Article

X chromosomal abnormalities in basal-like human breast cancer

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Abstract

Sporadic basal-like cancers (BLC) are a distinct class of human breast cancers that are phenotypically similar to BRCA1-associated cancers. Like BRCA1-deficient tumors, most BLC lack markers of a normal inactive X chromosome (Xi). Duplication of the active X chromosome and loss of Xi characterized almost half of BLC cases tested. Others contained biparental but nonheterochromatinized X chromosomes or gains of X chromosomal DNA. These abnormalities did not lead to a global increase in X chromosome transcription but were associated with overexpression of a small subset of X chromosomal genes. Other, equally aneuploid, but non-BLC rarely displayed these X chromosome abnormalities. These results suggest that X chromosome abnormalities contribute to the pathogenesis of BLC, both inherited and sporadic.

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... Three different sources of transcriptomic data were analyzed. Two of them, TBC (Tokushima Breast care Clinic study) and HBS (Harvard Breast SPORE blood and tissue repository), were publicly available [26,27] and the third one, SUH (Salamanca University Hospital), resulted from analyses of patient samples (fifteen tumor and one normal sample) obtained at our University Hospital in Salamanca. Briefly, 10-20 mg of each sample was used to isolate total RNA using PureLink RNA Mini Kit (Ambion, Life Technologies, Carlsbad, CA, USA) according to the manufacturer's instructions. ...
... gov/ gds), with accession no. GSE3744 and GSE38959, respectively [27]. The array data from the SUH was analyzed using the dChip software [28]. ...
... To identify surface proteins differentially expressed in TNBC, we used a combination of genomic and proteomic approaches ( Fig. 1A and Supplementary Fig. 1). The genomic studies were performed using gene expression patient data freely available from two different studies (herewith termed TBC -Tokushima Breast Care Clinic study- [26], and HBS -Harvard Breast SPORE blood and tissue repository- [27]) or obtained from microarray analysis of patient samples from the Salamanca University Hospital (SUH). These datasets were selected because when we started our study, they were the only ones that included transcriptomic data from tumoral as well as normal breast tissue, allowing comparative analyses. ...
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Background Despite the incorporation of novel therapeutics, advanced triple negative breast cancer (TNBC) still represents a relevant clinical problem. Considering this, as well as the clinical efficacy of antibody-drug conjugates (ADCs), we aimed at identifying novel ADC targets that could be used to treat TNBC. Methods Transcriptomic analyses were performed on TNBC and normal samples from three different studies. Plasma membrane proteins of three cell lines representative of the TNBC subtype were identified by cell surface biotinylation or plasma membrane isolation, followed by analyses of cell surface proteins using the Surfaceome online tool. Immunofluorescence and western studies were used to characterize the action of a CD98hc-directed ADC, which was prepared by in house coupling of emtansine to an antibody that recognized the ectodomain of CD98hc. Xenografted TNBC cells were used to analyze the antitumoral properties of the anti-CD98hc ADC. Results Comparative genomic studies between normal breast and TNBC tissues, together with proteomic and bioinformatic analyses resulted in the elaboration of a catalog of potential ADC targets. One of them, the CD98hc transmembrane protein, was validated as an ADC target. An antibody recognizing the ectodomain of CD98hc efficiently internalized and reached the lysosomal compartment. An emtansine-based ADC derived from such antibody was prepared and showed antitumoral properties in TNBC in vitro and in vivo models. Mechanistically, the anti-CD98hc ADC blocked cell cycle progression, that was followed by cell death caused by mitotic catastrophe. Conclusions This work describes a list of potential ADC targets in TNBC and validates one of them, the transmembrane protein CD98hc. The studies presented here also demonstrate the robustness of the multiomic approach herewith described to identify novel potential ADC targets.
... In the Curtis Breast Statistics (FC: 3.239) (23). In the Richardson Breast 2 Statistics data set, SLC7A5 was more upregulated in ductal breast carcinoma tissue than normal tissue (FC: 3.620) (24). In the Finak Breast Statistics data set, SLC7A8 was found to be highly expressed in invasive breast carcinoma (FC: 4.259) (22). ...
... SLC7A8 was found to be highly expressed in mixed lobular and ductal breast carcinoma (FC: 3.448) in TCGA, and mucinous breast carcinoma (FC: 2.323) in Curtis Breast data set versus normal samples (23). While in the Richardson Breast 2 Statistics data set, SLC7A8 was found to be lowly expressed in ductal breast carcinoma (FC: 2.135) (24 (24). In the Finak's data set (22), SLC38A2 was more lowly expressed in the ductal breast carcinoma samples (FC: 23.038) than the normal samples (see Table 1). ...
... SLC7A8 was found to be highly expressed in mixed lobular and ductal breast carcinoma (FC: 3.448) in TCGA, and mucinous breast carcinoma (FC: 2.323) in Curtis Breast data set versus normal samples (23). While in the Richardson Breast 2 Statistics data set, SLC7A8 was found to be lowly expressed in ductal breast carcinoma (FC: 2.135) (24 (24). In the Finak's data set (22), SLC38A2 was more lowly expressed in the ductal breast carcinoma samples (FC: 23.038) than the normal samples (see Table 1). ...
Article
Background: Breast cancer (BC) is a highly heterogeneous disease. Solute carriers (SLCs) have been involved in the tumor progression of various cancer types. This study aimed to evaluate the role of these SLC-related glutamine transporters in the prognosis of BC patients by bioinformatics analysis. Methods: This study examined the transcription and prognostic data for glutamine-related transporters in BC from Oncomine Database, which is currently the largest oncogene microarray database platform in the world. As well as Gene Expression Profiling Interactive Analysis (GEPIA), Kaplan-Meier (K-M), and cBioPortal online resources. The Tumor Immune Estimation Resource (TIMER) and GEPIA were also used to examine the relationship between SLCs and immune cell infiltration. Results: The expression levels of SLC1A5, SLC3A2, SLC7A5, SLC7A8, and SLC38A1 were higher in BC tissues than normal breast tissues, but the expression level of SLC6A14 was lower. The expression levels of SLC7A5, SLC7A8, SLC6A14, and SLC38A2 were related to a later clinical tumor stage. In the K-M analyses, The K-M curves revealed that patients with high SLC1A5 expression had a poor prognosis (OS HR =1.28, 95% CI: 1.06-1.54; P=0.01). The high expression of SLC3A2 was significantly correlated with a poor prognosis (DMFS HR =1.19, 95% CI: 1.02-1.39; P=0.027). Increased SLC7A5 mRNA levels and decreased SLC7A8 mRNA levels were significantly associated with a poor prognosis in terms of OS, RFS, DMFS and PPS. The high expression of SLC6A14 was significantly correlated with a poor prognosis (PPS HR =1.35, 95% CI: 1.07-1.7; P=0.011). The high expression of SLC38A1 was correlated with a better prognosis than low expression of SLC38A1 (RFS HR =0.84, 95% CI: 0.76-0.93; P=0.00077; DMFS HR =0.78, 95% CI: 0.67-0.91; P=0.0013). The infiltration of immune cells and their marker genes were associated with SLC1A5, SLC3A2, SLC7A5, SLC7A8, SLC6A14, SLC38A1, and SLC38A2 expression. SLC7A5, SLC7A8, SLC38A1, and SLC38A2 have the potential to regulate polarization in tumor-associated macrophages. Conclusions: SLC7A5, SLC7A8, SLC38A1, and SLC38A2 may regulate the polarization of tumor-associated macrophages (TAMs). SLC1A5, SLC3A2, SLC7A5, and SLC6A14 may be promising biomarkers for the BC diagnosis and may represent potential therapeutic targets for these patients.
... Certain genetic mutations typically lead to distinct subtypes of tumors. Sporadic basal-like cancer has phenotypically similarity and relationships with BRCA (BC susceptibility gene)-associated BC (Richardson et al., 2006;Alimonti et al., 2010). BRCA1 and BRCA2 are tumor suppressor genes with critical roles in DNA damage repair; their germline or somatic mutations are closely related to carcinogenesis, including BC and high-grade serous cancer of the gynecological tract (particularly the fallopian tube, ovary, and peritoneum) (Foulkes and Shuen, 2013). ...
... In the subsequent validation of the results, we used TNBC data from TCGA for internal validation and GEO datasets GSE3744 (Richardson et al., 2006;Alimonti et al., 2010) and GSE25307 for external validation. The research subjects used in our work and relevant clinical traits information are shown in Table 1. ...
... We identified highly connected genes within modules as candidate genes to analyze the changes in transcriptional expression levels in the BRCA1-MUT, BRCA2-MUT, and WT groups compared with normal samples. In the validation cohort, we performed DEG analysis between TNBC expression profiles and para-cancerous tissues to achieve internal validation of candidate genes; GSE3744 (Richardson et al., 2006;Alimonti et al., 2010) and GSE25307 were downloaded for external validation, using the limma package and P < 0.05 was taken as the criterion for a significant difference. Furthermore, we analyzed and evaluated the mRNA expression levels of candidate genes using an R package combined with standardized TPM expression data for several subtype groups (sub-division into three groups with TNBC included or excluded) to reflect the potential effects of TNBC subtypes on the final results. ...
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Background: BRCA 1/2 mutations are closely related to high lifetime risk of breast cancer (BC). The objective of this study was to identify the genes, regulators, and immune-associated patterns underlying disease pathology in BC with BRCA1/2 somatic mutations and their associations with clinical traits. Methods: RNA sequencing data and clinical information from The Cancer Genome Atlas (TCGA; N = 36 BRCA1 -mutant BC; N = 49 BRCA2 -mutant BC; and N = 117 BRCA1/2 -wild-type BC samples) were used for discovery, which included consensus network analysis, function enrichment, and analysis of hub genes; other TCGA data ( N = 117 triple-negative BC) and two Gene Expression Omnibus database expression profiles were used as validation cohorts. Results: Consensus network analysis helped to identify specific co-expressed modules that showed positive correlations with tumor stage, number of positive lymph nodes, and margin status in BRCA1/2 -mutant BC but lacking correlations in BRCA1/2 -wild-type BC. Functional enrichment suggested potential mechanisms in BRCA1/2 carriers that could regulate the cell cycle, immune response, cellular metabolic processes, and cell migration, via enriched pathways including p53 and JAK–STAT signaling. Consensus network analysis identified the specific and common carcinogenic mechanisms involving BRCA mutations. Regulators cross-linking these modules include E2F or IRF transcription factor family, associated with cell cycle or immune response regulation module, respectively. Eight hub genes, including ISG15 , BUB1 , and TTK , were upregulated in several BRCA1/2 -mutant BC datasets and showed prognostic value in BC. Furthermore, their genetic expression was related to higher levels of immune infiltration in BRCA1/2 -mutant BC, which manifested as recruitment of T helper cells (Th1 cells), follicular helper T cells, and regulatory T cells, and T cell exhaustion. Moreover, important indicators for evaluation of BC immunotherapy, tumor mutational burden and neoantigen load also positively correlated with expression of some hub genes. Conclusion: We constructed a BRCA1/2 mutation-type-specific co-expressed gene network with related transcription factors and immune-associated patterns that could regulate and influence tumor metastasis and immune microenvironment, providing novel insights into the pathological process of this disease and the corresponding BRCA mutations.
