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Integrated genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma (gene expression)

ABSTRACT: Genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma

ORGANISM(S): Homo sapiens

PROVIDER: GSE32548 | GEO | 2012/06/18

SECONDARY ACCESSION(S): PRJNA154427

REPOSITORIES: GEO

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Integrated genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma

Project description:This SuperSeries is composed of the following subset Series: GSE32535: Integrated genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma (genomic) GSE32548: Integrated genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma (gene expression) Refer to individual Series

2012-06-17 | E-GEOD-32549 | biostudies-arrayexpress

Integrated genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma (genomic)

Project description:Genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma

2012-06-18 | GSE32535 | GEO

Integrated genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma (gene expression)

Project description:Genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma 131 primary bladder cancer tumor samples were analyzed on Illumina gene expression Bead Arrays.

2012-06-17 | E-GEOD-32548 | biostudies-arrayexpress

Integrated genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma (genomic)

Project description:Genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma 146 primary bladder cancer tumor samples were analyzed on BAC array containing ~32 000 BAC clones. Arrays were produced at the Swegene Centre for Integrative Biology at Lund University (SCIBLU).

2012-06-17 | E-GEOD-32535 | biostudies-arrayexpress

Integrated genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma

Project description:Integrated genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma

| PRJNA147013 | ENA

Integrated genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma

Project description:This SuperSeries is composed of the SubSeries listed below.

2012-06-18 | GSE32549 | GEO

Integrated genomic and gene expression profiling identifies two major genomic circuits in urothelial carcinoma.

Project description:Similar to other malignancies, urothelial carcinoma (UC) is characterized by specific recurrent chromosomal aberrations and gene mutations. However, the interconnection between specific genomic alterations, and how patterns of chromosomal alterations adhere to different molecular subgroups of UC, is less clear. We applied tiling resolution array CGH to 146 cases of UC and identified a number of regions harboring recurrent focal genomic amplifications and deletions. Several potential oncogenes were included in the amplified regions, including known oncogenes like E2F3, CCND1, and CCNE1, as well as new candidate genes, such as SETDB1 (1q21), and BCL2L1 (20q11). We next combined genome profiling with global gene expression, gene mutation, and protein expression data and identified two major genomic circuits operating in urothelial carcinoma. The first circuit was characterized by FGFR3 alterations, overexpression of CCND1, and 9q and CDKN2A deletions. The second circuit was defined by E3F3 amplifications and RB1 deletions, as well as gains of 5p, deletions at PTEN and 2q36, 16q, 20q, and elevated CDKN2A levels. TP53/MDM2 alterations were common for advanced tumors within the two circuits. Our data also suggest a possible RAS/RAF circuit. The tumors with worst prognosis showed a gene expression profile that indicated a keratinized phenotype. Taken together, our integrative approach revealed at least two separate networks of genomic alterations linked to the molecular diversity seen in UC, and that these circuits may reflect distinct pathways of tumor development.

| S-EPMC3369837 | biostudies-literature

Homo sapiens

Project description:Integrated genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma (genomic)

| PRJNA154431 | ENA

Homo sapiens

Project description:Integrated genomic and gene expression profiling identifies two major gene/genomic circuits operating in urothelial carcinoma (gene expression)

| PRJNA154427 | ENA

Recurring urothelial carcinomas show genomic rearrangements incompatible with a direct relationship, implications for tumor development.

Project description:We made use of the fact that patients with non-muscle invasive tumors show frequent local recurrences and multiple tumors to study re-initiation of tumor growth from the same urothelium. By extensive genomic analyses we show that tumors from the same patient are clonal. We show that gross genomic chromosomal aberrations may appear abruptly and disappear with no transitional stages being observed. By analysis of incompatible changes i.e., genomic alterations that cannot be reversed, we show that almost all tumors from a single patient show such changes, thus the tumors cannot have originated from each other. As recurrent tumors share both genomic alterations and driver gene mutations, these must have been present in the histologically normal urothelium in periods with no tumor growth. We present a model that includes a growing and genomically evolving field of urothelial cells that occasionally, and locally, produce bursts of cellular growth leading to overt tumors. This gene expression data was used to check the molecular subtypes based on Lund taxonomy (LundTax) in the recurring urothelial carcinomas.

2020-03-13 | GSE146870 | GEO

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