Transcriptome analysis of normal kidney, primary and metastasis ccRCC
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE105261 | GEO | 2018/10/16
REPOSITORIES: GEO
Similar Datasets
Project description:In recent years, several approaches have been taken in the peptide-based immunotherapy of metastatic renal cell carcinoma (RCC), although little is known about HLA presentation on metastases compared to primary tumor and normal tissue of RCC. In this study we compared primary tumor, normal tissue and metastases with the aim of identifying similarities and differences between these tissues. We performed this comparison for two RCC patients on the level of the HLA ligandome using mass spectrometry and for three patients on the level of the transcriptome using oligonucleotide microarrays. The quantitative results show that primary tumor is more similar to metastasis than to normal tissue, both on the level of HLA ligand presentation and mRNA. We were able to characterize a total of 142 peptides in the qualitative analysis of HLA-presented peptides. Six of them were significantly overpresented on metastasis, among them a peptide derived from CD151; fourteen were overpresented on both primary tumor and metastasis compared to normal tissue, among them an HLA ligand derived from tumor protein p53. Thus, we could demonstrate that peptide-based immunotherapy might affect tumor as well as metastasis of RCC, but not healthy kidney tissue. Furthermore we were able to identify several peptides derived from tumor-associated antigens that are suitable for vaccination of metastatic RCC. Three clear cell renal cell carcinomas including autologous normal tissue and autologous metastasis were analyzed. This dataset is part of the TransQST collection.
2008-09-03 | E-GEOD-12606 | biostudies-arrayexpress
Project description:In recent years, several approaches have been taken in the peptide-based immunotherapy of metastatic renal cell carcinoma (RCC), although little is known about HLA presentation on metastases compared to primary tumor and normal tissue of RCC. In this study we compared primary tumor, normal tissue and metastases with the aim of identifying similarities and differences between these tissues. We performed this comparison for two RCC patients on the level of the HLA ligandome using mass spectrometry and for three patients on the level of the transcriptome using oligonucleotide microarrays. The quantitative results show that primary tumor is more similar to metastasis than to normal tissue, both on the level of HLA ligand presentation and mRNA. We were able to characterize a total of 142 peptides in the qualitative analysis of HLA-presented peptides. Six of them were significantly overpresented on metastasis, among them a peptide derived from CD151; fourteen were overpresented on both primary tumor and metastasis compared to normal tissue, among them an HLA ligand derived from tumor protein p53. Thus, we could demonstrate that peptide-based immunotherapy might affect tumor as well as metastasis of RCC, but not healthy kidney tissue. Furthermore we were able to identify several peptides derived from tumor-associated antigens that are suitable for vaccination of metastatic RCC.
2008-09-03 | GSE12606 | GEO
Project description:Gene array analysis of clear cell renal cell carcinoma tissue versus matched normal kidney tissue
2025-01-24 | E-GEOD-53757 | ExpressionAtlas
Project description:In order to address the progression, metastasis, and clinical heterogeneity of renal cell cancer (RCC), transcriptional profiling with oligonucleotide microarrays (22,283 genes) was done on 49 RCC tumors, 20 non-RCC renal tumors, and 23 normal kidney samples. Samples were clustered based on gene expression profiles and specific gene sets for each renal tumor type were identified. Gene expression was correlated to disease progression and a metastasis gene signature was derived. Gene signatures were identified for each tumor type with 100% accuracy. Differentially expressed genes during early tumor formation and tumor progression to metastatic RCC were found. Subsets of these genes code for secreted proteins and membrane receptors and are both potential therapeutic or diagnostic targets. A gene pattern ("metastatic signature") derived from primary tumors was very accurate in classifying tumors with and without metastases at the time of surgery. A previously described "global" metastatic signature derived by another group from various non-RCC tumors was validated in RCC. Unlike previous studies, we describe highly accurate and externally validated gene signatures for RCC subtypes and other renal tumors. Interestingly, the gene expression of primary tumors provides us information about the metastatic status in the respective patients and has the potential, if prospectively validated, to enrich the armamentarium of diagnostic tests in RCC. We validated in RCC, for the first time, a previously described metastatic signature and further showed the feasibility of applying a gene signature across different microarray platforms. Transcriptional profiling allows a better appreciation of the molecular and clinical heterogeneity in RCC. We used the following tissue samples to obtain transcriptional profiling of kidney tumors using Affymetrix HGU-133A chips: 23 Normal, 32 clear cell RCC (cRCC), 11 papillary RCC (pRCC), 6 chromophobe RCC (chrRCC), 12 Oncocytoma (OC), and 8 transitional cell carcinoma (TCC). The supplementary file 'GSE15641_mas5_data.txt' contains MAS5 signal values for the Samples included in Series GSE15641. This dataset is part of the TransQST collection.
