4C-seq revealed long-range interactions of a functional enhancer at the 8q24 prostate cancer risk locus

Mingyang Cai, Sewoon Kim, Kai Wang, Peggy J. Farnham, Gerhard A. Coetzee, Wange Lu

Research output: Contribution to journalArticle

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Abstract

Genome-wide association studies (GWAS) have identified >100 independent susceptibility loci for prostate cancer, including the hot spot at 8q24. However, how genetic variants at this locus confer disease risk hasn't been fully characterized. Using circularized chromosome conformation capture (4C) coupled with next-generation sequencing and an enhancer at 8q24 as "bait", we identified genome-wide partners interacting with this enhancer in cell lines LNCaP and C4-2B. These 4C-identified regions are distributed in open nuclear compartments, featuring active histone marks (H3K4me1, H3K4me2 and H3K27Ac). Transcription factors NKX3-1, FOXA1 and AR (androgen receptor) tend to occupy these 4C regions. We identified genes located at the interacting regions, and found them linked to positive regulation of mesenchymal cell proliferation in LNCaP and C4-2B, and several pathways (TGF beta signaling pathway in LNCaP and p53 pathway in C4-2B). Common genes (e.g. MYC and POU5F1B) were identified in both prostate cancer cell lines. However, each cell line also had exclusive genes (e.g. ELAC2 and PTEN in LNCaP and BRCA2 and ZFHX3 in C4-2B). In addition, BCL-2 identified in C4-2B might contribute to the progression of androgen-refractory prostate cancer. Overall, our work reveals key genes and pathways involved in prostate cancer onset and progression.

Original languageEnglish (US)
Article number22462
JournalScientific Reports
Volume6
DOIs
StatePublished - Mar 3 2016
Externally publishedYes

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Prostatic Neoplasms
Cell Line
Genes
Histone Code
Genome-Wide Association Study
Androgen Receptors
Transforming Growth Factor beta
Androgens
Transcription Factors
Chromosomes
Cell Proliferation
Genome

ASJC Scopus subject areas

  • General

Cite this

4C-seq revealed long-range interactions of a functional enhancer at the 8q24 prostate cancer risk locus. / Cai, Mingyang; Kim, Sewoon; Wang, Kai; Farnham, Peggy J.; Coetzee, Gerhard A.; Lu, Wange.

In: Scientific Reports, Vol. 6, 22462, 03.03.2016.

Research output: Contribution to journalArticle

Cai, Mingyang ; Kim, Sewoon ; Wang, Kai ; Farnham, Peggy J. ; Coetzee, Gerhard A. ; Lu, Wange. / 4C-seq revealed long-range interactions of a functional enhancer at the 8q24 prostate cancer risk locus. In: Scientific Reports. 2016 ; Vol. 6.
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