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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

Pathways in PDA.(a) Oncomaps and schematics of pathways with combined genetic lesions occurring at a frequency >15% in the PDA cohort. (b) Correlation between pathways in the PDA cohort reveals relatively weak interactions between pathways. (c) Random forest-based clustering of pathways. (d) Overall survival related to genetic alterations targeting KRAS and TP53 in clusters 1 and 2 versus all others. P value was obtained from Cox proportional hazard test.
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f5: Pathways in PDA.(a) Oncomaps and schematics of pathways with combined genetic lesions occurring at a frequency >15% in the PDA cohort. (b) Correlation between pathways in the PDA cohort reveals relatively weak interactions between pathways. (c) Random forest-based clustering of pathways. (d) Overall survival related to genetic alterations targeting KRAS and TP53 in clusters 1 and 2 versus all others. P value was obtained from Cox proportional hazard test.

Mentions: In addition to heterogeneity within the core KRAS pathway, we detected multiple additional pathways that were genetically altered at high frequency (>20%) in PDA (Fig. 5a, Supplementary Figs 31–33). Specifically, we found that the TGF-ß pathway is disrupted via a combination of largely mutually exclusive events in addition to the frequent disruption of SMAD4. This includes loss of TGFBR2/TGFBR1, as well as mutations in ACVR1B, which is a newly identified cancer-associated gene in the pathway18. Similarly, in concert with frequent deletion of CDKN2A and CDKN2B, CDK4 and CCND1 amplification and RB1 loss was observed in the RB pathway. Among signalling pathways, beta-catenin and NOTCH pathways exhibited frequent alterations indicative of oncogenic activation. Multiple Fanconi Anaemia genes as well as ATM, CHEK2, BCLAF1, BRCA1 and BRCA2 were observed to be mutated or deleted at relatively high frequency with alterations targeting some facet of DNA repair occurring in >35% of cases. Genetic lesions in chromatin remodelling SWI/SNF pathway occurred in 42% of the cases. In addition to these well-described pathways, we observed frequent aberrations that impinge on histone modification and the FAT/HIPPO pathway (Supplementary Figs 31–32). Each pathway was interrogated for association with outcome (Supplementary Fig. 34). Only DNA repair-associated pathways had a trend towards poor outcome, while beta-catenin signalling trended towards improved outcome. In general, the associations between pathways were limited as determined by Pearson's correlation (Fig. 5b). Random Forest and APC clustering were used to define subtypes of PDA based on altered pathways, and demonstrated marked diversity of combinations of deregulated pathways (Fig. 5c and Supplementary Fig. 35). While tumours with isolated KRAS-pathway alterations alone or in combination with TP53 have a poor prognosis, tumours with more complex pathway deregulations trended towards even poorer outcome (Fig. 5d). Many of the highlighted pathways represent therapeutic targets that are actionable in preclinical models and, in some cases, in the clinic (Table 2). For example, BRAF V600E has been shown to be a potential target in melanoma and other cancers. Loss of RNF43 or AXIN1 are associated with sensitivity to porcupine and tankyrase inhibitors targeting the beta-catenin pathway24, while deletion of CDKN2A or amplification of CDK4/CCND1 confer sensitivity to CDK4/6 inhibitors25. Deficits in Fanconi Anaemia genes can be targeted by cross-linking agents26, a finding readily observed in cell lines harbouring homozygous deletion of FANCF (Supplementary Fig. 36). Similarly, loss of BRCA function is associated with response to PARP inhibitors27. A number of these genetic alterations remain actionable in the presence of an activating KRAS mutation and could provide the opportunity for genetically targeted therapy in PDA.


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)

Pathways in PDA.(a) Oncomaps and schematics of pathways with combined genetic lesions occurring at a frequency >15% in the PDA cohort. (b) Correlation between pathways in the PDA cohort reveals relatively weak interactions between pathways. (c) Random forest-based clustering of pathways. (d) Overall survival related to genetic alterations targeting KRAS and TP53 in clusters 1 and 2 versus all others. P value was obtained from Cox proportional hazard test.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5: Pathways in PDA.(a) Oncomaps and schematics of pathways with combined genetic lesions occurring at a frequency >15% in the PDA cohort. (b) Correlation between pathways in the PDA cohort reveals relatively weak interactions between pathways. (c) Random forest-based clustering of pathways. (d) Overall survival related to genetic alterations targeting KRAS and TP53 in clusters 1 and 2 versus all others. P value was obtained from Cox proportional hazard test.
Mentions: In addition to heterogeneity within the core KRAS pathway, we detected multiple additional pathways that were genetically altered at high frequency (>20%) in PDA (Fig. 5a, Supplementary Figs 31–33). Specifically, we found that the TGF-ß pathway is disrupted via a combination of largely mutually exclusive events in addition to the frequent disruption of SMAD4. This includes loss of TGFBR2/TGFBR1, as well as mutations in ACVR1B, which is a newly identified cancer-associated gene in the pathway18. Similarly, in concert with frequent deletion of CDKN2A and CDKN2B, CDK4 and CCND1 amplification and RB1 loss was observed in the RB pathway. Among signalling pathways, beta-catenin and NOTCH pathways exhibited frequent alterations indicative of oncogenic activation. Multiple Fanconi Anaemia genes as well as ATM, CHEK2, BCLAF1, BRCA1 and BRCA2 were observed to be mutated or deleted at relatively high frequency with alterations targeting some facet of DNA repair occurring in >35% of cases. Genetic lesions in chromatin remodelling SWI/SNF pathway occurred in 42% of the cases. In addition to these well-described pathways, we observed frequent aberrations that impinge on histone modification and the FAT/HIPPO pathway (Supplementary Figs 31–32). Each pathway was interrogated for association with outcome (Supplementary Fig. 34). Only DNA repair-associated pathways had a trend towards poor outcome, while beta-catenin signalling trended towards improved outcome. In general, the associations between pathways were limited as determined by Pearson's correlation (Fig. 5b). Random Forest and APC clustering were used to define subtypes of PDA based on altered pathways, and demonstrated marked diversity of combinations of deregulated pathways (Fig. 5c and Supplementary Fig. 35). While tumours with isolated KRAS-pathway alterations alone or in combination with TP53 have a poor prognosis, tumours with more complex pathway deregulations trended towards even poorer outcome (Fig. 5d). Many of the highlighted pathways represent therapeutic targets that are actionable in preclinical models and, in some cases, in the clinic (Table 2). For example, BRAF V600E has been shown to be a potential target in melanoma and other cancers. Loss of RNF43 or AXIN1 are associated with sensitivity to porcupine and tankyrase inhibitors targeting the beta-catenin pathway24, while deletion of CDKN2A or amplification of CDK4/CCND1 confer sensitivity to CDK4/6 inhibitors25. Deficits in Fanconi Anaemia genes can be targeted by cross-linking agents26, a finding readily observed in cell lines harbouring homozygous deletion of FANCF (Supplementary Fig. 36). Similarly, loss of BRCA function is associated with response to PARP inhibitors27. A number of these genetic alterations remain actionable in the presence of an activating KRAS mutation and could provide the opportunity for genetically targeted therapy in PDA.

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