ArticleLiterature Review
To read the full-text of this research, you can request a copy directly from the authors.

Abstract

Over the past decade, comprehensive sequencing efforts have revealed the genomic landscapes of common forms of human cancer. For most cancer types, this landscape consists of a small number of “mountains” (genes altered in a high percentage of tumors) and a much larger number of “hills” (genes altered infrequently). To date, these studies have revealed ~140 genes that, when altered by intragenic mutations, can promote or “drive” tumorigenesis. A typical tumor contains two to eight of these “driver gene” mutations; the remaining mutations are passengers that confer no selective growth advantage. Driver genes can be classified into 12 signaling pathways that regulate three core cellular processes: cell fate, cell survival, and genome maintenance. A better understanding of these pathways is one of the most pressing needs in basic cancer research. Even now, however, our knowledge of cancer genomes is sufficient to guide the development of more effective approaches for reducing cancer morbidity and mortality.

No full-text available

Request Full-text Paper PDF

To read the full-text of this research,
you can request a copy directly from the authors.

... In a review of cancer genetics for the journal Science, Vogelstein et al. (2013) distinguished between four kinds of genetic heterogeneity in tumours mour to tumour, the overall picture of genetic alterations is assumed to be quite general. In a recurring metaphor, the distribution of mutated genes is analogised to a landscape of mountains, hills and valleys in a threedimensional coordinate system (Wood et al. 2007;Vogelstein et al. 2013). ...
... In a review of cancer genetics for the journal Science, Vogelstein et al. (2013) distinguished between four kinds of genetic heterogeneity in tumours mour to tumour, the overall picture of genetic alterations is assumed to be quite general. In a recurring metaphor, the distribution of mutated genes is analogised to a landscape of mountains, hills and valleys in a threedimensional coordinate system (Wood et al. 2007;Vogelstein et al. 2013). ...
... Many authors agree that mountains in the cancer genome landscape can be reliably interpreted as drivers, but concede that the interpretation of hills (let alone even rarer mutations) is challenging. In their review of cancer genome landscapes, previously quoted above, Vogelstein et al. (2013) write: ...
Thesis
The thesis addresses the relationship between populations and individuals in the philosophy of medicine. There is a long-standing tension in the fact that randomised, controlled trials in clinical populations count among the best evidence in medicine, while the goal of medical practice is to help individual patients who may differ from population averages. To what extent is evidence from populations a sufficient guide to the treatment of individuals, and how can it perhaps be improved upon? The thesis consists of five chapters that consider this problem from several complementary perspectives. The first chapter returns to the origins of population studies in medicine: The 1835 debate on medical statistics at the Académie Royale de Médecine in Paris. It argues that the existing literature has neglected core epistemological arguments on which the debate turned, and which made population studies a much more challenging methodological development than we today appreciate. The second chapter moves to a present-day version of the debate. It asks whether physicians ought more frequently to conduct so-called n-of-1 or single-case trials with individual patients. The conclusion is that while such studies are epistemologically sound, they are less useful than they may appear at first glance. The third chapter focuses on so-called molecular network reconstruction, a type of mechanistic discovery strategy that leverages large datasets. While it is often difficult to find strong associations between genetic variants and individual health outcomes, this literature suggests that a higher level of organisation -- the state of entire molecular networks -- can often be associated with individual outcomes. The fourth chapter presents an extended case study of periodontal disease, a common affliction that is well understood in some respects but also presents inter-individual heterogeneity that has been recalcitrant to explanation for decades. The puzzles of the case study lead into the fifth and final chapter, which locates the search for inter-individual variation in disease susceptibility and therapy response in an evolutionary context. It argues that evolutionary models of ultimate disease causation can serve as a heuristic tool for the study of the proximate causes of variation in health outcomes.
... This pool potentiates the selection of the sporadic cases where the OPEN ACCESS EDITED BY Anton A. Buzdin, European Organisation for Research and Treatment of Cancer, Belgium mutated genome promotes a growth advantage and protection from apoptotic mechanisms. However, since most variations do not confer a strong growth advantage (Vogelstein et al., 2013), the detection of the few key cancer-promoting variations hidden in a complex mutational landscape constitutes a major challenge in cancer genome research. ...
... Namely, mutations for oncogenes tend to recur at the same locus; while mutations for TSGs scatter along the coding sequence (CDS) Accordingly, in Catalogue of Somatic Mutations in Cancer (COSMIC) database (Forbes et al., 2010), mutations are classified with a so-called "20/20 rule": to classify a gene as an oncogene, 20% of all the mutations within a gene's CDS recorded in database, need to reside at the same locus.; whereas to classify one as a TSG, 20% of recorded mutations need to be inactivating mutations but they mostly do not overlap in their location (Vogelstein et al., 2013). ...
... With paired cancer types derived from different data sources, two cancer types out of nine -ovary serous cystadenocarcinoma (C7978) and glioblastoma (C3058) -were clustered together. Furthermore, a list of 29 canonical pathways from Supplementary Table S5 of (Vogelstein et al., 2013) were used as hallmarks in cancer development. For these pathways, clustering was performed without standardization to compare the influence among cancer types as well as between multiple resources (Supplementary Appendix Figure S1). ...
Article
Full-text available
Genome variation is the direct cause of cancer and driver of its clonal evolution. While the impact of many point mutations can be evaluated through their modification of individual genomic elements, even a single copy number aberration (CNA) may encompass hundreds of genes and therefore pose challenges to untangle potentially complex functional effects. However, consistent, recurring and disease-specific patterns in the genome-wide CNA landscape imply that particular CNA may promote cancer-type-specific characteristics. Discerning essential cancer-promoting alterations from the inherent co-dependency in CNA would improve the understanding of mechanisms of CNA and provide new insights into cancer biology and potential therapeutic targets. Here we implement a model using segmental breakpoints to discover non-random gene coverage by copy number deletion (CND). With a diverse set of cancer types from multiple resources, this model identified common and cancer-type-specific oncogenes and tumor suppressor genes as well as cancer-promoting functional pathways. Confirmed by differential expression analysis of data from corresponding cancer types, the results show that for most cancer types, despite dissimilarity of their CND landscapes, similar canonical pathways are affected. In 25 analyses of 17 cancer types, we have identified 19 to 169 significant genes by copy deletion, including RB1, PTEN and CDKN2A as the most significantly deleted genes among all cancer types. We have also shown a shared dependence on core pathways for cancer progression in different cancers as well as cancer type separation by genome-wide significance scores. While this work provides a reference for gene specific significance in many cancers, it chiefly contributes a general framework to derive genome-wide significance and molecular insights in CND profiles with a potential for the analysis of rare cancer types as well as non-coding regions.
... Twelve identity mutations and seven different mutations at the same location were found (Table S10), and PIK3CA (p.E542K) existed in 13 cancer types and 23 cervical cancer samples. In addition, detected somatic mutations were compared with reported driver genes in previous studies, including Cancer Gene Census [30], Bert Vogelstein's research [31], pancancer research [32], David Tamborero's research [33], and intOGen [34]. In general, the results of multi-region WES revealed that heterogeneities not only exist between individuals but also in different tumor regions of the same individual. ...
... However, in patients pa10 and pa11, one of the four regions in each patient harbored much more somatic mutations than the other tumor regions. Driver genes obtained from previous studies were labeled on the tree [30][31][32][33][34]. ...
Article
Full-text available
Cervical cancer is a heterogeneous malignancy mainly caused by human papillomavirus (HPV). While a few studies have revealed heterogeneity of cervical cancer in chromosome levels, the correlation between genetic heterogeneity and HPV integration in cervical cancer remains unknown. Here, we applied multi-region whole-exome sequencing and HPV integration analysis to explore intratumor heterogeneity in cervical cancer. We sequenced 20 tumor regions and 5 adjacent normal tissues from 5 cervical cancer patients, analysis based on somatic mutations and somatic copy number alterations (SCNAs) levels were performed. Variable heterogeneity was observed between the five patients with different tumor stages and HPV infection statuses. We found HPV integration has a positive effect on somatic mutation burden, but the relation to SCNAs remains unclear. Frequently mutated genes in cervical cancer were identified as trunk events, such as FBXW7, PIK3CA, FAT1 in somatic mutations and TP63, MECOM, PIK3CA, TBL1XR1 in SCNAs. New potential driver genes in cervical cancer were summarized including POU2F2, TCF7 and UBE2A. The SCNAs level has potential relation with tumor stage, and Signature 3 related to homologous recombination deficiency may be the appropriate biomarker in advanced cervical cancer. Mutation signature analysis also revealed a potential pattern that APOBEC-associated signature occurs in early stage and signatures associated with DNA damage repair arise at the later stage of cervical cancer evolution. In a conclusion, our study provides insights into the potential relationship between HPV infection and tumor heterogeneity. Those results enhanced our understanding of tumorigenesis and progression in cervical cancer.
... More precisely, somatic mutations form the basis of the development of cancer and are the result of lifelong processes, with thousands of point mutations and hundreds of larger chromosomal rearrangements found in individual cancers (Stephens et al., 2009;Stratton et al., 2009;Vogelstein et al., 2013;Martincorena and Campbell, 2015). However, a large fraction of these are either neutral or marginally deleterious 1 and only a few constitute a selective advantage, with Tomasetti et al. (2015) suggesting as few as three such driver gene mutations for lung and colon cancers while Fearon and Vogelstein (1990) suggest at least 4-5 for colon cancers. ...
... The mutations resulting from these causes leave distinct marks on the genome giving hints about the underlying mutational processes that gave rise to the cancer, called mutational signatures. As described by Vogelstein et al. (2013), carcinogens leave traces of their actions on the genome akin to fingerprints on a crime scene. ...
Thesis
The digital transformation of health care provides new opportunities to study dis- ease and gain unprecedented insights into the underlying biology. With the wealth of data generated, new statistical challenges arise. This thesis will address some of them, with a particular focus on Time-to-Event analysis. The Cox hazard model, one of the most widely used statistical tools in biomedicine, is extended to analyses for large-scale and high-dimensional data sets. Built on recent machine learning frame- works the approach scales readily to big data settings. The method is extensively evaluated in simulation- and case-studies, showcasing its applicability to different data modalities, ranging from hospital admission episodes to histopathological im- ages of tumour resections. The motivating application of this thesis are electronic health records (EHR), collections of various interlinked data at an individual level. With many countries starting to implement national health data resources, methods that can cope with these datasets become paramount. In particular, cancers could benefit significantly from these developments. The lifetime risk of developing a ma- lignancy is around 50%. However, the associated risks are not equally distributed with large differences between individuals. Hence, being able to utilise the data available in EHR could potentially help to stratify individuals by their risk profiles and screen or even intervene early. The proposed method is used to build a pre- dictive model for 20 primary cancer sites based on clinical disease histories, basic health parameters, and family histories covering 6.7 million Danish individuals over a combined 193 million life years. The obtained risk score can predict cancer inci- dence across most organ sites. Further, the information could potentially be used to create cohorts with similar efficiency while screening earlier, creating the possibility for risk-targeted screening programs. Additionally, the obtained result could also be transferred between health care systems, as shown here between Denmark and the UK. Taken together the thesis established a method to analyse the extensive amounts of data that is being generated nowadays as well as an evaluation of the potential these data sources can have in the context of cancer risk.
... More importantly, the hallmarks of carcinogenesis are the accumulation of genetic and epigenetic mutations that are commonly classified as a 'driver' or 'passenger' mutation according to their roles in promoting cell proliferation and invasion (29). Driver mutations have the capability to drive the cell lineage to cancer, but passenger mutations do not exhibit the proliferation-promoting benefit to cell lineage (30). Moreover, due to the large fraction of passenger mutations compared with driver mutations, the passenger genes contribute to the majority of experimentally confirmed neoantigens that showed high immunogenicity (31). ...
Article
Full-text available
The mutation of the crucial genes such as tumor suppressors or oncogenes plays an important role in the initiation and development of tumors. The non-synonymous mutations in the tumor cell genome will produce non-autologous proteins (neoantigen) to activate the immune system by activating CD4+ and CD8+ T cells. Neoantigen-based peptide vaccines have exhibited exciting therapeutic effects in treating various cancers alone or in combination with other therapeutic strategies. Furthermore, antigen-loaded DC vaccines are more powerful in inducing stronger immune responses than vaccines generated by antigens and adjuvants. Therefore, neoantigen-based dendritic cell (DC) vaccines could achieve promising effects in combating some malignant tumors. In this review, we summarized and discussed the recent research progresses of the neoantigen, neoantigen-based vaccines, and DC-based vaccine in pancreatic cancers (PCs). The combination of the neoantigen and DC-based vaccine in PC was also highlighted. Therefore, our work will provide more detailed evidence and novel opinions to promote the development of a personalized neoantigen-based DC vaccine for PC.
... However, in multicellular organisms the specific (de) phosphorylation of tyrosine residues became more and more the method of choice for regulation of cell division and cell diversity (Lim and Pawson, 2010). In line, the molecular causes in acquired or hereditary diseases of growth and development are regularly mapped on phosphotyrosine-mediated signaling routes (e.g., (Gelb and Tartaglia, 2006;Vogelstein et al., 2013)). Consequently, a considerable number of protein tyrosine kinase genes are now documented as proto-oncogenes or are linked to developmental disorders. ...
