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Wolfe AR, Cui T, Baie S, Corrales-Guerrero S, Webb A, Castro-Aceituno V, Shyu DL, Karasinska JM, Topham JT, Renouf DJ, Schaeffer DF, Halloran M, Packard R, Robb R, Chen W, Denko N, Lisanti M, Thompson TC, Frank P, Williams TM. Nutrient scavenging-fueled growth in pancreatic cancer depends on caveolae-mediated endocytosis under nutrient-deprived conditions. Sci Adv 2024; 10:eadj3551. [PMID: 38427741 PMCID: PMC10906919 DOI: 10.1126/sciadv.adj3551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 01/26/2024] [Indexed: 03/03/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by its nutrient-scavenging ability, crucial for tumor progression. Here, we investigated the roles of caveolae-mediated endocytosis (CME) in PDAC progression. Analysis of patient data across diverse datasets revealed a strong association of high caveolin-1 (Cav-1) expression with higher histologic grade, the most aggressive PDAC molecular subtypes, and worse clinical outcomes. Cav-1 loss markedly promoted longer overall and tumor-free survival in a genetically engineered mouse model. Cav-1-deficient tumor cell lines exhibited significantly reduced proliferation, particularly under low nutrient conditions. Supplementing cells with albumin rescued the growth of Cav-1-proficient PDAC cells, but not in Cav-1-deficient PDAC cells under low glutamine conditions. In addition, Cav-1 depletion led to significant metabolic defects, including decreased glycolytic and mitochondrial metabolism, and downstream protein translation signaling pathways. These findings highlight the crucial role of Cav-1 and CME in fueling pancreatic tumorigenesis, sustaining tumor growth, and promoting survival through nutrient scavenging.
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Affiliation(s)
- Adam R. Wolfe
- Department of Radiation Oncology, The University of Arkansas for Medical Sciences, The Winthrop P. Rockefeller Cancer Institute, Little Rock, AR, USA
| | - Tiantian Cui
- Department of Radiation Oncology, City of Hope, Duarte, CA, USA
| | - Sooin Baie
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH, USA
| | | | - Amy Webb
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | | | - Duan-Liang Shyu
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH, USA
| | | | | | - Daniel J. Renouf
- Pancreas Centre BC, Vancouver, BC, Canada
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - David F. Schaeffer
- Pancreas Centre BC, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Megan Halloran
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Rebecca Packard
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Ryan Robb
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wei Chen
- Department of Pathology, The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Nicholas Denko
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Arthur G. James Comprehensive Cancer Center and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Michael Lisanti
- Translational Medicine, University of Salford, Greater Manchester M5 4WT, UK
- Lunella Biotech, Inc., 145 Richmond Road, Ottawa, ON K1Z 1A1, Canada
| | - Timothy C. Thompson
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, USA
| | - Philippe Frank
- SGS France, Health & Nutrition, Saint-Benoît, France
- N2C, Nutrition Growth and Cancer, Faculté de Médecine, Université de Tours, Inserm, UMR, 1069 Tours, France
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2
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Topham JT, Lawlor RT, Lemaire D, Casolino R, Biankin AV. Data sharing in cancer research: perceived risks and the consequences of not sharing. Lancet Oncol 2024; 25:275-276. [PMID: 38423044 DOI: 10.1016/s1470-2045(24)00021-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 01/10/2024] [Indexed: 03/02/2024]
Affiliation(s)
| | - Rita T Lawlor
- ARC-Net Research Centre and Department of Engineering for Innovative Medicine, University of Verona, Verona, Italy
| | - Diana Lemaire
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Raffaella Casolino
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD, UK
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1BD, UK.
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Huey RW, Shah AT, Reddi HV, Dasari P, Topham JT, Hwang H, Dhillon N, Willett A, Smaglo BG, Estrella JS, Rashid A, Matamoros A, Overman MJ, Choquette L, Omerza G, Kelly K, Wang X, Loree JM, Rueter J, Varadhachary GR, Raghav K. Feasibility and value of genomic profiling in cancer of unknown primary: real-world evidence from prospective profiling study. J Natl Cancer Inst 2023; 115:994-997. [PMID: 37202363 PMCID: PMC10407690 DOI: 10.1093/jnci/djad095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/13/2023] [Accepted: 05/16/2023] [Indexed: 05/20/2023] Open
Abstract
Real-world evidence regarding the value of integrating genomic profiling (GP) in managing cancer of unknown primary (CUP) is limited. We assessed this clinical utility using a prospective trial of 158 patients with CUP (October 2016-September 2019) who underwent GP using next-generation sequencing designed to identify genomic alterations (GAs). Only 61 (38.6%) patients had sufficient tissue for successful profiling. GAs were seen in 55 (90.2%) patients of which GAs with US Food and Drug Administration-approved genomically matched therapy were seen in 25 (40.9%) patients. A change in therapy was recommended and implemented (primary endpoint of the study) in 16 (10.1%) and 4 (2.5%) patients of the entire study cohort, respectively. The most common reason for inability to implement the profiling-guided therapy was worsening of performance status (56.3%). Integrating GP in management of CUP is feasible but challenging because of paucity of tissue and aggressive natural history of the disease and requires innovative precision strategies.
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Affiliation(s)
- Ryan W Huey
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Aakash Tushar Shah
- Margaret M. and Albert B. Alkek Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Honey V Reddi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Priyadarsini Dasari
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Hyunsoo Hwang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nishat Dhillon
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anneleis Willett
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brandon G Smaglo
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jeannelyn S Estrella
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Asif Rashid
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Aurelio Matamoros
- Department of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael J Overman
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linda Choquette
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Greg Omerza
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Kevin Kelly
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Xuemei Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jonathan M Loree
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Jens Rueter
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Gauri R Varadhachary
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kanwal Raghav
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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4
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Boutin M, Topham JT, Feilotter H, Kennecke HF, Couture F, Harb M, Kavan P, Berry S, Lim HJ, Goffin JR, Ahmad C, Lott A, Renouf DJ, Jonker DJ, Tu D, O’Callaghan CJ, Chen EX, Loree JM. Optimizing the number of variants tracked to follow disease burden with circulating tumor DNA assays in metastatic colorectal cancer. Ther Adv Med Oncol 2023; 15:17588359231183682. [PMID: 37389190 PMCID: PMC10302520 DOI: 10.1177/17588359231183682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023] Open
Abstract
Background The number of somatic mutations detectable in circulating tumor DNA (ctDNA) is highly heterogeneous in metastatic colorectal cancer (mCRC). The optimal number of mutations required to assess disease kinetics is relevant and remains poorly understood. Objectives To determine whether increasing panel breadth (the number of tracked variants in a ctDNA assay) would alter the sensitivity in detecting ctDNA in patients with mCRC. Design We used archival tissue sequencing to perform an in silico assessment of the optimal number of tracked mutations to detect and monitor disease kinetics in mCRC using sequencing data from the Canadian Cancer Trials Group CO.26 trial. Methods For each patient, 1, 2, 4, 8, 12, or 16 of the most clonal (highest variant allele frequency) somatic variants were selected from archival tissue-based whole-exome sequencing and assessed for the proportion of variants detected in matched ctDNA at baseline, week 8, and progression timepoints. Results Data from 110 patients were analyzed. Genes most frequently encountered among the top four highest VAF variants in archival tissue were TP53 (51.9% of patients), APC (43.3%), KRAS (42.3%), and SMAD4 (9.6%). While the frequency of detecting at least one tracked variant increased when expanding beyond variant pool sizes of 1 and 2 in baseline (p = 0.0030) and progression (p = 0.0030) ctDNA samples, we observed no significant benefit to increases in variant pool size past four variants in any of the ctDNA timepoints (p < 0.05). Conclusion While increasing panel breadth beyond two tracked variants improved variant re-detection in ctDNA samples from patients with treatment refractory mCRC, increases beyond four tracked variants yielded no significant improvement in variant re-detection.
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Affiliation(s)
- Mélina Boutin
- Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada Centre Intégré de Cancérologie de la Montérégie, Université de Sherbrooke, QC, Canada
| | | | - Harriet Feilotter
- Canadian Cancer Trials Group, Queen’s University, Kingston, ON, Canada
| | | | | | | | | | - Scott Berry
- Department of Oncology, Queen’s University, Kingston, ON, Canada
| | - Howard J. Lim
- Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | | | | | | | - Daniel J. Renouf
- Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada Pancreas Center BC, Vancouver, BC, Canada
| | - Derek J. Jonker
- The Ottawa Hospital, University of Ottawa, Ottawa, ON, Canada
| | - Dongsheng Tu
- Canadian Cancer Trials Group, Queen’s University, Kingston, ON, Canada
| | | | - Eric X. Chen
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Jonathan M. Loree
- Division of Medical Oncology, BC Cancer, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada
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5
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Tsang ES, Csizmok V, Williamson LM, Pleasance E, Topham JT, Karasinska JM, Titmuss E, Schrader I, Yip S, Tessier-Cloutier B, Mungall K, Ng T, Sun S, Lim HJ, Loree JM, Laskin J, Marra MA, Jones SJM, Schaeffer DF, Renouf DJ. Homologous recombination deficiency signatures in gastrointestinal and thoracic cancers correlate with platinum therapy duration. NPJ Precis Oncol 2023; 7:31. [PMID: 36964191 PMCID: PMC10039042 DOI: 10.1038/s41698-023-00368-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 03/08/2023] [Indexed: 03/26/2023] Open
Abstract
There is emerging evidence about the predictive role of homologous recombination deficiency (HRD), but this is less defined in gastrointestinal (GI) and thoracic malignancies. We reviewed whole genome (WGS) and transcriptomic (RNA-Seq) data from advanced GI and thoracic cancers in the Personalized OncoGenomics trial (NCT02155621) to evaluate HRD scores and single base substitution (SBS)3, which is associated with BRCA1/2 mutations and potentially predictive of defective HRD. HRD scores were calculated by sum of loss of heterozygosity, telomeric allelic imbalance, and large-scale state transitions scores. Regression analyses examined the association between HRD and time to progression on platinum (TTPp). We included 223 patients with GI (n = 154) or thoracic (n = 69) malignancies. TTPp was associated with SBS3 (p < 0.01) but not HRD score in patients with GI malignancies, whereas neither was associated with TTPp in thoracic malignancies. Tumors with gBRCA1/2 mutations and a somatic second alteration exhibited high SBS3 and HRD scores, but these signatures were also present in several tumors with germline but no somatic second alterations, suggesting silencing of the wild-type allele or BRCA1/2 haploinsufficiency. Biallelic inactivation of an HR gene, including loss of XRCC2 and BARD1, was identified in BRCA1/2 wild-type HRD tumors and these patients had prolonged response to platinum. Thoracic cases with high HRD score were associated with high RECQL5 expression (p ≤ 0.025), indicating another potential mechanism of HRD. SBS3 was more strongly associated with TTPp in patients with GI malignancies and may be complementary to using HRD and BRCA status in identifying patients who benefit from platinum therapy.
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Affiliation(s)
- Erica S Tsang
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
- Pancreas Centre BC, Vancouver, BC, Canada
| | - Veronika Csizmok
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | | | | | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Intan Schrader
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Karen Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Tony Ng
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sophie Sun
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Howard J Lim
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Jonathan M Loree
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, BC, Canada
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Daniel J Renouf
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada.
- Pancreas Centre BC, Vancouver, BC, Canada.
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Titmuss E, Milne K, Jones MR, Ng T, Topham JT, Brown SD, Schaeffer DF, Kalloger S, Wilson D, Corbett RD, Williamson LM, Mungall K, Mungall AJ, Holt RA, Nelson BH, Jones SJM, Laskin J, Lim HJ, Marra MA. Immune Activation following Irbesartan Treatment in a Colorectal Cancer Patient: A Case Study. Int J Mol Sci 2023; 24:ijms24065869. [PMID: 36982943 PMCID: PMC10051648 DOI: 10.3390/ijms24065869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Colorectal cancers are one of the most prevalent tumour types worldwide and, despite the emergence of targeted and biologic therapies, have among the highest mortality rates. The Personalized OncoGenomics (POG) program at BC Cancer performs whole genome and transcriptome analysis (WGTA) to identify specific alterations in an individual's cancer that may be most effectively targeted. Informed using WGTA, a patient with advanced mismatch repair-deficient colorectal cancer was treated with the antihypertensive drug irbesartan and experienced a profound and durable response. We describe the subsequent relapse of this patient and potential mechanisms of response using WGTA and multiplex immunohistochemistry (m-IHC) profiling of biopsies before and after treatment from the same metastatic site of the L3 spine. We did not observe marked differences in the genomic landscape before and after treatment. Analyses revealed an increase in immune signalling and infiltrating immune cells, particularly CD8+ T cells, in the relapsed tumour. These results indicate that the observed anti-tumour response to irbesartan may have been due to an activated immune response. Determining whether there may be other cancer contexts in which irbesartan may be similarly valuable will require additional studies.
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Affiliation(s)
- E Titmuss
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - K Milne
- Deeley Research Centre, BC Cancer, Victoria, BC V8R 6V5, Canada
| | - M R Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - T Ng
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7, Canada
| | - J T Topham
- Pancreas Centre BC, Vancouver, BC V5Z 1G1, Canada
| | - S D Brown
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | | | - S Kalloger
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7, Canada
| | - D Wilson
- Department of Medical Oncology, BC Cancer, Vancouver, BC V5Z 4E6, Canada
| | - R D Corbett
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - L M Williamson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - K Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - A J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - R A Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - B H Nelson
- Deeley Research Centre, BC Cancer, Victoria, BC V8R 6V5, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - S J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - J Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, BC V5Z 4E6, Canada
| | - H J Lim
- Department of Medical Oncology, BC Cancer, Vancouver, BC V5Z 4E6, Canada
| | - M A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
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7
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Topham JT, O'Callaghan CJ, Feilotter H, Kennecke HF, Lee YS, Li W, Banks KC, Quinn K, Renouf DJ, Jonker DJ, Tu D, Chen EX, Loree JM. Circulating Tumor DNA Identifies Diverse Landscape of Acquired Resistance to Anti-Epidermal Growth Factor Receptor Therapy in Metastatic Colorectal Cancer. J Clin Oncol 2023; 41:485-496. [PMID: 36007218 PMCID: PMC9870216 DOI: 10.1200/jco.22.00364] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
PURPOSE Anti-epidermal growth factor receptor (EGFR) antibodies are effective treatments for metastatic colorectal cancer. Improved understanding of acquired resistance mechanisms may facilitate circulating tumor DNA (ctDNA) monitoring, anti-EGFR rechallenge, and combinatorial strategies to delay resistance. METHODS Patients with treatment-refractory metastatic colorectal cancer (n = 169) enrolled on the CO.26 trial had pre-anti-EGFR tissue whole-exome sequencing (WES) compared with baseline and week 8 ctDNA assessments with the GuardantOMNI assay. Acquired alterations were compared between patients with prior anti-EGFR therapy (n = 66) and those without. Anti-EGFR therapy occurred a median of 111 days before ctDNA assessment. RESULTS ctDNA identified 12 genes with increased mutation frequency after anti-EGFR therapy, including EGFR (P = .0007), KRAS (P = .0017), LRP1B (P = .0046), ZNF217 (P = .0086), MAP2K1 (P = .018), PIK3CG (P = .018), BRAF (P = .048), and NRAS (P = .048). Acquired mutations appeared as multiple concurrent subclonal alterations, with most showing decay over time. Significant increases in copy-gain frequency were noted in 29 genes after anti-EGFR exposure, with notable alterations including EGFR (P < .0001), SMO (P < .0001), BRAF (P < .0001), MET (P = .0002), FLT3 (P = .0002), NOTCH4 (P = .0006), ERBB2 (P = .004), and FGFR1 (P = .006). Copy gains appeared stable without decay 8 weeks later. There were 13 gene fusions noted among 11 patients, all but one of which was associated with prior anti-EGFR therapy. Polyclonal resistance was common with acquisition of ≥ 10 resistance related alterations noted in 21% of patients with previous anti-EGFR therapy compared with 5% in those without (P = .010). Although tumor mutation burden (TMB) did not differ pretreatment (P = .63), anti-EGFR exposure increased TMB (P = .028), whereas lack of anti-EGFR exposure resulted in declining TMB (P = .014). CONCLUSION Paired tissue and ctDNA sequencing identified multiple novel mutations, copy gains, and fusions associated with anti-EGFR therapy that frequently co-occur as subclonal alterations in the same patient.