... Next, we investigated the relationship between SIRT3 and HIF1A targets in human breast cancer cells. Gene expression profiling of seven normal breast samples and 40 ductal breast carcinomas revealed that SIRT3 expression is significantly lower (p = 3.53e −8 ) in breast carcinomas [52] ( Figure 5B). Several HIF1A target genes: SLC2A1/GLUT1, HK2, and LDHA, were significantly higher in the breast carcinomas than in the normal breast samples in the same data set [52] ( Figure 5B). ...
... Gene expression profiling of seven normal breast samples and 40 ductal breast carcinomas revealed that SIRT3 expression is significantly lower (p = 3.53e −8 ) in breast carcinomas [52] ( Figure 5B). Several HIF1A target genes: SLC2A1/GLUT1, HK2, and LDHA, were significantly higher in the breast carcinomas than in the normal breast samples in the same data set [52] ( Figure 5B). RNA-seq data showing HIF1A enrichment and glycolysis in NDV-infected cells recorded high expressions of HIF1A target genes ( Figure 5C). ...
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Lacking a self-contained metabolism network, viruses have evolved multiple mechanisms for rewiring the metabolic system of their host to hijack the host's metabolic resources for replication. Newcastle disease virus (NDV) is a paramyxovirus, as an oncolytic virus currently being developed for cancer treatment. However, how NDV alters cellular metabolism is still far from fully understood. In this study, we show that NDV infection reprograms cell metabolism by increasing glucose utilization in the glycolytic pathway. Mechanistically, NDV induces mitochondrial damage, elevated mitochondrial reactive oxygen species (mROS) and ETC dysfunction. Infection of cells depletes nucleotide triphosphate levels, resulting in elevated AMP:ATP ratios, AMP-activated protein kinase (AMPK) phosphorylation, and MTOR crosstalk mediated autophagy. In a time-dependent manner, NDV shifts the balance of mitochondrial dynamics from fusion to fission. Subsequently, PINK1-PRKN-dependent mitophagy was activated, forming a ubiquitin chain with MFN2 (mitofusin 2), and molecular receptor SQSTM1/p62 recognized damaged mitochondria. We also found that NDV infection induces NAD+-dependent deacetylase SIRT3 loss via mitophagy to engender HIF1A stabilization, leading to the switch from oxidative phosphorylation (OXPHOS) to aerobic glycolysis. Overall, these studies support a model that NDV modulates host cell metabolism through PINK1-PRKN-dependent mitophagy for degrading SIRT3.Abbreviations: AMPK: AMP-activated protein kinase; CCCP: carbonyl cyanide 3-chlorophenylhydrazone; ECAR: extracellular acidification rate; hpi: hours post infection LC-MS: liquid chromatography-mass spectrometry; mito-QC: mCherry-GFP-FIS1[mt101-152]; MFN2: mitofusin 2; MMP: mitochondrial membrane potential; mROS: mitochondrial reactive oxygen species; MOI: multiplicity of infection; 2-NBDG: 2-(N-(7-nitrobenz-2-oxa-1, 3-diazol-4-yl) amino)-2-deoxyglucose; NDV: newcastle disease virus; OCR: oxygen consumption rate; siRNA: small interfering RNA; SIRT3: sirtuin 3; TCA: tricarboxylic acid; TCID50: tissue culture infective doses.
... Additionally, Ramaswamy et al. [32] reported that the low mRNA level of EIF3F was found in different kinds of breast cancer (P < 0.001, fold change = −3.372). A low expression level of EIF3G was found in ductal breast carcinoma in the Richardson dataset [33]. Furthermore, Ma et al. [34] demonstrated that the mRNA expression of according to the data from TCGA, as well as in ductal breast carcinoma (P < 0.001, fold change = −2.071) ...
... Furthermore, Ma et al. [34] demonstrated that the mRNA expression of according to the data from TCGA, as well as in ductal breast carcinoma (P < 0.001, fold change = −2.071) based on the data from the study of Richardson et al [33]. Consistent with the results of GEPIA and TCGA, it indicated significantly higher EIF3B expression and lower EIF3D/ F/ L in breast cancer tissues. ...
Article
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The EIF3 gene family is essential in controlling translation initiation during the cell cycle. The significance of the EIF3 subunits as prognostic markers and therapeutic targets in breast cancer is not yet clear. We analyzed the expression of EIF3 subunits in breast cancer on the GEPIA and Oncomine databases and compared their expression in breast cancer and normal tissues using BRCA data downloaded from TCGA. Then we performed clinical survival analysis on the Kaplan–Meier Plotter database and clinicopathologic analysis on the bc-genexMiner v4.1 database. And EIF3B was chosen for mutation analysis via the Cancer SEA online tool. Meanwhile, we performed the immunohistochemical assay, real-time RT-PCR, and Western blotting to analyze EIF3B expression levels in breast cancer. An EIF3B knockdown and a negative control cell line were conducted for MTT assay and cell cycle analysis to assess cell growth. Specifically, the results of TCGA and online databases demonstrated that upregulated EIF3B was associated with poorer overall and advanced tumor progression. We also confirmed that EIF3B was more highly expressed in breast cancer cells and tissues than normal and correlated with a worse outcome. And knockdown of EIF3B expression inhibited the cell cycle and proliferation. Furthermore, EIF3B was highly mutated in breast cancer. Collectively, our results suggested EIF3B as a potential prognostic marker and therapeutic target for breast cancer.
... such as pancreatic cancer, samples of cancer metastasis, oesophageal cancer, and adrenocortical cancer, but these were not included in our scope of our panel of cancer samples. (Beier et al. 2007), GSE15209 (Pollard et al. 2009) 2-Breast Cancer Over-expressed GSE13915 ), GSE7904 (Richardson et al. 2006) 3-Breast Cancer Decreased GSE15131 (Crowder et al. 2009), GSE5051 (Jong et al. 2007), GSE6779 (Jönsson et al. 2007) In GSE15131 (Crowder et al. 2009) amplification study, MCF-7 showed decrease expression when compared with germ cells. In GSE5051 (Jong et al. 2007) MCF-7 also expressed downregulation. ...
... Several functions are executed by the proteins encoded by these genes. These include embryological development, cell cycle control, immune modulation, regulation of transcription, chromatin remodelling, and DNA repair (Richardson et al. 2006, Weinreba, Colgan 2004. Through DNA repair, these proteins will maintain the genome integrity, thus acting as tumour suppressors. ...
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Cancer imposes continuous challenges on global health, and the trend of its incidence will make it the leading cause of mortality in the twenty-first century (Robert, Vries & Hans 2010). Therefore, identifying novel-cancer antigens that can be used as biomarkers and targets for therapeutics has been a priority to minimize cancer morbidity and mortality rates (Grizzi et al. 2007). Cancer testis antigens genes’ (CTAs) characteristics of immune privilege restricted expression, aberrant expression in unrelated histological malignancies, and immunogenicity have made them a valuable family to be exploited for cancer research and clinical therapeutics (Joseph-Pietras et al. 2010; Shigematsu et al. 2010). Germ cell characteristics, such as global hypomethylation, telomerase activity, CTA expression, and the presence of several meiosis stage-specific proteins, are common features in cancer. Therefore, many sperm-specific proteins may contain novel-cancer testis antigens (Silina et al. 2011; Gjerstorff et al. 2010; Gjerstorff, Burns & Ditzel 2010). Through whole-genome profiling of male germline expression in mice, rats, and humans, several loci have shown a conserved sequence in meiotic and post-meiotic profiles. Though hybridization of the mice testis mRNA to human testis tissue, a microarray study revealed a positive signal of 81% from the clones (Sha et al. 2002). These are likely essential for sexual production, and several have detectable expression profiles in cancers. Therefore, as previously states, gametogenesis and carcinogenesis may share a similar molecular mechanism (Chalmel, Lardenois & Primig 2007). Given this, our research group has designed an in silico pipeline analysis that has identified a high number of candidate cancer-specific markers that could be promising in the oncology field. Using this approach, C4orf35, C13orf28, C18orf54, C20orf195, C22orf33, PPP4R4, SPACA1, and TMCO2 have been filtered. According to Hofmanna et al. (2008), gene expression in a CTA is restricted to the testis and cancer; furthermore, Mobasheri et al. (2007) found that a good CTA candidate should only be expressed in testis and cancer cell lines. Therefore, we analysed an expression profile of these genes in a panel of normal tissue samples by semi-quantitative RT-PCR using tailored primers for each candidate; b-actin was used as an unchanged and fixed endogenous gene reference. Only upon testis restricted gene expression will a gene be validated for screening in our designed panel of cancer samples. Our research is small in size, of an exploratory nature, and was not designed to quantify expression; rather, it is designed as a preliminary validation of several genes that were categorised for meiosis and cancer expression. However, our results should not be over-looked. In the given set of the experiment, the author has managed to identify C22orf33 and SPACA1 as potential candidates. In spite of having additional expression in the thymus, C18orf54 is also a good candidate. As will be demonstrated, all remaining genes, with the exception of TMCO2, could have potential use in the field of oncology field through the cautious interpretation of currently available data. Our study is not large enough to answer many questions related to these genes, provide further information on a putative function of these expressions, or validate the available data. As such, further experiments on a broader scale are warranted.
... To study the utility of the AMBB algorithm, a human gene expression dataset known as Pollen [21] and a mouse gene expression dataset, namely Buettner [22] are analyzed. The homo sapiens dataset also includes GDS3715 [23] and GSE7904 [24]. And we process all datasets to remove one-mapping multiple and duplicate genes. ...
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Biclustering algorithm is an effective tool for processing gene expression datasets. There are two kinds of data matrices, binary data and non-binary data, which are processed by biclustering method. A binary matrix is usually converted from pre-processed gene expression data, which can effectively reduce the interference from noise and abnormal data, and is then processed using a biclustering algorithm. However, biclustering algorithms of dealing with binary data have a poor balance between running time and performance. In this paper, we propose a new biclustering algorithm called the Adjacency Difference Matrix Binary Biclustering algorithm (AMBB) for dealing with binary data to address the drawback. The AMBB algorithm constructs the adjacency matrix based on the adjacency difference values, and the submatrix obtained by continuously updating the adjacency difference matrix is called a bicluster. The adjacency matrix allows for clustering of gene that undergo similar reactions under different conditions into clusters, which is important for subsequent genes analysis. Meanwhile, experiments on synthetic and real datasets visually demonstrate that the AMBB algorithm has high practicability.
... However, little is known about the dysregulation of the AKT Ser473 phosphorylation status in cancer cells. Several reports have indicated that PHLPP1 is downregulated in metastatic and aggressive breast cancer cells when compared with the levels in normal cells [17,18], but the mechanism of this downregulation of PHLPP1 in these cancer cells is not well studied. ...
