Jörg D Hoheisel's research while affiliated with German Cancer Research Center and other places

Publications (350)

Conference Paper
Background: Most of pancreatic cancer patients are diagnosed at late stage due to the inability of early diagnosis for pancreatic ductal adenocarcinoma (PDAC), finally leading to a very high mortality. Therefore the identification of effective biomarkers for the early diagnosis of PDAC has a critical significance for improving the outcome of PDAC p...
Fig. 1 NHC gold complexes are potent AHR ligands. a Heatmap of CYPs...
Fig. 2 Immunosuppressive effect of MC3 in human primary T cells. a...
Fig. 3 MC3-mediated immune suppression is TGFβ1 dependent. a Expression...
Fig. 4 In vitro and in vivo immunosuppression of CD4 + T cells by MC3....
Characterization of MC3-mediated immunosuppression in scurfy mice
a The...
Article
Full-text available
Gold compounds have a long history of use as immunosuppressants, but their precise mechanism of action is not completely understood. Using our recently developed liver-on-a-chip platform we now show that gold compounds containing planar N-heterocyclic carbene (NHC) ligands are potent ligands for the aryl hydrocarbon receptor (AHR). Further studies...
Figure 1.Methyltransferase-like 3 (METTL3)-dependent N...
Figure 2. Functional coordination of direct METTL3 targets with...
Figure 5. Pathways regulated by METTL3-silencing in GSCs. Gene set...
Article
Full-text available
Despite recent advances in N6-methyladenosine (m6A) biology, the regulation of crucial RNA processing steps by the RNA methyltransferase-like 3 (METTL3) in glioma stem-like cells (GSCs) remains obscure. An integrated analysis of m6A-RIP (RNA immunoprecipitation) and total RNA-Seq of METTL3-silenced GSCs identified that m6A modification in GSCs is p...
Article
Until recently, whole-proteome microarrays for comprehensive studies of protein interactions were mostly produced by individual cloning and cellular expression of very many open reading frames, followed by protein isolation and purification as well as array production. To overcome this cumbersome process, we have developed a method to generate micr...
Article
Glioblastoma (GBM) is the most aggressive form of adult brain tumors with a poor median survival of less than 15 months. The alkylating agent temozolomide is used for chemotherapy for GBM. Regardless of the rigorous therapeutic regime, almost all cases develop resistance and recur. The mechanisms of the inherent and acquired resistance are less und...
Figure 1. Parameters determined in the nanobody analysis. (A) A typical...
Figure 2. Fraction of aggregation-free nanobodies. (A) Size-ranked...
Figure 3. Nanobody aggregation kinetics, structure and mechanism. (A)...
Figure 4. Characterization of the ΔT m shift. (A) Concentration...
Figure 5. Structural determinants of nanobody thermoresistance. (A) A...
Article
Full-text available
Nanobodies represent the variable binding domain of camelid heavy-chain antibodies and are employed in a rapidly growing range of applications in biotechnology and biomedicine. Their success is based on unique properties including their reported ability to reversibly refold after heat-induced denaturation. This view, however, is contrasted by studi...
Figure 1. Generation of Ct whole-proteome microarrays. (a) In order to...
Figure 2. Microarray displaying the whole-proteome of Ct. (a) Results...
Figure 3. Proteome Immunoassays (PIA) using pools of five sera. In...
Figure 4. Reproducibility and stability of analyses on Ct...
Figure 5. Antibody patterns in individual sera with 130 selected Ct...
Article
Full-text available
Using Chlamydia trachomatis (Ct) as a complex model organism, we describe a method to generate bacterial whole-proteome microarrays using cell-free, on-chip protein expression. Expression constructs were generated by two successive PCRs directly from bacterial genomic DNA. Bacterial proteins expressed on microarrays display antigenic epitopes, ther...
Figure 1. Principle component analysis of the samples based on their...
Table 1 . Clinical characteristics of patient cohort
Figure 2. Tissue specificity of mRNA level variations. For each tissue...
Table 2 . Result of a Cox regression of 18 autophagy transcripts...
Figure 5. Prognosis of patient survival. Kaplan-Meier curves were...
Article
Full-text available
Transcriptional profiling was performed on 452 RNA preparations isolated from various types of pancreatic tissue from tumour patients and healthy donors, with a particular focus on peritumoral samples. Pancreatic ductal adenocarcinomas (PDAC) and cystic tumours were most different in these non-tumorous tissues surrounding them, whereas the actual t...
Table 1 : List of putative druggable target genes 
Figure 2: Upregulation of USP5 and its role in in pancreatic cancer....
Figure 3: USP5 knockdown leads to DNA damage, impaired cell cycle...
Figure 4: USP5 is essential for transformation and tumor growth. (A)...