Article
Full-text available
Protein tyrosine phosphatases, together with protein tyrosine kinases, control many molecular signaling steps that control life at cellular and organismal levels. Impairing alterations in the genes encoding the involved proteins is expected to profoundly affect the quality of life—if compatible with life at all. Here, we review the current knowledge on the effects of germline variants that have been reported for genes encoding a subset of the protein tyrosine phosphatase superfamily; that of the thirty seven classical members. The conclusion must be that the newest genome research tools produced an avalanche of data that suggest ‘guilt by association’ for individual genes to specific disorders. Future research should face the challenge to investigate these accusations thoroughly and convincingly, to reach a mature genotype-phenotype map for this intriguing protein family.
... The average number of the exonic somatic driver mutations in leukaemia was estimated to be around 9.6 per tumour [97], although subsequent analyses have shown that the number is probably an overestimate and that the number depends on the type of leukaemia. Mathematical models of mutations in self-renewing tissues, such as haematopoietic stem cells, indicate that more than half of the somatic mutations associated with malignancy occur before the initiation of the tumour. ...
Thesis
Introduction: Over the past decade, the availability of large population studies has allowed a detailed exploration of the relationship between genetics and clinical phenotypes. Clonal haematopoiesis (CH) is the expansion of blood cells with genetic features that are often observed in patients with haematological malignancies, particularly myeloid neoplasms. CH is a common finding in elderly individuals and associated with an elevated risk of developing haematological malignancies, cardiovascular diseases, and all-cause mortality. My study has four main aims. First, to characterise the inherited and environmental risk factors associated with myeloid CH. Second, to characterise the impact of myeloid CH on the risk of developing chronic inflammation-related diseases. Third, to investigate the utility of CH measures to predict the risk of myeloid malignancies. Fourth, to identify risk factors associated with age-related loss of the Y-chromosome (LOY) in men and its relationship to CH. Methods: The UK Biobank represents a unique genetic and phenotypic dataset of about 500,000 individuals with 94.6% white ethnicity. CH was defined in this study by the presence of mosaic chromosomal alterations (mCA) and/or somatic driver mutations. I utilised B-allele frequencies, and genotypic intensities from single nucleotide polymorphism array data (n = 486,941) to identify mCA, and diagnostic data to classify mCA according to their association with myeloid, lymphoid or neither of these diseases. Furthermore, I utilised whole exome sequencing data (WES, 1st release, n = 49,956; 2nd release, n=150,685) and publicly available databases to identify putative somatic driver mutations. LOY calls in men were provided by the UK Biobank from published data. Results: The frequency of myeloid CH increased per year of participant age and was associated with: two distinct germline predisposition signals within TERT, current smoking, and several blood features and clinical phenotypes indicative of chronic inflammation. Somatic loss-of-function mutations in ASXL1 were found to be strongly associated with current and past smoking status. Focusing on chronic kidney disease (CKD), myeloid CH was negatively associated with glomerular filtration rate (GFR) estimated from cystatin-C which is a marker of CKD but not with GFR estimated from creatinine which has previously been reported to be less informative. Furthermore, myeloid CH increased the risk of adverse outcomes, defined by a composite of all-cause mortality, myocardial infarction or stroke, in CKD cases compared to those without myeloid CH. Machine learning (ML) survival models which analysed high dimensional data including CH calls, blood counts and biochemistry markers were more predictive of myeloid malignancies in comparison to traditional regression-based models. Finally, LOY was significantly associated with CH and also with clonality inferred from non-CH somatic mutations. LOY was suggested to be causally associated with high levels of sex hormone binding globulin, and this relationship was linked to expression Quantitative Trait Locus (eQTL) associated with genes at the DLK1-MEG3 locus. Conclusion: This study demonstrates the wide scientific reach of CH and its broad impact on health outcomes. My results indicate that the type of CH, the identity of specific driver genes, inherited risk variants, and environmental factors are collectively determinants of the fitness of CH and influence the potential for development of myeloid neoplasms or non-malignant diseases. My findings also provide evidence that blood and serum measures hold additional information that helps to determine the clinical significance of CH. <br/
... The epigenetic marks on cells derived from the same tumor differ both at local and global levels, suggesting that the altered epigenetic marks can be oncogenic drivers or may lead to tumor cell heterogeneity and therapeutic resistance. Notably, genome-wide mapping of diverse tumors has established that almost half of the driver mutations are chromatin regulators [12]. An ample amount of literature on oncogenesis is devoted to the role of individual chromatin modifiers, transcription factors, and novel fusion proteins [1,[13][14][15]. ...
Article
Full-text available
A hallmark of cancers is uncontrolled cell proliferation, frequently associated with an underlying imbalance in gene expression. This transcriptional dysregulation observed in cancers is multifaceted and involves chromosomal rearrangements, chimeric transcription factors, or altered epigenetic marks. Traditionally, chromatin dysregulation in cancers has been considered a downstream effect of driver mutations. However, here we present a broader perspective on the alteration of chromatin organization in the establishment, diversification, and therapeutic resistance of cancers. We hypothesize that the chromatin organization controls the accessibility of the transcriptional machinery to regulate gene expression in cancerous cells and preserves the structural integrity of the nucleus by regulating nuclear volume. Disruption of this large-scale chromatin in proliferating cancerous cells in conventional chemotherapies induces DNA damage and provides a positive feedback loop for chromatin rearrangements and tumor diversification. Consequently, the surviving cells from these chemotherapies become tolerant to higher doses of the therapeutic reagents, which are significantly toxic to normal cells. Furthermore, the disorganization of chromatin induced by these therapies accentuates nuclear fragility, thereby increasing the invasive potential of these tumors. Therefore, we believe that understanding the changes in chromatin organization in cancerous cells is expected to deliver more effective pharmacological interventions with minimal effects on non-cancerous cells.
... Our main hypothesis is that the immune system played an important role in the regression of the metastases [21]. The frame shift mutation rate in dMMR CRC tumors is hundredfold higher than in proficient mismatch repair CRC tumors, which results in a high number of immunogenic neoantigens [22]. When these neoantigens are presented by an antigen-presenting cell and subsequently recognized by T cells, an immune antitumor response can occur [23]. ...
Article
Full-text available
Background: Cancer has become an important cause of death in solid organ transplant patients. The cause of malignancies in patients with solid organ transplants is multifactorial, but the use of intensive immunosuppression is regarded as an important factor. We describe the spontaneous, complete regression of colon cancer liver metastases, without initiation of antitumor therapy, in a solid organ transplant patient after modulation of immunosuppressants. Case Presentation. A 59-year-old female was admitted with fever, general discomfort, and elevated liver enzymes. She had received a single lung transplant, five years prior, for end-stage chronic obstructive pulmonary disease. Abdominal ultrasound and a computed tomography scan showed extensive liver lesions, and liver biopsy determined that the lesions were liver metastases originating from a colonic adenocarcinoma. Histopathologic analysis revealed that the primary tumor and liver metastases were mismatch repair-deficient (BRAFV600E mutant and MLH1/PMS2-deficient), also known as a microsatellite instable tumor. The patient's clinical condition deteriorated rapidly, and she was discharged home with palliative care. No antitumor treatment was initiated. Additionally, there was a short period without any immunosuppressants. Unexpectedly, her clinical condition improved, and complete regression of liver metastases was observed on imaging two months later. Unfortunately, the patient developed rejection of her lung transplant and succumbed to pulmonary disease six months following her cancer diagnosis. The autopsy confirmed the primary colon tumor location and complete regression of >40 liver metastases. Conclusions: Disinhibition and reset of the host immune response could have led to immune destruction of the liver metastases of this patient's immunogenic dMMR colon carcinoma. This case underscores the huge impact that temporary relief from immunosuppressive therapy could have on tumor homeostasis. Balanced management of care for organ transplant recipients with malignancies requires a multidisciplinary approach involving medical oncologists and transplant physicians to reach the best quality of care in these complex cases.
... Furthermore, in addition to abnormal AS, the accumulation of somatic mutation in characteristic genes has been observed to be a significant cause of cancer. Somatic mutations can be divided into mutations that result in selective growth advantages (drivers) and mutations that do not result in selective growth advantages (passengers) (56). Clinically, most drivers can generate carcinogenicity by regulating key small molecule enzymes or binding to cell signaling receptors (57). ...
Article
Full-text available
Background Testicular germ cell tumor (TGCT) is the most common tumor in young men, but molecular signatures, especially the alternative splicing (AS) between its subtypes have not yet been explored. Methods To investigate the differences between TGCT subtypes, we comprehensively analyzed the data of gene expression, alternative splicing (AS), and somatic mutation in TGCT patients from the TCGA database. The gene ontology (GO) enrichment analyses were used to explore the function of differentially expressed genes and spliced genes respectively, and Spearman correlation analysis was performed to explore the correlation between differential genes and AS events. In addition, the possible patterns in which AS regulates gene expression were elaborated by the ensemble database transcript atlas. And, we identified important transcription factors that regulate gene expression and AS and functionally validated them in TGCT cell lines. Results We found significant differences between expression and AS in embryonal carcinoma and seminoma, while mixed cell tumors were in between. GO enrichment analyses revealed that both differentially expressed and spliced genes were enriched in transcriptional regulatory pathways, and obvious correlation between expression and AS events was determined. By analyzing the transcript map and the sites where splicing occurs, we have demonstrated that AS regulates gene expression in a variety of ways. We further identified two pivot AS-related molecules (SOX2 and HDAC9) involved in AS regulation, which were validated in embryonal carcinoma and seminoma cell lines. Differences in somatic mutations between subtypes are also of concern, with our results suggesting that mutations in some genes (B3GNT8, CAPN7, FAT4, GRK1, TACC2, and TRAM1L1) occur only in embryonal carcinoma, while mutations in KIT, KARS, and NRAS are observed only in seminoma. Conclusions In conclusion, our analysis revealed the differences in gene expression, AS and somatic mutation among TGCT subtypes, providing a molecular basis for clinical diagnosis and precise therapy of TGCT patients.
... Gene amplification is an important mechanism in cancer, leading to increased gene expression and gain of function [33]. In our previous studies, using cell lines and breast tumors, we showed that STARD3 gene amplification and overexpression paralleled that of HER2 [14,15,34]. ...
Article
Full-text available
Unlabelled: Pathological complete response (pCR) after neoadjuvant systemic treatment (NST) is an important prognostic factor in HER2-positive breast cancer. The majority of HER2-positive breast cancers are amplified at the HER2 gene locus, several genes are co-amplified with HER2, and a subset of them are co-expressed. The STARD3 gene belongs to the HER2 amplicon, and its role as a predictive marker was never addressed. The objective of this study was to investigate the predictive value of STARD3 protein expression on NST pathological response in HER2-positive breast cancer. In addition, we studied the prognostic value of this marker. Methods: We conducted a retrospective study between 2007 and 2020 on 112 patients with non-metastatic HER2-positive breast cancer treated by NST and then by surgery. We developed an immunohistochemistry assay for STARD3 expression and subcellular localization and determined a score for STARD3-positivity. As STARD3 is an endosomal protein, its expression was considered positive if the intracellular signal pattern was granular. Results: In this series, pCR was achieved in half of the patients. STARD3 was positive in 86.6% of cases and was significantly associated with pCR in univariate analysis (p = 0.013) and after adjustment on other known pathological parameters (p = 0.044). Performances on pCR prediction showed high sensitivity (96%) and negative predictive value (87%), while specificity was 23% and positive predictive value was 56%. Overall, specific, relapse-free, and distant metastasis-free survivals were similar among STARD3 positive and negative groups, independently of other prognosis factors. Conclusion: NST is an opportunity for HER2-positive cancers. In this series of over a hundred HER2-positive and non-metastatic patients, a STARD3-negative score was associated with the absence of pathological complete response. This study suggests that determining STARD3 overexpression status on initial biopsies of HER2-positive tumors is an added value for the management of a subset of patients with high probability of no pathological response.
... The results indicated Of the three radiomic models we constructed, the ALN delta-radiomic model showed the highest predictive value. Intratumor heterogeneity drives neoplastic progression and therapeutic response [30,31] and changes dynamically accompanied by size changes after treatment 6 Visual nomogram of the delta-radiomic + clinical model in predicting apCR. The ** represents. ...
Article
Full-text available
Background The objective of this paper is to explore the value of a delta-radiomic model of the axillary lymph node (ALN) using dynamic contrast-enhanced (DCE) MRI for early prediction of the axillary pathological complete response (pCR) of breast cancer patients after neoadjuvant chemotherapy (NAC). Methods A total of 120 patients with ALN-positive breast cancer who underwent breast MRI before and after the first cycle of NAC between October 2018 and May 2021 were prospectively included in this study. Patients were divided into a training ( n = 84) and validation ( n = 36) cohort based on the temporal order of their treatments. Radiomic features were extracted from the largest slice of targeted ALN on DCE-MRI at pretreatment and after one cycle of NAC, and their changes (delta-) were calculated and recorded. Logistic regression was then applied to build radiomic models using the pretreatment (pre-), first-cycle(1st-), and changes (delta-) radiomic features separately. A clinical model was also built and combined with the radiomic models. The models were evaluated by discrimination, calibration, and clinical application and compared using DeLong test. Results Among the three radiomic models, the ALN delta-radiomic model performed the best with AUCs of 0.851 (95% CI: 0.770–0.932) and 0.822 (95% CI: 0.685–0.958) in the training and validation cohorts, respectively. The clinical model yielded moderate AUCs of 0.742 (95% CI: 0.637–0.846) and 0.723 (95% CI: 0.550–0.896), respectively. After combining clinical features to the delta-radiomics model, the efficacy of the combined model (AUC = 0.932) in the training cohort was significantly higher than that of both the delta-radiomic model (Delong p = 0.017) and the clinical model (Delong p < 0.001) individually. Additionally, in the validation cohort, the combined model had the highest AUC (0.859) of any of the models we tested although this was not statistically different from any other individual model’s validation AUC. Calibration and decision curves showed a good agreement and a high clinical benefit for the combined model. Conclusion This preliminary study indicates that ALN-based delta-radiomic model combined with clinical features is a promising strategy for the early prediction of downstaging ALN status after NAC. Future axillary MRI applications need to be further explored.
