Integrative sequencing reveals alterations in untreated and castration resistant prostate cancer

Study ID	Alternative Stable ID	Type
EGAS00001000526		Other

Study ID

Alternative Stable ID

Type

EGAS00001000526

Other

Study Description

We report the integrative sequencing of genomic, transcriptomic and DNA methylation changes in 28 untreated (PC) and 13 castration resistant prostate cancers (CRPC). AR, TGF-β and WNT signaling pathways were altered in CRPCs. We identified two new fusion genes, TMPRSS2-SKIL and DOT1L-HES6. Fusion analysis in an independent cohort validated SKIL as a recurrent 3’ fusion partner and oncogene in prostate cancer. The HES6 fusion was found in an AR-negative CRPC, and HES6 overexpression in vitro led to androgen independent growth. A distinct DNA methylation signature was found for CRPC. Transcriptome assembly uncovered 128 previously unannotated prostate cancer associated transcripts, including the ERG regulated transcript TPCAT-10-36067 whose knockdown had a dramatic effect on the growth, invasiveness, and rate of apoptosis of prostate cancer cells.

Dataset ID	Description	Technology	Samples
EGAD00001000609	Whole transcriptome sequencing of 28 untreated prostate cancers, 13 castration resistant prostate cancers, and 12 benign prostatic hyperplasias. Whole transcriptome sequencing of 28 untreated prostate cancers, 13 castration resistant prostate cancers, and 12 benign prostatic hyperplasias.	Illumina HiSeq 2000	53
EGAD00001000610	Methylated DNA immunoprecipitation sequencing of 28 untreated prostate cancers, 11 castration resistant prostate cancers, and 12 benign prostatic hyperplasias. Methylated DNA immunoprecipitation sequencing of 28 untreated prostate cancers, 11 castration resistant prostate cancers, and 12 benign prostatic hyperplasias.	Illumina HiSeq 2000	51
EGAD00001000611	Small RNA sequencing of 28 untreated prostate cancers, 12 castration resistant prostate cancers, and 3 benign prostatic hyperplasias. Small RNA sequencing of 28 untreated prostate cancers, 12 castration resistant prostate cancers, and 3 benign prostatic hyperplasias.	Illumina HiSeq 2000	43
EGAD00001000612	Low coverage whole genome sequencing of 27 untreated prostate cancers, 9 castration resistant prostate cancers, and 4 benign prostatic hyperplasias. Low coverage whole genome sequencing of 27 untreated prostate cancers, 9 castration resistant prostate cancers, and 4 benign prostatic hyperplasias.	Illumina HiSeq 2000	40
EGAD00001007921	Two sections of cryopreserved prostate cancer tissue from one untreated prostate cancer patient were profiled for spatial transcriptomics using the Visium Spatial library preparation protocol from 10x Genomics. The GRCh38 aligned sequencing reads from the two prostate cancer tissue sections are provided as BAM files. Two sections of cryopreserved prostate cancer tissue from one untreated prostate cancer patient were profiled for spatial transcriptomics using the Visium Spatial library preparation protocol from 10x Genomics. The GRCh38 aligned sequencing reads from the two prostate cancer tissue sections are provided as BAM files.	Illumina NovaSeq 6000	2

Dataset ID

Description

Technology

Samples

EGAD00001000609

Whole transcriptome sequencing of 28 untreated prostate cancers, 13 castration resistant prostate cancers, and 12 benign prostatic hyperplasias.

Illumina HiSeq 2000

EGAD00001000610

Methylated DNA immunoprecipitation sequencing of 28 untreated prostate cancers, 11 castration resistant prostate cancers, and 12 benign prostatic hyperplasias.

Illumina HiSeq 2000

EGAD00001000611

Small RNA sequencing of 28 untreated prostate cancers, 12 castration resistant prostate cancers, and 3 benign prostatic hyperplasias.

Illumina HiSeq 2000

EGAD00001000612

Low coverage whole genome sequencing of 27 untreated prostate cancers, 9 castration resistant prostate cancers, and 4 benign prostatic hyperplasias.

Illumina HiSeq 2000

EGAD00001007921

Two sections of cryopreserved prostate cancer tissue from one untreated prostate cancer patient were profiled for spatial transcriptomics using the Visium Spatial library preparation protocol from 10x Genomics. The GRCh38 aligned sequencing reads from the two prostate cancer tissue sections are provided as BAM files.

Illumina NovaSeq 6000

Study

Study Description

Study Datasets 5 datasets.

Who archives the data?

Publications

Citations

The European Genome-phenome Archive (EGA) is part of the ELIXIR infrastructure.