2009-04-28 | E-GEOD-15641 | biostudies-arrayexpress
Project description:In order to address the progression, metastasis, and clinical heterogeneity of renal cell cancer (RCC), transcriptional profiling with oligonucleotide microarrays (22,283 genes) was done on 49 RCC tumors, 20 non-RCC renal tumors, and 23 normal kidney samples. Samples were clustered based on gene expression profiles and specific gene sets for each renal tumor type were identified. Gene expression was correlated to disease progression and a metastasis gene signature was derived. Gene signatures were identified for each tumor type with 100% accuracy. Differentially expressed genes during early tumor formation and tumor progression to metastatic RCC were found. Subsets of these genes code for secreted proteins and membrane receptors and are both potential therapeutic or diagnostic targets. A gene pattern ("metastatic signature") derived from primary tumors was very accurate in classifying tumors with and without metastases at the time of surgery. A previously described "global" metastatic signature derived by another group from various non-RCC tumors was validated in RCC. Unlike previous studies, we describe highly accurate and externally validated gene signatures for RCC subtypes and other renal tumors. Interestingly, the gene expression of primary tumors provides us information about the metastatic status in the respective patients and has the potential, if prospectively validated, to enrich the armamentarium of diagnostic tests in RCC. We validated in RCC, for the first time, a previously described metastatic signature and further showed the feasibility of applying a gene signature across different microarray platforms. Transcriptional profiling allows a better appreciation of the molecular and clinical heterogeneity in RCC.
2009-04-28 | GSE15641 | GEO
Project description:Approximately 70% of clear cell renal cell carcinoma are characterised by the biallelic inactivation of VHL on chromosome 3p. ELOC-mutated renal cell carcinoma with biallelic ELOC inactivation on chromosome 8q are considered a novel subtype of renal cancer possessing a morphological overlap with ccRCC; however, the frequency and consequences of ELOC alterations in wtVHL and mutVHL is unclear. In this study, we characterise 123 renal tumours with clear cell morphology with known VHL mutation status to assess morphological and molecular consequences of ELOC inactivation. Using Oncoscan and whole exome sequencing we identify 18 ELOC deleted RCC, three of which contain ELOC mutations resulting in the biallelic inactivation of ELOC. Biallelic ELOC and biallelic VHL aberrations were mutually exclusive, although two ELOC-mutated RCC showed monoallelic VHL alterations. Using High Ambiguity Driven Biomolecular Docking we report a novel ELOC variant containing a duplication event disrupting ELOC-pVHL interaction alongside the frequently seen Y79C alteration. Using HRM mass spectrometry we show RCC with biallelic ELOC alterations have significantly reduced ELOC expression but similar CAIX and VEGFA expression when compared to classical ccRCC with VHL inactivation. These data demonstrate that RCC with ELOC and VHL alterations have comparable downstream effects with similar pathways to ccRCC tumourigenesis indicating that both entities are closely related.
