Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer

PMID: 22610119 · DOI: 10.1038/ng.2279 · Journal: Nature Genetics (2012)

TL;DR

This study performed whole-exome sequencing of 112 prostate tumor/normal pairs and identified recurrently mutated genes in prostate cancer, including SPOP (13%), FOXA1, and MED12. SPOP was the most frequently mutated gene, with all mutations clustering in the substrate-binding cleft. SPOP-mutant tumors lacked ETS rearrangements (P < 0.001) and exhibited a distinct pattern of genomic alterations enriched for 5q21 and 6q21 deletions, defining a new molecular subtype of prostate cancer.

Cohort & data

• 112 prostate adenocarcinoma/normal pairs, treatment-naive radical prostatectomy specimens from American and Australian patients (PMID:22610119)
• Cancer type: PRAD
• Dataset: prad_broad
• Mean exome coverage: 118x, 89.2% of targets at 20x or greater depth
• Additional validation cohorts comprising over 300 primary tumors and metastases from multiple US and European centers (Weill Cornell Medical College, University of Michigan, Uropath, University of Washington)
• Copy number profiling on 169 tumors via Affymetrix SNP 6.0 arrays
• RNA-seq performed on 22 exome-sequenced tumors and 41 independent samples
• 5,764 somatic mutations identified; median of 30 non-silent mutations per tumor (~1.4 per Mb)

Key findings

• Twelve genes were significantly enriched for mutations at q-value < 0.1 (PMID:22610119)
• SPOP was the most frequently mutated gene at 13% of cases (15/111 exomes), with all mutations affecting conserved residues in the substrate-binding cleft of this Cullin-based E3 ubiquitin ligase (PMID:22610119)
• SPOP mutation frequency was 6-15% across localized and advanced prostate tumors in multiple independent cohorts, including 14.5% (6/41) in metastatic disease (PMID:22610119)
• SPOP mutations and ETS rearrangements (TMPRSS2-ERG fusion) were mutually exclusive (P < 0.001, Fisher’s exact test), confirmed across all five cohorts (PMID:22610119)
• SPOP-mutant tumors were enriched for 5q21 deletions (containing CHD1; P = 1.4e-11) and 6q21 deletions (containing FOXO3, PRDM1; P = 3.4e-7) (PMID:22610119)
• TP53 lesions were generally absent in SPOP-mutant tumors (P = 0.015, Fisher’s exact test) (PMID:22610119)
• SPOP mutations trended inversely with PTEN loss and PIK3CA mutations in primary tumors (P = 0.044), though they co-occurred more frequently in metastatic tumors (PMID:22610119)
• FOXA1 harbored mutations in 4/111 exomes and 4/41 RNA-seq samples, all in the Forkhead domain near the DNA-binding surface (PMID:22610119)
• MED12 was mutated in 6/111 exomes, with a recurrent F1224L mutation in five samples (PMID:22610119)
• CDKN1B was somatically mutated in 3 samples and deleted in 16 others (PMID:22610119)
• Mutation calling validated at 95.6% accuracy (CI: 92-98%) by mass spectrometric genotyping (PMID:22610119)