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Affiliation(s)
- James T. Topham
- BC Cancer, University of British Columbia, Vancouver, BC, Canada
| | | | - Harriet Feilotter
- Canadian Cancer Trials Group, Queen's University, Kingston, ON, Canada
| | | | | | | | | | | | - Daniel J. Renouf
- BC Cancer, University of British Columbia, Vancouver, BC, Canada
| | - Derek J. Jonker
- The Ottawa Hospital, University of Ottawa, Ottawa, ON, Canada
| | - Dongsheng Tu
- Canadian Cancer Trials Group, Queen's University, Kingston, ON, Canada
| | - Eric X. Chen
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Jonathan M. Loree
- BC Cancer, University of British Columbia, Vancouver, BC, Canada,Jonathan M. Loree, MD, MS, University of British Columbia, BC Cancer, University of British Columbia, 600 West 10th Ave, Vancouver, BC V5Z 4E6, Canada; Twitter: @jonathanloree; e-mail:
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8
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Topham JT, Renouf DJ, Schaeffer DF. Circulating tumor DNA: toward evolving the clinical paradigm of pancreatic ductal adenocarcinoma. Ther Adv Med Oncol 2023; 15:17588359231157651. [PMID: 36895849 PMCID: PMC9989430 DOI: 10.1177/17588359231157651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 01/30/2023] [Indexed: 03/06/2023] Open
Abstract
Over a decade of sequencing-based genomics research has unveiled a diverse somatic mutation landscape across patients with pancreatic ductal adenocarcinoma (PDAC), and the identification of druggable mutations has aligned with the development of novel targeted therapeutics. However, despite these advances, direct translation of years of PDAC genomics research into the clinical care of patients remains a critical and unmet need. Technologies that enabled the initial mapping of the PDAC mutation landscape, namely whole-genome and transcriptome sequencing, remain overly expensive in terms of both time and financial resources. Consequentially, dependence on these technologies to identify the relatively small subset of patients with actionable PDAC alterations has greatly impeded enrollment for clinical trials testing novel targeted therapies. Liquid biopsy tumor profiling using circulating tumor DNA (ctDNA) generates new opportunities by overcoming these challenges while further addressing issues particularly relevant to PDAC, namely, difficulty of obtaining tumor tissue via fine-needle biopsy and the need for faster turnaround time due to rapid disease progression. Meanwhile, ctDNA-based approaches for tracking disease kinetics with respect to surgical and therapeutic interventions offer a means to elevate the current clinical management of PDAC toward higher granularity and accuracy. This review provides a clinically focused summary of ctDNA advances, limitations, and opportunities in PDAC and postulates ctDNA sequencing technology as a catalyst for evolving the clinical decision-making paradigm of this disease.
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Affiliation(s)
| | - Daniel J Renouf
- Pancreas Centre BC, Vancouver, BC, Canada.,Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - David F Schaeffer
- Division of Anatomic Pathology, Vancouver General Hospital, 910 West 10th Avenue, Vancouver, BC V5Z 1M9, Canada.,Pancreas Centre BC, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada
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9
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Metcalfe A, Karasinska JM, Topham JT, Kalloger SE, Ali H, Ashforth D, Marra MA, Laskin J, Tang PA, Goodwin R, Bathe OF, Renouf DJ, Schaeffer DF. Abstract B053: Targeting SMURF1 with low-dose proteasome inhibitors in pancreatic cancer organoids. Cancer Res 2022. [DOI: 10.1158/1538-7445.panca22-b053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Abstract
Global initiatives focused on whole genome and transcriptome analysis (WGTA) of metastatic pancreatic ductal adenocarcinoma (PDAC) tumor cohorts are driving progress in understanding the clinical impact of PDAC heterogeneity. This knowledge is key to continue the discovery of subsets of patients who could benefit from biomarker-informed targeted therapy and expand the currently limited PDAC treatment options. To identify clinically actionable subtypes in metastatic PDAC (mPDAC), our team analyzes prospectively collected WGTA data from patients enrolled in the PanGen trial (NCT02869802), in parallel with analysis of a set of patient-derived organoids (PDOs). In a cohort of 69 sequenced tumors, four cases (5.8%) had an amplification of chromosome 7q22, which included copy gains of transcriptional co-factor TRRAP, drug metabolizing cytochrome P450 genes CYP3A4 and CYP3A5, and SMURF1. SMURF1 is a ubiquitin-protein ligase that regulates TGFβ receptor signaling, in part via its interaction with SMAD7, and has been implicated in the epithelial-to-mesenchymal program and tumor invasiveness in PDAC. The proteasome inhibitor (PI) bortezomib has been shown to attenuate SMURF1 levels. We investigated whether SMURF1 signaling axis is associated with sensitivity to PIs in mPDAC, by analyzing the cytotoxic effects of the PIs bortezomib, carfilzomib and ixazomib in PDOs. Eight PDOs were treated with PIs at concentrations between 0.1pM-1mM. The presence of live and dead cells was quantified using the IN Cell Analyzer, and cell toxicity was analyzed using GRtoxic metrics (grcalculator.org). The PIs bind catalytic subunits of the 26S proteasome, primarily proteasome subunit beta-5, encoded by PSMB5. The cytotoxic activity of all three PIs negatively correlated with tumor biopsy PSMB5 expression (p<0.05), suggesting that PDOs established from tumors with low expression of PSMB5 are more sensitive to PI-induced cell death. There was a positive correlation between ixazomib cytotoxicity and SMURF1 expression (p<0.05). PanGen patients with high (>75th percentile) tumor SMURF1 expression showed shorter overall survival (OS) compared to the rest of the cohort (median OS 9 vs. 14 months, respectively; p=0.004). Immunohistochemistry analysis of a tumor tissue microarray comprising 175 resected PDAC cases detected an association of concomitant low SMURF1 and high SMAD7 protein levels with adjuvant therapy response (median OS: 40 vs. 12 months with no adjuvant treatment, p=0.002), suggesting that attenuation of SMURF1 in the presence of SMAD7 may improve chemotherapy response in early disease stages. In summary, we present data indicating increased sensitivity to PIs in a subset of tumors with low PSMB5 and high SMURF1 expression, and highlight the translational utility of the investigation of genomic and clinically annotated pre-clinical models in PDAC predictive biomarker discovery.
Citation Format: Andrew Metcalfe, Joanna M. Karasinska, James T. Topham, Steve E. Kalloger, Hassan Ali, Dawn Ashforth, Marco A. Marra, Janessa Laskin, Patricia A. Tang, Rachel Goodwin, Oliver F. Bathe, Daniel J. Renouf, David F. Schaeffer. Targeting SMURF1 with low-dose proteasome inhibitors in pancreatic cancer organoids [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B053.
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Affiliation(s)
| | | | | | | | - Hassan Ali
- 1Pancreas Centre BC, Vancouver, BC, Canada,
| | | | - Marco A. Marra
- 3BC Cancer Genome Sciences Centre, Vancouver, BC, Canada,
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Tao LV, Topham JT, Karasinska JM, Tsang ES, Metcalfe A, Ali H, Ashforth D, Goodwin R, Tang PA, Bathe OF, Laskin J, Marra M, Renouf DJ, Schaeffer DF. Abstract B066: Elucidating the role of insulin receptor isoform expression in metastatic pancreatic ductal adenocarcinoma. Cancer Res 2022. [DOI: 10.1158/1538-7445.panca22-b066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Abstract
Introduction: While type 2 diabetes mellitus (T2DM) has been shown to be both a risk factor and consequence of pancreatic ductal adenocarcinoma (PDAC), the bidirectional relationship between T2DM and PDAC remains to be fully understood. Due to spatial proximity of insulin-producing beta cells, PDAC tumor cells are presumably exposed to a highly concentrated insulin microenvironment, which may contribute to the dysregulation of the insulin receptor gene INSR. There are two isoforms of insulin receptor: IR-A and IR-B. IR-A activity has been associated with oncogenic function and is upregulated in several cancer types. This leads to questions regarding the role of INSR and more specifically, how the ratio of the two isoforms may potentiate tumor aggressiveness in PDAC. Results: Using data from whole-genome and RNA sequencing of metastatic PDAC (mPDAC) from both the PanGen (n=70; NCT01855477) and Personalized Oncogenomics (n=22; NCT02155621) trials, we identified somatic copy loss of INSR in 39/92 (42%) patient tumors, with the majority of such cases (35/39; 90%) showing heterozygous copy loss. There was no statistical association between INSR copy status and PDAC transcriptomic subtypes. INSR expression was lower in basal-like versus classical subtype tumors (p=1.1e-4), and INSR expression was further attenuated in basal-like tumors with heterozygous copy loss of INSR (p=0.0041). The ratio of IR-A:IR-B expression was heterogenous across samples, and heightened IR-A:IR-B ratio was significantly (p<0.05) associated with expression of genes linked to the PI3K-Akt signaling axis (CCDC88A, THEM4) and glucose metabolism (HK1, G6PC, PKLR) in basal-like tumors. Interestingly,HK1 and IGF1R were significantly upregulated, independent of IR-A:IR-B ratio, among basal-like (p 9.1e-9 and p=1.4e-5, respectively) compared to classical subtype tumors. Conclusion: These data indicate that heightened IR-A:IR-B ratio is associated with the expression of key pathways converging on PI3K signalling and glucose metabolism in mPDAC, while highlighting that several IR-A:IR-B-associated gene correlations are unique to basal-like tumors. Such findings warrant further investigation of relative INSR isoform expression in mPDAC and pre-clinical models to elucidate the role of the oncogenic isoform, IR-A, in driving tumor aggressiveness in basal-like subtype tumors.
Citation Format: Lan V. Tao, James T. Topham, Joanna M. Karasinska, Erica S. Tsang, Andrew Metcalfe, Hassan Ali, Dawn Ashforth, Rachel Goodwin, Patricia A. Tang, Oliver F. Bathe, Janessa Laskin, Marco Marra, Daniel J. Renouf, David F. Schaeffer. Elucidating the role of insulin receptor isoform expression in metastatic pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B066.
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Affiliation(s)
- Lan V. Tao
- 1BC Cancer Research Institute, Vancouver, BC, Canada,
| | | | | | | | | | - Hassan Ali
- 1BC Cancer Research Institute, Vancouver, BC, Canada,
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Topham JT, Tsang ES, Karasinska JM, Metcalfe A, Ali H, Kalloger SE, Csizmok V, Williamson LM, Titmuss E, Nielsen K, Negri GL, Spencer Miko SE, Jang GH, Denroche RE, Wong HL, O'Kane GM, Moore RA, Mungall AJ, Loree JM, Notta F, Wilson JM, Bathe OF, Tang PA, Goodwin R, Morin GB, Knox JJ, Gallinger S, Laskin J, Marra MA, Jones SJM, Schaeffer DF, Renouf DJ. Integrative analysis of KRAS wildtype metastatic pancreatic ductal adenocarcinoma reveals mutation and expression-based similarities to cholangiocarcinoma. Nat Commun 2022; 13:5941. [PMID: 36209277 PMCID: PMC9547977 DOI: 10.1038/s41467-022-33718-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 09/29/2022] [Indexed: 11/15/2022] Open
Abstract
Oncogenic KRAS mutations are absent in approximately 10% of patients with metastatic pancreatic ductal adenocarcinoma (mPDAC) and may represent a subgroup of mPDAC with therapeutic options beyond standard-of-care cytotoxic chemotherapy. While distinct gene fusions have been implicated in KRAS wildtype mPDAC, information regarding other types of mutations remain limited, and gene expression patterns associated with KRAS wildtype mPDAC have not been reported. Here, we leverage sequencing data from the PanGen trial to perform comprehensive characterization of the molecular landscape of KRAS wildtype mPDAC and reveal increased frequency of chr1q amplification encompassing transcription factors PROX1 and NR5A2. By leveraging data from colorectal adenocarcinoma and cholangiocarcinoma samples, we highlight similarities between cholangiocarcinoma and KRAS wildtype mPDAC involving both mutation and expression-based signatures and validate these findings using an independent dataset. These data further establish KRAS wildtype mPDAC as a unique molecular entity, with therapeutic opportunities extending beyond gene fusion events. KRAS wildtype metastatic pancreatic ductal adenocarcinoma (mPDAC) could represent a distinct molecular entity from other PDACs. Here, the authors analyse KRAS wildtype mPDAC tumours using genomics and transcriptomics and find molecular similarities with cholangiocarcinomas.