Article
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Transmembrane prostate androgen-induced protein (TMEPAI), also known as PMEPA1, is highly expressed in many types of cancer and promotes oncogenic abilities. However, the mechanisms whereby TMEPAI facilitates tumorigenesis are not fully understood. We previously established TMEPAI-knockout (KO) cells from human triple-negative breast cancer (TNBC) cell lines and found that TMEPAI-KO cells showed reduced tumorigenic abilities. Here, we report that TMEPAI-KO cells upregulated the expression of pleckstrin homology (PH) domain and leucine-rich repeat protein phosphatase 1 (PHLPP1) and suppressed AKT Ser473 phosphorylation, which was consistent with TCGA dataset analysis. Additionally, the knockdown (KD) of PHLPP1 in TMEPAI-KO cells partially but significantly rescued AKT Ser473 phosphorylation, as well as in vitro and in vivo tumorigenic activities, thus showing that TMEPAI functions as an oncogenic protein through the regulation of PHLPP1 subsequent to AKT activation. Furthermore, we demonstrated that TMEPAI PPxY (PY) motifs are essential for binding to NEDD4-2, an E3 ubiquitin ligase, and PHLPP1-downregulatory ability. Moreover, TMEPAI enhanced the complex formation of PHLPP1 with NEDD4-2 and PHLPP1 polyubiquitination, which leads to its proteasomal degradation. These findings indicate that the PY motifs of TMEPAI suppress the amount of PHLPP1 and maintain AKT Ser473 phosphorylation at high levels to enhance the tumorigenic potentiality of TNBC.
... Many chromosomal regions showing uniparental disomy (UPD) are consistent and specific for tumor types and appear more frequently in solid tumors than leukemia [47]. UPD has been previously reported in breast cancer [48] [49] and other tumors. Mutated genes in UPD have been considered indicative of patient outcome with implications in response to chemotherapy. ...
... As reported by Richardson, high ATF5 expression was found in ductal breast carcinoma compared with normal tissues (fold change=1.760) [24]. Likewise, in Curtis's dataset, ATF6 was overexpressed in multiple types of BrCa, including tubular breast carcinoma with a fold change of 1.780, ductal breast carcinoma in situ with a fold change of 1.751, invasive ductal and invasive lobular breast carcinoma with a fold change of 1.731, breast carcinoma with a fold change of 1.630, medullary breast carcinoma with a fold change of 1.618, invasive ductal breast carcinoma with a fold change of 1.613, invasive lobular breast carcinoma with a fold change of 1.591, and invasive breast carcinoma with a fold change of 1.570, compared with normal breast tissues [23]. ...
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Background: To obtain a thorough comprehension of the profile and prognosis of activating transcription factor (ATF) family members in breast cancer. Method: We searched Oncomine, GEPIA, cBioPortal, Kaplan-Meier plotter, and CancerSEA databases to assess expression level, prognostic value, and functions of ATFs in breast cancer. Results: In breast cancer, we found that the expression levels of genes like ATF1, ATF5, and ATF6, were higher than in normal tissues. While the expression levels of ATF3, ATF4, ATF7 were lower in the former than in the latter. Similarly, the ATFs protein expressions were consistent with this in the Human Protein Atlas database. High expressions of ATF2, ATF4, and ATF6-7 were associated with good relapse-free survival. Increased expressions of ATF4 and ATF7 had high overall survival. Conversely, the mRNA expression of ATF1 was negatively correlated with distant metastasis-free survival. Similarly, high expression of ATF2 had reduced post-progression survival. Conclusions: ATF1 was a target of potential therapeutic interest for breast cancer, and ATF4 and ATF6-7 were potential prognostic factors in evaluating breast cancer.
... In Radvany dataset, signi cant low expression of SCN2B was found in BC samples compared to normal tissues (fold change: -2.892, p=0.002) [21]. Similarly, in other seven datasets, signi cant downregulation of SCN4B was found in BC tissues (all p<0.01) [21][22][23][24][25][26] (HR=0.64, 95% CI: 0.55-0.75, ...
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Background: Voltage-gated sodium (Nav) channels encoded by SCNs are heteromeric protein complexes containing pore-forming α subunits together with non-pore-forming β subunits. Ion channels play an important role in the regulation of many cellular processes during normal physiology, and increasingly recognized for their contribution to pathophysiology, including cancers. Numerous studies in the last years have reported the expression of SCNs in metastatic cells of many cancers and their upregulation have been evident in promoting migration, invasion and metastasis, whereas it remains unclear whether distinct SCNs family members play an important role in the development and progression of BC. Results: The study investigated the roles of SCNs in the prognosis of BC using ONCOMINE, UALCAN, Kaplan-Meier Plotter, GEPIA, Metascape, LinkedOmics databases. The results showed that transcriptional and proteinic expressions of 9 SCNs were downregulated in patients with BC, including SCN1A~4A, 7A, 9A and SCN2B~4B. low expressions of 11 SCNs members were found to be significantly associated with poorer overall survival (OS) in BC patients (P<0.01), including SCN2A, 3A, 5A, 7A, 9A~11A and SCN1B~4B. Moreover, prognostic value of mRNA expression of SCNs could only be seen in HER2-negative BC patients when we performed subgroup analysis. Conclusions: These results indicated that SCNs could be prognostic biomarkers for survivals of BC patients. Some medicines that regulate SCNs might provide new targets for BC treatment.
... In the TCGA Breast dataset [22], SLC2A1 was overexpressed compared with that in the normal samples in intraductal cribriform breast adenocarcinoma (fold change = 2.172), in male breast carcinoma (fold change = 3.575), in invasive ductal breast carcinoma (fold change = 2.557) and in invasive breast carcinoma (fold change = 2.251). In the Richardson Breast 2 [23] dataset, SLC2A1 was also overexpressed in ductal breast carcinoma with a fold change of 2.340. The Curtis Breast dataset [24] indicated that compared to normal samples, SLC2A1 overexpression is also found in medullary breast carcinoma (fold change = 2.728), in mucinous breast carcinoma (fold change = 2.100) and in invasive breast carcinoma (fold change = 2.317). ...
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Background Current treatment methods for patients with triple-negative breast cancer (TNBC) are very limited, and the prognosis of TNBC is relatively poor. It has been reported that glucose transporter 1 (GLUT1) is overexpressed in breast cancer cells; however, its association with the prognosis is mostly unclear. Moreover, retinoblastoma gene 1 (RB1) might be used as a biomarker for the sensitivity of breast cancer cells to GLUT1 inhibitors, which brought us to the hypothesis that there might be a close correlation between the expression of GLUT1–4 and the expression of RB1. Methods In this study, we systematically analyzed the co-expression of GLUT1–4 and the influence of GLUT1–4 gene expression on the prognosis of breast cancer using data mining methods. We also explored possible relationships between GLUT1–4 and RB1 expression in breast cancer tissues. We used public databases such as ONCOMINE, GEPIA, LinkedOmics, and COEXPEDIA. Results According to the results, the mRNA expression of SLC2A1 was significantly higher in breast cancer, while the expression levels of SLC2A2–4 were downregulated. The results also indicate that GLUT1 expression does not have significant influence on the overall survival of patients with breast cancer. The mRNA expression of SLC2A1 and RB1 is significantly correlated, which means that tissues with high RB1 mRNA expression might have relatively higher mRNA expression of SLC2A1 ; however, further study analyzing their roles in the expression regulation pathways with human samples is needed to verify the hypothesis. Conclusions The mRNA expression of SLC2A1 was significantly higher in breast cancer. The overall survival of breast cancer patients wasn’t significantly correlated with GLUT1–4 expression. The mRNA expression of SLC2A1 and RB1 is significantly correlated according to the analysis conducted in LinkedOmics. It provides reference for future possible individualized treatment of TNBC using GLUT1 inhibitors, especially in patients with higher mRNA expression of RB1 . Further study analyzing the roles of these two genes in the regulation pathways is needed.
... Selected parameters from Oncomine included a fold-change of 3, a P-value of 0.001, and gene rank within the top 10%). (source: Richardson Breast Study 2, N=47 samples, and 19,574 measured genes) [28]. ...
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Breast cancer, comprising of several sub-phenotypes, is a leading cause of female cancer-related mortality in the UK and accounts for 15% of all cancer cases. Chemoresistant sub phenotypes of breast cancer remain a particular challenge. However, the rapidly-growing availability of clinical datasets, presents the scope to underpin a data driven precision medicine-based approach exploring new targets for diagnostic and therapeutic interventions. We report a survey of several publicly available databases probing the expression and prognostic role of Karyopherin-2 alpha (KPNA2) in breast cancer prognosis. Aberrant KPNA2 overexpression is directly correlated with aggressive tumour phenotypes and poor patient survival outcomes. We examined the existing information available on a range of commonly occurring mutations of KPNA2 and their correlation with patient survival. Our analysis of clinical gene expression datasets show that KPNA2 is frequently amplified in breast cancer, with differences in expression levels observed as a function of patient age and clinicopathologic parameters. We also found that aberrant KPNA2 overexpression is directly correlated with poor patient prognosis, warranting further investigation of KPNA2 as an actionable target for patient stratification or the design of novel chemotherapy agents. In the era of big data, the wealth of datasets available in the public domain can be used to underpin proof of concept studies evaluating the biomolecular pathways implicated in chemotherapy resistance in breast cancer.
... DNA methylation and gene expression linkage can be further modulated in tumor cells with copy number aberrations (CNA). The asymmetric inactivation of the X chromosomes serves as a classical model for such interplay 24,25 . We identified a cluster of X-linked promoters whose methylation profiles show specific correlation with a gene module including the XIST noncoding RNA and additional X-linked genes (Extended Data Fig. 9a, b, Supplementary Data 4) suggesting that they are involved in the maintenance of X methylation and its re-establishment following X-chromosome CNA. ...
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DNA methylation is aberrant in cancer, but the dynamics, regulatory role and clinical implications of such epigenetic changes are still poorly understood. Here, reduced representation bisulfite sequencing (RRBS) profiles of 1538 breast tumors and 244 normal breast tissues from the METABRIC cohort are reported, facilitating detailed analysis of DNA methylation within a rich context of genomic, transcriptional, and clinical data. Tumor methylation from immune and stromal signatures are deconvoluted leading to the discovery of a tumor replication-linked clock with genome-wide methylation loss in non-CpG island sites. Unexpectedly, methylation in most tumor CpG islands follows two replication-independent processes of gain (MG) or loss (ML) that we term epigenomic instability. Epigenomic instability is correlated with tumor grade and stage, TP53 mutations and poorer prognosis. After controlling for these global trans-acting trends, as well as for X-linked dosage compensation effects, cis -specific methylation and expression correlations are uncovered at hundreds of promoters and over a thousand distal elements. Some of these targeted known tumor suppressors and oncogenes. In conclusion, this study demonstrates that global epigenetic instability can erode cancer methylomes and expose them to localized methylation aberrations in-cis resulting in transcriptional changes seen in tumors.
... Oncomine data showed that the mRNA expression of MCM2-8 and MCM10 but not MCM1 and MCM9 in BC samples was significantly upregulated compared with normal samples (Figures 1 and 2). As shown in Table 1, previous reports indicated that MCM2-8 and MCM10 were upregulated in BC [3,[29][30][31][32][33][34][35]. e expression levels of MCMs with tumor stage for breast cancer were analyzed by Gene Expression Profiling Interactive Analysis (GEPIA) database. ...