Article
Full-text available
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal solid tumors. With an overall five-year survival rate remaining below 6%, there is an explicit need to search for new molecular targets for therapeutic interventions. We undertook a barcode labelled short-hairpin (shRNA) library screen in pancreatic cancer cells in order to identify...
Article
We are analyzing in detail the molecular communication between the different cell types in the microenvironment of pancreatic ductal adenocarcinomas (PDAC). Also, its regulation is being investigated, looking at aspects such as the kind and mixture of molecules needed for triggering a particular regulative function, and unraveling the inter- and in...
Article
Introduction and aims: Although the overall five-year survival of all patients with cancer stands at 63%, for pancreatic cancer patients, it is a disheartening 8% - a number that remains largely unchanged for three decades. Of the patients diagnosed with pancreatic cancer, about 85% exhibit pancreatic ductal adenocarcinoma (PDAC). Most of these pat...
Article
Full-text available
The CAF1-NOT complex of Trypanosoma brucei, like that of other eukaryotes, contains several NOT proteins (NOT1, NOT3, NOT3/5, NOT10, and NOT11), NOT9/CAF40, and the CAF1 deadenylase, which targets 3' poly(A) tails. Again like other eukaryotes, deadenylation is the first step in the degradation of most trypanosome mRNAs. In animal cells, destruction...
Figure 1. GSS analysis of nanobody stability and aliphatic indices. (A)...
Figure 2. GSS stability signature. (A) Sequence differences between the...
Figure 3. Stabilization of dromedary nanobodies by N-terminal mutations...
Figure 4. Mechanism of stabilization by N-terminal mutations Q1E and...
Figure 5. Species-dependent difference contact map of the nanobody...
Article
Full-text available
Background: Variable domains of camelid heavy-chain antibodies, commonly named nanobodies, have high biotechnological potential. In view of their broad range of applications in research, diagnostics and therapy, engineering their stability is of particular interest. One important aspect is the improvement of thermostability, because it can have im...
Figure 1. Principle and performance of the process of producing...
Figure 2. Protein microarray quality. (a) Microarray with 2016 proteins...
Figure 3. Detection of proteins generated in situ from individual...
Article
Full-text available
DNA sequencing has advanced to a state that permits studying the genomes of individual patients as nearly a matter of routine. Towards analysing a tissue’s protein content in a similar manner, we established a method for the production of microarrays that represent full-length proteins as they are encoded in individual specimens, exhibiting the par...
Figure 1: Proteins that are commonly regulated in secretome and...
Table 1 : Cell lines used in the study
Figure 2: AUC values of the 189 individual serum markers. Analysis by...
Table 2 : List of the most frequently predicted functions associated...
Figure 3: Proteins that were similarly regulated in both tumor cell...
Article
Full-text available
Pancreatic cancer is the currently most lethal malignancy. Toward an accurate diagnosis of the disease in body liquids, we studied the protein composition of the secretomes of 16 primary and established cell lines of pancreatic ductal adenocarcinoma (PDAC). Compared to the secretome of non-tumorous cells, 112 proteins exhibited significantly differ...
Figure 1. PAH_c.1222C>T COS-7 cell line was established as a PKU in...
Figure 2. Correction of the PAH_c.1222C>T variant in COS-7 cells. (a)...
Article
Full-text available
The CRISPR/Cas9 system is a recently developed genome editing technique. In this study, we used a modified CRISPR system, which employs the fusion of inactive Cas9 (dCas9) and the FokI endonuclease (FokI-dCas9) to correct the most common variant (allele frequency 21.4%) in the phenylalanine hydroxylase (PAH) gene - c.1222C>T (p.Arg408Trp) - as an a...
Quality control of anti-CHFR antibodies. (a) Binding intensities on the...
Immunohistochemistry analysis of GRIP2 abundance in pancreatic tissues....
Quality control of anti-GRP2 antibodies. (a) Binding intensities on the...
Visualisation of the antibody microarray analysis results as volcano...
Typical results of microarray analyses. (a) Overlay-image of the...
Article
Many diagnostic and therapeutic concepts require antibodies of high specificity. Recombinant binder libraries and related selection approaches allow the efficient isolation of antibodies against almost every target of interest. Nevertheless, it cannot be guaranteed that selected antibodies perform well and interact specifically enough with analytes...
Article
Background & aims: Incidence of and mortality from pancreatic ductal adenocarcinoma (PDAC), the most common form of pancreatic cancer, are almost equivalent, so better treatments are needed. We studied gene expression profiles of PDACs and the functions of genes with altered expression to identify new therapeutic targets. Methods: We performed m...
Figure 6: Melanosomal miR-211 induces CAF formation via upregulation of...
