Extensive germline-somatic interplay contributes to prostate cancer progression through HNF1B co-option of TMPRSS2-ERG

Giannareas, Nikolaos; Zhang, Qin; Yang, Xiayun; Na, Rong; Tian, Yijun; Yang, Yongfeng; Ruan, Xiaohao; Huang, Da; Yang, Xiaoqun; Wang, Chaofu; Zhang, Peng; Manninen, Aki; Wang, Liang; Wei, Gong-Hong

doi:10.1038/s41467-022-34994-z

Cited by 11 publications

(5 citation statements)

References 121 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…One potential issue of this study is inconsistent results in some tests among different cell lines. While these inconsistence may attribute to genetic heterogeneity, we also want to highlight that some candidates found exclusively in DU145 cells are reported to be functional in prostate cells (40). Additionally, to increase our gRNA library coverage, we may use a novel CRISPR systems with expanded PAM site compatibility.…”

Section: Discussionmentioning

confidence: 99%

Combined CRISPRi and proteomics screening reveal a cohesin-CTCF-bound allele contributing to increased expression ofRUVBL1and prostate cancer progression

Tian

Dong

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

Introduction: Genome-wide association studies along with expression quantitative trait loci (eQTL) have identified hundreds of single nucleotide polymorphisms (SNPs) and their target genes in prostate cancer (PrCa). Although these genetic associations to PrCa have been widely reported, functional characterization of these risk loci remains challenging. Methods: To screen for regulatory SNPs, we designed a library containing 9133 guide RNAs (gRNAs) to target 2,166 candidate SNP sites implicated in PrCa. We performed negative screening in dCas9-KRAB stable prostate cell lines and applied the RIGOR program to identify the essential SNPs for cell proliferation. We further characterized the regulatory role of a selected single nucleotide polymorphim (SNP, rs60464856) using luciferase reporter assay, ChIP-qPCR, and xCas9 base editing in prostate cells. Finally, we investigated the biological impact of the SNP-regulated gene RUVBL1 on cell proliferation and tumor growth via gene knockdown using in vitro and in vivo assays. Results: From interference of 2,166 candidate SNPs via CRISPR interference screening, the RIGOR program identified 117 SNPs that could regulate genes to promote growth advantage in prostate cancer cell lines. Compared to unselected SNPs, the 117 candidates tended to reside near 5 kb flanking the transcription start sites (p = 0.01). To characterize the regulatory role of these SNPs, we selected one SNP (rs60464856) for detailed analysis. This SNP was covered by multiple gRNAs significantly depleted in the screening (FDR<0.05). Pooled SNP association analysis in the PRACTICAL cohort showed significantly higher PrCa risk for the G allele (pvalue=1.2E-16). eQTL analysis showed that the G allele is associated with an increased expression of RUVBL1 in multiple datasets. To further validate the CRISPR interference effect, we transfected a gRNA targeting the rs60464856 site in the dCas9 stable cell lines and observed significant inhibition of the RUVBL1 expression. We also applied the xCas9 adenine base editor to convert the rs60464856 A into G allele and observed an increased RUVBL1 expression in subclones carrying the rs60464856 G allele in prostate cell lines. To test if any protein showed allele-specific binding at rs60464856, we used SILAC-based DNA pull-down proteomics and observed that cohesin subunits (including SMC3) preferred the A allele. ChIP qPCR assays showed significant enrichment of CTCF and SMC3 signals at the rs60464856 site with preferential binding to the A allele. To evaluate the potential role of this locus in maintaining long-range chromatin structure, we analyzed a HiC dataset and found that the rs60464856 locus enriched consistent chromatin interactions in prostate cell lines. To determine the potential role of the rs60464856 target gene, we knocked down the RUVBL1 via shRNA and observed significant proliferation inhibition in prostate cell lines. We also tested PC3 cells with RUVBL1 knockdown in nude mice xenografts and observed reduced tumorigenesis. Gene set enrichment analysis showed that RUVBL1 expression was associated with the enrichment of cell cycle related pathways in both cell line and TCGA prostate cancer cohorts. Lastly, we showed that an increased RUVBL1 expression and its relevant pathway activation were associated with poor survival. Conclusion: We applied the CRISPR interference screening at selected prostate cancer risk loci and identified over a hundred regulatory SNPs essential for prostate cell proliferation. Further analysis confirmed the important role of rs60464856 and its target gene RUVBL1 in prostate cell growth and tumorigenesis.

show abstract

Section: Discussionmentioning

confidence: 99%

Combined CRISPRi and proteomics screening reveal a cohesin-CTCF-bound allele contributing to increased expression ofRUVBL1and prostate cancer progression

Tian

Dong

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…To discover the susceptibility loci for PCa, many GWAS projects have been initiated since 2005 and over 270 risk loci have been reported [ 35 – 37 ]. By investigating the molecular mechanisms underlying the biological effect of these risk SNPs, previous studies including ours suggest that these SNPs may affect gene regulation by modulating the binding of key transcription factors such as HOXB13, AR, and the most frequent PCa-specific fusion protein TMPRSS2-ERG [ 40 , 41 , 103 ] as well as the influence of genetic variants on transcription factor DNA-binding in other types of diseases [ 89 , 104 ]. One of our pioneer studies demonstrates that the PCa risk-associated allele at rs339331 impacts PCa predisposition and progression by altering RFX6 expression through a functional interplay with the PCa susceptibility gene HOXB13 [ 40 ].…”

Section: Discussionmentioning

confidence: 99%

GATA2 co-opts TGFβ1/SMAD4 oncogenic signaling and inherited variants at 6q22 to modulate prostate cancer progression