... Highly significant enrichment is seen for the frequently mutated KMT2C, as observed previously [11]. The distribution of mutations to many sites, rather than a few selected sites, and the enrichment of alterations in conserved residues of the PHDs suggest that the mutations cause a loss-of-function and change-offunction, respectively [62]. The accumulation of alterations in conserved residues of the PHDs suggests that PHD dysfunction is an important contributor to KMT2A-D-driven malignancies. ...
Article
Full-text available
Histone lysine-specific methyltransferase 2 (KMT2A-D) proteins, alternatively called mixed lineage leukemia (MLL1-4) proteins, mediate positive transcriptional memory. Acting as the catalytic subunits of human COMPASS-like complexes, KMT2A-D methylate H3K4 at promoters and enhancers. KMT2A-D contain understudied highly conserved triplets and a quartet of plant homeodomains (PHDs). Here, we show that all clustered (multiple) PHDs localize to the well-defined loci of H3K4me3 and H3 acetylation-rich active promoters and enhancers. Surprisingly, we observe little difference in binding pattern between PHDs from promoter-specific KMT2A-B and enhancer-specific KMT2C-D. Fusion of the KMT2A CXXC domain to the PHDs drastically enhances their preference for promoters over enhancers. Hence, the presence of CXXC domains in KMT2A-B, but not KMT2C-D, may explain the promoter/enhancer preferences of the full-length proteins. Importantly, targets of PHDs overlap with KMT2A targets and are enriched in genes involved in the cancer pathways. We also observe that PHDs of KMT2A-D are mutated in cancer, especially within conserved folding motifs (Cys4HisCys2Cys/His). The mutations cause a domain loss-of-function. Taken together, our data suggest that PHDs of KMT2A-D guide the full-length proteins to active promoters and enhancers, and thus play a role in positive transcriptional memory. Graphical Abstract
... 11 Meanwhile, Gene Expression Omnibus (GEO), a large public database, can be used to screen different expression genes (DEGs) related to the initiation and progression of ALI from microarray data. 3,12 For example, Tu et al. (2021) identified 20 hubgenes up-regulated in ALI by GEO microarray database. 13 These hub-genes were mainly enriched in nuclear factor kappa B (NF-κB) and tumor necrosis factor-α (TNF-α) signaling pathway, indicating that they were important pathways affecting the pathogenesis of ALI. 13 It is possible to find potential therapeutic drugs targeting DEGs. ...
Article
Full-text available
Background/objective: Acute lung injury (ALI) is a critical clinical syndrome with high rates of incidence and mortality. However, its molecular mechanism remains unclear. The current work aimed to explore the molecular mechanisms of ALI by identifying different expression genes (DEGs) and candidate drugs using a combination of chip analysis and experimental validation. Methods: Three microarray datasets were downloaded from Gene Expression Omnibus (GEO) database to obtain DEGs. We conducted a Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway-enrichment analyses of overlapping DEGs among three databases. The expression level of key gene was verified by Western blotting analysis in LPS-treated ALI cell models. Finally, we predicted the candidate drugs targeting the key gene that might be effective for ALI treatment, and the role of candidate drug in treating ALI was verified by investigation. Results: A total 29 overlapping DEGs were up-regulated in LPS-induced ALI groups. They were enriched in inflammation and inflammation-related pathways. Serpin family A member 3 (SERPINA3) was defined as a key gene because it was associated with inflammation pathway and up-regulated in microarray datasets in LPS-induced ALI. In LPS-induced human bronchial epithelial cells transformed with Ad12-SV40-2B (BEAS-2B) cells, SERPINA3 was enhanced. Pyridoxal phosphate as an upstream drug of SERPINA3 could improve cell viability and reduce expression inflammatory factors in LPS-treated BEAS-2B cells. Conclusion: Our study suggested that pyridoxal phosphate could be a candidate drug targeting SERPINA3 gene in LPS-induced ALI. It has protective and anti-inflammatory effects in BEAS-2B cells, and may become a potential novel treatment for ALI.
... Several genes and pathways have been shown to be involved in tumor initiation and growth. A series of recurrent mutations in APC, KRAS, SMAD4, and TP53 are crucial recurrent driver events that accumulate during adenoma formation and progression to sporadic CRC, often correlating with specific stages of the cancer development process [16,17]. Molecular studies have also shown that alterations in WNT-β-catenin, membrane receptor tyrosine kinases (RTKs), and downstream MAPK and PI3K signaling pathways are nearly ubiquitous events in CRC [17,18]. ...
Article
Full-text available
Human epidermal growth factor receptor 2 (HER2) amplification has emerged as a biomarker in colorectal cancer (CRC), occurring in 1–4% of metastatic CRC (mCRC). In addition to conventional methods, such as immunohistochemistry and fluorescence in situ hybridization, next-generation sequencing-based tissue or circulating tumor DNA analysis has recently been used to identify HER2 amplification and assess HER2 overexpression. Prospective clinical trials have demonstrated the efficacy of HER2-targeted therapies in HER2-positive mCRC. The TRIUMPH study, a phase II study of dual HER2 antibodies, i.e., pertuzumab plus trastuzumab, demonstrated promising efficacy for patients with HER2-positive mCRC confirmed by tissue-and/or blood-based techniques, which led to the regulatory approval of this combination therapy in Japan. The mechanisms associated with efficacy and resistance have also been explored in translational studies that incorporate liquid biopsy in prospective trials. In particular, HER2 copy number and co-alterations have repeatedly been reported as biomarkers related to efficacy. To improve the therapeutic efficacy of the current strategy, many clinical trials with various HER2-targeted agents are ongoing. This review discusses the molecular basis of HER2-targeted therapeutic strategies for patients with HER2-positive mCRC.
... This can also be indicated by the fact that the standardized uptake value in positron examination was different between primary pancreatic cancer and metachronous liver metastasis. Intratumor heterogeneity has been identified in recent genetic studies [28]. Metastasis is a multistep process consisting of local invasion, intravasation, survival in circulation, extravasation, and distant colonization [29,30]. ...
Article
Full-text available
Background Although new-onset diabetes has been described in up to 20% of patients with newly diagnosed pancreatic cancer, reports regarding new-onset diabetes associated with newly developed liver metastasis from pancreatic cancer are limited. Case presentation A 60-year-old man was diagnosed with pancreatic tail cancer without impaired glycemic control. A curative-intent distal pancreatectomy with adjuvant S-1 chemotherapy was performed. Two years after surgery, a high HbA1c concentration and solitary liver metastasis were identified on follow-up examination. Two major chemotherapy regimens, gemcitabine/nab-paclitaxel and modified FOLFIRINOX, were sequentially administered to the patient; however, his carbohydrate 19-9 concentration continued to increase. Because the patient’s glycemic control rapidly worsened in synchrony with the tumor growth, insulin therapy was initiated. Although the liver metastasis was refractory to chemotherapy, curative-intent left hepatectomy was performed because only one tumor remained. His impaired glycemic control improved immediately after surgery, and insulin therapy was terminated. When writing this report (2 years after hepatectomy), the patient was alive and recurrence-free. Conclusions New-onset diabetes appeared with the progression of metachronous liver metastasis from pancreatic cancer, without recurrence at any other site. The patient’s diabetic state was improved by resection of the liver tumor, and liver metastasis itself was proven to have caused the glucometabolic disorder by increasing insulin resistance.
... Recent advances in DNA sequencing technologies have led to the development of reliable and cost-effective whole-genome sequencing methods and relevant analysis pipelines, which have been applied to numerous cancer types [1][2][3][4][5][6][7][8][9], precancerous lesions [4], normal tissues, cells, and stem cells [10,11]. The somatic mutation landscape from these data revealed various genotypic alterations, ranging from driver and passenger somatic mutations for cancer initiation and progression [12][13][14][15], mutation signatures [16], clonal Life 2023, 13, 71 2 of 15 and subclonal evolutions [17], to the findings on novel structural variations including kategis [18,19], chromothripsis [20], and whole-genome doubling [21,22]. Although mechanisms on how these aberrations arise have not been fully defined, a number of statistical and machine-learning approaches have shown that the somatic point mutation landscapes of multiple cancer types and precancerous lesions correlated with the chromatin mark landscape [23,24]. ...
Article
Full-text available
We present here COOBoostR, a computational method designed for the putative prediction of the tissue- or cell-of-origin of various cancer types. COOBoostR leverages regional somatic mutation density information and chromatin mark features to be applied to an extreme gradient boosting-based machine-learning algorithm. COOBoostR ranks chromatin marks from various tissue and cell types, which best explain the somatic mutation density landscape of any sample of interest. A specific tissue or cell type matching the chromatin mark feature with highest explanatory power is designated as a potential tissue- or cell-of-origin. Through integrating either ChIP-seq based chromatin data, along with regional somatic mutation density data derived from normal cells/tissue, precancerous lesions, and cancer types, we show that COOBoostR outperforms existing random forest-based methods in prediction speed, with comparable or better tissue or cell-of-origin prediction performance (prediction accuracy—normal cells/tissue: 76.99%, precancerous lesions: 95.65%, cancer cells: 89.39%). In addition, our results suggest a dynamic somatic mutation accumulation at the normal tissue or cell stage which could be intertwined with the changes in open chromatin marks and enhancer sites. These results further represent chromatin marks shaping the somatic mutation landscape at the early stage of mutation accumulation, possibly even before the initiation of precancerous lesions or neoplasia.
... Several missense variants of FGFR3 have been documented in genetic studies of patients with phenotypic disorders such as achondroplasia, thanatophoric dysplasia I and II, Muenke syndrome, hypochondroplasia, among others reported in the J o u r n a l P r e -p r o o f 5 Human Gene Mutation database (HGMD) and also in tumors listed in the Catalogue Of Somatic Mutations In Cancer (COSMIC) (Tate et al. 2019). Furthermore, FGFR3 has been categorized as a cancer driver gene involved in cell survival with a 99% oncogene score (van Rhijn et al. 2002a;van Rhijn et al. 2002b;Vogelstein et al. 2013). Over 7% of the sequenced tumors were positive for FGFR3 mutants, some of them affecting the same codon resulting in different amino acid substitutions (cancer.sanger.ac.uk, (Tate et al. 2019)), further highlighting the proliferative properties of FGFR3 mutations. ...
Article
Fibroblast growth factor receptors (FGFRs) initiate signal transduction via the RAS/MAPK pathway by their tyrosine-kinase activation known to determine cell-growth, tissue differentiation, and apoptosis. Recently, many missense mutations have been reported for FGFR3, but we only know the functional effect for a handful of them. Some mutations result in aberrant FGFR3 signaling and are associated with various genetic disorders and oncogenic conditions. Here, we employed micropatterned surfaces to specifically enrich fluorophore-tagged FGFR3 (mGFP-FGFR3) in certain areas of the plasma membrane of living cells. We quantified receptor activation via total internal reflection fluorescence microscopy of FGFR3 signaling at the cell membrane that captured the recruitment of the downstream signal transducer GRB2 tagged with mScarlet (GRB2-mScarlet) to FGFR3 micropatterns. With this system, we tested the activation of FGFR3 upon ligand addition (fgf1 and fgf2) for wildtype (WT) and four FGFR3 mutants associated with congenital disorders (G380R, Y373C, K650Q, and K650E). Our data showed that ligand addition increased GRB2 recruitment to WT FGFR3, with fgf1 having a stronger effect than fgf2. For all mutants, we found an increased basal receptor activity, and only for two of the four mutants (G380R and K650Q), activity was further increased upon ligand addition. Compared to previous reports, two mutant receptors (K650Q and K650E) had either an unexpectedly high or low activation state, respectively. This can be attributed to the different methodology, since micropatterning specifically captures signaling events at the plasma membrane. Collectively, our results provide further insight into the functional effects of mutations to FGFR3.
... The most deadly phase of cancer is when tumor cells disseminate throughout the organism and seed distant metastases. Despite initial expectations to identify genes specifically promoting migration and invasion of tumor cells, it appeared that most cancer-associated genes promoting cell migration also promote proliferation in a pleiotropic and perhaps even coupled manner [1,2]. ...
Article
Full-text available
Whole exome sequencing of invasive mammary carcinomas revealed the association of mutations in PTEN and ZFHX3 tumor suppressor genes (TSGs). We generated single and combined PTEN and ZFHX3 knock-outs (KOs) in the immortalized mammary epithelial cell line MCF10A to study the role of these genes and their potential synergy in migration regulation. Inactivation of PTEN, but not ZFHX3, induced the formation of large colonies in soft agar. ZFHX3 inactivation in PTEN KO, however, increased colony numbers and normalized their size. Cell migration was affected in different ways upon PTEN and ZFHX3 KO. Inactivation of PTEN enhanced coordinated cell motility and thus, the collective migration of epithelial islets and wound healing. In contrast, ZFHX3 knockout resulted in the acquisition of uncoordinated cell movement associated with the appearance of immature adhesive junctions (AJs) and the increased expression of the mesenchymal marker vimentin. Inactivation of the two TSGs thus induces different stages of partial epithelial-to-mesenchymal transitions (EMT). Upon double KO (DKO), cells displayed still another motile state, characterized by a decreased coordination in collective migration and high levels of vimentin but a restoration of mature linear AJs. This study illustrates the plasticity of migration modes of mammary cells transformed by a combination of cancer-associated genes.