Figure 7: Melanosomal miR-211 induces CAF formation via upregulation of...
Article
Full-text available
Melanoma originates in the epidermis and becomes metastatic after invasion into the dermis. Prior interactions between melanoma cells and dermis are poorly studied. Here, we show that melanoma cells directly affect the formation of the dermal tumour niche by microRNA trafficking before invasion. Melanocytes, cells of melanoma origin, are specialize...
Proteins that exhibited significant abundance variations between tumor...
Article
Full-text available
In this study, protein profiling was performed on gastric cancer tissue samples in order to identify proteins that could be utilized for an effective diagnosis of this highly heterogeneous disease and as targets for therapeutic approaches. To this end, 16 pairs of postoperative gastric adenocarcinomas and adjacent non-cancerous control tissues were...
Graphical summery of the results obtained in our study.
Article
Significance: Changes in platelet concentrate (PC) supernatants during storage have been so far only poorly addressed and high abundant proteins burden the identification of quantitative changes in the secretome. We applied a high-throughput antibody microarray allowing for the sensitive quantification of 673 extracellular factors. PCs account for...
Article
Pancreatic ductal adenocarcinoma (PDAC) is characterized by very early metastasis, suggesting the hypothesis that metastasis-associated changes may occur prior to actual tumor formation. In this study, we identified miR-192 as an epigenetically regulated suppressor gene with predictive value in this disease. miR-192 was downregulated by promoter me...
Article
Pancreatic ductal adenocarcinoma (PDAC) clinically has a very poor prognosis. No small molecule is available to reliably achieve cures. Meisoindigo is chemically related to the natural product indirubin and showed substantial efficiency in clinical chemotherapy for CML in China. However, its effect on PDAC is still unknown. Our results showed stron...
Article
Control of gene expression at the post-transcriptional level is essential in all organisms, and RNA-binding proteins play critical roles from mRNA synthesis to decay. To fully understand this process, it is necessary to identify the complete set of RNA-binding proteins and the functional consequences of the protein-mRNA interactions. Here, we provi...
Fig 1. Comparative Venn analysis of differentially expressed proteins....
Fig 2. Heat map demonstrating unsupervised hierarchical clustering...
Fig 3. Expression of VEGFA, RUNX1 and RUNX3. (A) Relative expression of...
Fig 4. Protein expression of RUNX3 in platelets of cITP patients (n =...
Fig 5. RUNX1 protein expression in platelets from patients with cITP (n...
Article
Full-text available
The pathological mechanisms underlying the development of immune thrombocytopenia (ITP) are unclear and its diagnosis remains a process of exclusion. Currently, there are no known specific biomarkers for ITP to support differential diagnosis and treatment decisions. Profiling of serum proteins may be valuable for identifying such biomarkers. Sera f...
Article
Introduction: Pancreatic ductal adenocarcinoma (PDAC) is by far the most common type of pancreatic cancer. It constitutes about 90% of tumors of the exocrine pancreas. The aggressive nature of PDAC along with its poor diagnostic markers contributes to a high lethality of this disease. Studies from other cancer entities implicate the role of viruses...
Table 2 Correlation of molecular (qRT-PCR) and histological cellular...
Table 3 Correlation of molecular (microarray signal intensity...
(a) Expression values of the five RNACellStrat genes in qRT-PCR...
Influence of tissue cell composition on the prognostic value of the...
(a) Expression results of RNACellStrat markers in microarray...
Article
Full-text available
Meaningful profiling of pancreatic cancer samples is particularly challenging due to their complex cellular composition. Beyond tumor cells, surgical biopsies contain desmoplastic stroma with infiltrating inflammatory cells, adjacent normal parenchyma, and "non-pancreatic tissues". The risk of misinterpretation rises when the heterogeneous cancer t...
Table 1 . Patient statistics. 
Figure 1. TBL1 is overexpressed in human and mouse PDAC. 
Figure 2. TBL1 controls pancreatic cancer cell growth and metabolic...
Table 2 . Over-representation analysis for TBL1 knockdown on GOPB terms. 
Article
Full-text available
Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer fatalities in Western societies, characterized by high metastatic potential and resistance to chemotherapy. Critical molecular mechanisms of these phenotypical features still remain unknown, thus hampering the development of effective prognostic and therapeutic measures i...
Article
To identify miRNAs whose expression are differentially regulated during trypanosome infections a microarray targeting more than 600 rat miRNA was used to analyze the miRNA expression profiles between uninfected rats and animals infected by Trypanosoma congolense and Trypanosoma brucei s.l. The potential targets of dysregulated miRNAs as well as the...
Figure 1: Schematic representation of the process of producing...
Figure 2: Immunoassays are shown that are currently used in clinical...
Figure 3: Workflow of an analysis by antibody microarray of the protein...