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The minichromosome maintenance (MCM) protein family plays a key role in eukaryotic DNA replication and has been confirmed to be associated with the occurrence and progression of many tumors. However, the expression levels, functions, and prognostic values of MCMs in breast cancer (BC) have not been clearly and systematically explained. In this article, we studied the transcriptional levels of MCMs in BC based on the Oncomine database. Kaplan-Meier plotter was used to analyze prognostic value of MCMs in human BC patients. Furthermore, we constructed a MCM coexpression gene network and performed functional annotation analysis through DAVID to reveal the functions of MCMs and coexpressed genes. The data showed that the expression of MCM2-8 and MCM10 but not MCM1 and MCM9 was upregulated in BC. Kaplan-Meier plotter analysis revealed that high transcriptional levels of MCM2, MCM4-7, and MCM10 were significantly related to low relapse-free survival (RFS) in BC patients. In contrast, high levels of MCM1 and MCM9 predicted high RFS for BC patients. This study suggests that MCM2, MCM4-7, and MCM10 possess great potential to be valuable prognostic biomarkers for BC and that MCM1 and MCM9 may serve as potential treatment targets for BC patients.
... There are 4 VGLL proteins in mammals, named VGLL1-4. These proteins bear no sequence similarity except for the TDU domain (the TEAD-interacting domain) [24][25][26][27][28]. Previous studies showed that VGLL1 promotes cell proliferation and exhibits high expression in basal-like breast cancer [29,30]. Similarly, VGLL3 is amplified in soft tissue sarcoma and inhibition of VGLL3 results in decreased cell proliferation and migration [31]. ...
... Through Oncomine analysis, we revealed that, in a dataset from Richardson et al. (Richardson et al., 2006), MMP-9 was highly expressed in several types of breast cancer relative to that in normal tissues. The fold change was 8.256 in ductal breast carcinoma ( Figure 6A), and the other datasets also demonstrated a similar profile (Xia et al., 2019). ...
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Objective: Chemoprevention curcumin Analog-1.1 (CCA-1.1) demonstrates antineoplastic effect toward cancer cells. By using triple-negative breast cancer (TNBC), 4T1, and human epidermal growth factor receptor 2 (HER2)-enriched metastatic cells (MCF-7/HER2), we evaluate the cytotoxic and antimigration activities from CCA-1.1. Methods: The cytotoxic activities from a single treatment of CCA-1.1 and in combination with doxorubicin were determined through MTT assay. We also calculated the selectivity index and combination index of CCA-1.1 from the cytotoxic data. Migrating cells were evaluated using wound healing assay, and the MMP2 and MMP9 secretion levels were determined through gelatin zymography. Results: As hypothesized, CCA-1.1 performed cytotoxic activity during treatment in 4T1 and MCF-7/HER2 cancer cells with good selectivity (Selectivity Index >2). In addition, CCA-1.1 demonstrated a synergistic effect in combinatorial treatment with a low dose of doxorubicin. A single treatment of CCA-1.1 repressed cell migration in 4T1 and MCF-7/HER2 cells. Under gelatin zymography, CCA-1.1 subsided the activities of MMP-9, thereby revealing the potency of CCA-1.1 as an anti-migratory agent. Moreover, MMP-9 was also eminently expressed in TNBC and HER2-enriched breast cancer cells when compared with that in other subtypes. Conclusion: Our preliminary study collectively reinforces the potential effect of CCA-1.1 through the inhibition of highly aggressive cell migration, particularly in breast cancer.
... Oncomine database analysis, as shown in Table 1, indicated significant differences in SOCS mRNA expression levels between tissues of different subtypes of breast cancer and normal breast tissues. With the thresholds of p-value< 0.05, fold change≥2, and gene rank = top 10%, SOCS1 was determined to be overexpressed in invasive breast carcinoma and invasive lobular breast carcinoma tissues compared with normal tissues based on data from TCGA; SOCS2 was determined to be down-regulated in breast carcinoma based on data from TCGA, Ma et al. [20], Curtis et al. [21], Karnoub et al. [22], Turashvili et al. [23], Gluck et al. [24] and Richardson et al. [25]; and SOCS3, SOCS4, SOCS5, SOCS6 and SOCS7 were determined to be highly expressed in breast carcinoma based on data from TCGA and Ma et al. [20], Finak et al. [26], Turashvili et al. [23], Radvanyi et al. [27]. In addition to the mRNA expression levels, we also assessed the protein expression levels of SOCS family members based on the immunohistochemical images of SOCS proteins in BRCA patients obtained from the HPA database. ...
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Background: Abnormal expression of suppressor of cytokine signaling (SOCS) proteins regulates tumor angiogenesis and development in cancers. In this study, we aimed to perform a comprehensive bioinformatic analysis of SOCS proteins in breast invasive carcinoma (BRCA). Methods: The gene expression, methylation level, copy number, protein expression and patient survival data related to SOCS family members in BRCA patients were obtained from the following databases: Oncomine, The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), Human Protein Atlas (HPA), Gene Expression Profiling Interactive Analysis (GEPIA), PCViz, cBioPortal and Kaplan-Meier plotter. Correlation analyses, identification of interacting genes and construction of regulatory networks were performed by functional and pathway enrichment analyses, weighted gene coexpression network analysis (WGCNA) and gene set enrichment analysis (GSEA). Results: Data related to 1109 BRCA tissues and 113 normal breast tissue samples were extracted from the TCGA database. SOCS2 and SOCS3 exhibited significantly lower mRNA expression levels in BRCA tissues than in normal tissues. BRCA patients with high mRNA levels of SOCS3 (p < 0.01) and SOCS4 (p < 0.05) were predicted to have significantly longer overall survival (OS) times. Multivariate analysis showed that SOCS3 was an independent prognostic factor for OS. High mRNA expression levels of SOCS2 (p < 0.001), SOCS3 (p < 0.001), and SOCS4 (p < 0.01), and a low expression level of SOCS5 (p < 0.001) were predicted to be significantly associated with better recurrence-free survival (RFS). Multivariate analysis showed that SOCS2 was an independent prognostic factor for RFS. Lower expression levels of SOCS2 and SOCS3 were observed in patients with tumors of more advanced clinical stage (p < 0.05). Functional and pathway enrichment analyses, together with WGCNA and GSEA, showed that SOCS3 and its interacting genes were significantly involved in the JAK-STAT signaling pathway, suggesting that JAK-STAT signaling might play a critical role in BRCA angiogenesis and development. Western blot results showed that overexpression of SOCS3 inhibited the activity of the JAK-STAT signaling pathway in vitro. Conclusions: SOCS family proteins play a very important role in BRCA. SOCS3 may be a prognostic factor and SOCS2 may be a potential therapeutic target in breast cancer.
... Pancreatic cancer is one of the highly malignant tumors of the digestive system. Although the prognosis has been slightly improved in recent years, the 5-year survival rate is still less than 8% [1] .Although pancreatic cancer is not among the top ve related deaths in China, its proportion in cancer-related deaths has increased by 9% in the past 10 years, and this proportion has increased sharply with the change of lifestyle and dietary habits of Chinese residents as well as the acceleration of population aging [2] .At present, the pathogenesis of pancreatic cancer is still unclear, which brings great limitations to the treatment of pancreatic cancer.In addition, serum tumor markers such as CA199 have poor speci city and sensitivity in the diagnosis of pancreatic cancer [3] .Therefore, we need to study new markers of pancreatic cancer, hoping to improve the speci city and sensitivity of pancreatic cancer diagnosis.AMIGO is originally a novel sequence induced by the neuron-promoting protein amphoterin [4][5] .The AMIGO2 gene is located on human chromosome 12q13 and is a member of the Amigo gene family that encodes type 1 transmembrane proteins.The extracellular region of AMIGO2 has a leucine-rich repetitive (LRR) domain [6] .Studies have shown that genes with LRR domain are involved in regulating the growth, invasion and metastasis of tumor cells.The expression of LRRC 3b, a member of the LRRC super family, is signi cantly down-regulated in human breast cancer [7] , glioma [8] , prostate cancer [9] , and lung cancer [10] .Another member of the LRRC super family, LGR5 has also been reported to be expressed in liver cancer [11] , gastric cancer [12] ,basal cell carcinoma [13] , colon cancer and ovarian cancer [14] .Overexpression of LGR5 promotes tumor cell proliferation [13] , while silencing its expression induces tumor cell apoptosis [12].In addition, studies have shown that the LRR domain of AMIGO2 plays a role in the process of collagen adhesion and migration of gastric cancer cells [15] .However, the role of AMIGO2 in pancreatic cancer has been rarely reported at home and abroad.For this purpose, we used the GEPIA2 [16] database, UALCAN [17] database, Kaplan-Meierplotter database [18] , Human protein Atlas database [19] , Timer database [20] , David database [21] , and Metascape database [22] , Harmonizome database [23] , and Jaspar database [24] were used to comprehensively analyze the expression and prognosis of mRAN and its proteins in pancreatic cancer.The possible mechanisms of AMIGO2 gene in pancreatic cancer were further studied.This study provides a theoretical basis for further study of AMIGO2 gene in pancreatic cancer. ...
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Background.The AMIGO2 extracellular domain has a leucine - rich repetitive domain (LRR) and encodes a type 1 transmembrane protein , and is a member of the AMIGO gene family .Although the abnormal expression of AMIGO2 is associated with multiple tumors , the relationship with pancreatic cancer is not clear . Methods.The expression of AMIGO2 mRNA and proteins in pancreatic cancer was analyzed using NCBI GEO database and GEPIA2、Human Protein Atlas database.The RNA sequencing data of pancreatic cancer and clinical data of pancreatic cancer patients in TCGA public database were retrospectively analyzed. AMIGO2 gene expression data and their corresponding clinical information in the sample were analyzed retrospectively. The diagnostic value of AMIGO2 expression in pancreatic cancer patients was determined by receiver operating characteristic (ROC) curve analysis. The effects of AMIGO2 expression differences on survival time of pancreatic cancer patients were analyzed by Kaplan-Meier Plotter database and GEPIA2 database.The correlation between AMIGO2 gene and TP53 mutation in pancreatic cancer was analyzed by UALCAN database and TIMER database. The similar genes of AMIGO2 in pancreatic cancer were analyzed by GEPIA2 database, and the biological behavior, cellular composition, molecular function enrichment analysis and protein interaction of similar genes were analyzed by DAVID database and Metascape database. enrichment analysis of AMIGO2 similar gene pathways using KEGG database. The MSIGDB cancer coexpression module in Harmonizome database and TIMER database were used to study the gene coexpression of AMIGO2 in pancreatic cancer. AMIGO2 transcription factors were predicted using the JASPER database. The pathway of AMIGO2 transcription factors and co-expression genes was studied by KEGG database. Results. The expression of AMIGO2 (GSE16515, GSE15471) in pancreatic cancer tissues was significantly higher than that in normal tissues (P < 0.05). The GEPIA2 database also confirmed that the expression of AMIGO2 in pancreatic cancer tissues was significantly higher than that in normal tissues. The expression level of AMIGO2 gene was correlated with lymph node metastasis and histological grade of pancreatic cancer (P<0.05). The high expression of AMIGO2 protein in pancreatic cancer was confirmed in Human Protein Atlas database. The overall survival rate and progression-free survival rate of pancreatic cancer patients with high expression of AMIGO2 were significantly shorter than those of patients with low expression of AMIGO2 in Kaplan-Meier Plotter database and GEPIA2 database. In the gene ontology analysis, it is found that AMIGO2 is involved in cell adhesion, proliferation, migration, apoptosis and other biological processes. KEGG analysis pathway is concentrated in the focal adhesion pathway, mitotic cell cycle changes, and the regulation of cell protein localization. Abnormal expression of AMIGO2 was found in pancreatic cancer caused by TP53 mutation in UALCAN and TIMER databases.In JASPAR database, we predicted that there are 10 transcription sites between AMIGO2 and transcription factor MYB. In addition, there are positive genes related to AMIGO2 in TIMER database and transcription factor MYB regulates tumor cell proliferation and apoptosis in PI3K-Akt signal transduction pathway and WNT signal pathway in pancreatic cancer.