... Therefore, the prevention, diagnosis, and therapy of breast cancer constitutes a serious challenge for modern oncology. An early diagnosis of breast tumors increases the chance of successful radical treatment and thus reduces mortality [2]. Notably, the 5-year survival rate for the tumors detected at one stage of clinical advancement earlier increases by approximately 25 percentage points. ...
Article
Full-text available
Mammography machines must meet high requirements to ensure the quality of the generated images. On the other hand, due to the use of ionizing radiation, there is a need to minimize the dose received by patients. To optimize both of these parameters (dose and image quality), the response characteristics of image detectors and, depending on the composition of the breasts, the physical contrast of the examined structures should be considered. This study aimed to determine the optimal voltage values for a given breast thickness during imaging with the use of a selenium image detector. Analysis was carried out using the Monte Carlo simulation method with the GEANT4 code. Our results reveal that the combination of Mo anode together with Mo filtration (the system recommended in analog mammography) was the least favorable combination among those used in digital mammography machines with a selenium detector. Moreover, the use of Rh filtration instead of Mo was advantageous regardless of the thickness of the breast and resulted in a significant improvement in image quality with the same dose absorbed in the breast. The most advantageous solution was found to be an X-ray tube with a W anode. The highest values of the image quality-to-dose ratio were observed for breasts with dimensions ranging from 53 mm to 60 mm in thickness. Lower image quality was observed for breasts with smaller dimensions due to high breast glandularity, resulting in the deterioration of the physical contrast.
... These studies are mainly based on the gene level; nevertheless, exploring the impacts of mutations on immunotherapy at the pathway level will provide us with more robust results than at the gene level because of tumour heterogeneity. This may be because even if patients have different genetic mutations, these mutated genes tend to be ultimately involved in certain pathways [16,17]. ...
Article
Full-text available
Background Immune checkpoint blockades (ICBs) have emerged as a promising treatment for cancer. Recently, tumour mutational burden (TMB) and neoantigen load (NAL) have been proposed to be potential biomarkers to predict the efficacy of ICB; however, they were limited by difficulties in defining the cut-off values and inconsistent detection platforms. Therefore, it is critical to identify more effective predictive biomarkers for screening patients who will potentially benefit from immunotherapy. In this study, we aimed to identify comutated signaling pathways to predict the clinical outcomes of immunotherapy. Methods Here, we comprehensively analysed the signaling pathway mutation status of 9763 samples across 33 different cancer types from The Cancer Genome Atlas (TCGA) by mapping the somatic mutations to the pathways. We then explored the comutated pathways that were associated with increased TMB and NAL by using receiver operating characteristic (ROC) curve analysis and multiple linear regressions. Results Our results revealed that comutation of the Spliceosome (Sp) pathway and Hedgehog (He) signaling pathway (defined as SpHe-comut⁺) could be used as a predictor of increased TMB and NAL and was associated with increased levels of immune-related signatures. In seven independent immunotherapy cohorts, we validated that SpHe-comut⁺ patients exhibited a longer overall survival (OS) or progression-free survival (PFS) and a higher objective response rate (ORR) than SpHe-comut⁻ patients. Moreover, a combination of SpHe-comut status with PD-L1 expression further improved the predictive value for ICB therapy. Conclusion Overall, SpHe-comut⁺ was demonstrated to be an effective predictor of immunotherapeutic benefit in seven independent immunotherapy cohorts and may serve as a potential and convenient biomarker for the clinical application of ICB therapy.
... Neoantigens are derived from tumor-specific somatic mutations and are exclusively expressed in cancer cells and absent in normal human tissue. The majority (95%) of somatic mutations are single-nucleotide variants (SNVs), which lead to aberrant protein and peptide expression with single amino acid substitutions [105]. ...
Article
Full-text available
Despite the recent successes and durable responses with immune checkpoint inhibitors (ICI), many cancer patients, including those with melanoma, do not derive long-term benefits from ICI therapies. The lack of predictive biomarkers to stratify patients to targeted treatments has been the driver of primary treatment failure and represents an unmet medical need in melanoma and other cancers. Understanding genomic correlations with response and resistance to ICI will enhance cancer patients' benefits. Building on insights into interplay with the complex tumor microenvironment (TME), the ultimate goal should be assessing how the tumor 'instructs' the local immune system to create its privileged niche with a focus on genomic reprogramming within the TME. It is hypothesized that this genomic reprogramming determines the response to ICI. Furthermore, emerging genomic signatures of ICI response, including those related to neoantigens, antigen presentation, DNA repair, and oncogenic pathways, are gaining momentum. In addition, emerging data suggest a role for checkpoint regulators, T cell functionality, chromatin modifiers, and copy-number alterations in mediating the selective response to ICI. As such, efforts to contextualize genomic correlations with response into a more insightful understanding of tumor immune biology will help the development of novel biomarkers and therapeutic strategies to overcome ICI resistance.
... In recent years, many avenues of epigenetics have been investigated, including non-coding mRNA expression, DNA methylation and in the case of Prof. Adrian Bracken's lab at Trinity College Dublin (TCD), histone modifications. Prof. Bracken began the talk showing recent rounds of NGS sequencing and the key oncogenes and tumour suppressors highlighted [30] and a reminder that chromatin-modifying proteins are one of the main contributors to that list. ...
Article
Full-text available
Innovation in both detection and treatment of cancer is necessary for the constant improvement in therapeutic strategies, especially in patients with novel or resistant variants of cancer. Cancer mortality rates have declined by almost 30% since 1991, however, depending on the cancer type, acquired resistance can occur to varying degrees. To combat this, researchers are looking towards advancing our understanding of cancer biology, in order to inform early detection, and guide novel therapeutic approaches. Through combination of these approaches, it is believed that a more complete and thorough intervention on cancer can be achieved. Here, we will discuss the advances and approaches in both detection and treatment of cancer, presented at the 58th Irish Association for Cancer Research (IACR) annual conference.
... In essence, the epigenome consists of numerous types of modifications to DNA, which act to regulate the genome [2]. The impact of epigenetics on the cancer genome has been referred to as "the most obvious source of dark matter" [3], exhibiting how elusive the field once was in its contribution to the cancer genome. Epigenetic mechanisms have now been ...
Article
Full-text available
Morphological, transcriptomic, and genomic defects are well-explored parameters of cancer biology. In more recent years, the impact of epigenetic influences, such as DNA methylation, is becoming more appreciated. Aberrant DNA methylation has been implicated in many types of cancers, influencing cell type, state, transcriptional regulation, and genomic stability to name a few. Traditionally, large populations of cells from the tissue of interest are coalesced for analysis, producing averaged methylome data. Considering the inherent heterogeneity of cancer, analysing populations of cells as a whole denies the ability to discover novel aberrant methylation patterns, identify subpopulations, and trace cell lineages. Due to recent advancements in technology, it is now possible to obtain methylome data from single cells. This has both research and clinical implications, ranging from the identification of biomarkers to improved diagnostic tools. As with all emerging technologies, distinct experimental, bioinformatic, and practical challenges present themselves. This review begins with exploring the potential impact of single-cell sequencing on understanding cancer biology and how it could eventually benefit a clinical setting. Following this, the techniques and experimental approaches which made this technology possible are explored. Finally, the present challenges currently associated with single-cell DNA methylation sequencing are described.
... Driver genes were a concept stronger than marker genes and were a relative new concept which had been intensely applied on nding important genes that caused or signi cantly promoted tumors, or even drove/driven-by particular terms such as tumor classi cation, mutations, and enhancers etc [42][43][44][45] . ...
Preprint
Full-text available
Purpose Androgen is important in the formation, development and progress of prostate cancer. Deprivation of androgen, also named castration, is an effective way in prostate cancer therapies. For patients undergoing castration therapies, castration was gradually becoming ineffective in prostate cancer treatment and therefore resulting in castration resistance for prostate cancer, which is beyond efficient therapies. Moreover, the mechanism on how castration resistance was originated and what promoted castration resistance was rarely reported. We designed the project to further understand the mechanism for castration resistance. Methods AR-V7 and PRPF6 were selected to be calibration markers and then performed with protein mass spectrometry to detect AR-V7 and PRPF6 binding proteins. Afterwards, we used transcriptome big data from prostate cancer and castration-resistant prostate cancer and then applied combined analysis of association rules method, gene co-expression analysis, linear matrix migration method and functional deep filtering on identifying candidate driver genes which were causally correlated with castration resistance. The predicted driver genes were intersected with protein mass spectrometry filtering results for both AR-V7 and PRPF6. Afterwards, the predicted driver genes were theoretically and experimentally validated. Results The 5 candidate driver genes RPL28, RPS4X, RPL11, RPL23A and RPSA were deemed as driver genes for castration resistance and were validated on being highly correlated and playing important role in the progress of castration resistance. Conclusion The new driver genes might assist on further understanding the mechanism and bringing new insight on the prevention and therapy for castration resistance on prostate cancer.
... The frequencies of the intrinsically rhythmic Ca 2+ activity of glioblastoma cell networks (mean: 12.5-12.7 mHz in vivo and 9.7-11.3 mHz in vitro; Fig. 2c) lie in the same range in which the MAPK and NF-κB pathways that enhance proliferation and cell survival 23,24 are maximally activated 20,25,26 . Indeed, the most upregulated signalling pathways in KCa3.1 high cells and tumours with a high expression of KCa3.1 in RNA-expression datasets of human glioblastoma included these two pathways, whereas the CaMKII and calpain pathways that are activated by considerably higher Ca 2+ spike frequencies 20,27,28 around 1-50 Hz were not upregulated ( Fig. 5f and Extended Data Fig. 9h,i). ...
Article
Full-text available
Diffuse gliomas, particularly glioblastomas, are incurable brain tumours1. They are characterized by networks of interconnected brain tumour cells that communicate via Ca2+ transients2–6. However, the networks’ architecture and communication strategy and how these influence tumour biology remain unknown. Here we describe how glioblastoma cell networks include a small, plastic population of highly active glioblastoma cells that display rhythmic Ca2+ oscillations and are particularly connected to others. Their autonomous periodic Ca2+ transients preceded Ca2+ transients of other network-connected cells, activating the frequency-dependent MAPK and NF-κB pathways. Mathematical network analysis revealed that glioblastoma network topology follows scale-free and small-world properties, with periodic tumour cells frequently located in network hubs. This network design enabled resistance against random damage but was vulnerable to losing its key hubs. Targeting of autonomous rhythmic activity by selective physical ablation of periodic tumour cells or by genetic or pharmacological interference with the potassium channel KCa3.1 (also known as IK1, SK4 or KCNN4) strongly compromised global network communication. This led to a marked reduction of tumour cell viability within the entire network, reduced tumour growth in mice and extended animal survival. The dependency of glioblastoma networks on periodic Ca2+ activity generates a vulnerability7 that can be exploited for the development of novel therapies, such as with KCa3.1-inhibiting drugs. A population of highly interconnected cells in glioblastoma makes these tumours resistant to general damage but vulnerable to targeted disruption of this small fraction of cells and their rhythmic Ca2+ oscillations.
... The data in the Cagan et al. paper [8] allow us to conclude that mice accumulate mutations at a higher rate than humans, and therefore individual mouse cells may acquire the requisite number of cancer-causing mutations in a much shorter time period. At face value, this interpretation would support the largely mutation-centric view of cancer as in the classical "Vogelgram", whereby each stage of cancer development requires a mutation in a particular pathway, eventually culminating in the emergence of the winner cells that become fully transformed [11]. The beauty of this model is that it fits nicely with the Armitage-Doll view of human cancer development as a series of around 6 rate-limiting steps [2], a conclusion widely interpreted to mean that cancer goes through a relatively small number of distinct stages before emergence of complete malignancy. ...
... The related consequences of germline gene mutations for embryonic development phases might be disastrous if stem cells avoid differentiation, increase divisions or permit highly deleterious errors to be transmitted to the daughter stem cells, thus affecting body development [40]. ...
Article
Full-text available
Hereditary gastric cancers (HGCs) are supposed to be rare and difficult to identify. Nonetheless, many cases of young patients with gastric cancer (GC) fulfill the clinical criteria for considering this diagnosis but do not present the defined pathogenic mutations necessary to meet a formal diagnosis of HGC. Moreover, GC in young people is a challenging medical situation due to the usual aggressiveness of such cases and the potential risk for their relatives when related to a germline variant. Aiming to identify additional germline alterations that might contribute to the early onset of GC, a complete exome sequence of blood samples from 95 GC patients under 50 and 94 blood samples from non-cancer patients was performed and compared in this study. The number of identified germline mutations in GC patients was found to be much higher than that from individuals without a cancer diagnosis. Specifically, the number of high functional impact mutations, including those affecting genes involved in medical diseases, cancer hallmark genes, and DNA replication and repair processes, was much higher, strengthening the hypothesis of the potential causal role of such mutations in hereditary cancers. Conversely, classically related HGC mutations were not found and the number of mutations in genes in the CDH1 pathway was not found to be relevant among the young GC patients, reinforcing the hypothesis that existing alternative germline contributions favor the early onset of GC. The LILRB1 gene variants, absent in the world’s cancer datasets but present in high frequencies among the studied GC patients, may represent essential cancer variants specific to the Amerindian ancestry’s contributions. Identifying non-reported GC variants, potentially originating from under-studied populations, may pave the way for additional discoveries and translations to clinical interventions for GC management. The newly proposed approaches may reduce the discrepancy between clinically suspected and molecularly proven hereditary GC and shed light on similar inconsistencies among other cancer types. Additionally, the results of this study may support the development of new blood tests for evaluating cancer risk that can be used in clinical practice, helping physicians make decisions about strategies for surveillance and risk-reduction interventions.