Article
Full-text available
After the establishment of DNA/RNA sequencing as a means of clinical diagnosis, the analysis of the proteome is next in line. As a matter of fact, proteome-based diagnostics is bound to be even more informative, since proteins are directly involved in the actual cellular processes that are responsible for disease. However, the structural variation...
Figure 1: GHSR methylation pattern, average methylation degree and ROC...
Table 1 : Characteristics of patients and samples
Figure 2: GHSR methylation degree in all samples analyzed. Methylation...
Table 2 : Crude and adjusted area under the ROC curve (AUC) values by...
Figure 3: GHSR methylation in cancer samples of different stages....
Article
Full-text available
Identification of a single molecular trait that is determinant of common malignancies may serve as a powerful diagnostic supplement to cancer type-specific markers. Here, we report a DNA methylation mark that is characteristic of seven studied malignancies, namely cancers of lung, breast, prostate, pancreas, colorectum, glioblastoma and B cell chro...
Figure 1: ROC curves for disease specific miRNAs. (A) The ROC curve for...
Table 1 Cohorts with International Classification of Diseases (ICD)-10...
Figure 2: Area-proportional Venn diagram for miRNAs with the highest...
Figure 3: Up- versus downregulations. The balloon plot shows, for the...
Figure 4: Classification in patients (cancer and non-cancer) and...
Article
Full-text available
BackgroundmiRNA profiles are promising biomarker candidates for a manifold of human pathologies, opening new avenues for diagnosis and prognosis. Beyond studies that describe miRNAs frequently as markers for specific traits, we asked whether a general pattern for miRNAs across many diseases exists.Methods We evaluated genome-wide circulating profil...
Article
GISTs have distinct gene expression patterns according to localisation, genotype and aggressiveness. DNA methylation at CpG dinucleotides is an important mechanism for regulation of gene expression. We performed targeted DNA methylation analysis of 1.505 CpG loci in 807 cancer-related genes in a cohort of 76 GISTs, combined with genome-wide mRNA ex...
Article
Stroke induces a profound neuroinflammatory reaction that leads to secondary cerebral tissue injury. Interleukin-10 (IL-10) is a key anti-inflammatory cytokine that is endogenously produced by immune cells and limits this inflammatory reaction. Previously, therapeutic administration of IL-10 has been shown to be neuroprotective in experimental stro...
Article
About 70% of newly diagnosed cases of bladder cancer are low-stage, low-grade, non muscle-invasive. Standard treatment is transurethral resection. About 60% of the tumours will recur, however, and in part progress to become invasive. Therefore, surveillance cystoscopy is performed after resection. However, in the USA and Europe alone, about 54,000...
Figure 1. Proof of concept of the tethering approach. ( A ) Schematic...
Table 1.  RNA-binding proteins and translation factors that increase...
Figure 2.  Schematic of the overexpression library and the growth...
Table 2.  Selected factors that suppress PGKB expression.
Figure 3.  Results for ZC3H11.
(A) Sequence reads that were linked to...
Article
Full-text available
In trypanosomatids, gene expression is regulated mainly by post-transcriptional mechanisms, which affect mRNA processing, translation and degradation. Currently, our understanding of factors that regulate either mRNA stability or translation is rather limited. We know that often, the regulators are proteins that bind to the 3'-untranslated region;...
Figure 1: Characterization of Caco-2 and HCT-116 exosomes. (A) Average...
Figure 2: Comparison of miRNA sets found in exosomes and their source...
Figure 3: Quantitative asymmetric distribution of miRNAs in CRC cells...
Figure 4: Biological functions of exosomal miRNAs in CRC. (A)...
Figure 5: Comparison of biological functions attributed to cellular DE...
Article
Full-text available
Exchange of molecules via exosomes is a means of eukaryotic intercellular communication, especially within tumour microenvironments. However, no data are available on alterations of exosomal molecular cargo by environmental cues (eg, pharmacological treatments). To approach this issue, we compared the abundance of 754 miRNAs and 741 cancer-related...
Schematic of RNAi screen with analysis of fumarate levels throughout...
Adenylate cyclases are synthetic lethal with FH in HEK293T cells. (A)...
Inhibition of adenylate cyclases is more toxic to FH-deficient than to...
Increase in cyclic-AMP production following FH deletion. (A) Cyclic-AMP...
Article
Full-text available
Synthetic lethality is an appealing technique for selectively targeting cancer cells which have acquired molecular changes that distinguish them from normal cells. High-throughput RNAi-based screens have been successfully used to identify synthetic lethal pathways with well-characterized tumor suppressors and oncogenes. The recent identification of...
