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Whole-exome sequencing of pancreatic cancer defines genetic diversity and therapeutic targets.

Witkiewicz AK, McMillan EA, Balaji U, Baek G, Lin WC, Mansour J, Mollaee M, Wagner KU, Koduru P, Yopp A, Choti MA, Yeo CJ, McCue P, White MA, Knudsen ES - Nat Commun (2015)

Bottom Line: Copy number alterations target multiple tumour suppressive/oncogenic loci; however, amplification of MYC is uniquely associated with poor outcome and adenosquamous subtype.KRAS mutations are observed in >90% of cases, but codon Q61 alleles are selectively associated with improved survival.Together, these data delineate new genetic diversity of PDA and provide insights into prognostic determinants and therapeutic targets.

View Article: PubMed Central - PubMed

Affiliation: 1] Simmons Cancer Center, UT Southwestern Medical Center, Dallas, Texas 75390, USA [2] Department of Pathology, UT Southwestern Medical Center, Dallas, Texas 75390, USA.

ABSTRACT
Pancreatic ductal adenocarcinoma (PDA) has a dismal prognosis and insights into both disease etiology and targeted intervention are needed. A total of 109 micro-dissected PDA cases were subjected to whole-exome sequencing. Microdissection enriches tumour cellularity and enhances mutation calling. Here we show that environmental stress and alterations in DNA repair genes associate with distinct mutation spectra. Copy number alterations target multiple tumour suppressive/oncogenic loci; however, amplification of MYC is uniquely associated with poor outcome and adenosquamous subtype. We identify multiple novel mutated genes in PDA, with select genes harbouring prognostic significance. RBM10 mutations associate with longer survival in spite of histological features of aggressive disease. KRAS mutations are observed in >90% of cases, but codon Q61 alleles are selectively associated with improved survival. Oncogenic BRAF mutations are mutually exclusive with KRAS and define sensitivity to vemurafenib in PDA models. High-frequency alterations in Wnt signalling, chromatin remodelling, Hedgehog signalling, DNA repair and cell cycle processes are observed. Together, these data delineate new genetic diversity of PDA and provide insights into prognostic determinants and therapeutic targets.

No MeSH data available.


Related in: MedlinePlus

Significantly mutated genes in PDA.(a) Mutational significance was determined for SNV and INDELS from the 109 sequenced cases using MutsigCV. Genes were subjected to unsupervised clustering, and the frequency and P value as determined by MutsigCV are shown. (b) Kaplan–Meier analysis of select significantly mutated genes. P value was obtained from Cox proportional hazard test. (c) IHC was used to confirm loss of ARID1A protein in a large cohort of PDA cases (scale bar, 150 μM). Diminished ARID1A protein level was associated with overall survival. P value was obtained from Cox proportional hazard test.
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f3: Significantly mutated genes in PDA.(a) Mutational significance was determined for SNV and INDELS from the 109 sequenced cases using MutsigCV. Genes were subjected to unsupervised clustering, and the frequency and P value as determined by MutsigCV are shown. (b) Kaplan–Meier analysis of select significantly mutated genes. P value was obtained from Cox proportional hazard test. (c) IHC was used to confirm loss of ARID1A protein in a large cohort of PDA cases (scale bar, 150 μM). Diminished ARID1A protein level was associated with overall survival. P value was obtained from Cox proportional hazard test.

Mentions: MutSigCV analysis16 of 109 PDA/normal tissue pairs revealed 24 significantly mutated genes occurring in >3.5% of cases (Fig. 3a, Supplementary Data 3). For comparison. similar analysis performed using data from prior sequencing effort4 revealed only four non-synonymous mutations (Supplementary Figs 17–18). The identification of KRAS, TP53, CDKN2A and SMAD4 confirmed that our approach detected known alterations promoting PDA tumorigenesis. GNAS mutations were present in all four colloid carcinomas and two conventional PDAs. Most GNAS mutations were in hotspot codon 201 (R201C and R201H) (Supplementary Figs 19 and 20). Consistent with recent studies17, all GNAS-mutated invasive carcinoma cases were derived from a common precursor, intraductal pancreatic neoplasm (IPMN). Four of the six PDAs harbouring GNAS alteration had concomitant mutations in KRAS (Supplementary Data 1). Two other genes reported as mutated in IPMN, RNF43 and RBM10, were detected in six and four conventional PDA cases, respectively. Notably, PDAs harbouring RNF43 and RBM10 alterations did not arise from IPMN and there was no association between these genes and GNAS mutations in this cohort. We also identified a number of ‘cancer genes'18 as significantly mutated in PDA, including BCLAF1 (5% of cases), IRF6 (4% of cases), FLG (10% of cases), AXIN1 (5% of cases), GLI3 (6% of cases) and PIK3CA (4% of cases).