2025-04-22 | GSE201277 | GEO
Project description:Generation of a new library of targeted mass spectrometry assays for accurate protein quantification in malignant and normal kidney tissue. Aliquots of primary tumor tissue lysates from 86 patients with initially localized renal cell carcinoma (RCC), 75 patients with metastatic RCC treated with sunitinib or pazopanib in the first line and 17 adjacent normal tissues treated at Masaryk Memorial Cancer Institute (MMCI) in Brno, Czech Republic, or University Hospital Pilsen (UHP), Czech Republic, were used to generate the spectral library. Two previously published datasets (dataset A and B) and two newly generated RCC datasets (dataset C and D) were analyzed using the newly generated library showing increased number of quantified peptides and proteins, depending on the size of the library and LC-MS/MS instrumentation. This PRIDE project also includes quantitative analysis results for all four datasets and raw files for dataset C and D. Dataset A is characterized in DOI: 10.1038/nm.3807. It consists of 18 samples from 9 RCC patients involving one cancer and non-cancerous sample per patient. Dataset B is characterized in DOI: 10.3390/biomedicines9091145. It consists of 16 tumor samples and 16 adjacent normal tissues from 16 mRCC patients treated at Masaryk Memorial Cancer Institute (MMCI) in Brno, Czech Republic. Dataset C involves only tumor tissues from dataset B. Half of them responded to sunitinib treatment in the first line three months after treatment initiation and half did not. Dataset D involves 16 RCC patients treated at University Hospital Pilsen (UHP), Czech Republic. All were localized at the time of initial diagnosis, half of the tumors developed distant metastasis in five years after the diagnosis.
2022-01-03 | PXD028411 | Pride
Project description:Renal cell carcinoma (RCC) is the most common and lethal cancer of the adult kidney. Its incidence is increasing and outcomes remain poor. Accurate discrimination of RCC patients with poor prognosis was very important for the appropriate and effective patient management. ccRCC originated from dysregulation of different gene expression. To screen novel prognosis markers, a dysregulated mRNA expression profile was identified by microarray in some pairs of different stages ccRCC.
2017-12-31 | GSE100666 | GEO
Project description:Renal cell carcinoma (RCC) is among the top 8 most diagnosed cancer in United States, which 79,000 patients newly were diagnosed and 13,920 deaths [1]. The clear-cell RCC (ccRCC) is the most common histopathological subtype representing approximately 85~90% in all diagnosed case [2]. In renal cancer treatment, metastasis is considered the most serious problem. Metastatic RCC (mRCC) is a fetal disease. It is known that about 25~30% of patients diagnosed with early kidney cancer have metastasized [3, 4]. The 5-year survival rate of patients with mRCC is 11.7%, and the prognosis is very poor [5]. Approximately 30% of patients have recurrence despite removal of the primary tumor, including 10-15% of patients found in T1 and clinically removed [4]. The mRCC patients show poor response to chemotherapy and radiotherapy, the rate of disappointing for treatment is increased from 15% to 25% [6, 7]. The common sites of RCC metastasis is known to the lung (40%), bone (30%), lymph node (22%) and liver (20%) [8].
2024-01-30 | PXD039207 | Pride
Project description:Renal cell carcinoma (RCC), the third most prevalent urological cancer, claims more than 100,000 lives/year worldwide. The clear cell (ccRCC) is the most common and aggressive subtype of renal cancer. Commonly asymptomatic, more than 30% of ccRCCs are diagnosed when they are already metastatic resulting in a 95% mortality rate and one-third of organ-confined cancers treated by nephrectomy develop metastasis during the follow-up. Diagnosis and monitoring requires expensive and frequent imaging examinations; thereby, finding of diagnostic and prognostic biomarkers to screen, diagnose and monitor renal cancers are clearly needed. Hepatitis A virus receptor/kidney injury molecule 1 (HAVCR1/KIM-1) gene has been claimed to be a susceptibility gene for ccRCC and HAVCR1/KIM-1 ectodomain shedding a predictive biomarker of tumor progression.
2020-09-27 | E-MTAB-2071 | biostudies-arrayexpress