Article
Full-text available
Tumor mutation burden is an imperfect proxy of tumor foreignness and has therefore failed to consistently demonstrate clinical utility in predicting responses in the context of immunotherapy. We evaluated mutations in regions of the genome that are unlikely to undergo loss in a pan-cancer analysis across 31 tumor types (n = 9,242) and eight immunotherapy-treated cohorts of patients with non-small-cell lung cancer, melanoma, mesothelioma, and head and neck cancer (n = 524). We discovered that mutations in single-copy regions and those present in multiple copies per cell constitute a persistent tumor mutation burden (pTMB) which is linked with therapeutic response to immune checkpoint blockade. Persistent mutations were retained in the context of tumor evolution under selective pressure of immunotherapy and tumors with a high pTMB content were characterized by a more inflamed tumor microenvironment. pTMB imposes an evolutionary bottleneck that cancer cells cannot overcome and may thus drive sustained immunologic tumor control in the context of immunotherapy. Genomic analyses in large cohorts of patients with cancer identify a new measure of tumor mutational burden, based on genomic regions that are unlikely to undergo loss, that is associated with therapeutic response to immunotherapy.
Article
Full-text available
Administration of targeted therapies provides a promising treatment strategy for urachal adenocarcinoma (UrC) or primary bladder adenocarcinoma (PBAC); however, the selection of appropriate drugs remains difficult. Here, we aimed to establish a routine compatible methodological pipeline for the identification of the most important therapeutic targets and potentially effective drugs for UrC and PBAC. Next‐generation sequencing, using a 161 cancer driver gene panel, was performed on 41 UrC and 13 PBAC samples. Clinically relevant alterations were filtered, and therapeutic interpretation was performed by in silico evaluation of drug‐gene interactions. After data processing, 45/54 samples passed the quality control. Sequencing analysis revealed 191 pathogenic mutations in 68 genes. The most frequent gain‐of‐function mutations in UrC were found in KRAS (33%), and MYC (15%), while in PBAC KRAS (25%), MYC (25%), FLT3 (17%) and TERT (17%) were recurrently affected. The most frequently affected pathways were the cell cycle regulation, and the DNA damage control pathway. Actionable mutations with at least one available approved drug were identified in 31/33 (94%) UrC and 8/12 (67%) PBAC patients. In this study, we developed a data‐processing pipeline for the detection and therapeutic interpretation of genetic alterations in two rare cancers. Our analyses revealed actionable mutations in a high rate of cases, suggesting that this approach is a potentially feasible strategy for both UrC and PBAC treatments. Precision oncology is an emerging treatment strategy for rare cancers such as urachal (UrC) and primary bladder adenocarcinoma (PBAC). In this study, we performed a multicentre sample collection and developed a DNA sequencing (161 gene Oncomine Comprehensive Assay Panel) and data processing pipeline for the detection and therapeutic interpretation of targetable genetic alterations in these two rare cancer entities. Our analyses revealed actionable alterations (e.g. EGFR, BRCA, CCND1/2/3, ERBB2, MET and METex14) in a high rate of cases, suggesting this approach to be feasible for both UrC and PBAC.
Article
Therapy-related myeloid neoplasms (t-MN) account for approximately 10-15% of all myeloid neoplasms and are associated with poor prognosis. Genomic characterization of t-MN to date has been limited in comparison to the considerable sequencing efforts performed for de novo myeloid neoplasms. Until recently, targeted deep sequencing (TDS) or whole exome sequencing (WES) have been the primary technologies utilized and thus limited the ability to explore the landscape of structural variants and mutational signatures. In the past decade, population-level studies have identified clonal hematopoiesis as a risk factor for the development of myeloid neoplasms. However, emerging research on clonal hematopoiesis as a risk factor for developing t-MN is evolving, and much is unknown about the progression of CH to t-MN. In this work, we will review the current knowledge of the genomic landscape of t-MN, discuss background knowledge of clonal hematopoiesis gained from studies of de novo myeloid neoplasms, and examine the recent literature studying the role of therapeutic selection of CH and its evolution under the effects of antineoplastic therapy. Finally, we will discuss the potential implications on current clinical practice and the areas of focus needed for future research into therapy-selected clonal hematopoiesis in myeloid neoplasms.
Article
There has been a surge of interest and efforts in the discovery of covalent ligands for diverse proteins as tool compounds or therapeutic candidates in recent years. We present two studies that involve applications of a target‐centric approach and a ligand‐centric approach toward covalent ligand discovery. By targeting a rare cysteine residue in a receptor tyrosine kinase EphB3, we were able to rapidly identify potent inhibitors of EphB3 with extraordinary proteomic selectivity supported by activity‐based probe profiling. While characterizing an activity‐based probe intended for EphB3 using ABPP, we made a surprising discovery that its primary cellular target was a catalytic subunit of V‐ATPase through its covalent engagement with a cryptic pocket on V‐ATPase. These two approaches will be increasingly used in combination to develop covalent ligands with high potency and yield comprehensive target profiles to accelerate the rate of therapeutic discovery in the future.
Article
Throughout the centuries, the world's outstanding scientists and research groups have gathered their efforts to characterise the initiation and progression of malignant neoplasms. The temporal dissection of tumourigenesis provided by phylogenetic studies is one of the milestones in understanding cancer; however, some black boxes are still unsolved. Currently, there is no consensus regarding the development of oral squamous cell carcinoma (OSCC), the leading cancer of the head and neck region. Oral epithelial dysplasia (OED) may precede oral cancer and, occasionally, be clinically evident as white, red or mixed mucosal lesions, called oral potentially malignant disorders (OPMD). In a stepwise view of oral carcinogenesis, OED and OPMD have been considered harbingers of oral cancer. Nevertheless, the malignant transformation of OPMD is a rare event. Most of these disorders remain benign and can even regress, making it challenging to formulate evolutionary hypotheses for OSCC initiation. Deciphering OED evolution is vital to highlight the potential drivers of oral carcinogenesis and molecular targets for OSCC preventative and therapeutic strategies. This narrative review synthesises the main concepts of evolutionary theories and discusses which of them better explains OED development and malignant transformation.
Preprint
Full-text available
Background Colon cancer is the most prevalent cancer and causes the highest cancer-associated mortality in both men and women globally. It has a high incidence and fatality rate, which places a significant burden on the healthcare system. Objective The current work was performed to understand the beneficial roles of nerolidol on the viability and cytotoxic mechanisms in the colon cancer HCT-116 cells. Methodology The MTT cytotoxicity assay was done to investigate the effect of nerolidol at different doses (5-100 µM) on the HCT-116 cell viability. The impacts of nerolidol on ROS accumulation and apoptosis was investigated using DCFH-DA, DAPI, and dual staining assays, respectively. The flow cytometry analysis was performed to study the influence of nerolidol on the cell cycle arrest in the HCT-116 cells. Results The outcomes of the MTT assay demonstrated that nerolidol at different doses (5-100 µM) substantially inhibited the HCT-116 cell viability with an IC50 level of 25 µM. The treatment with nerolidol appreciably boosted the ROS level in the HCT-116 cells. The findings of DAPI and dual staining revealed higher apoptotic incidences in the nerolidol-exposed HCT-116 cells, which supports its ability to stimulate apoptosis. The flow cytometry analysis demonstrated the considerable inhibition in cell cycle at G0/G1 phase in the nerolidol-exposed HCT-116 cells. Conclusion Our research showed that nerolidol can inhibit the cell cycle, increase ROS accumulation, and activate apoptosis in HCT-116 cells. In light of this, it may prove to be a potent salutary candidate to treat colon cancer.
Article
Full-text available
Curiosity concerning the process of human creation has been around for a long time. Relevant questions seemed to be resolved with the knowledge of how cells divide after fertilization obtained through in vitro fertilization experiments. However, we still do not know how human life is created at the cellular level. Recently, the value of cadavers as a resource from which to obtain “normal” cells and tissues has been established, and human research using postmortem bodies has attracted growing scientific attention. As the human genome can be analyzed at the level of nucleotides through whole-genome sequencing, individual cells in a postmortem body can be traced back to determine what developmental processes have transpired from fertilization. These retrospective lineage tracing studies have answered several unsolved questions on how humans are created. This review covers the methodologies utilized in lineage tracing research in a historical context and the conceptual basis for reconstructing the division history of cells in a retrospective manner using postzygotic somatic variants in postmortem tissue. We further highlight answers that postmortem research could potentially address and discuss issues that wait to be solved in the future.
Article
In patients with AFP-negative hepatocellular carcinoma (HCC), des-γ-carboxyprothrombin (DCP) is an important prognostic indicator for the preoperative assessment of transarterial chemoembolization (TACE). However, the association between the serum DCP levels and the degree of progression and prognosis of patients with AFP-negative HCC treated with TACE has not been thoroughly investigated to date, and the molecular mechanism is also unclear. The present study retrospectively analyzed the clinical data of 107 patients with AFP-negative HCC treated with TACE and divided them into two groups based on the median serum DCP levels. The association between DCP and the clinical characteristics of the patients was analyzed, and the survival data were analyzed using Kaplan-Meier curves and Cox regression models. The results demonstrated that the median follow-up time was 755 days (range, 64-1,556 days), and patients in the low-DCP group (n=11; 20.8%) had a lower mortality rate than those in the high-DCP group (n=20; 37.0%). Cox multivariate regression analysis suggested that preoperative lymph node metastasis [hazard ratio (HR), 3.903; 95% CI, 1.778-8.519; P=0.001] and DCP group (HR, 2.465; 95% CI, 1.038-5.854; P=0.041) were independent risk factors. Furthermore, the Gene Expression Omnibus database was utilized to screen differentially expressed mRNAs. Enrichment analyses were then performed, and a protein-protein interaction (PPI) network was constructed to identify hub genes. A total of 169 differentially expressed genes were screened. Enrichment analyses revealed that cancer-related and ribosomal pathways were significantly enriched. Furthermore, 10 hub genes were identified in the PPI network by counting the number of gene interactions, the majority of which belonged to the ribosomal protein (RPS) family, and the top three significant genes were RPS23, RPS11 and RPS3A. In patients with AFP-negative HCC, higher serum DCP levels were associated with poor prognosis after TACE. This may be associated with genes such as those belonging to the RPS family, which may contribute to future personalized therapy for this disease.
Article
Cancer is not a hard-wired phenomenon but an evolutionary disease. From the onset of carcinogenesis, cancer cells continuously adapt and evolve to satiate their ever-growing proliferation demands. This results in the formation of multiple subtypes of cancer cells with different phenotypes, cellular compositions, and consequently displaying varying degrees of tumorigenic identity and function. This phenomenon is referred to as cancer plasticity, during which the cancer cells exist in a plethora of cellular states having distinct phenotypes. With the advent of modern technologies equipped with enhanced resolution and depth, for example, single-cell RNA-sequencing and advanced computational tools, unbiased cancer profiling at a single-cell resolution are leading the way in understanding cancer cell rewiring both spatially and temporally. In this review, the processes and mechanisms that give rise to cancer plasticity include both intrinsic genetic factors such as epigenetic changes, differential expression due to changes in DNA, RNA, or protein content within the cancer cell, as well as extrinsic environmental factors such as tissue perfusion, extracellular milieu are detailed and their influence on key cancer plasticity hallmarks such as epithelial-mesenchymal transition (EMT) and cancer cell stemness (CSCs) are discussed. Due to therapy evasion and drug resistance, tumor heterogeneity caused by cancer plasticity has major therapeutic ramifications. Hence, it is crucial to comprehend all the cellular and molecular mechanisms that control cellular plasticity. How this process evades therapy, and the therapeutic avenue of targeting cancer plasticity must be diligently investigated.
Article
Objective: To assess a novel intraoperative core biopsy technique to provide enhanced guidance in partial glossectomies. Methods: All patients diagnosed with squamous cell carcinoma of the oral tongue were eligible for study participation. Following anesthesia, the planned resection and three points midway between the gross tumor and the intended ablation were marked. A core biopsy was performed with a needle spring on each point and sent for frozen sections. The initially planned resection was executed if the cores returned free of tumor. In case of a positive core biopsy, a new 1-1.5 cm margin was marked around that point. The main outcome measure was the closest final margin diameter, especially the deep ones. Other outcome measures were the core biopsies' sensitivity, specificity, and negative predictive value. Complications were recorded. Results: The final margins of 10 patients undergoing intraoperative core biopsies and 20 matched controls were analyzed. One patient had two positive cores and final negative margins after modifying the resection accordingly. Another patient had a positive biopsy diagnosed only on final pathology, and one close final margin. Patients that were operated with the new technique had larger margins compared to the controls: median (interquartile range) closest margin 5.95 (3.97; 9.63) mm versus 4 (2.25; 5) mm (p = 0.074) and median deep margin 8.6 (6.16; 10) mm versus 5 (3;10) mm (p = 0.411), respectively. There were no complications. Conclusion: A novel pre-resection intraoperative biopsy technique is presented. Core biopsies taken during glossectomies have the potential to prevent inadequate margins. Level of evidence: 3 Laryngoscope, 2022.