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Affiliation(s)
| | - Erica S Tsang
- Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | | | | | - Hassan Ali
- Pancreas Centre BC, Vancouver, BC, Canada
| | - Steve E Kalloger
- Pancreas Centre BC, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada
| | - Veronika Csizmok
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Karina Nielsen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | | | - Gun Ho Jang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Hui-Li Wong
- Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | | | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | | | - Faiyaz Notta
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Julie M Wilson
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Oliver F Bathe
- Departments of Surgery and Oncology, Cummings School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Patricia A Tang
- Departments of Surgery and Oncology, Cummings School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Rachel Goodwin
- The Ottawa Hospital Cancer Centre, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Gregg B Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Jennifer J Knox
- University Health Network, University of Toronto, Toronto, ON, Canada
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, ON, Canada.,University Health Network, University of Toronto, Toronto, ON, Canada
| | - Janessa Laskin
- Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada.,Division of Anatomic Pathology, Vancouver General Hospital, Vancouver, BC, Canada
| | - Daniel J Renouf
- Pancreas Centre BC, Vancouver, BC, Canada. .,Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada. .,Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
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Loree JM, Topham JT, Kennecke HF, Feilotter H, Lee YS, Virk S, Kopetz S, Duose DY, Manyam GC, Morris JS, Maru DM, Renouf D, Jonker DJ, Tu D, O'Callaghan CJ, Chen EX. Impact of consensus molecular subtyping (CMS) on survival in the CO.26 trial of durvalumab plus tremelimumab versus best supportive care (BSC) in metastatic colorectal cancer (mCRC). J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.3551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3551 Background: CO.26 was a phase 2 trial (2-sided α=0.1 and 80% power) that randomized 180 patients with refractory mCRC 2:1 to durvalumab + tremelimumab vs BSC with improved overall survival (OS) (HR 0.73, 90%CI 0.55-0.97, P=0.07). A Nanostring assay validated for use with FFPE was used to determine CMS for correlation with outcome. Methods: Archival FFPE from 163/180 (91%) of patients (pts) underwent RNA extraction and CMS subtyping. Cox proportional hazard models evaluated the prognostic and predictive impact of CMS on overall survival. Results: CMS distribution was skewed towards CMS4 (76%), with lower prevalence of CMS1 (2%), CMS2 (16%) and CMS3 (2%). There were 7/163 cases of indeterminate CMS (4%). Subgroup analysis was restricted to CMS2 and CMS4 based on sample size. With BSC alone, CMS2 showed trends to worse OS compared to all other patients pooled (HR 1.93, 90% CI 1.03-3.61, P=0.085), while CMS4 did not (HR 0.86, 90% CI 0.50-1.48, P=0.64). OS but not progression free survival (PFS) was improved with durvalumab + tremelimumab in the overall population. OS was improved with durvalumab + tremelimumab among patients with CMS2 tumors (HR 0.39, 90% CI 0.19-0.82, P=0.035) but not in patients with CMS4 tumors (HR 0.73, 90% CI 0.52-1.02, P=0.12) compared to BSC. Neither CMS2 (P-interaction=0.37) nor CMS4 (P-interaction=0.91) were predictive of OS benefit from durvalumab + tremelimumab compared to BSC. Disease control rate (DCR) trended to being better among CMS4 (24/85) than CMS2 cancers (1/15, OR 5.51, 90% CI 1.10-29.88, P=0.11) or CMS4 vs all non CMS4 cancers (1/21, OR 7.87, 90% CI 1.65-41.98, P=0.023) for patients on durvalumab + tremelimumab. PFS was not improved with durvalumab + tremelimumab in CMS2 (P=0.19) or CMS4 (P=0.29) cancers relative to BSC. Conclusions: In this trial of refractory colorectal cancer, we saw a shift in CMS subtype with more CMS4 than expected. Compared to CMS4, CMS2 showed stronger signals towards improved OS with durvalumab + tremelimumab but had a lower disease control rate. Differences in immune signaling by CMS may be important determinants of which component of immune regulation needs to be targeted in mCRC to improve outcomes. Clinical trial information: NCT02870920. [Table: see text]
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Affiliation(s)
| | | | | | - Harriet Feilotter
- Queen's University, Department of Pathology and Molecular Medicine, Kingston, ON, Canada
| | - Young S Lee
- Translational Medicine, AstraZeneca, Gaithersburg, MD
| | - Shakeel Virk
- Queen's University, Canadian Cancer Trials Group, Kingston, ON, Canada
| | - Scott Kopetz
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Dzifa Yawa Duose
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Daniel Renouf
- BC Cancer; University of British Columbia, Vancouver, BC, Canada
| | - Derek J. Jonker
- Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Dongsheng Tu
- Queen's University, Canadian Cancer Trials Group, Kingston, ON, Canada
| | | | - Eric Xueyu Chen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
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Fuentes Antrás J, Jang GH, Topham JT, Zhang A, Tsang ES, Wang Y, Hutchinson S, Dodd A, Wilson J, Notta F, Fischer S, Ramotar S, Moura S, Hakgor S, Siu LL, Zogopoulos G, Gallinger S, Renouf D, O'Kane GM, Knox JJ. Molecular characterization of long-term and short-term survivors of advanced pancreatic ductal adenocarcinoma. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.4024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
4024 Background: Median overall survival (mOS) for advanced pancreatic ductal adenocarcinoma (PDAC) is ≤1 year. However, there are patients (pts) who live for >2 years on chemotherapy and those who rapidly progress prior to a first scan, underscoring biological heterogeneity in PDAC subgroups. Understanding these differences is important in clinical trial design and provides prognostic information for pts. Methods: Clinical and molecular data (WGS and RNAseq) from pts with a diagnosis of locally advanced or metastatic PDAC enrolled in the COMPASS (NCT02750657) and POG/PanGen (NCT02155621, NCT02869802) studies were available for analysis as part of the TFRI’s EPPIC program and Marathon of Hope Cancer Centres Network, a multi-institutional collaborative network aiming to implement precision medicine in Canada. Clinical data were collected prospectively from both cohorts. Pts had an ECOG PS 0-1 and chemotherapy regimen was based on clinician’s preference. Profiling was performed on fresh biopsies and homologous recombination deficiency was identified with the HRDetect assay. We compared pts with very short OS (STS; ≤3 months, mo) vs long OS (LTS; ≥24 mo). Results: 341 pts were included in the analysis of which 47 were STS (mOS 1.6 mo) and 42 LTS (mOS 29.7 mo). There was no difference in median age, BMI or sex (p>0.1) between cohorts. STS were more likely to have an ECOG PS 1 vs 0 (p=0.03), higher tumor burden (RECIST) (p<0.001) and higher CA19.9 (p=0.04) at diagnosis. In STS, 71% had non evaluable responses as a result of clinical decline or death before first scan, and 28% PD as best response; in LTS, ORR to chemotherapy was 69%. Sixty-four % and 33% of LTS and 32% and 36% of STS had received mFFX and GA, respectively. There was no difference in the prevalence of KRAS mutations (90% vs 98%, ns) or specific mutant alleles, however amplification of mutant KRAS was more common in STS (35% vs 65%, p=0.01). The prevalence of inactivating driver mutations in TP53, CDKN2A, and SMAD4 (90% vs 98%, ns), and in genes involved in chromatin modification ( ARID1A, SMARCA4, PBRM1, KDM6A) (17% vs 30%, ns) was similar in both groups. However, STS had a higher prevalence of mutations resulting in activation of the PI3K/AKT/mTOR pathway ( PIK3CA, PTEN loss, STK11) (10% vs 26%, p=0.049). Genotypes consistent with HRD were present (17% vs 11%); however, in LTS 6/7 were a result of germline pathogenic variants, compared with only 1/5 in STS. Median structural variant loads, ploidy, TMB and substitution base signatures were similar in both cohorts. More basal-like PDAC were present in STS vs LTS (3% vs 30%, p=0.006). Conclusions: Pts who survive ≤3 mo with advanced PDAC are characterized by a higher tumor burden and molecular profiles consistent with enhanced RAS signaling, a deregulation of the PI3K/AKT/mTOR pathway, and a basal-like transcriptomic subtype. HRD genotypes are heterogeneous with germline carriers accounting for some of the LTS.
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Affiliation(s)
- Jesús Fuentes Antrás
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Gun Ho Jang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Amy Zhang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Erica S Tsang
- University of California San Francisco, San Francisco, CA
| | - Yifan Wang
- Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | | | - Anna Dodd
- Wallace McCain Center for Pancreatic Cancer, Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Julie Wilson
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Faiyaz Notta
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Sandra Fischer
- Laboratory Medicine Program, Toronto General Hospital, University Health Network, University of Toronto, Toronto, ON, Canada
| | | | - Shari Moura
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Sevan Hakgor
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Lillian L. Siu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - George Zogopoulos
- Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - Steven Gallinger
- Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Daniel Renouf
- BC Cancer; University of British Columbia, Vancouver, BC, Canada
| | | | - Jennifer J. Knox
- Wallace McCain Center for Pancreatic Cancer, Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
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Lau TTY, Sefid Dashti ZJ, Titmuss E, Pender A, Topham JT, Bridgers J, Loree JM, Feng X, Pleasance ED, Renouf DJ, Schrader KA, Sun S, Ho C, Marra MA, Laskin J, Karsan A. The Neoantigen Landscape of the Coding and Noncoding Cancer Genome Space. J Mol Diagn 2022; 24:609-618. [PMID: 35367630 DOI: 10.1016/j.jmoldx.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 01/12/2022] [Accepted: 02/25/2022] [Indexed: 11/18/2022] Open
Abstract
Tumor mutation burden (TMB) is a measure to predict patient responsiveness to immune checkpoint immunotherapy because with increased mutation frequency, the likelihood of a greater neoantigen burden is increased. Although neoantigen prediction tools exist, tumor neoantigen burden has not been adopted as a measure to predict immunotherapy response. With both measures, current guidelines are limited to the coding regions, but ectopic expression of sequences in the noncoding space may potentially be a source of neoantigens. A pan-cancer cohort of 574 advanced disease stage patients with whole genome and transcriptome sequencing was analyzed to report mutation burden and neoantigen counts within the coding and noncoding regions. The efficacy of tumor neoantigen burden, reported as tumor neoantigen count (TNC), including neoantigens derived from the expression of noncoding regions, compared with TMB as a predictor of response to immunotherapy for 80 patients who had received treatment, was evaluated. TMB was found to be the best predictor of response to immunotherapy, whereas expression-derived TNC from the noncoding regions did not improve prediction of response. Therefore, there is minimal benefit in extending the calculation of TNC to the noncoding space for the purposes of predicting response. However, it is likely that there is a wealth of neoantigens derived from the noncoding space that may impact patient outcomes and treatments.
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Affiliation(s)
- Tammy T Y Lau
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Zahra J Sefid Dashti
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Alexandra Pender
- Department of Medical Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - James T Topham
- Pancreas Centre BC, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Joshua Bridgers
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Jonathan M Loree
- Department of Medical Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Xiaolan Feng
- Department of Medical Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Erin D Pleasance
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Daniel J Renouf
- Department of Medical Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada; Pancreas Centre BC, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Kasmintan A Schrader
- Hereditary Cancer Program, BC Cancer Research Institute, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sophie Sun
- Hereditary Cancer Program, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Cheryl Ho
- Department of Medical Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Aly Karsan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada; Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
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Tsang ES, Topham JT, Karasinska J, Kalloger S, Csizmok V, Williamson L, Wong HL, O'Kane GM, Loree JM, Notta F, Bathe OF, Tang PA, Goodwin RA, Knox JJ, Gallinger S, Laskin JJ, Marra MA, Jones SJM, Schaeffer DF, Renouf DJ. Integrative analysis of KRAS-wildtype pancreatic ductal adenocarcinoma reveals unique similarities to extrahepatic cholangiocarcinoma. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.4_suppl.587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
587 Background: Oncogenic driver mutations in KRAS represent a hallmark genomic event in approximately 90% of pancreatic adenocarcinoma (PDAC). For the remaining 10% of patients with KRAS wildtype (wt) PDAC, distinct driver mutations have been described, but their transcriptional landscape has not been reported. Here, we leverage sequencing data from the PanGen trial to provide a comprehensive characterization of advanced KRASwt PDAC. Methods: 63 patients with advanced PDAC received whole genome and transcriptome sequencing prior to treatment for metastatic disease as part of the PanGen trial (NCT02869802). Clinical features, somatic mutation data and gene expression patterns were compared between KRASwt and mutant groups. PDAC samples were contrasted with 77 other metastatic carcinoma (colorectal and cholangiocarcinoma) samples from the Personalized OncoGenomics trial (NCT0215562). KRAS wt-associated genes were further investigated using 3 additional PDAC cohorts (COMPASS NCT02750657, TCGA, and ICGC). Results: 9 of 63 (14%) samples were KRASwt, with an earlier median age at diagnosis (51.4 vs. 60.9 years; p=0.03). Clinical features, including diabetes, family history of malignancy, and location of primary tumor, were comparable. CA 19-9 at baseline was lower in the KRASwt group, with median 58 vs. 4900 U/mL in the KRAS-mutant group ( p=0.03). Patients with KRASwt PDAC showed increased overall survival in univariable ( p=0.0024) and multivariable ( p=0.0089) analyses. 6 of 9 (67%) KRASwt tumors had fusions involving NRG1 (n = 3), FGFR2 (n = 1), BRAF (n = 1) or NTRK2 (n = 1), while known actionable fusions were not observed in KRAS mutant patients. KRASwt tumors showed increased expression of genes associated with cholangiocytes and grouped with cholangiocarcinoma samples in unsupervised clustering analysis. Validation using three independent PDAC cohorts revealed a core set of 70 KRAS wt-associated genes that converge on keratinization, ion transport, and hormone metabolism pathways. Conclusions: Patients with KRASwt PDAC show potentially targetable molecular traits with actionable fusions. We also highlight novel mutation and expression-based similarities between KRASwt PDAC and cholangiocarcinoma samples. Recurrent dysregulation of genes involved in cellular structure and metastasis provide impetus for further investigation into the developmental trajectory and potential therapeutic vulnerabilities of KRASwt PDAC.
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Affiliation(s)
| | | | | | | | - Veronika Csizmok
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Laura Williamson
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Hui-Li Wong
- Royal Melbourne Hospital, Melbourne, Australia
| | | | | | - Faiyaz Notta
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Patricia A. Tang
- Tom Baker Cancer Centre, University of Calgary, Calgary, AB, Canada
| | - Rachel Anne Goodwin
- National Cancer Institute of Canada Clinical Trials Group, The Ottawa Hospital, Ottawa, ON, Canada
| | - Jennifer J. Knox
- Wallace McCain Center for Pancreatic Cancer, Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | | | | | - Marco A. Marra
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | - David F. Schaeffer
- Department of Pathology & Laboratory Medicine Vancouver General Hospital, Vancouver, BC, Canada
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Ali HA, Metcalfe A, Topham JT, Warren CS, Karasinska JM, Schaeffer DF, Renouf DJ. Abstract PO-021: Targeting the mitochondrial pyruvate complex to alter metabolic programming in pancreatic cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.panca21-po-021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Pancreatic ductal adenocarcinoma (PDAC) can be stratified into distinct transcriptome subtypes, with the ‘basal-like’ or ‘squamous’ subtype being associated with worse prognosis, compared to the ‘classical’ subtype. Our group recently demonstrated that PDAC tumors have unique metabolic transcriptome profiles, and that genes involved in glycolysis and cholesterol synthesis pathways are positively correlated with basal-like and classical gene expression patterns, respectively. The mitochondrial pyruvate complex (MPC) mediates the transport of pyruvate into the mitochondria which attenuates the effect of glycolysis on tumor progression. The mitochondrial pyruvate carrier 1 (MPC1) gene, which encodes one of two subunits of MPC, is deleted in over 60% of metastatic PDAC and PDAC glycolytic tumors have lowest levels of MPC1 expression. Using PDAC tissue microarrays, we also found that reduced MPC1 protein expression correlates with reduced survival in patients. We hypothesized that targeting MPC1 will alter metabolic reprogramming and may modulate tumor aggressiveness and therapeutic vulnerability in PDAC tumor cells. Genomically and clinically annotated patient-derived tumor organoids (PDOs) were generated from metastatic biopsies from patients enrolled in the PanGen study (NCT02869802). PDOs from both basal and classical tumors were used in the study. In order to investigate glycolysis in PDOs, we adapted the Seahorse Glycolytic Stress Test. Glycolysis, glycolytic capacity and reserve were analyzed in PDOs under basal and treated conditions. To alter MPC1 activity, PDOs were treated for 48 hours with 5uM of UK-5099, an MPC1 inhibitor, or 2.5-5uM SRT1720. SRT1720 is an activator of sirtuin 1 (SIRT1) and the transcriptional coactivator peroxisome proliferator-activated receptor γ coactivator-1α (PGC1-α), which regulates the expression of MPC1. An unpaired t-test with an alpha of 0.05 was used for all statistical analysis. Glycolysis analysis revealed distinct glycolytic profiles in PDOs with differences in glycolytic capacity and reserves trending with different tumor subtypes. Treatment with UK-5099 resulted in an increase in both glycolytic rate and reserve in PDOs from basal and classical tumors. Treatment with SRT1720 resulted in significantly reduced glycolytic rate and capacity. These data suggest that PDAC PDOs exhibit distinct metabolic profiles and that targeting MPC1 can modulate glycolysis in PDOs. Our ongoing efforts aim to further characterize the subtype-specific effect of MPC1 modulators on glycolysis and chemotherapy response in PDAC PDOs.
Citation Format: Hassan A. Ali, Andrew Metcalfe, James T. Topham, Cassia S. Warren, Joanna M. Karasinska, David F. Schaeffer, Daniel J. Renouf. Targeting the mitochondrial pyruvate complex to alter metabolic programming in pancreatic cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2021 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2021;81(22 Suppl):Abstract nr PO-021.