Article
Full-text available
Genome sequencing has led to the identification of many proteins, which had not been recognized before. In consequence, the basic set of human proteins is generally known. Far less information, however, exists about protein-protein interactions, which are required and responsible for cellular activities and their control. Many protein isoforms that...
Figure 1: Schematic presentation of the various types of protein array...
Table 1 : Applications of protein arrays.
Figure 2: Schematic diagram illustrating the basic flow of a protein...
Article
Full-text available
Abstract The quest for a better understanding of organisms, and the human body in particular, at a comprehensive level has stimulated the development of techniques and processes that permit the analysis and assessment of biomedical information at high throughput. This has had substantial impact, not only by merely gathering knowledge but also by...
Figure 1: Barcoded in vivo RNAi screen with shRNA constructs. (a)...
Figure 2: SALL1 expression correlates with CDH1 levels in breast cancer...
Figure 3: Impact of SALL1 knockdown on cell migration and CSC...
Figure 4: Association of SALL1 expression with patient survival and...
Candidate tumor suppressor genes identified by means of in vivo RNAi screen
Article
Full-text available
The gold standard for determining the tumorigenic potential of human cancer cells is a xenotransplantation into immunodeficient mice. Higher tumorigenicity of cells is associated with earlier tumor onset. Here, we used xenotransplantation to assess the tumorigenic potential of human breast cancer cells following RNA interference-mediated inhibition...
Article
In this study, plasma samples from a multicentric case-control study on lymphoma were analyzed for the identification of proteins useful for diagnosis. The protein content in the plasma of 100 patients suffering from the three most common B-cell lymphomas and 100 control samples was studied with antibody microarrays composed of 810 antibodies that...
Figure 1 (See legend on next page.)
Table 1 Pathway enrichment analysis of candidate genes
The SUM-149 cell line contains a sub-population of cells with cancer...
Negative selection mammosphere formation shRNAi screen. (A) Schematic,...
ATG4A expression regulates mammosphere formation in breast cancer cell...
Article
Full-text available
Breast cancer stem cells are suspected to be responsible for tumour recurrence, metastasis formation as well as chemoresistance. Consequently, great efforts have been made to understand the molecular mechanisms underlying cancer stem cell maintenance. In order to study these rare cells in-vitro, they are typically enriched via mammosphere culture....
FIGURE 1. Venn diagram showing the number of proteins that were found...
FIGURE 2. Expression level variations of the 45 commonly regulated...
FIGURE 3. Immunohistochemical analysis of normal and PDAC tissues....
FIGURE 4. Immunoblot analysis showing the expression of ␣ -SMA in PSCs...
FIGURE 5. FACS sorting analysis revealed the percentage of PSCs (% of...
Article
Full-text available
Pancreatic stellate cells are key mediators in chronic pancreatitis and play a central role in the development of pancreatic fibrosis, stromal formation, and progression of pancreatic cancer. This study was aimed at investigating molecular changes at the level of the proteome that are associated with the activation of pancreatic stellate cells by p...
Figure 2. Induction of selected genes involved in metabolism. Primary...
Figure 3. Tumor volume and body weight development in MIA-PaCa-2...
Figure 4. Hematoxylin-eosine and immunohistochemical staining of tumor...
Closely related chemical structures of hyperforin (left) and nemorosone...
Primary human hepatocytes were treated with the indicated...
Article
Full-text available
Pancreatic cancer is one of the leading cancer-related causes of death in the western world with an urgent need for new treatment strategies. Recently, hyperforin and nemorosone have been described as promising anti-cancer lead compounds. While hyperforin has been thoroughly investigated in vitro and in vivo, in vivo data for nemorosone are still m...
Table 1 . Sample classification based on multiple diagnostic tests.
Figure 2. Cluster dendrogram for all samples. The samples were...
Table 2 . miRNAs with altered abundance in sleeping sickness.
Data for the miRNAs from Table 1 are illustrated, showing the Log2 fold...
The samples were classified according to miRNA expression patterns,...
Article
Full-text available
Simple, reliable tools for diagnosis of human African Trypanosomiases could ease field surveillance and enhance patient care. In particular, current methods to distinguish patients with (stage II) and without (stage I) brain involvement require samples of cerebrospinal fluid. We describe here an exploratory study to find out whether miRNAs from per...
Data
mRNAs with significantly altered abundance in sleeping sickness patients. Sheet 1: Results for individual patients are shown, with a corresponding result for pooled controls. Sheet 2: Annotations from GeneCARD for the regulated genes. (XLSX)
Data
Predicted targets of the miRNAs that were significantly changed in sleeping sickness samples. Only mRNAs that also showed a change in expression are included. (XLS)
Fig. 1. Barcode abundance and selection of candidate genes. ( A ) The...
Fig. 2. Validation of candidates. (A) Candidate genes were validated in...