Article
Full-text available
Triple-negative breast cancer (TNBC) is characterized by a high rate of systemic metastasis, insensitivity to conventional treatment and susceptibility to drug resistance, resulting in a poor patient prognosis. The immune checkpoint inhibitors (ICIs) represented by antibodies of programmed death receptor 1 (PD-1) and programmed death receptor ligand 1 (PD-L1) have provided new therapeutic options for TNBC. However, the efficacy of PD-1/PD-L1 blockade monotherapy is suboptimal immune response, which may be caused by reduced antigen presentation, immunosuppressive tumor microenvironment, interplay with other immune checkpoints and aberrant activation of oncological signaling in tumor cells. Therefore, to improve the sensitivity of TNBC to ICIs, suitable patients are selected based on reliable predictive markers and treated with a combination of ICIs with other therapies such as chemotherapy, radiotherapy, targeted therapy, oncologic virus and neoantigen-based therapies. This review discusses the current mechanisms underlying the resistance of TNBC to PD-1/PD-L1 inhibitors, the potential biomarkers for predicting the efficacy of anti-PD-1/PD-L1 immunotherapy and recent advances in the combination therapies to increase response rates, the depth of remission and the durability of the benefit of TNBC to ICIs.
Article
Evolutionary dynamics allows us to understand many changes happening in a broad variety of biological systems, ranging from individuals to complete ecosystems. It is also behind a number of remarkable organizational changes that happen during the natural history of cancers. These reflect tumour heterogeneity, which is present at all cellular levels, including the genome, proteome and phenome, shaping its development and interrelation with its environment. An intriguing observation in different cohorts of oncological patients is that tumours exhibit an increased proliferation as the disease progresses, while the timescales involved are apparently too short for the fixation of sufficient driver mutations to promote explosive growth. Here, we discuss how phenotypic plasticity, emerging from a single genotype, may play a key role and provide a ground for a continuous acceleration of the proliferation rate of clonal populations with time. We address this question by combining the analysis of real-time growth of non-small-cell lung carcinoma cells (N-H460) together with stochastic and deterministic mathematical models that capture proliferation trait heterogeneity in clonal populations to elucidate the contribution of phenotypic transitions on tumour growth dynamics.
Article
Full-text available
Colorectal cancer (CRC) is a leading cause of death worldwide. Despite advances in surgical and therapeutic management, tumor metastases and resistance to therapy still represent major hurdles. CRC risk is highly modifiable by lifestyle factors, including diet, which strongly influences both cancer incidence and related mortality. Galectin-3 (Gal-3) is a multifaceted protein involved in multiple pathophysiological pathways underlying chronic inflammation and cancer. Its versatility is given by the ability to participate in a wide range of tumor-promoting processes, including cell–cell/cell–matrix interactions, cell growth regulation and apoptosis, and the immunosuppressive tumor microenvironment. This review provides an updated summary of preclinical and observational human studies investigating the pathogenetic role of Gal-3 in intestinal inflammation and CRC, as well as the potential of Gal-3 activity inhibition by plant-source food-derived bioactive compounds to control CRC onset/growth. These studies highlight both direct and immuno-mediated effects of Gal-3 on tumor growth and invasiveness and its potential role as a CRC prognostic biomarker. Substantial evidence indicates natural food-derived Gal-3 inhibitors as promising candidates for CRC prevention and therapy. However, critical issues, such as their bioavailability and efficacy, in controlled human studies need to be addressed to translate research progress into clinical applications.
Article
IntroductionThe immune system plays an important role in breast cancer. Triple-negative and human epidermal growth factor receptor 2 (HER2)-positive breast cancers have a higher mutational burden and more neoantigens. This indicates that vaccination strategies are promising treatment options.Objective This article aims to discuss the principles of and evidence for vaccination strategies in breast cancer.Materials and methodsThe basic principles of therapeutic vaccination in breast cancer, different platforms and strategies, and clinical trial data available to date are presented.ResultsIn principle, either known shared antigens such as HER2 or mutant neoantigens can be used for vaccination. There are various vaccination platforms (e.g., synthetic peptides or mRNA) with different strengths and limitations. Randomized trial results are so far only available for peptide vaccines against HER2. In contrast, personalized mRNA vaccines against neoepitopes are promising, but proof of efficacy is still pending in randomized trials.Conclusion Vaccination strategies have the potential to improve survival of patients with breast cancer.
Article
Pseudokinases, so named because they lack conserved canonical amino acids that define their catalytically-active relatives, have evolved new biological functions in both prokaryotic and eukaryotic organisms. Human PSKH2 is closely related to the canonical kinase PSKH1, which maps to the CAMK family of protein kinases. Primates encode PSKH2 in the form of a pseudokinase, which is predicted to be catalytically inactive due to loss of the invariant catalytic Asp residue. Although the biological role(s) of vertebrate PSKH2 proteins remains unclear, we previously identified species-level adaptions in PSKH2 that have led to the appearance of kinase or pseudokinase variants in vertebrate genomes alongside a canonical PSKH1 paralog. In this paper we confirm that PSKH2 lacks detectable protein phosphotransferase activity, and exploit structural informatics, biochemistry and cellular proteomics to characterise vertebrate PSKH2 orthologues. AlphaFold 2-based structural analysis predicts roles for both the PSKH2 N- and C- regions that flank the pseudokinase core, and cellular truncation analysis confirms that the N-terminal domain, which contains a conserved myristoylation site, is required for stable human PSKH2 expression and localisation to a membrane-rich subcellular fraction containing mitochondrial proteins. Using mass spectrometry-based proteomics, we confirm that PSKH2 is part of a cellular mitochondrial protein network, and that its expression is regulated through client-status within the HSP90/Cdc37 molecular chaperone system. HSP90 interactions are mediated through binding to the PSKH2 C-terminal tail, land we predict that this region acts as both a cis and trans regulatory element, driving outputs from the PSKH2 pseudokinase domain are important for functional signalling.
Article
Full-text available
To characterize somatic alterations in colorectal carcinoma, we conducted a genome-scale analysis of 276 samples, analysing exome sequence, DNA copy number, promoter methylation and messenger RNA and microRNA expression. A subset of these samples (97) underwent low-depth-of-coverage whole-genome sequencing. In total, 16% of colorectal carcinomas were found to be hypermutated: three-quarters of these had the expected high microsatellite instability, usually with hypermethylation and MLH1 silencing, and one-quarter had somatic mismatch-repair gene and polymerase μ (POLE) mutations. Excluding the hypermutated cancers, colon and rectum cancers were found to have considerably similar patterns of genomic alteration. Twenty-four genes were significantly mutated, and in addition to the expected APC, TP53, SMAD4, PIK3CA and KRAS mutations, we found frequent mutations in ARID1A, SOX9 and FAM123B. Recurrent copy-number alterations include potentially drug-targetable amplifications of ERBB2 and newly discovered amplification of IGF2. Recurrent chromosomal translocations include the fusion of NAV2 and WNT pathway member TCF7L1. Integrative analyses suggest new markers for aggressive colorectal carcinoma and an important role for MYC-directed transcriptional activation and repression.
Article
Full-text available
Cell-based therapy has been viewed as a promising alternative to organ transplantation, but cell transplantation aimed at organ repair is not always possible. Here we show that the mouse lymph node can support the engraftment and growth of healthy cells from multiple tissues. Direct injection of hepatocytes into a single mouse lymph node generated enough ectopic liver mass to rescue the survival of mice with lethal metabolic disease. Furthermore, thymuses transplanted into single lymph nodes of athymic nude mice generated functional immune systems that were capable of rejecting allogeneic and xenogeneic grafts. Additionally, pancreatic islets injected into the lymph nodes of diabetic mice restored normal glucose control. Collectively, these results suggest the practical approach of targeting lymph nodes to restore, maintain or improve tissue and organ functions.
Article
Full-text available
Fibroblast growth factors are a family of ligands that bind to four different types of cell surface receptor entitled, FGR1, FGFR2, FGFR3, and FGFR4. These receptors differ in their ligand binding affinity and tissue distribution. The prototypical receptor structure is that of an extracellular region comprising three immunoglobulin-like domains, a hydrophobic transmembrane segment and a split intracellular tyrosine kinase domain. Alternative gene splicing affecting the extracellular third immunoglobulin loop also creates different receptor isoforms entitled FGFRIIIb and FGFRIIIc.Somatic FGFR mutations are implicated in different types of cancer and germline FGFR mutations occur in developmental syndromes particularly those in which craniosynostosis is a feature. The mutations found in both conditions are often identical. Many somatic FGFR mutations in cancer are gain-of-function mutations of established pre-clinical oncogenic potential. Gene amplification can also occur with 19-22% of squamous cell lung cancers for example having amplification of FGFR1. Ontologic comparators can be informative such as aberrant spermatogenesis being implicated in both spermatocytic seminomas and Apert syndrome. The former arises from somatic FGFR3 mutations and Apert syndrome arises from germline FGFR2 mutations. Finally therapeutics directed at FGF/FGFR inhibition are a promising subject for clinical trials.
Article
Full-text available
The demonstration of induced pluripotency and direct lineage conversion has led to remarkable insights regarding the roles of transcription factors and chromatin regulators in mediating cell state transitions. Beyond its considerable implications for regenerative medicine, this body of work is highly relevant to multiple stages of oncogenesis, from the initial cellular transformation to the hierarchical organization of established malignancies. Here, we review conceptual parallels between the respective biological phenomena, highlighting important interrelationships among transcription factors, chromatin regulators, and preexisting epigenetic states. The shared mechanisms provide insights into oncogenic transformation, tumor heterogeneity, and cancer stem cell models.
Article
Full-text available
Although it has been hypothesized that some of the somatic mutations found in tumors may occur before tumor initiation, there is little experimental or conceptual data on this topic. To gain insights into this fundamental issue, we formulated a mathematical model for the evolution of somatic mutations in which all relevant phases of a tissue's history are considered. The model makes the prediction, validated by our empirical findings, that the number of somatic mutations in tumors of self-renewing tissues is positively correlated with the age of the patient at diagnosis. Importantly, our analysis indicates that half or more of the somatic mutations in certain tumors of self-renewing tissues occur before the onset of neoplasia. The model also provides a unique way to estimate the in vivo tissue-specific somatic mutation rates in normal tissues directly from the sequencing data of tumors. Our results have substantial implications for the interpretation of the large number of genome-wide cancer studies now being undertaken.
Article
Full-text available
Head and neck squamous cell carcinoma (HNSCC) is a common, morbid, and frequently lethal malignancy. To uncover its mutational spectrum, we analyzed whole-exome sequencing data from 74 tumor-normal pairs. The majority exhibited a mutational profile consistent with tobacco exposure; human papillomavirus was detectable by sequencing DNA from infected tumors. In addition to identifying previously known HNSCC genes (TP53, CDKN2A, PTEN, PIK3CA, and HRAS), our analysis revealed many genes not previously implicated in this malignancy. At least 30% of cases harbored mutations in genes that regulate squamous differentiation (for example, NOTCH1, IRF6, and TP63), implicating its dysregulation as a major driver of HNSCC carcinogenesis. More generally, the results indicate the ability of large-scale sequencing to reveal fundamental tumorigenic mechanisms.
Article
Full-text available
Many individuals with multiple or large colorectal adenomas or early-onset colorectal cancer (CRC) have no detectable germline mutations in the known cancer predisposition genes. Using whole-genome sequencing, supplemented by linkage and association analysis, we identified specific heterozygous POLE or POLD1 germline variants in several multiple-adenoma and/or CRC cases but in no controls. The variants associated with susceptibility, POLE p.Leu424Val and POLD1 p.Ser478Asn, have high penetrance, and POLD1 mutation was also associated with endometrial cancer predisposition. The mutations map to equivalent sites in the proofreading (exonuclease) domain of DNA polymerases ɛ and δ and are predicted to cause a defect in the correction of mispaired bases inserted during DNA replication. In agreement with this prediction, the tumors from mutation carriers were microsatellite stable but tended to acquire base substitution mutations, as confirmed by yeast functional assays. Further analysis of published data showed that the recently described group of hypermutant, microsatellite-stable CRCs is likely to be caused by somatic POLE mutations affecting the exonuclease domain.
Article
Full-text available
Purpose: Vemurafenib, a selective inhibitor of BRAF(V600), has shown significant activity in BRAF(V600) melanoma but not in less than 10% of metastatic BRAF(V600) colorectal cancers (CRC), suggesting that studies of the unique hypermethylated phenotype and concurrent oncogenic activation of BRAF(mut) CRC may provide combinatorial strategies. Experimental design: We conducted comparative proteomic analysis of BRAF(V600E) melanoma and CRC cell lines, followed by correlation of phosphoinositide 3-kinase (PI3K) pathway activation and sensitivity to the vemurafenib analogue PLX4720. Pharmacologic inhibitors and siRNA were used in combination with PLX4720 to inhibit PI3K and methyltransferase in cell lines and murine models. Results: Compared with melanoma, CRC lines show higher levels of PI3K/AKT pathway activation. CRC cell lines with mutations in PTEN or PIK3CA were less sensitive to growth inhibition by PLX4720 (P = 0.03), and knockdown of PTEN expression in sensitive CRC cells reduced growth inhibition by the drug. Combined treatment of PLX4720 with PI3K inhibitors caused synergistic growth inhibition in BRAF-mutant CRC cells with both primary and secondary resistance. In addition, methyltransferase inhibition was synergistic with PLX4720 and decreased AKT activation. In vivo, PLX4720 combined with either inhibitors of AKT or methyltransferase showed greater tumor growth inhibition than PLX4720 alone. Clones with acquired resistance to PLX4720 in vitro showed PI3K/AKT activation with EGF receptor (EGFR) or KRAS amplification. Conclusions: We show that activation of the PI3K/AKT pathway is a mechanism of both innate and acquired resistance to BRAF inhibitors in BRAF(V600E) CRC and suggest combinatorial approaches to improve outcomes in this poor prognosis subset of patients.