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Affiliation(s)
- Hassan A. Ali
- 1University of British Columbia, Vancouver, BC, Canada,
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Grant RC, Denroche R, Jang GH, Nowak KM, Zhang A, Borgida A, Holter S, Topham JT, Wilson J, Dodd A, Jang R, Prince R, Karasinska JM, Schaeffer DF, Wang Y, Zogopoulos G, Berry S, Simeone D, Renouf DJ, Notta F, O'Kane G, Knox J, Fischer S, Gallinger S. Clinical and genomic characterisation of mismatch repair deficient pancreatic adenocarcinoma. Gut 2021; 70:1894-1903. [PMID: 32933947 DOI: 10.1136/gutjnl-2020-320730] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 08/05/2020] [Accepted: 08/09/2020] [Indexed: 12/27/2022]
Abstract
OBJECTIVE To describe the clinical, pathological and genomic characteristics of pancreatic cancer with DNA mismatch repair deficiency (MMRD) and proficiency (MMRP). DESIGN We identified patients with MMRD and MMRP pancreatic cancer in a clinical cohort (N=1213, 519 with genetic testing, 53 with immunohistochemistry (IHC)) and a genomic cohort (N=288 with whole-genome sequencing (WGS)). RESULTS 12 out of 1213 (1.0%) in the clinical cohort were MMRD by IHC or WGS. Of the 14 patients with Lynch syndrome, 3 (21.4%) had an MMRP pancreatic cancer by IHC, and 4 (28.6%) were excluded because tissue was unavailable for testing. MMRD cancers had longer overall survival after surgery (weighted HR after coarsened exact matching 0.11, 95% CI 0.02 to 0.78, p=0.001). One patient with an unresectable MMRD cancer has an ongoing partial response 3 years after starting treatment with PD-L1/CTLA-4 inhibition. This tumour showed none of the classical histopathological features of MMRD. 9 out of 288 (3.1%) tumours with WGS were MMRD. Despite markedly higher tumour mutational burden and neoantigen loads, MMRD cancers were significantly less likely to have mutations in usual pancreatic cancer driver genes like KRAS and SMAD4, but more likely to have mutations in genes that drive cancers with microsatellite instability like ACV2RA and JAK1. MMRD tumours were significantly more likely to have a basal-like transcriptional programme and elevated transcriptional markers of immunogenicity. CONCLUSIONS MMRD pancreatic cancers have distinct clinical, pathological and genomic profiles. Patients with MMRD pancreatic cancer should be considered for basket trials targeting enhanced immunogenicity or the unique genomic drivers in these malignancies.
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Affiliation(s)
- Robert C Grant
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Robert Denroche
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gun Ho Jang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Klaudia M Nowak
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Amy Zhang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Ayelet Borgida
- Ontario Pancreas Cancer Study, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Spring Holter
- Ontario Pancreas Cancer Study, Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - Julie Wilson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Anna Dodd
- Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Raymond Jang
- Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Rebecca Prince
- Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | | | | | - Yifan Wang
- Goodman Cancer Research Centre, Montreal, Quebec, Canada
| | | | - Scott Berry
- Department of Oncology, Queen's University, Kingston, Ontario, Canada
| | | | - Daniel J Renouf
- Pancreas Centre BC, Vancouver, Ontario, Canada.,BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Faiyaz Notta
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Grainne O'Kane
- Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Jennifer Knox
- Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Sandra Fischer
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada .,Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada.,Ontario Pancreas Cancer Study, Mount Sinai Hospital, Toronto, Ontario, Canada
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Renouf DJ, Loree JM, Knox JJ, Kavan P, Jonker DJ, Welch S, Couture F, Lemay F, Tehfe M, Harb M, Aucoin N, Ko YJ, Tang PA, Topham JT, Jia S, Du P, Schaeffer DF, Gill S, Tu D, O'Callaghan CJ. Predictive value of germline ATM mutations in the CCTG PA.7 trial: Gemcitabine (GEM) and nab-paclitaxel (Nab-P) versus GEM, nab-P, durvalumab (D) and tremelimumab (T) as first-line therapy in metastatic pancreatic ductal adenocarcinoma (mPDAC). J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.4135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
4135 Background: PA.7 evaluated whether combining PD-L1 and CTLA-4 inhibition with GEM and Nab-P increases efficacy. A previous analysis of the PA.7 data demonstrated high plasma based TMB (≥9 mut/Mb) was associated with improved OS in the Gem, Nab-P, D+T arm. DNA repair pathway aberrations beyond mismatch repair have been associated with potential immune sensitivity. We assessed the predictive value of germline ATM mutations in the PA.7 trial. Methods: This randomized phase II study (ClinicalTrials.gov NCT02879318) assessed the efficacy and safety of GEM, Nab-P, D, and T (arm A) vs. GEM and Nab-P (arm B) in patients (pts) with mPDAC (n = 180). The primary endpoint was overall survival (OS). Pre-treatment plasma was sequenced with the Predicine ATLAS next generation assay (600 gene, 2.4 Mb panel). 2-sided alpha set at 0.1. Results: 180 pts were randomized (119 to arm A and 61 to arm B) There was no significant difference in OS (9.8 months in arm A vs. 8.8 months in arm B, p-value 0.72) or PFS (5.5 months and 5.4 months respectively, HR 0.98, p-value 0.91). Plasma analysis was performed on 174/180 pts with available samples. 16/174 (9.2%) pts had germline ATM mutations, 12 in arm A and 4 in arm B. GEM, Nab-P, D+T was associated with improved OS in patients with ATM mutations (HR 0.10, 90% CI 0.03-0.37; median OS 13.9 months vs. 4.9 months) while no activity was seen in pts with ATM Wild Type (HR 0.99, 90% CI 0.73-1.33; median OS 9.79 months vs. 10.2 months); interaction p = 0.014. Germline ATM mutation status was independent of plasma TMB levels (Wilcoxon p = 0.76). Conclusions: Germline ATM mutation appeared predictive of benefit from the addition of dual immune checkpoint inhibitors (D and T) to Gem and Nab-P, with a significant interaction p-value. In addition to previous data from this trial regarding the predictive value of high plasma TMB (≥9 mut/Mb), this data further supports that there may be independent subgroups of PDAC, beyond MSI-H, that may benefit from immunotherapy, and trials evaluating immunotherapy in subgroups of PDAC with these profiles are warranted. Clinical trial information: NCT02879318.
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Affiliation(s)
| | | | - Jennifer J. Knox
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | | | | | | | - Felix Couture
- Centre Hospitalier Universitaire de Québec, Quebec City, QC, Canada
| | - Frederic Lemay
- Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
| | - Mustapha Tehfe
- Centre Hospitalier de l'Université de Montréal (CHUM), Montréal, QC, Canada
| | | | | | - Yoo-Joung Ko
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Patricia A. Tang
- Tom Baker Cancer Centre, University of Calgary, Calgary, AB, Canada
| | | | | | - Pan Du
- Predicine, Inc, Hayward, CA
| | - David F. Schaeffer
- Department of Pathology & Laboratory Medicine Vancouver General Hospital, Vancouver, BC, Canada
| | | | - Dongsheng Tu
- Queen's University, Canadian Cancer Trials Group, Kingston, ON, Canada
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Naso JR, Topham JT, Karasinska JM, Lee MK, Kalloger SE, Wong H, Nelson J, Moore RA, Mungall AJ, Jones SJ, Laskin J, Marra MA, Renouf DJ, Schaeffer DF. Tumor infiltrating neutrophils and gland formation predict overall survival and molecular subgroups in pancreatic ductal adenocarcinoma. Cancer Med 2021; 10:1155-1165. [PMID: 33372414 PMCID: PMC7897949 DOI: 10.1002/cam4.3695] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/20/2020] [Accepted: 12/06/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND RNA-sequencing-based classifiers can stratify pancreatic ductal adenocarcinoma (PDAC) into prognostically significant subgroups but are not practical for use in clinical workflows. Here, we assess whether histomorphological features may be used as surrogate markers for predicting molecular subgroup and overall survival in PDAC. METHODS Ninety-six tissue samples from 50 patients with non-resectable PDAC were scored for gland formation, stromal maturity, mucin, necrosis, and neutrophil infiltration. Prognostic PDAC gene expression classifiers were run on all tumors using whole transcriptome sequencing data from the POG trial (NCT02155621). Findings were validated using digital TCGA slides (n = 50). Survival analysis used multivariate Cox proportional-hazards tests and log-rank tests. RESULTS The combination of low gland formation and low neutrophil infiltration was significantly associated with the poor prognosis PDAC molecular subgroup (basal-like or squamous) and was an independent predictor of shorter overall survival, in both frozen section (n = 47) and formalin-fixed paraffin-embedded (n = 49) tissue samples from POG patients, and in the TCGA samples. This finding held true in the subgroup analysis of primary (n = 17) and metastatic samples (n = 79). The combination of high gland formation and high neutrophils had low sensitivity but high specificity for favorable prognosis subgroups. CONCLUSIONS The assessment of gland formation and neutrophil infiltration on routine histological sections can aid in prognostication and allow inferences to be made about molecular subtype, which may help guide patient management decisions and contribute to our understanding of heterogeneity in treatment response.
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Affiliation(s)
- Julia R. Naso
- Division of Anatomic PathologyVancouver General HospitalVancouverBCCanada
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverBCCanada
| | | | | | | | - Steve E. Kalloger
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverBCCanada
- Pancreas Centre BCVancouverBCCanada
| | - Hui‐li Wong
- Division of Medical OncologyBC CancerVancouverBCCanada
| | - Jessica Nelson
- Canada's Michael Smith Genome Sciences CentreVancouverBCCanada
| | | | | | | | - Janessa Laskin
- Division of Medical OncologyBC CancerVancouverBCCanada
- Canada's Michael Smith Genome Sciences CentreVancouverBCCanada
| | - Marco A. Marra
- Canada's Michael Smith Genome Sciences CentreVancouverBCCanada
- Department of Medical GeneticsUniversity of British ColumbiaVancouverBCCanada
| | - Daniel J. Renouf
- Pancreas Centre BCVancouverBCCanada
- Division of Medical OncologyBC CancerVancouverBCCanada
| | - David F. Schaeffer
- Division of Anatomic PathologyVancouver General HospitalVancouverBCCanada
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverBCCanada
- Pancreas Centre BCVancouverBCCanada
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Renouf DJ, Loree JM, Knox JJ, Kavan P, Jonker DJ, Welch S, Couture F, Lemay F, Tehfe M, Harb M, Aucoin N, Ko YJ, Tang PA, Topham JT, Jia S, Du P, Schaeffer DF, Gill S, Tu D, O'Callaghan CJ. Predictive value of plasma tumor mutation burden (TMB) in the CCTG PA.7 trial: Gemcitabine (GEM) and nab-paclitaxel (Nab-P) vs. GEM, nab-P, durvalumab (D) and tremelimumab (T) as first line therapy in metastatic pancreatic ductal adenocarcinoma (mPDAC). J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.3_suppl.411] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
411 Background: PA.7 evaluated whether combining PD-L1 and CTLA-4 inhibition with GEM and Nab-P increases efficacy as first line therapy in mPDAC. High TMB is associated with immunotherapy sensitivity, with a threshold of ≥10 mut/Mb receiving FDA accelerated approved for pembrolizumab in a tissue agnostic setting. We assessed the predictive value of plasma TMB in the PA.7 trial. Methods: This randomized phase II study (ClinicalTrials.gov NCT02879318) assessed the efficacy and safety of GEM, Nab-P, D, and T (arm A) vs. GEM and Nab-P (arm B) in patients (pts) with mPDAC (n = 180). The primary endpoint was overall survival (OS). Pre-treatment plasma was sequenced with the CLIA-certified PredicineATLAS cfDNA next generation assay (600 genes, 2.4 Mb panel). A pre-specified cut point of 5 mut/MB was selected based on distribution of TMB in the trial. 2-sided alpha set at 0.1. Results: 180 pts were randomized (119 to arm A and 61 to arm B). There was no significant difference in OS (9.8 months in arm A vs. 8.8 months in arm B, p-value 0.72) or PFS (5.5 months and 5.4 months respectively, HR 0.98, p-value 0.91). Plasma TMB analysis was performed on 174/180 pts with available samples, and tumor derived variants were detected in 173/174 pts (99.4%). 172 pts were microsatellite stable and 1 pt was microsatellite high (MSI-H) (plasma TMB 52.9 muts/Mb). Using the pre-specified cut-point of 5 mut/Mb there was no significant predictive value from plasma TMB (interaction p = 0.91). Using a minimum p-value approach, a cut-point of 9 mut/MB appeared predictive (p-interaction = 0.064; significant at pre-specified p = 0.1). 8/174 (4.6%) pts had a plasma TMB ≥9 mut/Mb (5/115 (4.4%) in arm A and 3/59 (5%) in arm B). GEM, Nab-P, D+T was associated with improved OS in patients with plasma TMB ≥9 mut/Mb (HR 0.30, 90% CI 0.06-1.37) while no activity was seen in pts with < 9 mut/Mb, (HR 0.97, 90% CI 0.73-1.29). TMB cut-point analysis revealed a clear trend for a decreasing HR favoring the GEM, Nab-P, D and T arm above the selected cut point, with no benefit in the low TMB group. Conclusions: Plasma TMB analysis was successful in over 99% of pts with available samples. Plasma TMB ≥9 mut/Mb was predictive of benefit from the addition of dual immune checkpoint inhibitors (D and T) to Gem and Nab-P, with a significant interaction p-value. While only present in a subgroup of pts (4.6%), this data defines a group beyond MSI-H PDAC that may benefit from immunotherapy. The optimal cut-point for high TMB in this setting requires validation. A clinical trial specifically assessing the role of chemotherapy combined with immune checkpoint inhibition in high TMB mPDAC is warranted. Clinical trial information: NCT02879318.