Genes & alterations

• SPOP: Recurrent missense mutations in the MATH domain substrate-binding cleft (Y87, W131, F133 among others); F133V was the most common variant. Mutant SPOP or SPOP knockdown increased cell invasion in vitro. Mutated in 6-15% of prostate cancers across cohorts (PMID:22610119)
• FOXA1: Missense mutations restricted to the Forkhead domain near the DNA-binding surface in 4/111 exomes. FOXA1 modulates AR-driven transcription and activates CDKN1B expression (PMID:22610119)
• MED12: Recurrent F1224L mutation in 5/6 mutated samples. Encodes a mediator complex subunit; mutations in prostate cancer affected distinct codons from those in uterine leiomyomas and occurred in epithelial cells (PMID:22610119)
• TP53: Recurrently mutated and deleted; generally absent in SPOP-mutant tumors (PMID:22610119)
• PTEN: Recurrently mutated and deleted; inversely associated with SPOP mutations in primary tumors (P = 0.044) (PMID:22610119)
• PIK3CA: Recurrently mutated; absent in SPOP-mutant tumors (PMID:22610119)
• CDKN1B: Somatic substitutions in 3 samples and deletions in 16; first report of somatic point mutations in this cell cycle regulator in prostate cancer (PMID:22610119)
• CHD1: Located at the 5q21 locus enriched for deletions in SPOP-mutant tumors; encodes a chromatin-modifying enzyme (PMID:22610119)
• TMPRSS2-ERG: ETS rearrangements present in up to 50% of prostate cancers; mutually exclusive with SPOP mutations (PMID:22610119)
• NKX3-1: Known losses at 8p21 in prostate cancer, confirmed as background alteration (PMID:22610119)
• AR: Gains of the AR gene noted as a common prostate cancer alteration (PMID:22610119)
• MSH6: One tumor harbored a frameshift MSH6 mutation with hypermutator phenotype (997 somatic mutations) (PMID:22610119)
• THSD7B, SCN11A, ZNF595: Novel genes enriched for mutations in this cohort, not previously known to be somatically altered in prostate cancer (PMID:22610119)

Clinical implications

• SPOP mutations define a distinct molecular subtype of ETS-negative prostate cancer with specific co-occurring genomic alterations (5q21/6q21 deletions, absence of TP53 lesions), potentially enabling molecular stratification of patients (PMID:22610119)
• The mutual exclusivity of SPOP mutations and ETS rearrangements suggests divergent early driver events in prostate carcinogenesis, which may have implications for disease modeling and patient stratification in clinical trials (PMID:22610119)
• SPOP mutations were found in high-grade prostatic intraepithelial neoplasia (HG-PIN), suggesting they are early events that could serve as early detection biomarkers (PMID:22610119)
• The different co-alteration landscape in SPOP-mutant primary versus metastatic tumors (PTEN/PIK3CA co-occurrence in metastases) may have implications for understanding disease progression (PMID:22610119)

Limitations & open questions

• The specific ubiquitin ligase functions and cellular pathways deregulated by SPOP mutation remain to be determined; whether mutations cause gain-of-function, dominant-negative effects, or altered substrate specificity is unknown (PMID:22610119)
• Functional consequences of FOXA1 Forkhead domain mutations on DNA binding and AR-driven transcription were not directly tested
• The inverse relationship between SPOP mutations and PTEN/PIK3CA alterations was evident in primary tumors but not metastatic tumors, requiring validation in larger cohorts
• The study focused on treatment-naive radical prostatectomy specimens; representation of advanced/castration-resistant disease was limited to a smaller validation cohort
• Novel significantly mutated genes (THSD7B, SCN11A, ZNF595) require further functional characterization

Citations from this paper used in the wiki

• “SPOP was the most frequently mutated gene, with mutations involving the SPOP substrate binding cleft in 6-15% of tumors across multiple independent cohorts.” (PMID:22610119)
• “SPOP-mutant prostate cancers lacked ETS rearrangements and exhibited a distinct pattern of genomic alterations.” (PMID:22610119)
• “all exomes with SPOP mutations lacked the TMPRSS2-ERG fusion or other ETS rearrangements…This mutually exclusive relationship between SPOP mutation and ERG rearrangement (P < 0.001, Fisher’s exact test) was confirmed in evaluable samples across all five cohorts tested” (PMID:22610119)
• “Recurrent somatic deletions at 5q21 and 6q21 were enriched in SPOP-mutant tumors (P = 1.4x10-11 and P = 3.4x10-7, respectively, Fisher’s exact test)” (PMID:22610119)
• “FOXA1 harbored nonsilent mutations in 4 of 111 exomes and 4 of 41 independent RNA-seq samples…Mutations strictly affected residues in the Forkhead domain” (PMID:22610119)
• “Mutations affecting MED12 were observed in 6 out of 111 exomes, with a recurrent F1224L mutation in five samples” (PMID:22610119)

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