Article
Full-text available
Dissecting Diversity Solid tumors are composed of functionally diverse tumor cells. The prevailing view is that this "intratumoral heterogeneity" arises from the accumulation of mutations during tumor growth, resulting in multiple genetically defined subclones of cells that respond in different ways to selective pressures such as chemotherapy. Kreso et al. (p. 543 , published online 13 December; see the Perspective by Marusyk and Polyak ) simultaneously monitored the genetic profiles and growth behavior of human colorectal cancer cells that were serially passaged in mice. Individual tumor cells within a uniform genetic lineage displayed extensive variation in survival, growth dynamics, and response to a chemotherapeutic drug. Thus, additional diversity-generating mechanisms such as epigenetic regulation or microenvironmental variability appear to operate within a genetic clone, endowing a subset of tumor cells with robust survival potential, especially during stress.
Article
Full-text available
Pancreatic cancer is a highly lethal malignancy with few effective therapies. We performed exome sequencing and copy number analysis to define genomic aberrations in a prospectively accrued clinical cohort (n = 142) of early (stage I and II) sporadic pancreatic ductal adenocarcinoma. Detailed analysis of 99 informative tumours identified substantial heterogeneity with 2,016 non-silent mutations and 1,628 copy-number variations. We define 16 significantly mutated genes, reaffirming known mutations (KRAS, TP53, CDKN2A, SMAD4, MLL3, TGFBR2, ARID1A and SF3B1), and uncover novel mutated genes including additional genes involved in chromatin modification (EPC1 and ARID2), DNA damage repair (ATM) and other mechanisms (ZIM2, MAP2K4, NALCN, SLC16A4 and MAGEA6). Integrative analysis with in vitro functional data and animal models provided supportive evidence for potential roles for these genetic aberrations in carcinogenesis. Pathway-based analysis of recurrently mutated genes recapitulated clustering in core signalling pathways in pancreatic ductal adenocarcinoma, and identified new mutated genes in each pathway. We also identified frequent and diverse somatic aberrations in genes described traditionally as embryonic regulators of axon guidance, particularly SLIT/ROBO signalling, which was also evident in murine Sleeping Beauty transposon-mediated somatic mutagenesis models of pancreatic cancer, providing further supportive evidence for the potential involvement of axon guidance genes in pancreatic carcinogenesis.
Article
Full-text available
Changes in DNA methylation, whether hypo- or hyper-methylation, have been shown to be associated with progression of colorectal cancer. Methylation changes substantially in the progression from normal mucosa, to adenoma and to carcinoma. This phenomenon has not been studied extensively, and studies have been restricted to individual CpG islands rather than taking a whole genome approach. We aimed to study genome wide methylation changes in colorectal cancerWe obtained 10 fresh frozen normal tissue-cancer sample pairs, and 5 fresh frozen adenoma samples. These were run on the lllumina HumanMethylation27 whole genome methylation analysis system. Differential methylation between normal tissue, adenoma and carcinoma was analysed using Bayesian regression modelling, Gene Set Enrichment Analysis (GSEA) and Hierarchical clustering (HC). The highest-rated individual gene for differential methylation in carcinomas versus normal tissue and adenomas versus normal tissue was GRASP (p(adjusted) = 1.59x10(-5) , BF = 12.62, p(adjusted) = 1.68x10(-6) , BF = 14.53). The highest rated -gene when comparing carcinomas vs. adenomas was ATM (p(adjusted) = 2.0x10(-4) , BF = 10.17). Hierarchical clustering demonstrated poor clustering by the CIMP criteria for methylation. GSEA demonstrated methylation changes in the Netrin/DCC and SLIT/ROBO pathways. Widespread changes in DNA methylation are seen in the transition from adenoma to carcinoma. The finding that GRASP, which encodes the general receptor for phosphoinositides-1 associated scaffold proteinwas differentially methylated in colorectal cancer is interesting. This may be a potential biomarker for colorectal cancer. Copyright © 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Article
Full-text available
Substantial evidence supports the concept that cancers are organized in a cellular hierarchy with cancer stem cells (CSCs) at the apex. To date, the primary evidence for CSCs derives from transplantation assays, which have known limitations. In particular, they are unable to report on the fate of cells within the original human tumor. Due to the difficulty in measuring tumor characteristics in patients, cellular organization and other aspects of cancer dynamics have not been quantified directly, although they likely play a fundamental role in tumor progression and therapy response. As such, new approaches to study CSCs in patient-derived tumor specimens are needed. In this study we exploited ultra-deep single-molecule genomic data derived from multiple microdissected colorectal cancer glands per tumor, along with a novel quantitative approach to measure tumor characteristics, define patient-specific tumor profiles, and infer tumor ancestral trees. We demonstrate that each cancer is unique in terms of its cellular organization, molecular heterogeneity, time from malignant transformation, and rate of mutation and apoptosis. Importantly, we estimated CSC fractions between 0.5% and 4%, indicative of a hierarchical organization responsible for long-lived CSC lineages, with variable rates of symmetric cell division. We also observed extensive molecular heterogeneity, both between and within individual cancer glands, suggesting a complex hierarchy of mitotic clones. Our framework enables the measurement of clinically relevant patient-specific characteristics in vivo, providing insight into the cellular organization and dynamics of tumor growth, with implications for personalized patient care.
Article
Full-text available
We analysed primary breast cancers by genomic DNA copy number arrays, DNA methylation, exome sequencing, messenger RNA arrays, microRNA sequencing and reverse-phase protein arrays. Our ability to integrate information across platforms provided key insights into previously defined gene expression subtypes and demonstrated the existence of four main breast cancer classes when combining data from five platforms, each of which shows significant molecular heterogeneity. Somatic mutations in only three genes (TP53, PIK3CA and GATA3) occurred at >10% incidence across all breast cancers; however, there were numerous subtype-associated and novel gene mutations including the enrichment of specific mutations in GATA3, PIK3CA and MAP3K1 with the luminal A subtype. We identified two novel protein-expression-defined subgroups, possibly produced by stromal/microenvironmental elements, and integrated analyses identified specific signalling pathways dominant in each molecular subtype including a HER2/phosphorylated HER2/EGFR/phosphorylated EGFR signature within the HER2-enriched expression subtype. Comparison of basal-like breast tumours with high-grade serous ovarian tumours showed many molecular commonalities, indicating a related aetiology and similar therapeutic opportunities. The biological finding of the four main breast cancer subtypes caused by different subsets of genetic and epigenetic abnormalities raises the hypothesis that much of the clinically observable plasticity and heterogeneity occurs within, and not across, these major biological subtypes of breast cancer.
Article
Full-text available
Scientists working with single-nucleotide variants (SNVs), inferred by next-generation sequencing software, often need further information regarding true variants, artifacts and sequence coverage gaps. In clinical diagnostics, e.g. SNVs must usually be validated by visual inspection or several independent SNV-callers. We here demonstrate that 0.5-60% of relevant SNVs might not be detected due to coverage gaps, or might be misidentified. Even low error rates can overwhelm the true biological signal, especially in clinical diagnostics, in research comparing healthy with affected cells, in archaeogenetic dating or in forensics. For these reasons, we have developed a package called pibase, which is applicable to diploid and haploid genome, exome or targeted enrichment data. pibase extracts details on nucleotides from alignment files at user-specified coordinates and identifies reproducible genotypes, if present. In test cases pibase identifies genotypes at 99.98% specificity, 10-fold better than other tools. pibase also provides pair-wise comparisons between healthy and affected cells using nucleotide signals (10-fold more accurately than a genotype-based approach, as we show in our case study of monozygotic twins). This comparison tool also solves the problem of detecting allelic imbalance within heterozygous SNVs in copy number variation loci, or in heterogeneous tumor sequences.
Article
Full-text available
Small-cell lung cancer (SCLC) is an exceptionally aggressive disease with poor prognosis. Here, we obtained exome, transcriptome and copy-number alteration data from approximately 53 samples consisting of 36 primary human SCLC and normal tissue pairs and 17 matched SCLC and lymphoblastoid cell lines. We also obtained data for 4 primary tumors and 23 SCLC cell lines. We identified 22 significantly mutated genes in SCLC, including genes encoding kinases, G protein-coupled receptors and chromatin-modifying proteins. We found that several members of the SOX family of genes were mutated in SCLC. We also found SOX2 amplification in ∼27% of the samples. Suppression of SOX2 using shRNAs blocked proliferation of SOX2-amplified SCLC lines. RNA sequencing identified multiple fusion transcripts and a recurrent RLF-MYCL1 fusion. Silencing of MYCL1 in SCLC cell lines that had the RLF-MYCL1 fusion decreased cell proliferation. These data provide an in-depth view of the spectrum of genomic alterations in SCLC and identify several potential targets for therapeutic intervention.
Article
Full-text available
Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide and shows a propensity to metastasize and infiltrate adjacent and more distant tissues. HCC is associated with multiple risk factors, including hepatitis B virus (HBV) infection, which is especially prevalent in China. Here, we used exome sequencing to identify somatic mutations in ten HBV-positive individuals with HCC with portal vein tumor thromboses (PVTTs), intrahepatic metastases. Both C:G>A:T and T:A>A:T transversions were frequently found among the 331 non-silent mutations. Notably, ARID1A, which encodes a component of the SWI/SNF chromatin remodeling complex, was mutated in 14 of 110 (13%) HBV-associated HCC specimens. We used RNA interference to assess the roles of 91 of the confirmed mutated genes in cellular survival. The results suggest that seven of these genes, including VCAM1 and CDK14, may confer growth and infiltration capacity to HCC cells. This study provides a view of the landscape of somatic mutations that may be implicated in advanced HCC.
Article
Full-text available
Esophageal cancer ranks sixth in cancer death. To explore its genetic origins, we conducted exomic sequencing on 11 esophageal adenocarcinomas (EAC) and 12 esophageal squamous cell carcinomas (ESCC) from the United States. Interestingly, inactivating mutations of NOTCH1 were identified in 21% of ESCCs but not in EACs. There was a substantial disparity in the spectrum of mutations, with more indels in ESCCs, A:T>C:G transversions in EACs, and C:G>G:C transversions in ESCCs (P < 0.0001). Notably, NOTCH1 mutations were more frequent in North American ESCCs (11 of 53 cases) than in ESCCs from China (1 of 48 cases). A parallel analysis found that most mutations in EACs were already present in matched Barrett esophagus. These discoveries highlight key genetic differences between EACs and ESCCs and between American and Chinese ESCCs, and suggest that NOTCH1 is a tumor suppressor gene in the esophagus. Finally, we provide a genetic basis for the evolution of EACs from Barrett esophagus. Significance: This is the first genome-wide study of mutations in esophageal cancer. It identifies key genetic differences between EACs and ESCCs including general mutation spectra and NOTCH1 loss-of-function mutations specific to ESCCs, shows geographic disparities between North American and Chinese ESCCs, and shows that most mutations in EACs are already present in matched Barrett esophagus. Cancer Discov; 2(10); 899–905. ©2012 AACR. Read the Commentary on this article by Collisson and Cho, p. 870. This article is highlighted in the In This Issue feature, p. 857.
Article
Full-text available
Colorectal tumours that are wild type for KRAS are often sensitive to EGFR blockade, but almost always develop resistance within several months of initiating therapy. The mechanisms underlying this acquired resistance to anti-EGFR antibodies are largely unknown. This situation is in marked contrast to that of small-molecule targeted agents, such as inhibitors of ABL, EGFR, BRAF and MEK, in which mutations in the genes encoding the protein targets render the tumours resistant to the effects of the drugs. The simplest hypothesis to account for the development of resistance to EGFR blockade is that rare cells with KRAS mutations pre-exist at low levels in tumours with ostensibly wild-type KRAS genes. Although this hypothesis would seem readily testable, there is no evidence in pre-clinical models to support it, nor is there data from patients. To test this hypothesis, we determined whether mutant KRAS DNA could be detected in the circulation of 28 patients receiving monotherapy with panitumumab, a therapeutic anti-EGFR antibody. We found that 9 out of 24 (38%) patients whose tumours were initially KRAS wild type developed detectable mutations in KRAS in their sera, three of which developed multiple different KRAS mutations. The appearance of these mutations was very consistent, generally occurring between 5 and 6 months following treatment. Mathematical modelling indicated that the mutations were present in expanded subclones before the initiation of panitumumab treatment. These results suggest that the emergence of KRAS mutations is a mediator of acquired resistance to EGFR blockade and that these mutations can be detected in a non-invasive manner. They explain why solid tumours develop resistance to targeted therapies in a highly reproducible fashion.