... Alternatively, another gene that lies centromeric to the latter genes within the duplicated segment, VBP1, has also been raised as a potential suspect possibly underlying that patient's development of multiple tumors. Such a speculation was based on a combination of facts pertaining to VBP1: it encodes a tumor-suppressor protein involved in repairing DNA damage, has been associated with the development of multiple cancers, and is not included in the gene panels commonly used to screen for hereditary or genetic cancers [10,31,32]. ...
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The int22h1/int22h2-mediated Xq28 duplication syndrome is a rare X-linked intellectual disability syndrome (XLIDS) arising from a duplication of the segment between intron 22 homologous regions 1 and 2, on the q28 subregion of the X chromosome. The main clinical features of the syndrome include intellectual disability, neurobehavioral abnormalities, and dysmorphic facial features. Due to the X-linked nature of the syndrome, affected males exhibit more severe phenotypes compared with heterozygous females. A unique distinguishing feature of the syndrome across the sexes, however, is a peculiar combination of recurrent sinopulmonary infections and atopy exclusively seen in a subset of affected males. In addition to the ‘typical’ 0.5 Mb duplication detected in most cases reported to date with the syndrome, a shortened centromeric version, and another 0.2 Mb telomerically shifted one, have been recently identified, with most detected duplications being maternally inherited, except for three recent cases found to have de novo duplications. Interestingly, a recently reported case of an affected male suggests a possible association of the syndrome with multiple malignancies, an observation that has been recently replicated in two pediatric patients. As a result, a better understanding of the pathogenesis of int22h1/int22h2-mediated Xq28 duplication syndrome may grant us a better understanding of the sex-specific differences in immunological responses, as well as the potential role of the genes involved by the duplication, in oncogenesis.
... To determine the difference in the expression of GLUT1 in tumors and normal tissues, the Oncomine database was used to analyze the levels of GLUT1 mRNA in tumors and normal tissues of various cancer types. This analysis showed that bladder (24,25), breast (26)(27)(28), colorectal (29,30), esophageal (31,32), gastric (33), head and neck (34,35), kidney (36)(37)(38)(39), leukemia (40), lung (41)(42)(43)(44)(45)(46), lymphoma (47), ovarian (48) and pancreatic cancer (49)(50)(51)(52) have higher expression of GLUT1 compared with normal tissues. In addition, there are data showing that the expression is lower in breast (53), esophageal cancer (54) and leukemia tumors (55) ( Figure 1A). ...
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Background Glucose transporter 1 (GLUT1) is encoded by the solute carrier family 2A1 (SLC2A1) gene and is one of the glucose transporters with the greatest affinity for glucose. Abnormal expression of GLUT1 is associated with a variety of cancers. However, the biological role of GLUT1 in esophageal carcinoma (ESCA) remains to be determined. Methods We analyzed the expression of GLUT1 in pan-cancer and ESCA as well as clinicopathological analysis through multiple databases. Use R and STRING to perform GO/KEGG function enrichment and PPI analysis for GLUT1 co-expression. TIMER and CIBERSORT were used to analyze the relationship between GLUT1 expression and immune infiltration in ESCA. The TCGA ESCA cohort was used to analyze the relationship between GLUT1 expression and m6A modification in ESCA, and to construct a regulatory network in line with the ceRNA hypothesis. Results GLUT1 is highly expressed in a variety of tumors including ESCA, and is closely related to histological types and histological grade. GO/KEGG functional enrichment analysis revealed that GLUT1 is closely related to structural constituent of cytoskeleton, intermediate filament binding, cell-cell adheres junction, epidermis development, and P53 signaling pathway. PPI shows that GLUT1 is closely related to TP53, GIPC1 and INS, and these three proteins all play an important role in tumor proliferation. CIBERSORT analysis showed that GLUT1 expression is related to the infiltration of multiple immune cells. When GLUT1 is highly expressed, the number of memory B cells decreases. ESCA cohort analysis found that GLUT1 expression was related to 7 m6A modifier genes. Six possible crRNA networks in ESCA were constructed by correlation analysis, and all these ceRNA networks contained GLUT1. Conclusion GLUT1 can be used as a biomarker for the diagnosis and treatment of ESCA, and is related to tumor immune infiltration, m6A modification and ceRNA network.
... Notably, few studies have addressed the role of ABHD2 in malignant tumors. It is reported that the expressions of ABHD2 in breast cancer and melanoma are obviously higher than those in normal tissues [39][40][41] , but whether it has molecular functions in these two cancers is still unknown. The Obinata team has reported that ABHD2 is an androgen-responsive gene, and it can promote the growth and migration of prostate cancer 42 . ...
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TAR DNA-Binding Protein 43 (TDP-43) has been well studied in neurodegenerative diseases, but its potential role in malignance is still unclear. Here, we demonstrate that TDP-43 contributes to the suppression of apoptosis by facilitating lipid metabolism in hepatocellular carcinoma (HCC). In HCC cells, TDP-43 is able to suppress apoptosis while deletion of it markedly induces apoptosis. RNA-sequencing identifies the lipid metabolism gene abhydrolase domain containing 2 (ABHD2) as the target gene of TDP-43. Tissue microarray analysis shows the positive correlation of TDP-43 and ABHD2 in HCC. Mechanistically, TDP-43 binds with the UG-rich sequence1 of ABHD2 3’UTR to enhance the mRNA stability of ABHD2, thereby upregulating ABHD2. Afterwards, TDP-43 promotes the production of free fatty acid and fatty acid oxidation-originated reactive oxygen species (ROS) in an ABHD2-dependent manner, so as to suppress apoptosis of HCC. Our findings provide insights into the mechanism of HCC progression and reveal TDP-43/ABHD2 as potential targets for the precise treatment of HCC. TDP-43 acts as an RNA-binding protein that regulates the RNA stability of ABHD2 and affects the release of fatty acids and ROS, which in turn regulates apoptosis and affects the growth of liver tumors.
... Through "differential analysis" module, students' t-test was used to analyze the differential expression of CXC chemokines in BC and normal tissues by setting the significance threshold of P < 0.05, multiple change of 2 and gene ranking in the top 10%. The samples involved 10 studies (13)(14)(15)(16)(17)(18)(19)(20)(21)(22). ...
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The increasing incidence and mortality rate of Breast cancer (BC) make it a major public health problem around the world. CXC chemokines can mediate the migration of immune cells and regulate apoptosis in tumor. However, the expression and prognostic value of them in BC and their targeted drugs have not been clarified. Therefore, in this study, ONCOMINE, GEPIA2.0, UALCAN, Venny2.1.0, cBioPortal, STRING, Gene MANIA, Pathway Commons, DAVID6.8, Omicshare, Cytoscape3.6.1, TIMER2.0, Drug Bank, TCMSP, RSCBPDB, PubChem, pkCSM, Chem Draw, AutoDockTools-1.5.6 and PyMOL were utilized for analysis. The expression of CXCL1-3, CXCL9-13 between BC and normal tissues was significantly different in all the three databases. And the expression of CXCL1-2, CXCL12-13 was correlated with the stages of BC. But only CXCL1-3 were prone to mutation, and negatively correlated with survival and prognosis of BC patients. Taken together, CXCL1-2 might be therapeutic targets and biomarkers for BC patients. In addition, both of them were associated with immune infiltration. The results of molecular docking showed that Quercetin was most likely to be developed as drugs that interacted directly with CXCL1-2. And GLU29 of CXCL1, ASP-1, PRO-96, TRP-47 and LEU-45 of CXCL2 were the most potential sites, which provided valuable reference for further study of pharmacodynamics and mechanism. In addition, the inhibitory effect of Quercetin on proliferation and promoting apoptosis of BC related cell lines were confirmed in vitro . Western blot and Real-Time PCR confirmed that it increased the expression of CXCL1-2 in MDA-MB-231 and MCF-7 cells.
... The mRNA expression levels of TIMM8A were signi cantly upregulated in patients with breast cancer based on TCGA and GTEx database (Fig. 1B). Richardson's study found that TIMM8A is highly expressed in breast cancer compared with normal tissues (Fig. 1C) [22]. Moreover, the normal ductal epithelial (N-Ductal) and lobular epithelial (N-Lobular) tissues exhibited signi cantly lower expression of TIMM8A relative to ductal carcinoma (Fig. 1D) [23]. ...
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Background: Breast cancer is notorious for its increasing incidence for decades. Ascending evidence has demonstrated that translocase of inner mitochondrial membrane (TIMM) proteins play vital roles in progression of several types of human cancer. However, the biological behaviors and molecular mechanisms of TIMM8A in breast cancer remain not fully illustrated. Methods: Pan-cancer analysis was firstly performed for TIMM8A’s expression and prognosis by Oncomine database. Subsequently, TIMM8A-related noncoding RNAs (ncRNAs) were identified by a series of bioinformatics analyses and dual-luciferase reporter assay, including expression analysis, correlation analysis, and survival analysis. Moreover, the effect of TIMM8A on breast cancer proliferation and apoptosis was evaluated in vitro by CCK-8 assays, colony formation assays and Western blot assays and the in vivo effect was revealed through a patient-derived xenograft mouse model. Results: We found that TIMM8A showed higher expression level in breast cancer and the higher TIMM8A mRNA expression group had a poorer prognosis than the lower TIMM8A group. hsa-circ-0107314/hsa-circ-0021867/hsa-circ-0122013 might be the three most potential upstream circRNAs of hsa-miR-34c-5p/hsa-miR-449a-TIMM8A axis in breast cancer. TIMM8A promotes proliferation of breast cancer cells in vitro and tumor growth in vivo. Conclusion: Our results confirmed that ncRNAs-mediated upregulation of TIMM8A correlated with poor prognosis and act as an oncogene in breast cancer.
... Meta-Analysis Based on the Databases of GEO and TCGA. Firstly, GSE7904 [14], GSE45827 [15], GSE65194 [16,17], GSE22820 [18,19], and GSE38959 were selected from the GEO database. Then, difference analysis was performed using GEO2R, with cut-off values of Log | FC | >1 and adjusted p value <0.05 for the screening of differential genes (Supplementary Table 1 -5). ...
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Breast cancer (BRCA) is a malignant tumor with a high incidence and poor prognosis in females. However, its pathogenesis remains unclear. In this study, based on bioinformatic analysis, we found that LINC00467 was highly expressed in BRCA and was associated with tumor metastasis and poor prognosis. The genomic and epigenetic analysis showed that LINC00467 may also be regulated by copy number amplification (CNA), chromatin openness, and DNA methylation. In vitro experiments showed that it could promote the proliferation, migration, and invasion of BRCA cells. Competitive endogenous RNA (ceRNA) regulatory network analysis and weighted gene coexpression network analysis (WGCNA) suggested that LINC00467 may play a role in signaling pathways of peroxisomal lipid metabolism, immunity, and others through microRNAs (miRNAs) targeting transforming growth factor beta 2 (TGFB2). In addition, copy number amplification and high expression of LINC00467 were associated with the low infiltration of CD8+ and CD4+ T cells. In conclusion, we found that LINC00467, driven by copy number amplification and DNA demethylation, may be a potential biomarker for the diagnosis and prognosis of BRCA and a tumor promoter acting as a potential therapeutic target for BRCA as well.