Whole-exome sequencing of pancreatic cancer defines genetic diversity and therapeutic targets.

Witkiewicz AK, McMillan EA, Balaji U, Baek G, Lin WC, Mansour J, Mollaee M, Wagner KU, Koduru P, Yopp A, Choti MA, Yeo CJ, McCue P, White MA, Knudsen ES - Nat Commun (2015)

Significantly mutated genes in PDA.(a) Mutational significance was determined for SNV and INDELS from the 109 sequenced cases using MutsigCV. Genes were subjected to unsupervised clustering, and the frequency and P value as determined by MutsigCV are shown. (b) Kaplan–Meier analysis of select significantly mutated genes. P value was obtained from Cox proportional hazard test. (c) IHC was used to confirm loss of ARID1A protein in a large cohort of PDA cases (scale bar, 150 μM). Diminished ARID1A protein level was associated with overall survival. P value was obtained from Cox proportional hazard test.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4403382&req=5

f3: Significantly mutated genes in PDA.(a) Mutational significance was determined for SNV and INDELS from the 109 sequenced cases using MutsigCV. Genes were subjected to unsupervised clustering, and the frequency and P value as determined by MutsigCV are shown. (b) Kaplan–Meier analysis of select significantly mutated genes. P value was obtained from Cox proportional hazard test. (c) IHC was used to confirm loss of ARID1A protein in a large cohort of PDA cases (scale bar, 150 μM). Diminished ARID1A protein level was associated with overall survival. P value was obtained from Cox proportional hazard test.
Mentions: MutSigCV analysis16 of 109 PDA/normal tissue pairs revealed 24 significantly mutated genes occurring in >3.5% of cases (Fig. 3a, Supplementary Data 3). For comparison. similar analysis performed using data from prior sequencing effort4 revealed only four non-synonymous mutations (Supplementary Figs 17–18). The identification of KRAS, TP53, CDKN2A and SMAD4 confirmed that our approach detected known alterations promoting PDA tumorigenesis. GNAS mutations were present in all four colloid carcinomas and two conventional PDAs. Most GNAS mutations were in hotspot codon 201 (R201C and R201H) (Supplementary Figs 19 and 20). Consistent with recent studies17, all GNAS-mutated invasive carcinoma cases were derived from a common precursor, intraductal pancreatic neoplasm (IPMN). Four of the six PDAs harbouring GNAS alteration had concomitant mutations in KRAS (Supplementary Data 1). Two other genes reported as mutated in IPMN, RNF43 and RBM10, were detected in six and four conventional PDA cases, respectively. Notably, PDAs harbouring RNF43 and RBM10 alterations did not arise from IPMN and there was no association between these genes and GNAS mutations in this cohort. We also identified a number of ‘cancer genes'18 as significantly mutated in PDA, including BCLAF1 (5% of cases), IRF6 (4% of cases), FLG (10% of cases), AXIN1 (5% of cases), GLI3 (6% of cases) and PIK3CA (4% of cases).

Bottom Line: Copy number alterations target multiple tumour suppressive/oncogenic loci; however, amplification of MYC is uniquely associated with poor outcome and adenosquamous subtype.KRAS mutations are observed in >90% of cases, but codon Q61 alleles are selectively associated with improved survival.Together, these data delineate new genetic diversity of PDA and provide insights into prognostic determinants and therapeutic targets.

View Article: PubMed Central - PubMed

Affiliation: 1] Simmons Cancer Center, UT Southwestern Medical Center, Dallas, Texas 75390, USA [2] Department of Pathology, UT Southwestern Medical Center, Dallas, Texas 75390, USA.

ABSTRACT
Pancreatic ductal adenocarcinoma (PDA) has a dismal prognosis and insights into both disease etiology and targeted intervention are needed. A total of 109 micro-dissected PDA cases were subjected to whole-exome sequencing. Microdissection enriches tumour cellularity and enhances mutation calling. Here we show that environmental stress and alterations in DNA repair genes associate with distinct mutation spectra. Copy number alterations target multiple tumour suppressive/oncogenic loci; however, amplification of MYC is uniquely associated with poor outcome and adenosquamous subtype. We identify multiple novel mutated genes in PDA, with select genes harbouring prognostic significance. RBM10 mutations associate with longer survival in spite of histological features of aggressive disease. KRAS mutations are observed in >90% of cases, but codon Q61 alleles are selectively associated with improved survival. Oncogenic BRAF mutations are mutually exclusive with KRAS and define sensitivity to vemurafenib in PDA models. High-frequency alterations in Wnt signalling, chromatin remodelling, Hedgehog signalling, DNA repair and cell cycle processes are observed. Together, these data delineate new genetic diversity of PDA and provide insights into prognostic determinants and therapeutic targets.

No MeSH data available.


Related in: MedlinePlus