Fig. 3. Validation of RAD17 in cell lines BxPC-3, MiaPaca-2 and...
Fig. 4. Depletion of cells arrested in early S phase. Long-term BrdU...
Fig. 5. Forced mitotic entry and sub-G1 increase. Knockdown of RAD17...
Article
Full-text available
Chemotherapy of advanced pancreatic cancer has mainly been gemcitabine-based for the past fifteen years, with only limited effect. Recently, combination therapy that also targets checkpoint kinase 1 (CHK1) has become an attractive option. The central role of CHK1 in many DNA damage response pathways, however, may result in undesired cytotoxicity in...
Data
Histomorphological examination of pancreatic tumor tissue sections with Hematoxylin and Eosin stains. Representative photomicrographs of three sections with low, medium and high tumor contents are shown. (TIF)
Data
Clinico-pathological details and tumor mutational status of all pancreatic cancer patients. (DOC)
Figure 1. Kaplan-Meier survival curves showing difference in overall...
Figure 1.  Kaplan-Meier survival curves showing difference in overall...
Table 1.  Clinical-pathological parameters of pancreatic cancer patients.
Table 2.  Multivariate Cox regression analysis for the effect of...
Table 3.  Multivariate Cox regression analysis for the effect of...
Article
Full-text available
KRAS mutations are major factors involved in initiation and maintenance of pancreatic tumors. The impact of different mutations on patient survival has not been clearly defined. We screened tumors from 171 pancreatic cancer patients for mutations in KRAS and CDKN2A genes. Mutations in KRAS were detected in 134 tumors, with 131 in codon 12 and only...
Data
Kaplan-Meier survival curves showing difference in overall survival in exocrine cancer patients with and without mutations. (A) Median survival of patients with KRAS mutations was 17 months against 30 months for patients without mutations in the gene. (B) Median survival of patients with KRAS codon 12 GGT>GAT (G12D) mutations was 16 months against...
Data
Mutation frequency by clinic pathology and effect on survival of pancreatic cancer patients. (DOC)
Data
Representative SSCP of KRAS codon 12 and codon 61 in pancreatic tumors. (A) The lanes 1–4 contain amplified fragments of exon 2 (codon 12) and lanes 5–6 contain amplified fragments of exon 3 (codon 61) from tumor DNA samples. The shifted bands seen in lane 1 contain GGT>GAT (G12D) mutation, lane 2 contains GGT>CGT (G12R), lane 3 contains GGT>GTT (G...
Data
Primer sequences and SSCP conditions for detection of mutations in the KRAS and CDKN2A genes. (DOC)
Article
There is strong epidemiologic evidence indicating that common genetic variability could be implicated in pancreatic cancer risk and, to date, various loci have been proposed. In particular, there is increasing evidence of the involvement of ABO gene variability and pancreatic cancer risk. In a large multicentric study of 1,028 pancreatic ductal ade...
Figure 1: Detection of DNA methylation patterns.A.Bar graphs showing...
Figure 2: Differentially methylated genes in DCM patients.A, B.Bar...
Figure 3: MassARRAY-based validation of differential methylation in...
Figure 4: MassARRAY-based validation of differential methylation in...
Figure 5: CpG island methylation of control subjects before and after...
Article
Full-text available
Dilated cardiomyopathies (DCM) show remarkable variability in their age of onset, phenotypic presentation, and clinical course. Hence, disease mechanisms must exist that modify the occurrence and progression of DCM, either by genetic or epigenetic factors that may interact with environmental stimuli. In the present study, we examined genome-wide ca...
Article
Based on about a decade of technical developments in analysing the human proteome with antibody microarrays and experience in performing such analyses, now there are the means at hand for detailed and simultaneously global investigations of this kind. Many technical aspects have been dealt with of both the microarray format itself - such as overcom...
Data
Expression and overlap of CD44/CD24/ESA/CD133 in JoPaca-1. A. Expression of putative stem cell markers CD44, CD24, ESA, and CD133 was determined by FACS using the respective antibodies conjugated to fluorescent dyes: Phycoerythrin-Cy7 to anti CD44, FITC to anti-CD24, APC to anti-ESA, and phycoerythrin to anti-CD133. Depicted here are two-dimensiona...
Data
Most commonly observed mutations in pancreatic cancer listed for BxPC-3 and JoPaca-1. Listed here are non-synonymous coding mutations of the top-17 mutated genes for pancreatic cancer (according to the COSMIC database) as well as BRCA1/2, PALLD and PALB2 (OMIM database) for BxPC-3 and JoPaca-1. Mutated bases are shown beneath each cell line with th...