... Data mining confirmed the significant downregulation of NURR1 in transformed breast (BC) cells compared to clinically healthy normal breast epithelia derived from breast reduction mammoplasty (GEO datasets: GDS3139 and GDS3716). Whereas, analysis of datasets (GDS2739 and GDS2635) showed no statistically significant downregulation of NURR1 expression in tumor tissues (Alimonti et al. 2010;Graham et al. 2010;Richardson et al. 2006;Tripathi et al. 2008;Turashvili et al. 2007). These findings propose that TANTs are pre-neoplastic breast epithelia in their transcriptome. ...
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Evidence and in silico analyses showed that TUSC7, miR-211, and Nurr1 may be involved in BC pathogenesis by ceRNET signaling axis. This study aimed to investigate the potential role of TUSC7/miR-211/Nurr1 ceRNET and rs2615499 variant as a novel cer-SNP in BC subjects. The expression assays were conducted by qPCR on tumor tissues (n = 50), tumor-adjacent normal tissues (TANTs) (n = 50), and clinically healthy control tissues (n = 50). The expression of TUSC7 and Nurr1 significantly decreased, but the level of miR-211 significantly increased in tumor tissues compared to TANTs and healthy normal tissues. Altered expression of TUSC7 and miR-211 was associated with poor prognosis of patients. The Nurr1 exhibited a double-edged sword-like activity in BC. In addition, TUSC7, Nurr1, and miR-211 expressions were significantly related to a novel BC-associated rs2615499 (A > C) located in the miR-211 binding site on Nurr1 3′-UTR. In the second part of the study, a case–control study was performed on BC patients (n = 100) and matched healthy controls (n = 100). The genomic DNA was isolated and genotyping was performed using Tetra-Primer ARMS PCR. The CC and AC genotypes were associated with higher expression levels of Nurr1 and worse outcomes of the disease. Our findings revealed that TUSC7 functions as a tumor suppressor in BC potentially via miR-211/Nurr1, which might be disturbed by the cer-SNP rs2615499. However, functional studies are needed to validate these results.
... 1D, E and Supplementary S1B, C). In addition, we analyzed the mRNA expression of cGAS and STING in different tumor and their adjacent normal tissues [25][26][27][28][29][30][31][32]. We found that cGAS expression in a variety of tumor tissues (including breast cancer and pancreatic cancer) was higher than that of normal tissues (Figs. ...
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The cytosolic DNA-sensing cGAS-STING pathway has been proved to be involved in tumor progression and influence the effect of cancer immunotherapy. However, little attentions have been paid to the role of cGAS-STING pathway on cancer stemness. Herein, we found that the cGAS-STING pathway was activated in different tumor cells. cGAS-or STING-knockout impaired the capability of tumor formation in vivo and tumorsphere formation in vitro. In addition, loss of cGAS-STING cascade promoted tumor apoptosis, but inhibited tumor growth and metastasis. We further demonstrated that cGAS-STING pathway potentiated tumor formation by sustaining cancer stemness. Moreover, analysis of RNA-seq showed that cGAS-STING pathway maintained cancer stemness probably by activating STAT3. Our findings highlight the role of intrinsic activation of cGAS-STING pathway in tumorigenesis, and reveal a new mechanism of its regulation of tumor progression via sustaining cancer stemness through STAT3 activation.
... The Oncomine database contains and compares available microarray data from multiple cancer types, including BC, with those from normal samples. The expression of MCMs in cancer cells is shown in Fig. 1 [27][28][29][30][31], followed by MCM2 in 8 datasets [28,29,31] and MCM10 in 7 datasets [28,29,31]. However, owing to the relatively small sample size, whether the expression of MCM5, MCM6 and MCM8 was elevated in BC remains controversial. ...
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Abstract Objective: Breast cancer (BC) is one of the most health-threatening neoplasms for women worldwide. Despite advances in detection and treatment strategies over the past few decades, the current biomarkers of BC are less than satisfactory for effective prognosis and individualized treatment. This study aimed to investigate the new biomarkers to meet this urgent demand. Methods: The current study investigated the transcriptional levels of minichromosome maintenance genes (MCMs) in BC patients from the Oncomine, UALCAN database, and Gene Expression Profiling Interactive Analysis (GEPIA); protein expression levels of MCM proteins in BC patients were derived from the Human Protein Atlas (HPA) database. Further, survival analysis was evaluated with Kaplan-Meier Plotter. BC genome atlas data were obtained from cBioPortal databases. Gene regulatory network analysis was performed using the STRING online tool, and gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using DAVID. Results: Based on multiple database analysis, mRNA and protein levels of MCM2, MCM4 and MCM10 were much higher in BC patient, and survival analysis showed that high transcription levels of most MCMs were found to be associated with poor prognosis for BC patients; moreover, the MCMs genetic alterations, especially of MCM2, MCM4 and MCM10, were found in 45% of BC patients. In addition, dysregulation of MCMs was considered to possibly affect DNA damage/repair, cell cycle dysregulation and chromosome instability. Conclusions: In summary, this study indicated that MCM2, MCM4, and MCM10 are potential prognostic markers and therapeutic targets for BC.
... To better explore the potential value of CENPW in breast carcinoma patients, we further explored the expression and function of CENPW in breast carcinoma through several means. According to the Richardson Breast two dataset (Richardson et al., 2006), the CENPW expression in ductal breast cancer was distinctly higher than that in normal tissues ( Figure 2A). In addition, the Curtis Breast dataset (Curtis et al., 2012) showed a 2.698-fold (p = 1.70E−09) increase in CENPW mRNA expression in medullary breast carcinoma ( Figure 2B). ...
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Breast invasive carcinoma (BRCA) is a carcinoma with a fairly high incidence, and the therapeutic schedules are generally surgery and chemotherapy. However, chemotherapeutic drugs tend to produce serious toxic side effects, which lead to the cessation of treatment. Therefore, it is imperative to develop treatment strategies that are more effective and have fewer side effects at the genetic level. Centromeric protein W (CENPW) is an oncogene that plays an important part in nucleosome assembly. To date, no studies have reported the prognostic significance of CENPW in breast carcinoma. In this study, we verified that CENPW expression is up-regulated in breast carcinoma and positively associated with the level of immune cell infiltration. The clinicopathological characteristics further suggest that CENPW expression is correlated with a worse prognosis of breast carcinoma. Interestingly, the CENPW mutation contributes to the poor prognosis. Next, we discovered that the genes interacting with CENPW are mainly concentrated in the cell cycle pathway, and CENPW is co-expressed with CDCA7, which is also highly expressed in breast carcinoma and leads to a worse prognosis. Our subsequent studies verified that knockdown of CENPW significantly inhibits the proliferation and migration of breast carcinoma cells and promotes their apoptosis rate. Notably, inhibition of CEMPW sensitizes breast cancer cells to chemotherapeutic drugs that have been found to induce cell cycle arrest. In summary, these results provide extensive data and experimental evidence that CENPW can serve as a novel predictor of breast cancer and may act as a prospective therapeutic target.
... The only improvement in the first tumour was that one chromosome 16 was replaced by a chromosome derivative consisting of 16p and 1q (Pandis et al., 1992). Active X chromosome duplication and Xi loss characterized almost half of the cases of sporadic basallike cancers studied (Richardson et al., 2006). Grade I and tubular breast carcinomas have a limited number of genomic alterations with extremely recurring 16q losses, while grade III breast carcinomas also have complex genotypes with 11q, 14q, 8p, 13q loss; 17q, 8q, 5p gain; and high-level gains (amplification) on 17q12, 17q22-24, 6q22, 8q22, 11q13, and 20q13 . ...
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... The mRNA expression levels of TIMM8A were significantly upregulated in patients with breast cancer based on TCGA and GTEx database (Fig. 1B). Richardson's study found that TIMM8A is highly expressed in breast cancer compared with normal tissues (Fig. 1C) [22]. Moreover, the lobular epithelial (N-Lobular) tissues exhibited significantly lower expression of TIMM8A relative to ductal carcinoma (Fig. 1D) [23]. ...
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... The corresponding sample information is downloaded from ArrayExpress [13,14]. All the 10 datasets are based on Affymetrix Hgu133plus2 platform [15][16][17][18][19][20][21][22][23][24]. The raw data from each dataset is normalized by RMA algorithm and batch-corrected by the removeBatchEffect function from R package Limma [25,26]. ...
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The human Six-Transmembrane Epithelial Antigen of the Prostate (STEAP) family comprises STEAP1-4. Several studies have pointed out STEAP proteins as putative biomarkers, as well as therapeutic targets in several types of human cancers, particularly in prostate cancer. However, the relationships and significance of the expression pattern of STEAP1-4 in cancer cases are barely known. Herein, the Oncomine database and cBioPortal platform were selected to predict the differential expression levels of STEAP members and clinical prognosis. The most common expression pattern observed was the combination of the over- and underexpression of distinct STEAP genes, but cervical and gastric cancer and lymphoma showed overexpression of all STEAP genes. It was also found that STEAP genes’ expression levels were already deregulated in benign lesions. Regarding the prognostic value, it was found that STEAP1 (prostate), STEAP2 (brain and central nervous system), STEAP3 (kidney, leukemia and testicular) and STEAP4 (bladder, cervical, gastric) overexpression correlate with lower patient survival rate. However, in prostate cancer, overexpression of the STEAP4 gene was correlated with a higher survival rate. Overall, this study first showed that the expression levels of STEAP genes are highly variable in human cancers, which may be related to different patients’ outcomes.
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Phenotypic plasticity is a crucial feature of aggressive cancer, providing the means for cancer progression. Stochastic changes in tumor cell transcriptional programs increase the chances of survival under any condition. I hypothesize that unstable chromatin permits stochastic transitions between transcriptional programs in aggressive cancers and supports non‐genetic heterogeneity of tumor cells as a basis for their adaptability. I present a mechanistic model for unstable chromatin which includes destabilized nucleosomes, mobile chromatin fibers and random enhancer‐promoter contacts, resulting in stochastic transcription. I suggest potential markers for “unsettled” chromatin in tumors associated with poor prognosis. Although many of the characteristics of unstable chromatin have been described, they were mostly used to explain changes in the transcription of individual genes. I discuss approaches to evaluate the role of unstable chromatin in non‐genetic tumor cell heterogeneity and suggest using the degree of chromatin instability and transcriptional noise in tumor cells to predict cancer aggressiveness. Non‐mutational phenotypic changes allow cells of aggressive tumors to invade, to metastasize and to regrow after treatment. This behavior can be explained by stochastic gene expression (SGE): random switches between transcriptional programs. We propose mechanistic model of SGE based on specific volatile chromatin state permissive for random promoter/enhancer contacts.