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Affiliation(s)
| | | | - Jennifer J. Knox
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | | | | | | | - Felix Couture
- Centre Hospitalier Universitaire de Québec, Quebec City, QC, Canada
| | - Frederic Lemay
- Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
| | - Mustapha Tehfe
- Centre Hospitalier Universite de Montreal- Hopital Notre Dame, Montréal, QC, Canada
| | | | | | - Yoo-Joung Ko
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Patricia A. Tang
- Tom Baker Cancer Centre, University of Calgary, Calgary, AB, Canada
| | | | | | - Pan Du
- Huidu Shanghai Medical Sciences, Ltd., Shanghai, CA, China
| | - David F. Schaeffer
- Department of Pathology & Laboratory Medicine Vancouver General Hospital, Vancouver, BC, Canada
| | | | - Dongsheng Tu
- Queen's University, Canadian Cancer Trials Group, Kingston, ON, Canada
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Topham JT, O'Callaghan CJ, Feilotter H, Kennecke HF, Lee YS, Li W, Banks K, Renouf DJ, Jonker D, Tu D, Chen EX, Loree JM. ctDNA-based mutational landscape following anti-EGFR antibodies in metastatic colorectal cancer (mCRC) to uncover novel resistance mechanisms in the CCTG CO.26 trial. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.3_suppl.117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
117 Background: Previous studies have identified MAPK and PIK3CA/AKT/mTOR pathways as common mechanisms of acquired resistance to anti-EGFR antibodies (EGFRab) in mCRC. However, such alterations do not account for all patients that become treatment resistant. Using paired whole-exome (WES; tissue) and circulating tumor DNA (ctDNA; plasma) sequencing, we performed characterization of the EGFRab resistance landscape in patients with mCRC. Methods: Post-treatment (ctDNA; plasma) sequencing was performed for 169 patients with mCRC, with 112 (66%) patients also receiving pre-treatment (WES; primary tumor) sequencing as part of the CO.26 trial. 66 (39%) patients received EGFRab previously at a median of 132.0 days prior to plasma sampling. Using bespoke bioinformatics pipelines (WES) coupled with the GuardantOMNI assay (plasma), we compared somatic mutation (SNV/indel, CNV and fusion) frequencies between pre- and post-EGFRab timepoints, and contrasted results between the two groups. Results: Significant increases in de novo acquisition of EGFR (p = 5.6e-4), KRAS (p = 0.011), ZNF217 (p = 0.0022), MAP2K1 (p = 0.0078) and LRP1B (p = 0.017) SNV/indels were unique to the EGFRab group and often occurred as multiple, low allele frequency events in the same patient. De novo copy number amplification of known resistance genes EGFR/ BRAF/ MET were observed in EGFRab-treated patients (p < 0.05), along with SMO (p = 6.8e-7), PTEN inhibitory gene PREX2 (p = 5.6e-4), FLT3 (p = 2.0e-5), NOTCH4 (p = 6.3e-5), ERBB2 (7.4e-4), KMT2A (p = 3.7e-4) and ARID1B (p = 0.0014). Genes impacted by fusion events in EGFRab-treated patients included BRAF-KIAA1549 (1 patient) and MET-CAV1 (1 patient), and these events were not detected in matched pre-treatment samples. EGFRab-treated patients were found to acquire a combination of multiple (≥5) mutation events (SNV/indel, CNV or fusion) at much higher frequency compared to non-EGFRab-treated patients (67% versus 25% of patients, p = 8.7e-8). Tumor mutation burden (TMB) was not significantly different (p = 0.71) between treatment groups prior to therapy initiation, while post-treatment TMB was significantly higher (p = 1.8e-7) in EGFRab-treated patients (median 25.4 versus 13.1 mut/mb). Conclusions: In addition to previously established resistance pathways, we identified acquired alterations in additional genes such as SMO, PREX2 and epigenetic modifiers KMT2A/ARID1B in EGFRab-treated patients . Moreover, we highlight the phenomenon by which EGFRab-treated tumors acquire multiple concurrent resistance mutations and heightened TMB. Our analysis provides novel insight into the landscape of resistance mechanisms to EGFRab in mCRC while highlighting the potential role for immunotherapy post-EGFRab. Clinical trial information: NCT02870920.
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Affiliation(s)
| | | | - Harriet Feilotter
- Queen's University, Department of Pathology and Molecular Medicine, Kingston, ON, Canada
| | | | | | | | | | | | | | - Dongsheng Tu
- Queen's University, Canadian Cancer Trials Group, Kingston, ON, Canada
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Loree JM, Topham JT, Kennecke HF, Feilotter H, Keshavarz-Rahaghi F, Lee YS, Li W, Quinn K, Banks K, Renouf DJ, Jonker DJ, Tu D, O'Callaghan CJ, Chen EX. Tissue and plasma tumor mutation burden (TMB) as predictive biomarkers in the CO.26 trial of durvalumab + tremelimumab (D+T) versus best supportive care (BSC) in metastatic colorectal cancer (mCRC). J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.3_suppl.61] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
61 Background: Pembrolizumab was recently granted tissue agnostic FDA accelerated approval for metastatic cancers with TMB≥10 mut/Mb. However, limited data supports immunotherapy in microsatellite stable (MSS) mCRC with TMB≥10 mut/Mb. We assessed tissue TMB and contrasted it to plasma derived TMB in the CO.26 trial. Methods: CO.26 was a phase 2 trial (2-sided ⍺ = 0.1 and 80% power) that randomized 180 patients (pts) 2:1 to D+T or BSC in refractory mCRC. Pre-treatment plasma was sequenced with the GuardantOMNI assay and archival tissue underwent exome sequencing with TMB assessed per the TMB harmonization project. MSI-H cases were excluded. For plasma TMB, we used a previously published cut point (≥28). Results: Overall survival (OS) but not progression free survival (PFS) was improved with D+T in the entire population. Of 180 pts, 163 were evaluable for plasma and 110 for tissue TMB. Median time between archival tissue and plasma collection was 3.1 yrs (IQR 1.9-5.1). Median tissue TMB was 6.6 muts/Mb (IQR 4.1-12.0), while median plasma TMB was 16.3 muts/Mb (IQR 9.4-25.9). Tissue and plasma TMB (r = -0.039, P = 0.69) were not correlated. Tissue TMB≥10 was not prognostic in the BSC arm (HR 1.01, 90%CI 0.52-1.92, P = 0.99) and OS was not improved in pts with tissue TMB≥10 (32/110 pts) following D+T vs BSC. A test of interaction suggested this threshold was not predictive (P = 0.85). Using a minimum P-value approach, no threshold supported high tissue TMB as predictive in MSS mCRC. In fact, the optimal cut point suggested low tissue TMB ( < 4.1 muts/Mb) had the greatest benefit from D+T (P-interaction = 0.048) and pts with TMB ≥4.1 mut/Mb (HR 0.50, 90%CI 0.26-0.96, P = 0.083) trended to better OS in the BSC arm. In contrast, 35/163 pts (21%) were identified in a high plasma TMB group associated with worse OS (HR 2.56, 90%CI 1.45-4.54, P = 0.007) in the BSC arm but improved OS following D+T compared to BSC with P-interaction = 0.082. Only 1 response was noted following D+T in a pt with tissue TMB = 16 mut/Mb and plasma TMB = 13 mut/Mb. Conclusions: Archival tissue TMB≥10 mut/Mb does not appear predictive of D+T benefit in MSS mCRC. Plasma derived TMB may better reflect evolutionary changes following intervening therapy than archival tissue. Clinical trial information: NCT02870920. [Table: see text]
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Affiliation(s)
| | | | | | - Harriet Feilotter
- Queen's University, Department of Pathology and Molecular Medicine, Kingston, ON, Canada
| | | | | | | | | | | | | | | | - Dongsheng Tu
- Queen's University, Canadian Cancer Trials Group, Kingston, ON, Canada
| | | | - Eric Xueyu Chen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
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Tsang ES, Csizmok V, Williamson L, Pleasance ED, Topham JT, Karasinska J, Titmuss E, Schrader KA, Cafferty F, Yip S, Tessier-Cloutier B, Mungall K, Sun S, Lim HJ, Loree JM, Laskin JJ, Marra MA, Jones SJM, Schaeffer DF, Renouf DJ. Beyond BRCA? clinical utility of homologous recombination deficiency in gastrointestinal cancers. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.3_suppl.472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
472 Background: There is emerging evidence about the predictive role of homologous recombination deficiency (HRD) in multiple cancers. The clinical utility of HRD is less well defined in gastrointestinal (GI) malignancies. Methods: We reviewed the whole genome (WGS) and transcriptomic (RNA-Seq) data of patients with advanced GI cancers between 2012-2018 in the Personalized Oncogenomics trial (NCT02155621). Scores were calculated as the sum of loss of heterozygosity, telomeric allelic imbalance, and large-scale state transitions scores. HRD was defined as a score ≥34. Mutational analysis was performed to determine the presence of mutational signature 3, which is usually strongly associated with BRCA status. Retrospective chart review was conducted to extract treatment and survival outcomes. Overall survival (OS) from initiation of first-line systemic therapy and time to progression on platinum therapy (TTPp) were calculated. Linear and multivariable regression analyses were conducted. Results: Of 154 patients with GI primaries, 56% were male and 105 (68%) were exposed to a platinum agent in the metastatic setting. Primary sites included upper GI (N=20, 9%), pancreas (N=35, 16%), colorectal (N=74, 33%), and other GI primary (N=25, 11%). Ten patients (6%) had a BRCA1/2 mutation, 20 (13%) had a high HRD score, and 11 (7%) had a high signature 3 score (>0.05). Six patients had both high HRD and high signature 3 scores (Table). On linear regression, high HRD scores and mutational signature 3 were independently associated with longer TTPp (β=4.17, 95% CI 0.15-8.19, p=0.04; β=8.03, 95% CI 2.87-13.18, p<0.05, respectively). On multivariable linear regression, after adjusting for HRD score, BRCA1/2 status, and tumor site, only cases with a mutational signature 3 retained significance ( p<0.05). HRD status was not prognostic for OS (HR 1.02, 95% CI 0.65-1.62, p=0.92). Conclusions: Within a cohort of patients with GI malignancies characterized by WGS and RNA-Seq, mutational signature 3 was more strongly associated with TTPp compared to HRD score. These data highlight potential predictive implications of Signature 3 to complement HRD and BRCA status in identifying patients who may benefit from exposure to platinum therapy. [Table: see text]
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Affiliation(s)
| | - Veronika Csizmok
- Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Laura Williamson
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Erin D. Pleasance
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | | | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | | | | | | | - Karen Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | - Howard John Lim
- British Columbia Cancer Vancouver, and CCTG Co-Chair, Vancouver, BC, Canada
| | | | | | - Marco A. Marra
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | - David F. Schaeffer
- Department of Pathology & Laboratory Medicine Vancouver General Hospital, Vancouver, BC, Canada
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24
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Topham JT, Karasinska JM, Lee MKC, Csizmok V, Williamson LM, Jang GH, Denroche RE, Tsang ES, Kalloger SE, Wong HL, O'Kane GM, Moore RA, Mungall AJ, Notta F, Loree JM, Wilson JM, Bathe O, Tang PA, Goodwin R, Knox JJ, Gallinger S, Laskin J, Marra MA, Jones SJM, Renouf DJ, Schaeffer DF. Subtype-Discordant Pancreatic Ductal Adenocarcinoma Tumors Show Intermediate Clinical and Molecular Characteristics. Clin Cancer Res 2021; 27:150-157. [PMID: 33051307 DOI: 10.1158/1078-0432.ccr-20-2831] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/09/2020] [Accepted: 10/09/2020] [Indexed: 01/03/2023]
Abstract
PURPOSE RNA-sequencing-based subtyping of pancreatic ductal adenocarcinoma (PDAC) has been reported by multiple research groups, each using different methodologies and patient cohorts. "Classical" and "basal-like" PDAC subtypes are associated with survival differences, with basal-like tumors associated with worse prognosis. We amalgamated various PDAC subtyping tools to evaluate the potential of such tools to be reliable in clinical practice. EXPERIMENTAL DESIGN Sequencing data for 574 PDAC tumors was obtained from prospective trials and retrospective public databases. Six published PDAC subtyping strategies (Moffitt regression tools, clustering-based Moffitt, Collisson, Bailey, and Karasinska subtypes) were used on each sample, and results were tested for subtype call consistency and association with survival. RESULTS Basal-like and classical subtype calls were concordant in 88% of patient samples, and survival outcomes were significantly different (P < 0.05) between prognostic subtypes. Twelve percent of tumors had subtype-discordant calls across the different methods, showing intermediate survival in univariate and multivariate survival analyses. Transcriptional profiles compatible with that of a hybrid subtype signature were observed for subtype-discordant tumors, in which classical and basal-like genes were concomitantly expressed. Subtype-discordant tumors showed intermediate molecular characteristics, including subtyping gene expression (P < 0.0001) and mutant KRAS allelic imbalance (P < 0.001). CONCLUSIONS Nearly 1 in 6 patients with PDAC have tumors that fail to reliably fall into the classical or basal-like PDAC subtype categories, based on two regression tools aimed toward clinical practice. Rather, these patient tumors show intermediate prognostic and molecular traits. We propose close consideration of the non-binary nature of PDAC subtypes for future incorporation of subtyping into clinical practice.
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Affiliation(s)
| | | | - Michael K C Lee
- Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Veronika Csizmok
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, British Columbia, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, British Columbia, Canada
| | - Gun Ho Jang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Erica S Tsang
- Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Steve E Kalloger
- Pancreas Centre BC, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hui-Li Wong
- Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | | | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, British Columbia, Canada
| | - Faiyaz Notta
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jonathan M Loree
- Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Julie M Wilson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Oliver Bathe
- The University of Calgary, Calgary, Alberta, Canada
| | | | - Rachel Goodwin
- The Ottawa Hospital Cancer Centre, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Jennifer J Knox
- University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Janessa Laskin
- Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada.,Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel J Renouf
- Pancreas Centre BC, Vancouver, British Columbia, Canada.,Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada.,Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver, British Columbia, Canada. .,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Division of Anatomic Pathology, Vancouver General Hospital, Vancouver, British Columbia, Canada
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25
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Tsang ES, Grisdale CJ, Pleasance E, Topham JT, Mungall K, Reisle C, Choo C, Carreira M, Bowlby R, Karasinska JM, MacMillan D, Williamson LM, Chuah E, Moore RA, Mungall AJ, Zhao Y, Tessier-Cloutier B, Ng T, Sun S, Lim HJ, Schaeffer DF, Renouf DJ, Yip S, Laskin J, Marra MA, Jones SJM, Loree JM. Uncovering Clinically Relevant Gene Fusions with Integrated Genomic and Transcriptomic Profiling of Metastatic Cancers. Clin Cancer Res 2020; 27:522-531. [PMID: 33148671 DOI: 10.1158/1078-0432.ccr-20-1900] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 09/11/2020] [Accepted: 10/29/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Gene fusions are important oncogenic drivers and many are actionable. Whole-genome and transcriptome (WGS and RNA-seq, respectively) sequencing can discover novel clinically relevant fusions. EXPERIMENTAL DESIGN Using WGS and RNA-seq, we reviewed the prevalence of fusions in a cohort of 570 patients with cancer, and compared prevalence to that predicted with commercially available panels. Fusions were annotated using a consensus variant calling pipeline (MAVIS) and required that a contig of the breakpoint could be constructed and supported from ≥2 structural variant detection approaches. RESULTS In 570 patients with advanced cancer, MAVIS identified 81 recurrent fusions by WGS and 111 by RNA-seq, of which 18 fusions by WGS and 19 by RNA-seq were noted in at least 3 separate patients. The most common fusions were EML4-ALK in thoracic malignancies (9/69, 13%), and CMTM8-CMTM7 in colorectal cancer (4/73, 5.5%). Combined genomic and transcriptomic analysis identified novel fusion partners for clinically relevant genes, such as NTRK2 (novel partners: SHC3, DAPK1), and NTRK3 (novel partners: POLG, PIBF1). CONCLUSIONS Utilizing WGS/RNA-seq facilitates identification of novel fusions in clinically relevant genes, and detected a greater proportion than commercially available panels are expected to find. A significant benefit of WGS and RNA-seq is the innate ability to retrospectively identify variants that becomes clinically relevant over time, without the need for additional testing, which is not possible with panel-based approaches.