Data
Selected SNPs from genome wide association studies in pancreatic cancer listed for BxPC-3 and JoPaca-1. The table lists significant non-coding variations for PDAC and their degree of mutation in the cell lines BxPC-3 and JoPaca-1. Mutations were selected from genome wide association studies up to January 2012. Sources can be identified by the first...
Data
FACS histograms of CD133 content in JoPaca-1. The content of CD133+ cells in JoPaca-1 was determined in increasing passages. Histograms are shown of cells stained with phycoerythrin-conjugated CD133-antibody (blue) and unstained cells (red) determined by FACS. (TIF)
Data
Chromosomal aberrations observed in the karyograms of 26 JoPaca-1 cells. Listed here are all observed aberrations and their prevalence in 26 karyograms. “t” marks translocations and “i” stands for inversions. (DOCX)
Figure 1. Growth behaviour and cell morphology. Phase contrast images...
Table 1 . CD133+ and overlap with CD44+/CD24+/ESA+ and ALDHbr.
Figure 2. Karyogram and common chromosomal aberrations. A...
Table 2 . Expression of CD133 in established pancreatic cancer cell lines.
Figure 3. Response to gemcitabine dependent on time and growth rate....
Article
Full-text available
Standard cancer cell lines do not model the intratumoural heterogeneity situation sufficiently. Clonal selection leads to a homogeneous population of cells by genetic drift. Heterogeneity of tumour cells, however, is particularly critical for therapeutically relevant studies, since it is a prerequisite for acquiring drug resistance and reoccurrence...
Data
FACS contour plots of cell lines with low CD133 content. The CD133+ content of established pancreatic cell lines was measured by FACS. Depicted here are contour plots of unstained cells (red) and cells stained with phycoerythrin-conjugated CD133-antibody (blue). Outliers of the contour are shown as dots and were include in the analysis. The gate fo...
Data
Sanger sequencing of KRAS codon 12. Electropherograms are presented for codons 11, 12, and 13 of the KRAS locus of JoPaca-1 parental cells and three JoPaca-1 subclones as well as four established cell lines. Sanger sequencing of JoPaca-1 parental cells detected both mutated (dT) and wildtype (dG) basepairs at the second position of codon 12, wherea...
Table 1 Characteristics of samples
Table 2 CpGs with the most differential methylation patterns between...
Table 3 The AUC values 
Fig. 4 Effects of GHSR on viability and invasion of breast cancer cells...
Article
Full-text available
DNA methylation patterns have been recognised as cancer-specific markers with high potential for clinical applications. We aimed at identifying methylation variations that differentiate between breast cancers and other breast tissue entities to establish a signature for diagnosis. Candidate genomic loci were analysed in 117 fresh-frozen breast spec...
Data
Full-text available
Table S2. The optimal GLS models found for each of the examined genes by a stepwise backward reduction of the full model described in Material and Methods.
Data
Full-text available
Table S1. Demographic and clinical characteristics of CLL patients and healthy donors.
Table 1 Sequences of the PCR and pyrosequencing primers used in this study
Maps of the studied sequences. (A) Schematic representations of the...
Methylation of the inhibitor genes in patient CLL samples. Methylation...
Results of Sanger bisulphite sequencing of patient and control samples....
Quantification of methylation degrees and expression of the inhibitor...
Article
Full-text available
Background The Wnt/β-catenin signalling is aberrantly activated in primary B cell chronic lymphocytic leukaemia (CLL). Epigenetic silencing of pathway inhibitor genes may be a mechanism for its activation. In this study, we investigated systematically and quantitatively the methylation status of 12 Wnt/β-catenin pathway inhibitor genes – CDH1, DACT...
Conference Paper
Aims Gastrointestinal stromal tumors (GISTs) have distinct gene expression patterns according to anatomical localisation and genotype, with potential impact on biological aggressiveness. DNA methylation of CpG dinucleotides in the promoter region of genes is an important mechanism for regulation of gene expression. We performed a large-scale analys...

Citations

... The activation and induction of fibrogenesis of PSC was triggered by the addition of TNF-α and as described previously [35]. In brief, PSCs were maintained in IMDM supplemented with heat-inactivated fetal bovine serum (10%), penicillin (50 units/ml), and streptomycin (50 μg/ ml) at 37°C and 5% CO 2 . ...
... Strategies that enable VHHs to cross the blood-brain barrier have recently shown promise. These findings have driven tremendous growth in the use of VHHs for treating central nervous system diseases (44)(45)(46). A limiting factor for the clinical use of VHH domains is that the hydrodynamic radius of VHHs falls below the kidney's glomerular filtration limit, which can contribute to rapid renal clearance and a weak pharmacokinetic (PK) profile, considerably affecting their therapeutic effectiveness. ...