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Background: The solute carrier (SLC) 7 family genes play central roles in cancer cell metabolism as glucose and glutamate transporters. However, their expression and prognostic value in breast cancer (BC) remains to be elucidated. Methods: Clinical data from BC patients were downloaded from The Cancer Genome Atlas (TCGA) and the Kaplan-Meier (KM) plotter database. The mechanisms underlying the association between SLC7A expression and overall survival (OS) were explored using Cox regression and log-rank tests. ESTIMATE gives a measure of the immune-cell infiltrates. Single-sample (ss) Gene Set Enrichment Analysis (GSEA) was conducted to quantify immune cell infiltration. Results: High SLC7A5 expression was associated with a poorer survival time in BC patients according to the TCGA and KM plotter data. SLC7A4 was associated with good progression-free interval (PFI) and disease-specific survival (DSS) according to the TCGA data. Furthermore, SLC7A4 was correlated with good prognosis of OS, distant metastasis-free survival (DMFS), relapse-free survival (RFS), and post-progression survival (PPS) according to the KM plotter data. SLC7A3 expression was positively associated with OS, but was not strongly associated with PFI nor DSS in the TCGA data. However, SLC7A3 was positively correlated with DMFS and RFS in the KM database analysis. SLC7A had excellent diagnostic value in BC patients and was strongly correlated with tumor infiltration. T helper 2 (Th2) cells, CD56 bright natural killer (NK) cells, and NK cells were the most strongly correlated with the SLC7A family genes, suggesting that these genes play a crucial role in BC partly by modulating immune infiltration. Conclusions: SLC7A4 and SLC7A5 expression levels may be sensitive biomarkers for predicting BC outcomes. SLC7A3 may be a potential diagnostic and prognostic biomarker in BC, but further studies are warranted to verify these results.
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Background: The successful identification of breast cancer (BRCA) prognostic biomarkers is essential for the strategic interference of BRCA patients. Recently, various methods have been proposed for exploring a small prognostic gene set that can distinguish the high-risk group from the low-risk group. Methods: Regularized Cox proportional hazards (RCPH) models were proposed to discover prognostic biomarkers of BRCA from gene expression data. Firstly, the maximum connected network with 1142 genes by mapping 956 differentially expressed genes (DEGs) and 677 previously BRCA-related genes into the gene regulatory network (GRN) was constructed. Then, the 72 union genes of the four feature gene sets identified by Lasso-RCPH, Enet-RCPH, [Formula: see text]-RCPH and SCAD-RCPH models were recognized as the robust prognostic biomarkers. These biomarkers were validated by literature checks, BRCA-specific GRN and functional enrichment analysis. Finally, an index of prognostic risk score (PRS) for BRCA was established based on univariate and multivariate Cox regression analysis. Survival analysis was performed to investigate the PRS on 1080 BRCA patients from the internal validation. Particularly, the nomogram was constructed to express the relationship between PRS and other clinical information on the discovery dataset. The PRS was also verified on 1848 BRCA patients of ten external validation datasets or collected cohorts. Results: The nomogram highlighted that the importance of PRS in guiding significance for the prognosis of BRCA patients. In addition, the PRS of 301 normal samples and 306 tumor samples from five independent datasets showed that it is significantly higher in tumors than in normal tissues ([Formula: see text]). The protein expression profiles of the three genes, i.e., ADRB1, SAV1 and TSPAN14, involved in the PRS model demonstrated that the latter two genes are more strongly stained in tumor specimens. More importantly, external validation illustrated that the high-risk group has worse survival than the low-risk group ([Formula: see text]) in both internal and external validations. Conclusions: The proposed pipelines of detecting and validating prognostic biomarker genes for BRCA are effective and efficient. Moreover, the proposed PRS is very promising as an important indicator for judging the prognosis of BRCA patients.
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Patients with triple-negative breast cancer have a poor prognosis as only a few efficient targeted therapies are available. Cancer cells are characterized by their unregulated proliferation and require large amounts of nucleotides to replicate their DNA. One-carbon metabolism contributes to purine and pyrimidine nucleotide synthesis by supplying one carbon atom. Although mitochondrial one-carbon metabolism has recently been focused on as an important target for cancer treatment, few specific inhibitors have been reported. In this study, we aimed to examine the effects of DS18561882 (DS18), a novel, orally active, specific inhibitor of methylenetetrahydrofolate dehydrogenase (MTHFD2), a mitochondrial enzyme involved in one-carbon metabolism. Treatment with DS18 led to a marked reduction in cancer-cell proliferation; however, it did not induce cell death. Combinatorial treatment with DS18 and inhibitors of checkpoint kinase 1 (Chk1), an activator of the S phase checkpoint pathway, efficiently induced apoptotic cell death in breast cancer cells and suppressed tumorigenesis in a triple-negative breast cancer patient-derived xenograft model. Mechanistically, MTHFD2 inhibition led to cell cycle arrest and slowed nucleotide synthesis. This finding suggests that DNA replication stress occurs due to nucleotide shortage and that the S-phase checkpoint pathway is activated, leading to cell-cycle arrest. Combinatorial treatment with both inhibitors released cell-cycle arrest, but induced accumulation of DNA double-strand breaks, leading to apoptotic cell death. Collectively, a combination of MTHFD2 and Chk1 inhibitors would be a rational treatment option for patients with triple-negative breast cancer.
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Objective: To investigate the role of vascular endothelial growth factor (VEGF) in regulating triple-negative breast cancer (TNBC) stem cells and the possible pathways involved in this regulatory mechanism. Methods: The Oncomine database, UALCAN database and Human Protein Atlas (HPA) database were used to analyze the expression of VEGF in breast cancer and its association with the molecular subtypes and prognosis of breast cancer. Sphere formation assay was carried out to examine the effects of hVEGF165 on sphere formation ability of TNBC MDA-MB-231 cell line; Western blotting and RT-qPCR were performed to detect the expression of the tumor stem cell markers including CD44, c-Myc, Nanog, and ALDH1 and the activation of the related pathways. Results: Data from the online databases all showed a significant increase of VEGF expression in breast cancer tissues than in the adjacent tissues (P < 0.0001), and its expression level was associated with the molecular subtypes of breast cancer. Specifically, the expression of VEGF was markedly higher in TNBC than in other subtypes of breast cancer. Survival analysis showed that breast cancer patients with a high VEGF expression had a significantly shortened overall survival (P < 0.0001). In the cell experiments, the sphere formation ability of MDA-MB-231 cells was significantly enhanced after treatment with hVEGF165 (P=0.0029). Compared with the monolayer cells, MDA-MB-231 spheres showed significantly increased expressions of VEGF, NRP-1, CD44, Nanog and c-Myc. Treatment with hVEGF165 resulted in significant time-dependent up-regulation of the expressions of CD44, c-Myc, Nanog and ALDH1 and down-regulation of CD24 expression in the cells. The results of Western blotting demonstrated that treatment with hVEGF165 caused significant activation of the ERK/MAPK pathway in MDA-MB-231 cells. Conclusion: VEGF promotes cancer stemness of triple-negative breast cancer possibly through the ERK/MAPK pathway.
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Characteristic patterns of gene expression measured by DNA microarrays have been used to classify tumors into clinically relevant subgroups. In this study, we have refined the previously defined subtypes of breast tumors that could be distinguished by their distinct patterns of gene expression. A total of 115 malignant breast tumors were analyzed by hierarchical clustering based on patterns of expression of 534 "intrinsic" genes and shown to subdivide into one basal-like, one ERBB2-overexpressing, two luminal-like, and one normal breast tissue-like subgroup. The genes used for classification were selected based on their similar expression levels between pairs of consecutive samples taken from the same tumor separated by 15 weeks of neoadjuvant treatment. Similar cluster analyses of two published, independent data sets representing different patient cohorts from different laboratories, uncovered some of the same breast cancer subtypes. In the one data set that included information on time to development of distant metastasis, subtypes were associated with significant differences in this clinical feature. By including a group of tumors from BRCA1 carriers in the analysis, we found that this genotype predisposes to the basal tumor subtype. Our results strongly support the idea that many of these breast tumor subtypes represent biologically distinct disease entities.
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In female mammalian cells, inactivation of one of the X chromosomes compensates the increased dosage of X-linked genes as compared with their male counterparts. This process is initiated by the X-inactive specific transcripts of the xist/XIST gene in cis, resulting in methylation of specific sites of genes to be silenced. However, in male germ cells, X inactivation is established by xist/XIST expression only. We investigated the X inactivation pattern in human testicular tumors of different histogenesis by analysis of XIST expression and methylation of the androgen receptor gene. XIST was expressed only in tumors derived from the germ cell lineage with supernumerical X chromosomes: seminomas, nonseminomas, and spermatocytic seminomas. Although low expression was present in testicular parenchyma with spermatogenesis, XIST was expressed at a higher level in parenchyma with carcinoma in situ, the precursor lesion of seminomas and nonseminomas. Despite the consistent expression of XIST in germ-cell-derived tumors with gain of X chromosomes, methylation of the androgen receptor gene was present in all differentiated but only in a proportion of the undifferentiated nonseminomas. This differential pattern of methylation was also found in a number of representative cell lines. Our data indicate that the counting mechanism resulting in X inactivation is functional in testicular cancers of different histogenesis. Moreover, the differentiation-dependent pattern of X inactivation as reported during normal development in the case of multiple X chromosomes by methylation is retained in these tumors. We conclude therefore that X inactivation allows the excessive gain of X chromosomes found in germ-cell-derived tumors of the adult testis. In addition, this offers an interesting model to study the fundamental mechanisms of these processes.
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Previous studies have shown that the chloride channel gene Clc4 is X-linked and subject to X inactivation in Mus spretus, but that the same gene is autosomal in laboratory strains of mice. This exception to the conservation of linkage of the X chromosome in one of two interfertile mouse species was exploited to compare expression of Clc4 from the X chromosome to that from the autosome. Clc4 was found to be highly expressed in brain tissues of both mouse species. Quantitative analyses of species-specific expression of Clc4 in brain tissues from mice resulting from M. spretus × laboratory strain crosses, demonstrate that each autosomal locus has half the level of Clc4 expression as compared with the single active X-linked locus. In contrast expression of another chloride channel gene, Clc3, which is autosomal in both mouse species is equal between alleles in F1 animals. There is no evidence of imprinting of the Clc4 autosomal locus. These results are consistent with Ohno’s hypothesis of an evolutionary requirement for a higher expression of genes on the single active X chromosome to maintain balance with autosomal gene expression [Ohno, S. (1967) Sex Chromosomes and Sex-Linked Genes (Springer, Berlin)].
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Klinefelter's syndrome (KS, XXY) as a risk factor for developing breast cancer was evaluated in a retrospective study of 93 unselected male breast cancer patients from the Healthcare region of Western Sweden. Archival normal material from lymph nodes or skin and subcutaneous tissue was examined using the FISH (fluorescence in situ hybridisation)-technique. The best yield of intact nuclei was obtained from lymph node tissue. The prevalence rate of KS in males with breast cancer was found to be 7.5 per cent, a much higher rate than previously reported (approximately 3 per cent). Methodological differences are suggested to cause the increased prevalence rate. Based on our finding and on the prevalence of KS in the normal population as well as on the incidence of MBC, a 50-fold increased risk of developing breast cancer in males with KS relative to normal males was found. The same median age at diagnosis, 72 years, was established for both groups of patients. No differences in survival were seen.