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Affiliation(s)
- Erica S Tsang
- Department of Medical Oncology, BC Cancer, Vancouver, Canada
| | - Cameron J Grisdale
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | | | - Karen Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Caralyn Reisle
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Caleb Choo
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Marcus Carreira
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | | | - Daniel MacMillan
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada
| | | | - Tony Ng
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Sophie Sun
- Department of Medical Oncology, BC Cancer, Vancouver, Canada
| | - Howard J Lim
- Department of Medical Oncology, BC Cancer, Vancouver, Canada
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Daniel J Renouf
- Department of Medical Oncology, BC Cancer, Vancouver, Canada.,Pancreas Centre BC, Vancouver, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
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26
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Pender A, Titmuss E, Pleasance ED, Fan KY, Pearson H, Brown SD, Grisdale CJ, Topham JT, Shen Y, Bonakdar M, Taylor GA, Williamson LM, Mungall KL, Chuah E, Mungall AJ, Moore RA, Lavoie JM, Yip S, Lim H, Renouf DJ, Sun S, Holt RA, Jones SJM, Marra MA, Laskin J. Genome and Transcriptome Biomarkers of Response to Immune Checkpoint Inhibitors in Advanced Solid Tumors. Clin Cancer Res 2020; 27:202-212. [PMID: 33020056 DOI: 10.1158/1078-0432.ccr-20-1163] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 07/06/2020] [Accepted: 09/30/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Immune checkpoint inhibitors (ICI) have revolutionized the treatment of solid tumors with dramatic and durable responses seen across multiple tumor types. However, identifying patients who will respond to these drugs remains challenging, particularly in the context of advanced and previously treated cancers. EXPERIMENTAL DESIGN We characterized fresh tumor biopsies from a heterogeneous pan-cancer cohort of 98 patients with metastatic predominantly pretreated disease through the Personalized OncoGenomics program at BC Cancer (Vancouver, Canada) using whole genome and transcriptome analysis (WGTA). Baseline characteristics and follow-up data were collected retrospectively. RESULTS We found that tumor mutation burden, independent of mismatch repair status, was the most predictive marker of time to progression (P = 0.007), but immune-related CD8+ T-cell and M1-M2 macrophage ratio scores were more predictive for overall survival (OS; P = 0.0014 and 0.0012, respectively). While CD274 [programmed death-ligand 1 (PD-L1)] gene expression is comparable with protein levels detected by IHC, we did not observe a clinical benefit for patients with this marker. We demonstrate that a combination of markers based on WGTA provides the best stratification of patients (P = 0.00071, OS), and also present a case study of possible acquired resistance to pembrolizumab in a patient with non-small cell lung cancer. CONCLUSIONS Interpreting the tumor-immune interface to predict ICI efficacy remains challenging. WGTA allows for identification of multiple biomarkers simultaneously that in combination may help to identify responders, particularly in the context of a heterogeneous population of advanced and previously treated cancers, thus precluding tumor type-specific testing.
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Affiliation(s)
- Alexandra Pender
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Erin D Pleasance
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Kevin Y Fan
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hillary Pearson
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Scott D Brown
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Cameron J Grisdale
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | | | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Melika Bonakdar
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Gregory A Taylor
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Jean-Michel Lavoie
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Howard Lim
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Daniel J Renouf
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
- Pancreas Centre BC, Vancouver, British Columbia, Canada
| | - Sophie Sun
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Robert A Holt
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada.
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27
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Kalloger SE, Karasinska JM, Keung MS, Thompson DL, Ho J, Chow C, Gao D, Topham JT, Warren C, Wong HL, Lee MKC, Renouf DJ, Schaeffer DF. Stroma vs epithelium-enhanced prognostics through histologic stratification in pancreatic ductal adenocarcinoma. Int J Cancer 2020; 148:481-491. [PMID: 32955725 DOI: 10.1002/ijc.33304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/10/2020] [Accepted: 09/07/2020] [Indexed: 01/05/2023]
Abstract
The mixture of epithelial and stromal components in pancreatic ductal adenocarcinoma (PDAC) may confound sequencing-based studies of tumor gene expression. Virtual microdissection has been suggested as a bioinformatics approach to segment the aforementioned components, and subsequent prognostic gene sets have emerged from this research. We examined the prognostic signature from the epithelial gene set of one such study using laser capture microdissected (LCM) epithelial samples. We also examined this gene set in matched stromal samples to determine whether prognostic findings were specific to the epithelium. LCM samples from 48 long-term and 48 short-term PDAC survivors were obtained. The resultant epithelial and stromal components were subjected to direct mRNA quantification using a 49 gene published PDAC classifier. Component-specific unsupervised hierarchical clustering was used to derive groups and survival differences were quantified. Immunohistochemical validation of particular genes was performed in an independent cohort. Clustering in the epithelial component yielded prognostic differences in univariable analysis (P = .02), but those differences were not significant when controlled for other clinicopathologic covariates (P = .06). Clustering in the stromal component yielded prognostic differences that persisted in the presence of other clinicopathologic covariates (P = .0005). Validation of selected genes in the epithelium (KRT6A-negative prognostic [P = .004]) and stroma (LY6D-improved prognostic [P = .01] and CTSV-negative prognostic [P = .0002]) demonstrated statistical independence in multivariable analysis. Although the genes used in this study were originally identified as being representative of the epithelial component of PDAC, their expression in the stroma appears to provide additional information that may aid in improved prognostication.
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Affiliation(s)
- Steve E Kalloger
- Pancreas Centre BC, Vancouver General Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Joanna M Karasinska
- Pancreas Centre BC, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Martin S Keung
- Pancreas Centre BC, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Danielle L Thompson
- Pancreas Centre BC, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Julie Ho
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christine Chow
- Genetic Pathology Evaluation Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dongxia Gao
- Genetic Pathology Evaluation Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - James T Topham
- Pancreas Centre BC, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Cassia Warren
- Pancreas Centre BC, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Hui-Li Wong
- Pancreas Centre BC, Vancouver General Hospital, Vancouver, British Columbia, Canada.,Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Michael Kuan-Ching Lee
- Pancreas Centre BC, Vancouver General Hospital, Vancouver, British Columbia, Canada.,Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.,Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel J Renouf
- Pancreas Centre BC, Vancouver General Hospital, Vancouver, British Columbia, Canada.,Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.,Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver General Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Division of Anatomical Pathology, Vancouver General Hospital, Vancouver, British Columbia, Canada.,Genetic Pathology Evaluation Centre, University of British Columbia, Vancouver, British Columbia, Canada
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28
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Tsang ES, Topham JT, Karasinska JM, Lee MKC, Williamson LM, Mendis S, Denroche RE, Jang GH, Kalloger SE, Moore RA, Mungall AJ, Bathe OF, Tang PA, Notta F, Wilson JM, Laskin J, O'Kane GM, Knox JJ, Goodwin RA, Loree JM, Jones SJM, Marra MA, Gallinger S, Schaeffer DF, Renouf DJ. Delving into Early-onset Pancreatic Ductal Adenocarcinoma: How Does Age Fit In? Clin Cancer Res 2020; 27:246-254. [PMID: 32958704 DOI: 10.1158/1078-0432.ccr-20-1042] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/15/2020] [Accepted: 09/14/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE With the rising incidence of early-onset pancreatic cancer (EOPC), molecular characteristics that distinguish early-onset pancreatic ductal adenocarcinoma (PDAC) tumors from those arising at a later age are not well understood. EXPERIMENTAL DESIGN We performed bioinformatic analysis of genomic and transcriptomic data generated from 269 advanced (metastatic or locally advanced) and 277 resectable PDAC tumor samples. Patient samples were stratified into EOPC (age of onset ≤55 years; n = 117), intermediate (age of onset 55-70 years; n = 264), and average (age of onset ≥70 years; n = 165) groups. Frequency of somatic mutations affecting genes commonly implicated in PDAC, as well as gene expression patterns, were compared between EOPC and all other groups. RESULTS EOPC tumors showed significantly lower frequency of somatic single-nucleotide variant (SNV)/insertions/deletions (indel) in CDKN2A (P = 0.0017), and were more likely to achieve biallelic mutation of CDKN2A through homozygous copy loss as opposed to heterozygous copy loss coupled with a loss-of-function SNV/indel mutation, the latter of which was more common for tumors with later ages of onset (P = 1.5e-4). Transcription factor forkhead box protein C2 (FOXC2) was significantly upregulated in EOPC tumors (P = 0.032). Genes significantly correlated with FOXC2 in PDAC samples were enriched for gene sets related to epithelial-to-mesenchymal transition (EMT) and included VIM (P = 1.8e-8), CDH11 (P = 6.5e-5), and CDH2 (P = 2.4e-2). CONCLUSIONS Our comprehensive analysis of sequencing data generated from a large cohort of PDAC patient samples highlights a distinctive pattern of biallelic CDKN2A mutation in EOPC tumors. Increased expression of FOXC2 in EOPC, with the correlation between FOXC2 and EMT pathways, represents novel molecular characteristics of EOPC.See related commentary by Lou, p. 8.
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Affiliation(s)
- Erica S Tsang
- BC Cancer, Vancouver, British Columbia, Canada.,Pancreas Centre BC, Vancouver, British Columba, Canada
| | | | | | - Michael K C Lee
- BC Cancer, Vancouver, British Columbia, Canada.,Pancreas Centre BC, Vancouver, British Columba, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Shehara Mendis
- BC Cancer, Vancouver, British Columbia, Canada.,Pancreas Centre BC, Vancouver, British Columba, Canada
| | | | - Gun Ho Jang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | | | | | - Faiyaz Notta
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Julie M Wilson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | | | - Jennifer J Knox
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Rachel A Goodwin
- The Ottawa Hospital Cancer Centre, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Jonathan M Loree
- BC Cancer, Vancouver, British Columbia, Canada.,Pancreas Centre BC, Vancouver, British Columba, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | | | - David F Schaeffer
- Pancreas Centre BC, Vancouver, British Columba, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel J Renouf
- BC Cancer, Vancouver, British Columbia, Canada. .,Pancreas Centre BC, Vancouver, British Columba, Canada
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29
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Topham JT, Titmuss E, Pleasance ED, Williamson LM, Karasinska JM, Culibrk L, Lee MKC, Mendis S, Denroche RE, Jang GH, Kalloger SE, Wong HL, Moore RA, Mungall AJ, O'Kane GM, Knox JJ, Gallinger S, Loree JM, Mager DL, Laskin J, Marra MA, Jones SJM, Schaeffer DF, Renouf DJ. Endogenous Retrovirus Transcript Levels Are Associated with Immunogenic Signatures in Multiple Metastatic Cancer Types. Mol Cancer Ther 2020; 19:1889-1897. [PMID: 32518206 DOI: 10.1158/1535-7163.mct-20-0094] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/28/2020] [Accepted: 06/04/2020] [Indexed: 11/16/2022]
Abstract
Next-generation sequencing of solid tumors has revealed variable signatures of immunogenicity across tumors, but underlying molecular characteristics driving such variation are not fully understood. Although expression of endogenous retrovirus (ERV)-containing transcripts can provide a source of tumor-specific neoantigen in some cancer models, associations between ERV levels and immunogenicity across different types of metastatic cancer are not well established. We performed bioinformatics analysis of genomic, transcriptomic, and clinical data across an integrated cohort of 199 patients with metastatic breast, colorectal, and pancreatic ductal adenocarcinoma tumors. Within each cancer type, we identified a subgroup of viral mimicry tumors in which increased ERV levels were coupled with transcriptional signatures of autonomous antiviral response and immunogenicity. In addition, viral mimicry colorectal and pancreatic tumors showed increased expression of DNA demethylation gene TET2 Taken together, these data demonstrate the existence of an ERV-associated viral mimicry phenotype across three distinct metastatic cancer types, while indicating links between ERV abundance, epigenetic dysregulation, and immunogenicity.
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Affiliation(s)
| | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Erin D Pleasance
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | | | - Luka Culibrk
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Michael K C Lee
- Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Shehara Mendis
- Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | | | - Gun-Ho Jang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Steve E Kalloger
- Pancreas Centre BC, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hui-Li Wong
- Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Grainne M O'Kane
- University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Jennifer J Knox
- University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan M Loree
- Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Dixie L Mager
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Janessa Laskin
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.,Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Division of Anatomic Pathology, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Daniel J Renouf
- Pancreas Centre BC, Vancouver, British Columbia, Canada. .,Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada.,Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Chan-Seng-Yue M, Kim JC, Wilson GW, Ng K, Figueroa EF, O'Kane GM, Connor AA, Denroche RE, Grant RC, McLeod J, Wilson JM, Jang GH, Zhang A, Liang SB, Borgida A, Chadwick D, Kalimuthu S, Lungu I, Bartlett JMS, Krzyzanowski PM, Sandhu V, Tiriac H, Froeling FEM, Karasinska JM, Topham JT, Renouf DJ, Schaeffer DF, Jones SJM, Marra MA, Laskin J, Chetty R, Stein LD, Zogopoulos G, Haibe-Kains B, Campbell PJ, Tuveson DA, Knox JJ, Fischer SE, Gallinger S, Notta F. Author Correction: Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution. Nat Genet 2020; 52:463. [PMID: 32051610 DOI: 10.1038/s41588-020-0588-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Michelle Chan-Seng-Yue
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jaeseung C Kim
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Genomics Technology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gavin W Wilson
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Karen Ng
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Grainne M O'Kane
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Centre University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Ashton A Connor
- Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Ontario, Canada
| | - Robert E Denroche
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Robert C Grant
- Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Centre University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Jessica McLeod
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Julie M Wilson
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gun Ho Jang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Amy Zhang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Sheng-Ben Liang
- UHN Program in BioSpecimen Sciences, University Health Network, Toronto, Ontario, Canada
| | - Ayelet Borgida
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Dianne Chadwick
- UHN Program in BioSpecimen Sciences, University Health Network, Toronto, Ontario, Canada
| | - Sangeetha Kalimuthu
- Department of Pathology, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Ilinca Lungu
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - John M S Bartlett
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Paul M Krzyzanowski
- Genomics Technology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Vandana Sandhu
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Hervé Tiriac
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY, USA.,Department of Surgery, University of California San Diego, NCI-designated Comprehensive Cancer Center, La Jolla, CA, USA
| | - Fieke E M Froeling
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY, USA.,Department of Surgery and Cancer, Imperial College London, London, UK
| | | | | | - Daniel J Renouf
- Pancreas Centre BC, Vancouver, British Columbia, Canada.,Department of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Runjan Chetty
- Department of Pathology, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Lincoln D Stein
- Bioinformatics, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - George Zogopoulos
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.,The Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK.,Department of Haematology, University of Cambridge, Cambridge, UK
| | - David A Tuveson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY, USA
| | - Jennifer J Knox
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Centre University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Sandra E Fischer
- Department of Pathology, University Health Network and University of Toronto, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Steven Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada. .,Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Ontario, Canada. .,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada. .,Department of Surgery, University of Toronto, Toronto, Ontario, Canada.
| | - Faiyaz Notta
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada. .,PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
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Mendis S, Alcaide M, Topham JT, Johnson B, Morin RD, Chu J, Bosdet I, Kopetz S, Karsan A, Gill S, Laskin J, Jones SJM, Marra MA, Schaeffer DF, Renouf DJ, Loree JM. Integration of Whole-Genome Sequencing With Circulating Tumor DNA Analysis Captures Clonal Evolution and Tumor Heterogeneity in Non-V600 BRAF Mutant Colorectal Cancer. Clin Colorectal Cancer 2020; 19:132-136.e3. [PMID: 32151517 DOI: 10.1016/j.clcc.2020.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/22/2020] [Accepted: 02/01/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Shehara Mendis
- Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Miguel Alcaide
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | | | - Benny Johnson
- Department of Gastrointestinal Medical Oncology, The University of M.D. Anderson Cancer Center, Houston, TX
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Jenny Chu
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Ian Bosdet
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of M.D. Anderson Cancer Center, Houston, TX
| | - Aly Karsan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sharlene Gill
- Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Janessa Laskin
- Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Daniel J Renouf
- Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada; Pancreas Centre BC, Vancouver, British Columbia, Canada
| | - Jonathan M Loree
- Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada.
