MicroRNA expression data from human renal cell cancer subtypes
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ABSTRACT:
ORGANISM(S): synthetic construct Homo sapiens
PROVIDER: GSE41282 | GEO | 2012/10/03
SECONDARY ACCESSION(S): PRJNA176439
REPOSITORIES: GEO
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Project description:MicroRNAs play a vital role in the process of tumorigenesis. To identify and characterize miRNA Expression in renal cell cancer, we performed microarray based screening of miRNA expression profiles in clear cell, papillary type 1 and papillary type 2 renal cell cancer. We selected cases of confirmed clear cell, papillary type 1 and papillary type 2 renal cell carcinoma and generated pairs of tumor and corresponding normal tissue by manual microdissection.
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Project description:Renal cell carcinoma is the most common neoplasm of the adult kidney. A few subtypes of RCC include papillary RCC (pRCC), chromophobe RCC (chRCC) and the benign oncocytoma tumor. In some cases, distinguishing between the RCC subyptes is difficult. We performed a mircroRNA (miRNA) microarray to determine differential miRNA expression between pRCC, chRCC, and oncocytoma. We performed a miRNA microarray on 10 tumor samples of each papillary renal cell carcinoma (pRCC), chromophobe renal cell carcinoma (chRCC), and oncocytoma.
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Project description:Clear cell papillary renal cell carcinoma (CCPRCC) is a low-grade renal neoplasm with morphological characteristics mimicking both clear cell renal cell carcinoma (CCRCC) and papillary renal cell carcinoma (PRCC). However, despite some overlapping features, their morphological, immunohistochemical, and molecular profiles are distinct. To better understand the biology of this tumor, we analyze the miRNA expression profiles of a set of CCPRCC by microarrays.
2017-02-28 | GSE95385 | GEO
Project description:Copy number variant (CNV) analysis was performed on renal cell carcinoma (RCC) specimens (chromophobe, clear cell, oncocytoma, papillary type 1, papillary type 2) using high resolution arrays (1.85 million probes). RCC samples exhibited diverse genomic changes within and across tumor types ranging from 106 CNV segments in a clear cell specimen to 2238 CNV segments in a papillary type 2 specimen. Despite the genomic heterogeneity, distinct CNV segments were common within each of 4 tumor classifications: chromophobe (7 segments), clear cell (3 segments), oncocytoma (9 segments), and papillary type 2 (2 segments). Shared segments ranged from a 6.1 Kb deletion among oncocytomas to a 208.3 Kb deletion common to chromophobes. Among common tumor type-specific variations, chromophobe, clear cell and oncocytomas comprised exclusively non-coding DNA. No CNV regions were common to papillary type 1 specimens although there were 12 amplifications and 12 deletions in 5 of 6 samples. Three microRNAs and 12 mRNA genes had M-bM-^IM-% 98% of their coding region contained within CNV regions including multiple gene families (chromophobe: amylase 1A, 1B, 1C; oncocytoma: general transcription factor 2H2, 2B, 2C, 2D). Gene deletions involved in histone modification and chromatin remodeling affected individual subtypes (clear cell: SFMBT, SETD2; papillary type 2: BAZ1A) as well as the collective RCC group (KDM4C). The genomic amplifications/deletions identified in each renal tumor type represent potential diagnostic and/or prognostic biomarkers. Tissue samples were obtained from the University of Pittsburgh Health Sciences Tissue Bank (HSTB) using an honest broker system and according to IRB approved protocol #970480. Samples were acquired as surgical specimens, flash-frozen in a 1.8 ml cryotube (NalgeNunc, Inc., Rochester, NY) followed by immediate storage at -80C. Each tumor sample (n=27) was classified into one of 5 renal cancer subtypes (chromophobe: n=5, clear cell: n=5, oncocytoma: n=5, papillary type 1: n=6, papillary type 2: n=6) by consensus evaluation of correlative hematoxylin and eosin stained slides performed independently by 3 anatomical pathologists. The three pathologists also confirmed the absence of pathological features in adjacent normal renal samples (n=9) and this normal reference group was expanded by inclusion of 14 normal thyroid samples and 8 normal lung specimens. DNA from each of these specimens was analyzed using genotyping microarrays (SNP 6.0, Affymetrix, Sunnyvale, CA).
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Project description:Renal cell carcinoma is the most common neoplasm of the adult kidney. A few subtypes of RCC include papillary RCC (pRCC), chromophobe RCC (chRCC) and the benign oncocytoma tumor. In some cases, distinguishing between the RCC subyptes is difficult. We performed a mircroRNA (miRNA) microarray to determine differential miRNA expression between pRCC, chRCC, and oncocytoma.
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Project description:Copy number variant (CNV) analysis was performed on renal cell carcinoma (RCC) specimens (chromophobe, clear cell, oncocytoma, papillary type 1, papillary type 2) using high resolution arrays (1.85 million probes). RCC samples exhibited diverse genomic changes within and across tumor types ranging from 106 CNV segments in a clear cell specimen to 2238 CNV segments in a papillary type 2 specimen. Despite the genomic heterogeneity, distinct CNV segments were common within each of 4 tumor classifications: chromophobe (7 segments), clear cell (3 segments), oncocytoma (9 segments), and papillary type 2 (2 segments). Shared segments ranged from a 6.1 Kb deletion among oncocytomas to a 208.3 Kb deletion common to chromophobes. Among common tumor type-specific variations, chromophobe, clear cell and oncocytomas comprised exclusively non-coding DNA. No CNV regions were common to papillary type 1 specimens although there were 12 amplifications and 12 deletions in 5 of 6 samples. Three microRNAs and 12 mRNA genes had ≥ 98% of their coding region contained within CNV regions including multiple gene families (chromophobe: amylase 1A, 1B, 1C; oncocytoma: general transcription factor 2H2, 2B, 2C, 2D). Gene deletions involved in histone modification and chromatin remodeling affected individual subtypes (clear cell: SFMBT, SETD2; papillary type 2: BAZ1A) as well as the collective RCC group (KDM4C). The genomic amplifications/deletions identified in each renal tumor type represent potential diagnostic and/or prognostic biomarkers.
2012-04-29 | GSE34676 | GEO
Project description:Between 80% and 90% of renal carcinomas are either clear cell renal cell carcinoma or papillary RCC although there are at least 20 other distinct forms of RCC recognised by the World Health Organization (WHO). Emerging or provisional entities have been considered as variants of PRCC, including papillary renal neoplasm with reversed polarity (PRNRP). However, the molecular basis of PRNRP, and miRNA expression profile, is unknown. We used microarray analysis to elucidate the non-coding RNA (ncRNA) profiles of 10 PRNRP cases and compared them with other renal neoplasms. Cases were only considered for this study after fulfilment of strict inclusive histological and immunohistochemical criteria. We used Affymetrix miRNA v.4.0 arrays to elucidate the expression of these samples.
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Project description:Papillary renal cell carcinoma (pRCC) is the second most frequent renal cell carcinomas (RCC) after clear cell RCC. In contrast to clear cell RCC, there is no consensual protocol using targeted therapy for metastatic pRCC. Moreover, diagnosis of some pRCC, especially pRCC of type 2 (pRCC2) may be challenging. Our aim was to identify molecular biomarkers that could be helpful for the diagnosis and treatment of pRCC.
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