Article
Full-text available
Characterization of the prostate cancer transcriptome and genome has identified chromosomal rearrangements and copy number gains and losses, including ETS gene family fusions, PTEN loss and androgen receptor (AR) amplification, which drive prostate cancer development and progression to lethal, metastatic castration-resistant prostate cancer (CRPC). However, less is known about the role of mutations. Here we sequenced the exomes of 50 lethal, heavily pre-treated metastatic CRPCs obtained at rapid autopsy (including three different foci from the same patient) and 11 treatment-naive, high-grade localized prostate cancers. We identified low overall mutation rates even in heavily treated CRPCs (2.00 per megabase) and confirmed the monoclonal origin of lethal CRPC. Integrating exome copy number analysis identified disruptions of CHD1 that define a subtype of ETS gene family fusion-negative prostate cancer. Similarly, we demonstrate that ETS2, which is deleted in approximately one-third of CRPCs (commonly through TMPRSS2:ERG fusions), is also deregulated through mutation. Furthermore, we identified recurrent mutations in multiple chromatin- and histone-modifying genes, including MLL2 (mutated in 8.6% of prostate cancers), and demonstrate interaction of the MLL complex with the AR, which is required for AR-mediated signalling. We also identified novel recurrent mutations in the AR collaborating factor FOXA1, which is mutated in 5 of 147 (3.4%) prostate cancers (both untreated localized prostate cancer and CRPC), and showed that mutated FOXA1 represses androgen signalling and increases tumour growth. Proteins that physically interact with the AR, such as the ERG gene fusion product, FOXA1, MLL2, UTX (also known as KDM6A) and ASXL1 were found to be mutated in CRPC. In summary, we describe the mutational landscape of a heavily treated metastatic cancer, identify novel mechanisms of AR signalling deregulated in prostate cancer, and prioritize candidates for future study.
Article
Full-text available
All cancers carry somatic mutations in their genomes. A subset, known as driver mutations, confer clonal selective advantage on cancer cells and are causally implicated in oncogenesis, and the remainder are passenger mutations. The driver mutations and mutational processes operative in breast cancer have not yet been comprehensively explored. Here we examine the genomes of 100 tumours for somatic copy number changes and mutations in the coding exons of protein-coding genes. The number of somatic mutations varied markedly between individual tumours. We found strong correlations between mutation number, age at which cancer was diagnosed and cancer histological grade, and observed multiple mutational signatures, including one present in about ten per cent of tumours characterized by numerous mutations of cytosine at TpC dinucleotides. Driver mutations were identified in several new cancer genes including AKT2, ARID1B, CASP8, CDKN1B, MAP3K1, MAP3K13, NCOR1, SMARCD1 and TBX3. Among the 100 tumours, we found driver mutations in at least 40 cancer genes and 73 different combinations of mutated cancer genes. The results highlight the substantial genetic diversity underlying this common disease.
Article
Full-text available
To correlate the variable clinical features of oestrogen-receptor-positive breast cancer with somatic alterations, we studied pretreatment tumour biopsies accrued from patients in two studies of neoadjuvant aromatase inhibitor therapy by massively parallel sequencing and analysis. Eighteen significantly mutated genes were identified, including five genes (RUNX1, CBFB, MYH9, MLL3 and SF3B1) previously linked to haematopoietic disorders. Mutant MAP3K1 was associated with luminal A status, low-grade histology and low proliferation rates, whereas mutant TP53 was associated with the opposite pattern. Moreover, mutant GATA3 correlated with suppression of proliferation upon aromatase inhibitor treatment. Pathway analysis demonstrated that mutations in MAP2K4, a MAP3K1 substrate, produced similar perturbations as MAP3K1 loss. Distinct phenotypes in oestrogen-receptor-positive breast cancer are associated with specific patterns of somatic mutations that map into cellular pathways linked to tumour biology, but most recurrent mutations are relatively infrequent. Prospective clinical trials based on these findings will require comprehensive genome sequencing.
Article
Full-text available
Blockade of programmed death 1 (PD-1), an inhibitory receptor expressed by T cells, can overcome immune resistance. We assessed the antitumor activity and safety of BMS-936558, an antibody that specifically blocks PD-1. We enrolled patients with advanced melanoma, non-small-cell lung cancer, castration-resistant prostate cancer, or renal-cell or colorectal cancer to receive anti-PD-1 antibody at a dose of 0.1 to 10.0 mg per kilogram of body weight every 2 weeks. Response was assessed after each 8-week treatment cycle. Patients received up to 12 cycles until disease progression or a complete response occurred. A total of 296 patients received treatment through February 24, 2012. Grade 3 or 4 drug-related adverse events occurred in 14% of patients; there were three deaths from pulmonary toxicity. No maximum tolerated dose was defined. Adverse events consistent with immune-related causes were observed. Among 236 patients in whom response could be evaluated, objective responses (complete or partial responses) were observed in those with non-small-cell lung cancer, melanoma, or renal-cell cancer. Cumulative response rates (all doses) were 18% among patients with non-small-cell lung cancer (14 of 76 patients), 28% among patients with melanoma (26 of 94 patients), and 27% among patients with renal-cell cancer (9 of 33 patients). Responses were durable; 20 of 31 responses lasted 1 year or more in patients with 1 year or more of follow-up. To assess the role of intratumoral PD-1 ligand (PD-L1) expression in the modulation of the PD-1-PD-L1 pathway, immunohistochemical analysis was performed on pretreatment tumor specimens obtained from 42 patients. Of 17 patients with PD-L1-negative tumors, none had an objective response; 9 of 25 patients (36%) with PD-L1-positive tumors had an objective response (P=0.006). Anti-PD-1 antibody produced objective responses in approximately one in four to one in five patients with non-small-cell lung cancer, melanoma, or renal-cell cancer; the adverse-event profile does not appear to preclude its use. Preliminary data suggest a relationship between PD-L1 expression on tumor cells and objective response. (Funded by Bristol-Myers Squibb and others; ClinicalTrials.gov number, NCT00730639.).
Article
Full-text available
All cancers carry somatic mutations. The patterns of mutation in cancer genomes reflect the DNA damage and repair processes to which cancer cells and their precursors have been exposed. To explore these mechanisms further, we generated catalogs of somatic mutation from 21 breast cancers and applied mathematical methods to extract mutational signatures of the underlying processes. Multiple distinct single- and double-nucleotide substitution signatures were discernible. Cancers with BRCA1 or BRCA2 mutations exhibited a characteristic combination of substitution mutation signatures and a distinctive profile of deletions. Complex relationships between somatic mutation prevalence and transcription were detected. A remarkable phenomenon of localized hypermutation, termed “kataegis,” was observed. Regions of kataegis differed between cancers but usually colocalized with somatic rearrangements. Base substitutions in these regions were almost exclusively of cytosine at TpC dinucleotides. The mechanisms underlying most of these mutational signatures are unknown. However, a role for the APOBEC family of cytidine deaminases is proposed. PaperClip
Article
Full-text available
Cancer evolves dynamically as clonal expansions supersede one another driven by shifting selective pressures, mutational processes, and disrupted cancer genes. These processes mark the genome, such that a cancer's life history is encrypted in the somatic mutations present. We developed algorithms to decipher this narrative and applied them to 21 breast cancers. Mutational processes evolve across a cancer's lifespan, with many emerging late but contributing extensive genetic variation. Subclonal diversification is prominent, and most mutations are found in just a fraction of tumor cells. Every tumor has a dominant subclonal lineage, representing more than 50% of tumor cells. Minimal expansion of these subclones occurs until many hundreds to thousands of mutations have accumulated, implying the existence of long-lived, quiescent cell lineages capable of substantial proliferation upon acquisition of enabling genomic changes. Expansion of the dominant subclone to an appreciable mass may therefore represent the final rate-limiting step in a breast cancer's development, triggering diagnosis. PaperClip
Article
Full-text available
Cancer Gene Islands Human tumors are riddled with genomic alterations that rearrange, remove, amplify, or otherwise disrupt a wide spectrum of genes, and a key challenge is identifying which of these alterations are causally involved in tumorigenesis. The role of recurrent hemizygous focal deletions is especially puzzling because these deletions preferentially affect certain chromosomal regions and result in the loss of one copy of a whole cluster of adjacent genes. Solimini et al. (p. 104 , published online 24 May; see the Perspective by Greenman ) found that these deletions span genomic regions that are enriched in genes that negatively regulate cell proliferation. The cumulative reduction in dosage and tumor suppressive function of the genes within these “cancer gene islands” may represent a critical factor driving tumor growth.
Article
Full-text available
The use of a priori knowledge in the alignment of targeted sequencing data is investigated using computational experiments. Adapting a Needleman–Wunsch algorithm to incorporate the genomic position information from the targeted capture, we demonstrate that alignment can be done to just the target region of interest. When in addition use is made of direct string comparison, an improvement of up to a factor of 8 in alignment speed compared to the fastest conventional aligner (Bowtie) is obtained. This results in a total alignment time in targeted sequencing of around 7 min for aligning approximately 56 million captured reads. For conventional aligners such as Bowtie, BWA or MAQ, alignment to just the target region is not feasible as experiments show that this leads to an additional 88% SNP calls, the vast majority of which are false positives (∼92%).
Article
Full-text available
The large chromosomal deletions frequently observed in cancer genomes are often thought to arise as a "two-hit" mechanism in the process of tumor-suppressor gene (TSG) inactivation. Using a murine model system of hepatocellular carcinoma (HCC) and in vivo RNAi, we test an alternative hypothesis, that such deletions can arise from selective pressure to attenuate the activity of multiple genes. By targeting the mouse orthologs of genes frequently deleted on human 8p22 and adjacent regions, which are lost in approximately half of several other major epithelial cancers, we provide evidence suggesting that multiple genes on chromosome 8p can cooperatively inhibit tumorigenesis in mice, and that their cosuppression can synergistically promote tumor growth. In addition, in human HCC patients, the combined down-regulation of functionally validated 8p TSGs is associated with poor survival, in contrast to the down-regulation of any individual gene. Our data imply that large cancer-associated deletions can produce phenotypes distinct from those arising through loss of a single TSG, and as such should be considered and studied as distinct mutational events.
Article
Full-text available
More than half of the cancer occurring today is preventable by applying knowledge that we already have. Tobacco, obesity, and physical inactivity are the modifiable causes of cancer that generate the most disease. Cancer burden can be reduced by alterations in individual and population behaviors and by public health efforts as long as these changes are driven by sound scientific knowledge and social commitment to change. The obstacles to these efforts are societal and arise from the organization of institutions, including academia, and in the habits of daily life. To achieve maximal possible cancer prevention, we will need better ways to implement what we know and improved infrastructure that will better incentivize and support transdisciplinary, multilevel research and successful intervention.
Article
Full-text available
Clear cell renal cell carcinoma (ccRCC) is the most common kidney cancer and has very few mutations that are shared between different patients. To better understand the intratumoral genetics underlying mutations of ccRCC, we carried out single-cell exome sequencing on a ccRCC tumor and its adjacent kidney tissue. Our data indicate that this tumor was unlikely to have resulted from mutations in VHL and PBRM1. Quantitative population genetic analysis indicates that the tumor did not contain any significant clonal subpopulations and also showed that mutations that had different allele frequencies within the population also had different mutation spectrums. Analyses of these data allowed us to delineate a detailed intratumoral genetic landscape at a single-cell level. Our pilot study demonstrates that ccRCC may be more genetically complex than previously thought and provides information that can lead to new ways to investigate individual tumors, with the aim of developing more effective cellular targeted therapies.
Article
Full-text available
Recurrent mutations in isocitrate dehydrogenase 1 (IDH1) and IDH2 have been identified in gliomas, acute myeloid leukaemias (AML) and chondrosarcomas, and share a novel enzymatic property of producing 2-hydroxyglutarate (2HG) from α-ketoglutarate. Here we report that 2HG-producing IDH mutants can prevent the histone demethylation that is required for lineage-specific progenitor cells to differentiate into terminally differentiated cells. In tumour samples from glioma patients, IDH mutations were associated with a distinct gene expression profile enriched for genes expressed in neural progenitor cells, and this was associated with increased histone methylation. To test whether the ability of IDH mutants to promote histone methylation contributes to a block in cell differentiation in non-transformed cells, we tested the effect of neomorphic IDH mutants on adipocyte differentiation in vitro. Introduction of either mutant IDH or cell-permeable 2HG was associated with repression of the inducible expression of lineage-specific differentiation genes and a block to differentiation. This correlated with a significant increase in repressive histone methylation marks without observable changes in promoter DNA methylation. Gliomas were found to have elevated levels of similar histone repressive marks. Stable transfection of a 2HG-producing mutant IDH into immortalized astrocytes resulted in progressive accumulation of histone methylation. Of the marks examined, increased H3K9 methylation reproducibly preceded a rise in DNA methylation as cells were passaged in culture. Furthermore, we found that the 2HG-inhibitable H3K9 demethylase KDM4C was induced during adipocyte differentiation, and that RNA-interference suppression of KDM4C was sufficient to block differentiation. Together these data demonstrate that 2HG can inhibit histone demethylation and that inhibition of histone demethylation can be sufficient to block the differentiation of non-transformed cells.
Article
Recent technologic advances have permitted higher resolution and more rapid analysis of individual cancer genomes at the single-nucleotide level. Such advances have shown bewildering intertumor heterogeneity with limited somatic alterations shared between tumors of the same histopathologic subtype. Exacerbating such complexity, increasing evidence of intratumor genetic heterogeneity (ITH) is emerging, both within individual tumor biopsies and spatially separated between biopsies of the same tumor. Sequential analysis of tumors has also revealed evidence that ITH temporally evolves during the disease course. ITH has implications for predictive or prognostic biomarker strategies, where the tumor subclone that may ultimately influence therapeutic outcome may evade detection because of its absence or presence at low frequency at diagnosis or because of its regional separation from the tumor biopsy site. In this review, the implications of "trunk and branch" tumor evolution for drug discovery approaches and emerging evidence that low-frequency somatic events may drive t