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32
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Lee M, Wong HL, Tsang ES, Addison SMF, Topham JT, Karasinska J, Kalloger S, Loree JM, Schaeffer DF, Renouf DJ. Clinicopathological features of pancreatic cancer-related diabetes. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.4_suppl.675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
675 Background: Epidemiological studies suggest pancreatic ductal adenocarcinoma (PDAC) may be strongly interrelated with diabetes. However, little is known about the clinicopathological features of pancreatic cancer related diabetes. Methods: A retrospective chart review was undertaken of all patients with advanced PDAC treated with at least one cycle of palliative chemotherapy at BC Cancer, Vancouver between Jan 2012- Dec 2015. Diagnosis of diabetes was determined by consultation documentation and/or fasting glucose > 7mmol/L or HbA1c > 48mmol/L. Peripancreatic diabetes is defined as diabetes diagnosis < 3 years prior to PDAC diagnosis. Results: 578 patients were identified with median age 66 (49-81), 54.6% male, 39.5% non-smoker and 63.5% ECOG 0/1. 27.3% confirmed diabetics, of which 75.8% (119/157) have peripancreatic diabetes. At initial diagnosis, 11.2% were deemed upfront resectable, 44.0% borderline/locally advanced, and 55.1% metastatic. Median overall survival (OS) for the cohort based on stage of disease at initial diagnosis for borderline, locally advanced and metastatic was 22 months (16.1-27.9), 12 months (10.1-13.9) and 6 months (5.0-7.0) respectively. There was no association with diabetes status and OS noted (p = 0.58). Statistical differences were noted in BMI (24.1 v 26.1, p = 0.003), and proportion of Charlson comorbidity index (CCI) of 2 (2.2 v 88.3%, p < 0.01) between non-diabetic and diabetic patients respectively. Statistical difference between peripancreatic diabetes compared to long-term diabetes were noted in resectable status (18.6 v 7.6%, p = 0.048), weight loss > 2kg (78.6 v 60.5%, p = 0.035), hypertension (25.9 v 59.8%, p = 0.002) and dyslipidemia (18.5 v 42.7%, p = 0.024). Conclusions: The majority of patients diagnosed with advanced PDAC with diabetes appeared to develop diabetes within 3 years prior to diagnosis. Further studies to assess the potential role of pancreatic cancer screening investigations in newly diagnosed diabetics are warranted.
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Affiliation(s)
| | - Hui-Li Wong
- Royal Melbourne Hospital, Melbourne, Australia
| | | | | | | | | | | | | | - David F. Schaeffer
- Department of Pathology & Laboratory Medicine Vancouver General Hospital, Vancouver, BC, Canada
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Lee M, Topham JT, Kalloger S, Mendis SR, Tsang ES, Karasinska J, Loree JM, Schaeffer DF, Renouf DJ. Whole genome and transcriptome analysis and the link between insulin receptor aberration and diabetes in PDAC. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.4_suppl.743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
743 Background: Pancreatic ductal adenocarcinoma’s (PDAC) association with diabetes development remains poorly understood. The insulin receptor ( INSR) can divert insulin signaling from metabolic to oncogenic pathway activation through alternative splicing of INSR in several cancer types. Methods: 54 treatment naïve patients with metastatic PDAC underwent fresh tumour biopsy in the BC Cancer Personalized Oncogenomics (POG) and PanGen studies (NCT02155621, NCT02869802) for whole genome (WGA) and transcriptome analysis (RNASeq). Copy status and expression of INSR were correlated with T2DM status, Moffitt subtypes, and overall survival (OS). The findings were then correlated with 92 resected PDAC from the International Cancer Genome Consortium (ICGC). Results: 13/54 (24%) had confirmed T2DM at enrollment, and had poorer OS compared to non-diabetic PDAC patients, independent of Moffitt subtype, HR 3.2 (1.5-6.5), p =0.001. Diabetics were more likely to have hypertension (64 v 11%, p <0.001), dyslipidemia (57 v 16%, p=0.013), and to be older (61.5 v 58 years, p=0.014) and smokers (71.4 v 21.6%, p=0.015). WGA revealed significant enrichment of heterozygous INSR copy loss in T2DM (69%) compared to all other patients (24%; p=0.03) and an enrichment of INSR copy loss for metastatic PDAC relative to resected PDAC in ICGC (35 v 18%, p=0.03). Heterozygous INSR copy loss (n = 17/54) was an independent predictor of worse OS (10.8 v 15.1 months, HR 2.29 (1.20-4.36), p=0.012), and it interacted with diabetes status (p=0.023). Moffitt basal (vs. classical) subtype (n = 17/54, of which 8/17 have INSR copy loss) was also an independent predictor of OS with HR 4.3 (2.1-8.7), p<0.001. Whilst there was no interaction between INSR status and Moffitt subtype on OS (p=0.727), INSR expression is lower in basal subtype, p<0.001. Conclusions: Presence of T2DM in our cohort is an independent predictor of worse OS, consistent with published literature. Alteration in the insulin signalling pathway with heterozygous copy loss of INSR was associated with poorer prognosis, diabetes development and overlapped with Moffitt basal subtype.
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Affiliation(s)
| | | | | | | | | | | | | | - David F. Schaeffer
- Department of Pathology & Laboratory Medicine Vancouver General Hospital, Vancouver, BC, Canada
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34
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Chan-Seng-Yue M, Kim JC, Wilson GW, Ng K, Figueroa EF, O'Kane GM, Connor AA, Denroche RE, Grant RC, McLeod J, Wilson JM, Jang GH, Zhang A, Dodd A, Liang SB, Borgida A, Chadwick D, Kalimuthu S, Lungu I, Bartlett JMS, Krzyzanowski PM, Sandhu V, Tiriac H, Froeling FEM, Karasinska JM, Topham JT, Renouf DJ, Schaeffer DF, Jones SJM, Marra MA, Laskin J, Chetty R, Stein LD, Zogopoulos G, Haibe-Kains B, Campbell PJ, Tuveson DA, Knox JJ, Fischer SE, Gallinger S, Notta F. Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution. Nat Genet 2020; 52:231-240. [PMID: 31932696 DOI: 10.1038/s41588-019-0566-9] [Citation(s) in RCA: 293] [Impact Index Per Article: 73.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 12/04/2019] [Indexed: 02/08/2023]
Abstract
Pancreatic adenocarcinoma presents as a spectrum of a highly aggressive disease in patients. The basis of this disease heterogeneity has proved difficult to resolve due to poor tumor cellularity and extensive genomic instability. To address this, a dataset of whole genomes and transcriptomes was generated from purified epithelium of primary and metastatic tumors. Transcriptome analysis demonstrated that molecular subtypes are a product of a gene expression continuum driven by a mixture of intratumoral subpopulations, which was confirmed by single-cell analysis. Integrated whole-genome analysis uncovered that molecular subtypes are linked to specific copy number aberrations in genes such as mutant KRAS and GATA6. By mapping tumor genetic histories, tetraploidization emerged as a key mutational process behind these events. Taken together, these data support the premise that the constellation of genomic aberrations in the tumor gives rise to the molecular subtype, and that disease heterogeneity is due to ongoing genomic instability during progression.
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Affiliation(s)
- Michelle Chan-Seng-Yue
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jaeseung C Kim
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Genomics Technology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gavin W Wilson
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Karen Ng
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Grainne M O'Kane
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Centre University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Ashton A Connor
- Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Ontario, Canada
| | - Robert E Denroche
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Robert C Grant
- Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Centre University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Jessica McLeod
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Julie M Wilson
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gun Ho Jang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Amy Zhang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Anna Dodd
- Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Centre University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Sheng-Ben Liang
- UHN Program in BioSpecimen Sciences, University Health Network, Toronto, Ontario, Canada
| | - Ayelet Borgida
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Dianne Chadwick
- UHN Program in BioSpecimen Sciences, University Health Network, Toronto, Ontario, Canada
| | - Sangeetha Kalimuthu
- Department of Pathology, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Ilinca Lungu
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - John M S Bartlett
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Paul M Krzyzanowski
- Genomics Technology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Vandana Sandhu
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Hervé Tiriac
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY, USA.,Department of Surgery, University of California San Diego, NCI-designated Comprehensive Cancer Center, La Jolla, CA, USA
| | - Fieke E M Froeling
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY, USA.,Department of Surgery and Cancer, Imperial College London, London, UK
| | | | | | - Daniel J Renouf
- Pancreas Centre BC, Vancouver, British Columbia, Canada.,Department of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Runjan Chetty
- Department of Pathology, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Lincoln D Stein
- Bioinformatics, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - George Zogopoulos
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.,The Goodman Cancer Research Centre of McGill University, Montreal, Quebec, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK.,Department of Haematology, University of Cambridge, Cambridge, UK
| | - David A Tuveson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY, USA
| | - Jennifer J Knox
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Centre University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Sandra E Fischer
- Department of Pathology, University Health Network and University of Toronto, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Steven Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada. .,Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Ontario, Canada. .,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada. .,Department of Surgery, University of Toronto, Toronto, Ontario, Canada.
| | - Faiyaz Notta
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada. .,PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
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Karasinska JM, Topham JT, Kalloger SE, Jang GH, Denroche RE, Culibrk L, Williamson LM, Wong HL, Lee MK, O'Kane GM, Moore RA, Mungall AJ, Moore MJ, Warren C, Metcalfe A, Notta F, Knox JJ, Gallinger S, Laskin J, Marra MA, Jones SJ, Renouf DJ, Schaeffer DF. Abstract A24: Gene expression along the glycolysis-cholesterol synthesis axis and outcome in pancreatic cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.panca19-a24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Reprogramming of metabolic pathways allows cancer cells to survive and thrive in the tumor microenvironment. Glycolysis-inducing factors including oncogenic KRAS mutations, loss of function in TP53 and hypoxia are prevalent in PDAC. Cholesterol and its metabolites support tumor cell growth and the mevalonate pathway, which uses glycolysis products for de novo cholesterol synthesis, has been found to be upregulated in cancer. However, whether intertumoral heterogeneity in these metabolic networks influences outcome in pancreatic cancer has not been well established. We profiled the expression of glycolytic and cholesterogenic genes in 325 resected and metastatic pancreatic ductal adenocarcinoma (PDAC) tumors and identified four distinct subgroups: quiescent, glycolytic, cholesterogenic, and mixed. Glycolytic tumors were associated with the shortest median survival in resectable and metastatic disease settings. Patients with cholesterogenic tumors had the longest median survival. KRAS and MYC amplified tumors had higher expression of glycolytic genes than tumors with normal or lost copies of these oncogenes. The mitochondrial uptake of pyruvate, the end product of glycolysis, facilitates the generation of acetyl-CoA for cholesterol synthesis. PDAC tumors with a glycolytic gene signature had the lowest expression of mitochondrial pyruvate carriers MPC1 and MPC2. Glycolytic and cholesterogenic gene expression correlated with the expression of reported prognostic PDAC subtype classifier genes. Our results indicate that PDAC tumors have unique metabolic profiles that influence disease outcome and provide functional correlate to previously identified subtypes. The findings also raise the possibility of a shift in balance between the glycolytic and cholesterogenic pathways as a factor in PDAC progression and a potential target for therapy.
Citation Format: Joanna M. Karasinska, James T. Topham, Steve E. Kalloger, Gun Ho Jang, Robert E. Denroche, Luka Culibrk, Laura M. Williamson, Hui-li Wong, Michael K.C. Lee, Grainne M. O'Kane, Richard A. Moore, Andrew J. Mungall, Malcolm J. Moore, Cassia Warren, Andrew Metcalfe, Faiyaz Notta, Jennifer J. Knox, Steven Gallinger, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, Daniel J. Renouf, David F. Schaeffer. Gene expression along the glycolysis-cholesterol synthesis axis and outcome in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr A24.
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Affiliation(s)
| | | | | | - Gun Ho Jang
- 2Ontario Institute for Cancer Research, Toronto, ON, Canada,
| | | | - Luka Culibrk
- 3Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada,
| | | | | | | | | | - Richard A. Moore
- 3Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada,
| | - Andrew J. Mungall
- 3Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada,
| | | | | | | | - Faiyaz Notta
- 2Ontario Institute for Cancer Research, Toronto, ON, Canada,
| | | | | | | | - Marco A. Marra
- 3Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada,
| | - Steven J.M. Jones
- 3Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada,
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Topham JT, Titmuss E, Pleasance E, Williamson LM, Karasinska JM, Culibrk L, Lee MK, Kalloger SE, Mendis S, Moore RA, Mungall AJ, Laskin J, Loree JM, Mager DL, Marra MA, Jones SJ, Schaeffer DF, Renouf DJ. Abstract B56: Endogenous retrovirus transcript levels are associated with immunogenic signatures in multiple metastatic cancer types. Cancer Res 2019. [DOI: 10.1158/1538-7445.panca19-b56] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Variability in the immunogenic landscape of metastatic cancer lesions has revealed insight into detection of potential immunotherapy-responsive patients, though underlying mechanisms driving such variation are not fully understood. Endogenous retrovirus (ERV)-containing transcripts have recently emerged as a potential source of tumor-associated antigen that are orthogonal to somatic mutation-derived neoantigens. To characterize the intersection between ERV levels and predicted immunogenicity in metastatic cancer, we comprehensively profiled the transcript abundance of 702,533 ERV loci in 199 metastatic tumors from breast, colorectal, and pancreatic cancer patients. In all three cancer types, overall ERV transcript load was associated with upregulation of genes involved in innate antiviral response pathways as well as genes involved in both adaptive and innate immune signaling. In colorectal and pancreatic tumors, samples with concomitant increases in ERV load and antiviral response gene expression, termed viral mimicry tumors, showed high expression of the DNA demethylation gene TET2, a gene previously described to promote transcription of ERV-containing transcripts. Collectively, these data are compatible with the notion that an increased level of ERV-containing transcripts may account for increased immunogenicity in a subset of metastatic tumors and support the relationship between DNA demethylation and ERV load in colorectal and pancreatic tumors.
Citation Format: James T. Topham, Emma Titmuss, Erin Pleasance, Laura M. Williamson, Joanna M. Karasinska, Luka Culibrk, Michael K.C. Lee, Steve E. Kalloger, Shehara Mendis, Richard A. Moore, Andrew J. Mungall, Janessa Laskin, Jonathan M. Loree, Dixie L. Mager, Marco A. Marra, Steven J.M. Jones, David F. Schaeffer, Daniel J. Renouf. Endogenous retrovirus transcript levels are associated with immunogenic signatures in multiple metastatic cancer types [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr B56.