... Some studies have suggested that overexpression of METTL3 profoundly inhibited the proliferation, tumorigenicity and migration ability of glioma [144,145], breast cancer [146] or bladder cancer cells [147] by altering the mRNA expression of genes or proteins. Paradoxically, other studies have shown that by silencing METTL3 [148][149][150][151][152][153] or WTAP (only in glioma) [154], similar cell growth and aggressiveness inhibition was achieved (Fig. 4). ...
... Furthermore, a number of miRNAs which suppress proliferation, invasion, and migration of cancer cells, were downregulated due to promoter hypermethylation in different types of cancer. Among these miRNAs are let-7a, miR-9, miR-34b/c, miR-338-3p, miR-596, miR-125a-5p, miR-375, miR-27b-3p, miR-495-3p, miR-490-3p and miR-124a in gastric cancer [87][88][89][90][91][92][93][94][95][96][97], let-7a, miR-9, miR-124 s, miR-125a-5p, miR-192, miR-615-5p, miR-1247, miR-142-3p, miR-148a, miR-132, miR-200, miR-152, miR-17 and miR-92 in pancreatic cancer [98][99][100][101][102][103][104][105][106][107][108][109], miR-9, let-7a, miR-191, miR-203, miR-335, miR-137, miR-142, miR-148a, miR-375, miR-195, miR-183, miR-497, miR-124, miR-125, miR-378, miR-639 in HCC [110][111][112][113][114][115][116][117][118][119][120], and let-7a, miR-107, miR-203a, miR-1258, miR − 9, miR-107, miR-124-3p, miR-125b-5p, miR-127-5p, miR-129-5p, miR-130b, miR-132-3p, miR-137, miR-148a-3p, miR-339-3p, miR-375, miR-34a, miR-203a, miR-34b/c, miR-191-5p, miR-193a-5p, miR-193a-3p, miR-196, miR-508-3p, miR-424/503 cluster in ovarian cancer [121][122][123][124][125][126][127][128][129][130][131][132]. It has been shown by numerous studies that there is a significant change in the expression profile of the miRNA not just in tumor samples but also in the blood and urine of patients with bladder neoplasm [133,134]. ...
... GIST is the second common gastrointestinal tumor showing variable clinical outcomes because of complicated molecular alteration [21]. The involvement of DNA methylation has been found in GIST [22]. In the current study, we explored the role of EZH2-mediated PAX8 methylation in GIST, and found it a facilitator for GIST progression via downregulation of Wnt4. ...
... Although autophagy can prevent tumour cell proliferation in early tumorigenesis steps [55], it seems to act as a pro-tumour player in later stages of tumour formation [4]. Moreover, CSCs represent a particular cell population that has higher basal autophagy levels than other cancer cells, as they use it as a way to proceed to quiescence in order to survive under drastic conditions within the tumour core [56,57]. Wolf et al. [57] thus showed that inhibiting ATG4A expression led to a decrease of the CSC-like phenotype in breast cancer tumours in vivo, suggesting its importance in maintenance of CSCs. ...
... The fabrication of protein microarrays was performed applying the multiple spotting technique, an approach that uses DNA templates to synthesize proteins directly on microarray slides [17,37]. The protein microarrays were spotted on epoxysilane coated slides (SCHOTT Nexterion AG, Jena, Germany) using a microarray non-contact printer, the Nanoplotter 2 (GeSIM, Radeberg, Germany) following the protocol described by Hufnagel et al. [38]. The protein microarrays manufacture process is outlined in Figure 5. ...
... It does not appear to bind any of the eIF4G candidates and was found to migrate with the heavy polysomal complexes in sucrose gradients, thus could be associated with the stabilization of polysomes in Leishmania. Genome-wide tethering assay in Trypanosoma brucei classified LeishIF4E-2 as a putative translation repressor [18], but in Leishmania its role still remains elusive [19]. ...
... This technique can be applied for the simultaneous detection of multiple proteins, and has the advantage of high-throughput applicability. 25 We accordingly used this advanced antibody array detection chip technology to identify protein markers associated with sperm apoptosis and sperm damage, and showed that Fas/Fasl, Bcl-2/Bax, caspase-3, caspase-8, p53, p21, TNF-α, TNF-β, sTNF-R1, and sTNF-R2 were all significantly upregulated in line with increasing BMI in men. Interestingly, livin, which was upregulated in the overweight group, was significantly downregulated in the obese group. ...
... IET covers the most detrimental malignancies including pancreatic ductal adenocarcinoma (PDAC), breast cancer 2 , and ovarian cancer 3 . The 5-year overall survival rate of IET, take PDAC as an example, is around 5% 4,5 . Emerging advances in immunotherapy including immune-checkpoint blockade (ICB) have shown promise in melanoma, lung cancer and urothelial carcinoma 6 . ...