Yang

Zhang

et al. 2023

J Exp Clin Cancer Res

Self Cite

View full text Add to dashboard Cite

Background Aberrant somatic genomic alteration including copy number amplification is a hallmark of cancer genomes. We previously profiled genomic landscapes of prostate cancer (PCa), yet the underlying causal genes with prognostic potential has not been defined. It remains unclear how a somatic genomic event cooperates with inherited germline variants contribute to cancer predisposition and progression. Methods We applied integrated genomic and clinical data, experimental models and bioinformatic analysis to identify GATA2 as a highly prevalent metastasis-associated genomic amplification in PCa. Biological roles of GATA2 in PCa metastasis was determined in vitro and in vivo. Global chromatin co-occupancy and co-regulation of GATA2 and SMAD4 was investigated by coimmunoprecipitation, ChIP-seq and RNA-seq assays. Tumor cellular assays, qRT-PCR, western blot, ChIP, luciferase assays and CRISPR-Cas9 editing methods were performed to mechanistically understand the cooperation of GATA2 with SMAD4 in promoting TGFβ1 and AR signaling and mediating inherited PCa risk and progression. Results In this study, by integrated genomics and experimental analysis, we identified GATA2 as a prevalent metastasis-associated genomic amplification to transcriptionally augment its own expression in PCa. Functional experiments demonstrated that GATA2 physically interacted and cooperated with SMAD4 for genome-wide chromatin co-occupancy and co-regulation of PCa genes and metastasis pathways like TGFβ signaling. Mechanistically, GATA2 was cooperative with SMAD4 to enhance TGFβ and AR signaling pathways, and activated the expression of TGFβ1 via directly binding to a distal enhancer of TGFβ1. Strinkingly, GATA2 and SMAD4 globally mediated inherited PCa risk and formed a transcriptional complex with HOXB13 at the PCa risk-associated rs339331/6q22 enhancer, leading to increased expression of the PCa susceptibility gene RFX6. Conclusions Our study prioritizes causal genomic amplification genes with prognostic values in PCa and reveals the pivotal roles of GATA2 in transcriptionally activating the expression of its own and TGFβ1, thereby co-opting to TGFβ1/SMAD4 signaling and RFX6 at 6q22 to modulate PCa predisposition and progression.

show abstract

“…Accumulating evidence suggests that genetic alterations play a crucial role in driving the progression of normal cells from the hyperplastic and dysplastic stages to metastatic disease, including invasive cancer. [31,32] Therefore, the analysis of gene alterations is essential for gaining novel insights into the role of oncogenes in cancer development. [33] In line with this, we investigated the muta- tion types of GSC across various cancers and observed that missense mutations were the most frequently occurring mutation type in multiple cancer types.…”

Section: Discussionmentioning

confidence: 99%

Oncogene goosecoid is transcriptionally regulated by E2F1 and correlates with disease progression in prostate cancer

Ge,

Ma,

Zhou

et al. 2023

Chinese Medical Journal

View full text Add to dashboard Cite

Background: Although some well-established oncogenes are involved in cancer initiation and progression such as prostate cancer (PCa), the long tail of cancer genes remains to be defined. Goosecoid (GSC) has been implicated in cancer development. However, the comprehensive biological role of GSC in pan-cancer, specifically in PCa, remains unexplored. The aim of this study was to investigate the role of GSC in PCa development. Methods: We performed a systematic bioinformatics exploration of GSC using datasets from The Cancer Genome Atlas, Genotype-Tissue Expression, Gene Expression Omnibus, German Cancer Research Center, and our in-house cohorts. First, we evaluated the expression of GSC and its association with patient prognosis, and identified GSC-relevant genetic alterations in cancers. Further, we focused on the clinical characterization and prognostic analysis of GSC in PCa. To understand the transcriptional regulation of GSC by E2F transcription factor 1 (E2F1), we performed chromatin immunoprecipitation quantitative polymerase chain reaction (qPCR). Functional experiments were conducted to validate the effect of GSC on the tumor cellular phenotype and sensitivity to trametinib. Results: GSC expression was elevated in various tumors and significantly correlated with patient prognosis. The alterations of GSC contribute to the progression of various tumors especially in PCa. Patients with PCa and high GSC expression exhibited worse progression-free survival and biochemical recurrence outcomes. Further, GSC upregulation in patients with PCa was mostly accompanied with higher Gleason score, advanced tumor stage, lymph node metastasis, and elevated prostate-specific antigen (PSA) levels. Mechanistically, the transcription factor, E2F1, stimulates GSC by binding to its promoter region. Detailed experiments further demonstrated that GSC acted as an oncogene and influenced the response of PCa cells to trametinib treatment. Conclusions: GSC was highly overexpressed and strongly correlated with patient prognosis in PCa. We found that GSC, regulated by E2F1, acted as an oncogene and impeded the therapeutic efficacy of trametinib in PCa.

show abstract

Extensive germline-somatic interplay contributes to prostate cancer progression through HNF1B co-option of TMPRSS2-ERG

Cited by 11 publications

References 121 publications

Combined CRISPRi and proteomics screening reveal a cohesin-CTCF-bound allele contributing to increased expression ofRUVBL1and prostate cancer progression

Combined CRISPRi and proteomics screening reveal a cohesin-CTCF-bound allele contributing to increased expression ofRUVBL1and prostate cancer progression

GATA2 co-opts TGFβ1/SMAD4 oncogenic signaling and inherited variants at 6q22 to modulate prostate cancer progression

Oncogene goosecoid is transcriptionally regulated by E2F1 and correlates with disease progression in prostate cancer

Contact Info

Product

Resources

About