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Affiliation(s)
| | - Emma Titmuss
- 2Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada,
| | - Erin Pleasance
- 2Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada,
| | | | | | - Luka Culibrk
- 2Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada,
| | | | | | | | - Richard A. Moore
- 2Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada,
| | - Andrew J. Mungall
- 2Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada,
| | | | | | | | - Marco A. Marra
- 2Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada,
| | - Steven J.M. Jones
- 2Canada’s Michael Smith Genome Sciences Centre, Vancouver, BC, Canada,
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Chun HJE, Johann PD, Milne K, Zapatka M, Buellesbach A, Ishaque N, Iskar M, Erkek S, Wei L, Tessier-Cloutier B, Lever J, Titmuss E, Topham JT, Bowlby R, Chuah E, Mungall KL, Ma Y, Mungall AJ, Moore RA, Taylor MD, Gerhard DS, Jones SJM, Korshunov A, Gessler M, Kerl K, Hasselblatt M, Frühwald MC, Perlman EJ, Nelson BH, Pfister SM, Marra MA, Kool M. Identification and Analyses of Extra-Cranial and Cranial Rhabdoid Tumor Molecular Subgroups Reveal Tumors with Cytotoxic T Cell Infiltration. Cell Rep 2019; 29:2338-2354.e7. [PMID: 31708418 PMCID: PMC6905433 DOI: 10.1016/j.celrep.2019.10.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 08/20/2019] [Accepted: 10/02/2019] [Indexed: 11/23/2022] Open
Abstract
Extra-cranial malignant rhabdoid tumors (MRTs) and cranial atypical teratoid RTs (ATRTs) are heterogeneous pediatric cancers driven primarily by SMARCB1 loss. To understand the genome-wide molecular relationships between MRTs and ATRTs, we analyze multi-omics data from 140 MRTs and 161 ATRTs. We detect similarities between the MYC subgroup of ATRTs (ATRT-MYC) and extra-cranial MRTs, including global DNA hypomethylation and overexpression of HOX genes and genes involved in mesenchymal development, distinguishing them from other ATRT subgroups that express neural-like features. We identify five DNA methylation subgroups associated with anatomical sites and SMARCB1 mutation patterns. Groups 1, 3, and 4 exhibit cytotoxic T cell infiltration and expression of immune checkpoint regulators, consistent with a potential role for immunotherapy in rhabdoid tumor patients. Chun et al. report similarities between the MYC subgroup of cranial and extracranial rhabdoid tumors (RTs) at genetic, gene-expression, and epigenetic levels. They identify five DNA methylation subgroups of RTs across multiple organ sites, and some subgroups exhibit increased levels of immune cell infiltration and immune checkpoint expression.
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Affiliation(s)
- Hye-Jung E Chun
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Pascal D Johann
- Hopp Children's Cancer Center, Heidelberg 69120, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg 69120, Germany; Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | - Katy Milne
- Deeley Research Centre, BC Cancer, Victoria, BC V8R 6V5, Canada
| | - Marc Zapatka
- Department of Molecular Genetics, DKFZ, Heidelberg 69120, Germany
| | - Annette Buellesbach
- Hopp Children's Cancer Center, Heidelberg 69120, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg 69120, Germany; Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | - Naveed Ishaque
- Center for Digital Health, Berlin Institute of Health and Charité-Universitätsmedizin Berlin, Berlin 10117, Germany; Heidelberg Center for Personalized Oncology, DKFZ, Heidelberg 69120, Germany
| | - Murat Iskar
- Department of Molecular Genetics, DKFZ, Heidelberg 69120, Germany
| | - Serap Erkek
- Hopp Children's Cancer Center, Heidelberg 69120, Germany
| | - Lisa Wei
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Jake Lever
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - James T Topham
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Michael D Taylor
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | | | - Manfred Gessler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry; and Comprehensive Cancer Center Mainfranken, University of Wuerzburg, Wuerzburg 97074, Germany
| | - Kornelius Kerl
- Department of Pediatric Hematology and Oncology, University Children's Hospital Muenster, Muenster 48149, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Muenster, Muenster 48149, Germany
| | - Michael C Frühwald
- University Children's Hospital Augsburg, Swabian Children's Cancer Center, Augsburg 86156, Germany
| | - Elizabeth J Perlman
- Department of Pathology and Laboratory Medicine, Lurie Children's Hospital, Northwestern University's Feinberg School of Medicine and Robert H. Lurie Cancer Center, Chicago, IL 60611, USA
| | - Brad H Nelson
- Deeley Research Centre, BC Cancer, Victoria, BC V8R 6V5, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada; Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 3E6, Canada
| | - Stefan M Pfister
- Hopp Children's Cancer Center, Heidelberg 69120, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg 69120, Germany; Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada.
| | - Marcel Kool
- Hopp Children's Cancer Center, Heidelberg 69120, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg 69120, Germany.
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Karasinska JM, Topham JT, Kalloger SE, Jang GH, Denroche RE, Culibrk L, Williamson LM, Wong HL, Lee MKC, O'Kane GM, Moore RA, Mungall AJ, Moore MJ, Warren C, Metcalfe A, Notta F, Knox JJ, Gallinger S, Laskin J, Marra MA, Jones SJM, Renouf DJ, Schaeffer DF. Altered Gene Expression along the Glycolysis-Cholesterol Synthesis Axis Is Associated with Outcome in Pancreatic Cancer. Clin Cancer Res 2019; 26:135-146. [PMID: 31481506 DOI: 10.1158/1078-0432.ccr-19-1543] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/11/2019] [Accepted: 08/28/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Identification of clinically actionable molecular subtypes of pancreatic ductal adenocarcinoma (PDAC) is key to improving patient outcome. Intertumoral metabolic heterogeneity contributes to cancer survival and the balance between distinct metabolic pathways may influence PDAC outcome. We hypothesized that PDAC can be stratified into prognostic metabolic subgroups based on alterations in the expression of genes involved in glycolysis and cholesterol synthesis. EXPERIMENTAL DESIGN We performed bioinformatics analysis of genomic, transcriptomic, and clinical data in an integrated cohort of 325 resectable and nonresectable PDAC. The resectable datasets included retrospective The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) cohorts. The nonresectable PDAC cohort studies included prospective COMPASS, PanGen, and BC Cancer Personalized OncoGenomics program (POG). RESULTS On the basis of the median normalized expression of glycolytic and cholesterogenic genes, four subgroups were identified: quiescent, glycolytic, cholesterogenic, and mixed. Glycolytic tumors were associated with the shortest median survival in resectable (log-rank test P = 0.018) and metastatic settings (log-rank test P = 0.027). Patients with cholesterogenic tumors had the longest median survival. KRAS and MYC-amplified tumors had higher expression of glycolytic genes than tumors with normal or lost copies of the oncogenes (Wilcoxon rank sum test P = 0.015). Glycolytic tumors had the lowest expression of mitochondrial pyruvate carriers MPC1 and MPC2. Glycolytic and cholesterogenic gene expression correlated with the expression of prognostic PDAC subtype classifier genes. CONCLUSIONS Metabolic classification specific to glycolytic and cholesterogenic pathways provides novel biological insight into previously established PDAC subtypes and may help develop personalized therapies targeting unique tumor metabolic profiles.See related commentary by Mehla and Singh, p. 6.
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Affiliation(s)
| | | | - Steve E Kalloger
- Pancreas Centre BC, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gun Ho Jang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Luka Culibrk
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Hui-Li Wong
- Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Michael K C Lee
- Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Grainne M O'Kane
- University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Malcolm J Moore
- Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Cassia Warren
- Pancreas Centre BC, Vancouver, British Columbia, Canada
| | | | - Faiyaz Notta
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jennifer J Knox
- University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Janessa Laskin
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.,Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel J Renouf
- Pancreas Centre BC, Vancouver, British Columbia, Canada.,Division of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada.,Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver, British Columbia, Canada. .,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Division of Anatomic Pathology, Vancouver General Hospital, Vancouver, British Columbia, Canada
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McDonald PC, Chafe SC, Brown WS, Saberi S, Swayampakula M, Venkateswaran G, Nemirovsky O, Gillespie JA, Karasinska JM, Kalloger SE, Supuran CT, Schaeffer DF, Bashashati A, Shah SP, Topham JT, Yapp DT, Li J, Renouf DJ, Stanger BZ, Dedhar S. Regulation of pH by Carbonic Anhydrase 9 Mediates Survival of Pancreatic Cancer Cells With Activated KRAS in Response to Hypoxia. Gastroenterology 2019; 157:823-837. [PMID: 31078621 DOI: 10.1053/j.gastro.2019.05.004] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 05/05/2019] [Accepted: 05/06/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND & AIMS Most pancreatic ductal adenocarcinomas (PDACs) express an activated form of KRAS, become hypoxic and dysplastic, and are refractory to chemo and radiation therapies. To survive in the hypoxic environment, PDAC cells upregulate enzymes and transporters involved in pH regulation, including the extracellular facing carbonic anhydrase 9 (CA9). We evaluated the effect of blocking CA9, in combination with administration of gemcitabine, in mouse models of pancreatic cancer. METHODS We knocked down expression of KRAS in human (PK-8 and PK-1) PDAC cells with small hairpin RNAs. Human and mouse (KrasG12D/Pdx1-Cre/Tp53/RosaYFP) PDAC cells were incubated with inhibitors of MEK (trametinib) or extracellular signal-regulated kinase (ERK), and some cells were cultured under hypoxic conditions. We measured levels and stability of the hypoxia-inducible factor 1 subunit alpha (HIF1A), endothelial PAS domain 1 protein (EPAS1, also called HIF2A), CA9, solute carrier family 16 member 4 (SLC16A4, also called MCT4), and SLC2A1 (also called GLUT1) by immunoblot analyses. We analyzed intracellular pH (pHi) and extracellular metabolic flux. We knocked down expression of CA9 in PDAC cells, or inhibited CA9 with SLC-0111, incubated them with gemcitabine, and assessed pHi, metabolic flux, and cytotoxicity under normoxic and hypoxic conditions. Cells were also injected into either immune-compromised or immune-competent mice and growth of xenograft tumors was assessed. Tumor fragments derived from patients with PDAC were surgically ligated to the pancreas of mice and the growth of tumors was assessed. We performed tissue microarray analyses of 205 human PDAC samples to measure levels of CA9 and associated expression of genes that regulate hypoxia with outcomes of patients using the Cancer Genome Atlas database. RESULTS Under hypoxic conditions, PDAC cells had increased levels of HIF1A and HIF2A, upregulated expression of CA9, and activated glycolysis. Knockdown of KRAS in PDAC cells, or incubation with trametinib, reduced the posttranscriptional stabilization of HIF1A and HIF2A, upregulation of CA9, pHi, and glycolysis in response to hypoxia. CA9 was expressed by 66% of PDAC samples analyzed; high expression of genes associated with metabolic adaptation to hypoxia, including CA9, correlated with significantly reduced survival times of patients. Knockdown or pharmacologic inhibition of CA9 in PDAC cells significantly reduced pHi in cells under hypoxic conditions, decreased gemcitabine-induced glycolysis, and increased their sensitivity to gemcitabine. PDAC cells with knockdown of CA9 formed smaller xenograft tumors in mice, and injection of gemcitabine inhibited tumor growth and significantly increased survival times of mice. In mice with xenograft tumors grown from human PDAC cells, oral administration of SLC-0111 and injection of gemcitabine increased intratumor acidosis and increased cell death. These tumors, and tumors grown from PDAC patient-derived tumor fragments, grew more slowly than xenograft tumors in mice given control agents, resulting in longer survival times. In KrasG12D/Pdx1-Cre/Tp53/RosaYFP genetically modified mice, oral administration of SLC-0111 and injection of gemcitabine reduced numbers of B cells in tumors. CONCLUSIONS In response to hypoxia, PDAC cells that express activated KRAS increase expression of CA9, via stabilization of HIF1A and HIF2A, to regulate pH and glycolysis. Disruption of this pathway slows growth of PDAC xenograft tumors in mice and might be developed for treatment of pancreatic cancer.
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Affiliation(s)
- Paul C McDonald
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Shawn C Chafe
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Wells S Brown
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Saeed Saberi
- Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Mridula Swayampakula
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Geetha Venkateswaran
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Oksana Nemirovsky
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Jordan A Gillespie
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Joanna M Karasinska
- Pancreas Centre BC, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Steve E Kalloger
- Pancreas Centre BC, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Claudiu T Supuran
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Sesto Fiorentino, Florence, Italy
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver General Hospital, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ali Bashashati
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sohrab P Shah
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - James T Topham
- Pancreas Centre BC, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Donald T Yapp
- Department of Experimental Therapeutics, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Jinyang Li
- Gastroenterology Division, Department of Medicine and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Daniel J Renouf
- Medical Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Ben Z Stanger
- Gastroenterology Division, Department of Medicine and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Shoukat Dedhar
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
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Jones MR, Williamson LM, Topham JT, Lee MKC, Goytain A, Ho J, Denroche RE, Jang G, Pleasance E, Shen Y, Karasinska JM, McGhie JP, Gill S, Lim HJ, Moore MJ, Wong HL, Ng T, Yip S, Zhang W, Sadeghi S, Reisle C, Mungall AJ, Mungall KL, Moore RA, Ma Y, Knox JJ, Gallinger S, Laskin J, Marra MA, Schaeffer DF, Jones SJM, Renouf DJ. NRG1 Gene Fusions Are Recurrent, Clinically Actionable Gene Rearrangements in KRAS Wild-Type Pancreatic Ductal Adenocarcinoma. Clin Cancer Res 2019; 25:4674-4681. [PMID: 31068372 DOI: 10.1158/1078-0432.ccr-19-0191] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/07/2019] [Accepted: 04/15/2019] [Indexed: 01/28/2023]
Abstract
PURPOSE Gene fusions involving neuregulin 1 (NRG1) have been noted in multiple cancer types and have potential therapeutic implications. Although varying results have been reported in other cancer types, the efficacy of the HER-family kinase inhibitor afatinib in the treatment of NRG1 fusion-positive pancreatic ductal adenocarcinoma is not fully understood. EXPERIMENTAL DESIGN Forty-seven patients with pancreatic ductal adenocarcinoma received comprehensive whole-genome and transcriptome sequencing and analysis. Two patients with gene fusions involving NRG1 received afatinib treatment, with response measured by pretreatment and posttreatment PET/CT imaging. RESULTS Three of 47 (6%) patients with advanced pancreatic ductal adenocarcinoma were identified as KRAS wild type by whole-genome sequencing. All KRAS wild-type tumors were positive for gene fusions involving the ERBB3 ligand NRG1. Two of 3 patients with NRG1 fusion-positive tumors were treated with afatinib and demonstrated a significant and rapid response while on therapy. CONCLUSIONS This work adds to a growing body of evidence that NRG1 gene fusions are recurrent, therapeutically actionable genomic events in pancreatic cancers. Based on the clinical outcomes described here, patients with KRAS wild-type tumors harboring NRG1 gene fusions may benefit from treatment with afatinib.See related commentary by Aguirre, p. 4589.
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Affiliation(s)
- Martin R Jones
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Laura M Williamson
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | | | - Michael K C Lee
- BC Cancer, Division of Medical Oncology, Vancouver, British Columbia, Canada
| | - Angela Goytain
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Julie Ho
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Robert E Denroche
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - GunHo Jang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Erin Pleasance
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Yaoquing Shen
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | | | - John P McGhie
- BC Cancer, Division of Medical Oncology, Vancouver, British Columbia, Canada
| | - Sharlene Gill
- BC Cancer, Division of Medical Oncology, Vancouver, British Columbia, Canada
| | - Howard J Lim
- BC Cancer, Division of Medical Oncology, Vancouver, British Columbia, Canada
| | - Malcolm J Moore
- Division of Medical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Hui-Li Wong
- BC Cancer, Division of Medical Oncology, Vancouver, British Columbia, Canada
| | - Tony Ng
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Wei Zhang
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Sara Sadeghi
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Carolyn Reisle
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Karen L Mungall
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Richard A Moore
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Yussanne Ma
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Jennifer J Knox
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Division of Medical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Steven Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Janessa Laskin
- BC Cancer, Division of Medical Oncology, Vancouver, British Columbia, Canada
| | - Marco A Marra
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - David F Schaeffer
- Pancreas Centre British Columbia, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, British Columbia, Canada
| | - Daniel J Renouf
- Pancreas Centre British Columbia, Vancouver, Canada.
- BC Cancer, Division of Medical Oncology, Vancouver, British Columbia, Canada
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41
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Abstract
In a Perspective, James Topham and Marco Marra discuss progress in the use of genomic information to guide cancer treatment.
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Affiliation(s)
- James T. Topham
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Marco A. Marra
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- * E-mail:
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