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Hereditary breast and ovarian cancer syndromes can be caused by loss-of-function germline mutations in one of two tumour-suppressor genes, BRCA1 and BRCA2 (ref. 1). Each gene product interacts with recombination/DNA repair proteins in pathways that participate in preserving intact chromosome structure. However, it is unclear to what extent such functions specifically suppress breast and ovarian cancer. Here we analyse what is known of BRCA gene function and highlight some unanswered questions in the field.
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The XIST gene is implicated in X chromosome inactivation, yet the RNA contains no apparent open reading frame. An accumulation of XIST RNA is observed near its site of transcription, the inactive X chromosome (Xi). A series of molecular cytogenetic studies comparing properties of XIST RNA to other protein coding RNAs, support a critical distinction for XIST RNA; XIST does not concentrate at Xi simply because it is transcribed and processed there. Most notably, morphometric and 3-D analysis reveals that XIST RNA and Xi are coincident in 2- and 3-D space; hence, the XIST RNA essentially paints Xi. Several results indicate that the XIST RNA accumulation has two components, a minor one associated with transcription and processing, and a spliced major component, which stably associates with Xi. Upon transcriptional inhibition the major spliced component remains in the nucleus and often encircles the extra-prominent heterochromatic Barr body. The continually transcribed XIST gene and its polyadenylated RNA consistently localize to a nuclear region devoid of splicing factor/poly A RNA rich domains. XIST RNA remains with the nuclear matrix fraction after removal of chromosomal DNA. XIST RNA is released from its association with Xi during mitosis, but shows a unique highly particulate distribution. Collective results indicate that XIST RNA may be an architectural element of the interphase chromosome territory, possibly a component of nonchromatin nuclear structure that specifically associates with Xi. XIST RNA is a novel nuclear RNA which potentially provides a specific precedent for RNA involvement in nuclear structure and cis-limited gene regulation via higher-order chromatin packaging.
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Gene expression array profiles identify subclasses of breast cancers with different clinical outcomes and different molecular features. The present study attempted to correlate genomic alterations (loss of heterozygosity; LOH) with subclasses of breast cancers having distinct gene expression signatures. Hierarchical clustering of expression array data from 89 invasive breast cancers identified four major expression subclasses. Thirty-four of these cases representative of the four subclasses were microdissected and allelotyped using genome-wide single nucleotide polymorphism detection arrays (Affymetrix, Inc.). LOH was determined by comparing tumor and normal single nucleotide polymorphism allelotypes. A newly developed statistical tool was used to determine the chromosomal regions of frequent LOH. We found that breast cancers were highly heterogeneous, with the proportion of LOH ranging widely from 0.3% to >60% of heterozygous markers. The most common sites of LOH were on 17p, 17q, 16q, 11q, and 14q, sites reported in previous LOH studies. Signature LOH events were discovered in certain expression subclasses. Unique regions of LOH on 5q and 4p marked a subclass of breast cancers with “basal-like” expression profiles, distinct from other subclasses. LOH on 1p and 16q occurred preferentially in a subclass of estrogen receptor-positive breast cancers. Finding unique LOH patterns in different groups of breast cancer, in part defined by expression signatures, adds confidence to newer schemes of molecular classification. Furthermore, exclusive association between biological subclasses and restricted LOH events provides rationale to search for targeted genes.
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Germline mutations of the Brca1 tumor suppressor gene predispose women to breast and ovarian cancers. To study mechanisms underlying BRCA1-related tumorigenesis, we derived mouse embryonic fibroblast cells carrying a targeted deletion of exon 11 of the Brca1 gene. We show that the mutant cells maintain an intact G1–S cell cycle checkpoint and proliferate poorly. However, a defective G2–M checkpoint in these cells is accompanied by extensive chromosomal abnormalities. Mutant fibroblasts contain multiple, functional centrosomes, which lead to unequal chromosome segregation, abnormal nuclear division, and aneuploidy. These data uncover an essential role of BRCA1 in maintaining genetic stability through the regulation of centrosome duplication and the G2–M checkpoint and provide a molecular basis for the role of BRCA1 in tumorigenesis.
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Male breast cancer is 100 times less frequent than its female counterpart and accounts for less than 1% of all cancers in men. Although men with breast cancer also often have gynecomastia, it is still unknown whether gynecomastia per se predisposes the male breast to malignant disease. We describe the cytogenetic analysis of three gynecomastias and four breast cancers in men. No chromosome abnormalities were detected in two cases of gynecomastia, with no other concomitant breast disease. The third gynecomastia sample, taken from a site where a breast carcinoma had previously been removed, had a t(2;11)(p24;p13) as the sole chromosome change; this is the first time that an abnormal karyotype has been described in gynecomastia. All four cancers had clonal chromosome abnormalities. Several cytogenetically unrelated clones were found in the breast tumor and in a metastasis from case 1. In the carcinoma of case 2, a single abnormal clone was found, characterized by loss of the Y chromosome, monosomy 17, and a deletion of the long arm of chromosome 18. In the carcinoma of case 3, a clone with loss of the Y chromosome as the sole change dominated, accompanied by the gain of an X chromosome in a subclone. In the lymph node metastasis examined from case 4, a single clone carrying trisomies for chromosomes 5 and 16 was detected. Our findings, especially when collated with data on the six karyotypically abnormal breast carcinomas in men described previously, indicate that gain of the X chromosome, gain of chromosome 5, loss of the Y chromosome, loss of chromosome 17, and del(18)(q21) are nonrandom abnormalities in male breast carcinomas. Genes Chromosomes Cancer 23:16–20, 1998. © 1998 Wiley-Liss, Inc.
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Gain of an X chromosome is observed as a secondary, acquired karyotypic alteration in a significant proportion of malignant lymphomas. To determine the potential involvement of X-linked genes in neoplastic development, we have analyzed the inactivation status of the supernumerary X chromosome in lymphomas in both male and female patients. In males, neither methylation of FMR1 nor expression of XIST was detected, demonstrating that the duplicated chromosome was not subject to inactivation. In females, both expressed polymorphisms and polymorphisms associated with methylation differences between the active and inactive X chromosome were analyzed to determine whether the duplicated chromosome was active or inactive. To facilitate this analysis, allele-specific PCR primers were designed for detection of previously described polymorphisms in the IDSX and G6PD genes. The female lymphomas were shown to be clonal in origin, and duplication of either the active (5 cases) or inactive (4 cases) X chromosome was observed. Correlations between clinical status and the inactivation status of the X chromosome involved in the duplication were not observed in our relatively small sample, although 4/4 informative cases with a t(14;18) showed duplication of the active X chromosome. In the course of these studies, we detected hypermethylation of the androgen receptor (AR) locus in an extremely high proportion of both male (7/9) and female (9/10) samples. These results are discussed with respect to whether sex chromosome aneuploidies in tumors are involved in, or simply the result of, the neoplastic process. Genes Chromosomes Cancer 28:246–257, 2000. © 2000 Wiley-Liss, Inc.
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Some difficulties with the classical model for the evolution of a genetically invert Y chromosome are discussed. An alternative model is proposed, which is based on the principle of Mullers ratchet; this involves the accumulation of chromosomes bearing deleterious mutant genes in a finite population in the absence of crossing-over. This process would result in the gradual increase, with time, in the number of mutant loci carried in an average Y chromosome, although the frequency of individual deleterious alleles at most loci remains low. It is shown that this creates a selection pressure for differentially increasing the activity of the X chromosome in heterogametic individuals at the expense of that of the Y, leading eventually to a genetically inert Y chromosome and to the evolution of dosage compensation.
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The study was undertaken to investigate the relationship between Barr body distribution and estrogen receptor protein content of mammary carcinoma. The proportion of cells with one or more Barr body was determined in 105 specimens of mammary carcinoma from Guard stained imprints. Receptor protein content of the specimen was measured by the dextran charcoal method and compared with histopathologic features of the carcinomas. Primary carcinomas with Barr bodies in more than 10 percent of tumor cells were more likely to have higher levels of receptor protein than those with a lower proportion of Barr body containing cells (P less than 0.005). The results obtained for primary carcinoma may explain why patients with carcinomas that have a high proportion of Barr body positive cells are more likely to respond to hormonal therapy. Furthermore, these observations, when correlated with other available data about ERP suggest that an X-chromosome is involved in the synthesis of and/or carries the locus of action for estrogen receptor protein.
Article
The human androgen-receptor gene (HUMARA; GenBank) contains a highly polymorphic trinucleotide repeat in the first exon. We have found that the methylation of HpaII and HhaI sites less than 100 bp away from this polymorphic short tandem repeat (STR) correlates with X inactivation. The close proximity of the restriction-enzyme sites to the STR allows the development of a PCR assay that distinguishes between the maternal and paternal alleles and identifies their methylation status. The accuracy of this assay was tested on (a) DNA from hamster/human hybrid cell lines containing either an active or inactive human X chromosome; (b) DNA from normal males and females; and (c) DNA from females showing nonrandom patterns of X inactivation. Data obtained using this assay correlated substantially with those obtained using the PGK, HPRT, and M27 beta probes, which detect X inactivation patterns by Southern blot analysis. In order to demonstrate one application of this assay, we examined X inactivation patterns in the B lymphocytes of potential and obligate carriers of X-linked agammaglobulinemia.
Article
To determine the clonal nature of hematopoiesis and to assess lineage involvement in patients with myelodysplastic syndromes (MDS), we used restriction fragment length polymorphisms of the X-linked genes phosphoglycerate kinase (PGK1) and hypoxanthine phosphoribosyltransferase (HPRT) and the X-linked probe M27 beta. Eleven female MDS patients heterozygous for at least one of these probes were studied: 3 with refractory anemia (RA), 2 with RA with ringed sideroblasts (RARS), 2 with chronic myelomonocytic leukemia (CMML), and 4 with RA with excess of blasts in transformation (RAEB-t). All exhibited clonal hematopoiesis as determined by Southern analysis of DNA prepared from peripheral blood (PB) and/or bone marrow (BM) cells. In three of the six patients heterozygous for the PGK1 gene, purified cell suspensions of polymorphonuclear cells (PMN), monocytes, lymphocytes, and/or T cells prepared from PB were tested. In addition, five of these patients were analyzed by a polymerase chain reaction (PCR)-based procedure as described recently. This method was slightly adapted to facilitate the analysis of cell lysates of fluorescence-activated cell sorted (FACS) monocytes, T and B lymphocytes, and natural killer (NK) cells. The outcome of Southern and PCR analysis was concordant, showing that PMN and monocytes were clonally derived, whereas circulating T and B lymphocytes and NK cells exhibited random X-chromosome inactivation compatible with a polyclonal pattern. To address the question of whether T cells are derived from unaffected progenitor cells or that their origin had antedated the onset of MDS, naive and memory T cells were analyzed separately. Both subsets showed a polyclonal pattern. However, in one patient analysis of constitutive DNA suggested a skewed methylation, and the presence of clonal lymphocytes against a background of polyclonal lymphoid cells cannot be ruled out in this patient. PCR analysis of PB and BM cells showed a nonrandom, unilateral pattern of X-inactivation, compatible with a mixture of clonally (myeloid) and polyclonally (lymphoid) derived cells. In conclusion, in some patients, MDS represents a disorder with clonal hematopoiesis restricted to cells of myeloid origin, whereas a random X-inactivation pattern is found in lymphoid cells.