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Gene expression profiling of clear cell renal cell carcinoma with sarcomatoid transformation

ABSTRACT: Gene expression profiling of clear cell renal cell carcinoma with sarcomatoid transformation

PROVIDER: PRJNA1206208 | ENA |

REPOSITORIES: ENA

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Gene expression profiling of clear cell renal cell carcinoma with sarcomatoid transformation

Project description:Renal cell carcinoma (RCC) with sarcomatoid transformation features a biphasic tumour with both sarcomatoid and carcinomatous components. Clear cell RCC (ccRCC) is the most common RCC subtype, frequently exhibits sarcomatoid transformation. The pathogenesis of sarcomatoid ccRCC remains unclear. This study aimed to identify the genes and pathways involved in sarcomatoid ccRCC using gene expression profiling. We analysed three distinct regions including sarcomatoid component, clear cell component and matched normal kidney tissue from formalin-fixed, paraffin-embedded (FFPE) tissue samples of four patients. RNA was extracted and gene expression profiles were analysed using the NanoString nCounter® PanCancer Pathways Panel on the NanoString nCounter® Analysis System. Data analysis was performed using NanoString nSolver™ Analysis Software. Significant gene expression differences were defined with a threshold of fold change ˃ 4 and P-value ˂ 0.05. Compared to normal kidney tissue, 17 genes were significantly different in the clear cell component, with 5 were upregulated and 12 downregulated. The most significantly upregulated and downregulated genes were GDF6 and SFRP1 respectively. In the sarcomatoid component, 85 genes showed differences, with 38 upregulated and 47 downregulated. COL11A1 and LRP2 were the most significantly overexpressed and underexpressed genes respectively. When comparing sarcomatoid component with clear cell component, there were 53 significantly dysregulated genes, including epithelial-mesenchymal transition markers such as MMP9 and FN1. Pathway analysis indicated that PI3K was the most frequently deregulated pathway in the sarcomatoid component, suggesting its role in sarcomatoid transformation. This study provides insights into the gene expression patterns in ccRCC with sarcomatoid transformation.

2025-01-21 | GSE285848 | GEO

Genome wide analysis of sarcomatoid and non-sarcomatoid clear cell renal cell carcinoma

Project description:Genome wide analysis of sarcomatoid and non-sarcomatoid clear cell renal cell carcinoma

| PRJNA254826 | ENA

Genome wide DNA copy number analysis of sarcomatoid renal cell carcinoma.

Project description:The genome wide DNA copy number profiles of the biphasic epithelioid (E-) and sarcomatoid (S-) components of sarcomatoid clear cell renal cell carcinoma were analyzed using SNP arrays. The E- and S- components showed a similar DNA copy number profile, despite morphologic differences.

2015-06-18 | GSE59265 | GEO

Genome wide transcriptomic analysis of sarcomatoid (E/S), rhabdoid (E/R) and non-sarcomatoid (E*) clear cell renal cell carcinoma

Project description:An analysis of the biphasic epithelioid (E-) and sarcomatoid(S-) components of sarcomatoid RCC and advanced stage non-sarcomatoid RCC (E*) showed that: the E- and S- components shared a similar transcriptomic signature, despite morphologic differences; and that the transcriptome of sarcomatoid RCC was sharply distinct from non-sarcomatoid RCC. The E- and R- components of rhabdoid RCC were also transcriptomically similar but distinct from RCC lacking rhabdoid/sarcomatoid features (E*). Total RNA processed and spotted on Illumina microarrays from the following patient samples: 38 sarcomatoid RCC (37 paired E- and S and 1 unpaired S-), 4 rhabdoid RCC (paired E- and R-) and 56 non-sarcomatoid RCC. There are 8 replicate samples (7 sarcomatoid RCC and 1 rhabdoid RCC).

2015-06-18 | E-GEOD-59264 | biostudies-arrayexpress

RNA-seq transcriptomic analysis of sarcomatoid (E/S), rhabdoid (E/R) and non-sarcomatoid (E*) clear cell renal cell carcinoma

Project description:The biphasic epithelioid (E-) and sarcomatoid(S-) components of sarcomatoid RCC and epithelioid (E-) and rhabdoid (R-) components of rhabdoid RCC shared a similar transcriptomic signature, despite morphologic differences; by contrast, the transcriptome of sarcomatoid and rhabdoid RCC was sharply distinct from non-sarcomatoid RCC. Total RNA was processed for RNA-seq from the following patient samples: 7 sarcomatoid RCC (E- and S- pairs), 4 rhabdoid RCC (E- and R- pairs) and 15 non-sarcomatoid RCC.

2015-05-20 | E-GEOD-59066 | biostudies-arrayexpress

Genome wide transcriptomic analysis of sarcomatoid (E/S), rhabdoid (E/R) and non-sarcomatoid (E*) clear cell renal cell carcinoma

2015-06-18 | GSE59264 | GEO

RNA-seq transcriptomic analysis of sarcomatoid (E/S), rhabdoid (E/R) and non-sarcomatoid (E*) clear cell renal cell carcinoma

2015-05-20 | GSE59066 | GEO

Transcriptome RNA sequencing data of sarcomatoid renal cell carcinoma cell line SRCC and its subclones with different phenotypes.

Project description:Two subsets of early genetic mutations closely related to the malignant behavior of renal sarcomatoid carcinoma were identified by exon sequencing, transcriptome sequencing, protein profiling and clonal evolution of self-established renal sarcomatoid carcinoma cell lines and subclones of different secretion states

2024-12-30 | GSE193006 | GEO

Clear-cell renal cell carcinomas tumors

Project description:Whole genome expression of 39 clear-cell renal cell carcinomas tumors 39 frozen tissue from recent nephrectomies for clear-cell renal cell carcinoma; association with clinical characteristics

2011-05-28 | E-GEOD-29609 | biostudies-arrayexpress

Genomic characterization of sarcomatoid transformation in clear cell renal cell carcinoma.

Project description:The presence of sarcomatoid features in clear cell renal cell carcinoma (ccRCC) confers a poor prognosis and is of unknown pathogenesis. We performed exome sequencing of matched normal-carcinomatous-sarcomatoid specimens from 21 subjects. Two tumors had hypermutation consistent with mismatch repair deficiency. In the remainder, sarcomatoid and carcinomatous elements shared 42% of somatic single-nucleotide variants (SSNVs). Sarcomatoid elements had a higher overall SSNV burden (mean 90 vs. 63 SSNVs, P = 4.0 × 10(-4)), increased frequency of nonsynonymous SSNVs in Pan-Cancer genes (mean 1.4 vs. 0.26, P = 0.002), and increased frequency of loss of heterozygosity (LOH) across the genome (median 913 vs. 460 Mb in LOH, P < 0.05), with significant recurrent LOH on chromosomes 1p, 9, 10, 14, 17p, 18, and 22. The most frequent SSNVs shared by carcinomatous and sarcomatoid elements were in known ccRCC genes including von Hippel-Lindau tumor suppressor (VHL), polybromo 1 (PBRM1), SET domain containing 2 (SETD2), phosphatase and tensin homolog (PTEN). Most interestingly, sarcomatoid elements acquired biallelic tumor protein p53 (TP53) mutations in 32% of tumors (P = 5.47 × 10(-17)); TP53 mutations were absent in carcinomatous elements in nonhypermutated tumors and rare in previously studied ccRCCs. Mutations in known cancer drivers AT-rich interaction domain 1A (ARID1A) and BRCA1 associated protein 1 (BAP1) were significantly mutated in sarcomatoid elements and were mutually exclusive with TP53 and each other. These findings provide evidence that sarcomatoid elements arise from dedifferentiation of carcinomatous ccRCCs and implicate specific genes in this process. These findings have implications for the treatment of patients with these poor-prognosis cancers.

| S-EPMC4776463 | biostudies-literature

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