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Kumar-Sinha C, Vats P, Tran N, Robinson DR, Gunchick V, Wu YM, Cao X, Ning Y, Wang R, Rabban E, Bell J, Shankar S, Mannan R, Zhang Y, Zalupski MM, Chinnaiyan AM, Sahai V. Genomics driven precision oncology in advanced biliary tract cancer improves survival. Neoplasia 2023; 42:100910. [PMID: 37267699 PMCID: PMC10245336 DOI: 10.1016/j.neo.2023.100910] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 06/04/2023]
Abstract
BACKGROUND Biliary tract cancers (BTCs) including intrahepatic, perihilar, and distal cholangiocarcinoma as well as gallbladder cancer, are rare but aggressive malignancies with few effective standard of care therapies. METHODS We implemented integrative clinical sequencing of advanced BTC tumors from 124 consecutive patients who progressed on standard therapies (N=92 with MI-ONCOSEQ and N=32 with commercial gene panels) enrolled between 2011-2020. RESULTS Genomic profiling of paired tumor and normal DNA and tumor transcriptome (RNA) sequencing identified actionable somatic and germline genomic alterations in 54 patients (43.5%), and potentially actionable alterations in 79 (63.7%) of the cohort. Of these, patients who received matched targeted therapy (22; 40.7%) had a median overall survival of 28.1 months compared to 13.3 months in those who did not receive matched targeted therapy (32; P < 0.01), or 13.9 months in those without actionable mutations (70; P < 0.01). Additionally, we discovered recurrent activating mutations in FGFR2, and a novel association between KRAS and BRAF mutant tumors with high expression of immune modulatory protein NT5E (CD73) that may represent novel therapeutic avenues. CONCLUSIONS Overall, the identification of actionable/ potentially actionable aberrations in a large proportion of cases, and improvement in survival with precision oncology supports molecular analysis and clinical sequencing for all patients with advanced BTC.
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Affiliation(s)
- Chandan Kumar-Sinha
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pankaj Vats
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nguyen Tran
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dan R Robinson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Valerie Gunchick
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yi-Mi Wu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yu Ning
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rui Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Erica Rabban
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Janice Bell
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sunita Shankar
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rahul Mannan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yuping Zhang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mark M Zalupski
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Vaibhav Sahai
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
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Cobain EF, Wu YM, Vats P, Chugh R, Worden F, Smith DC, Schuetze SM, Zalupski MM, Sahai V, Alva A, Schott AF, Caram MEV, Hayes DF, Stoffel EM, Jacobs MF, Kumar-Sinha C, Cao X, Wang R, Lucas D, Ning Y, Rabban E, Bell J, Camelo-Piragua S, Udager AM, Cieslik M, Lonigro RJ, Kunju LP, Robinson DR, Talpaz M, Chinnaiyan AM. Assessment of Clinical Benefit of Integrative Genomic Profiling in Advanced Solid Tumors. JAMA Oncol 2021; 7:525-533. [PMID: 33630025 PMCID: PMC7907987 DOI: 10.1001/jamaoncol.2020.7987] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Question What is the clinical utility of genomic profiling for patients with advanced solid tumors? Findings In this cohort study of 1015 patients who underwent integrative genomic profiling, a high rate of pathogenic germline variants and a subset of patients who derive substantial clinical benefit from sequencing information were identified. Meaning These findings support (1) directed germline testing for inherited cancer predisposition in all patients with advanced cancer and (2) use of integrative genomic profiling as a component of standard of care for patients with cancer of unknown origin and other rare malignant neoplasms. Importance Use of next-generation sequencing (NGS) to identify clinically actionable genomic targets has been incorporated into routine clinical practice in the management of advanced solid tumors; however, the clinical utility of this testing remains uncertain. Objective To determine which patients derived the greatest degree of clinical benefit from NGS profiling. Design, Setting, and Participants Patients in this cohort study underwent fresh tumor biopsy and blood sample collection for genomic profiling of paired tumor and normal DNA (whole-exome or targeted-exome capture with analysis of 1700 genes) and tumor transcriptome (RNA) sequencing. Somatic and germline genomic alterations were annotated and classified according to degree of clinical actionability. Results were returned to treating oncologists. Data were collected from May 1, 2011, to February 28, 2018, and analyzed from May 1, 2011, to April 30, 2020. Main Outcomes and Measures Patients’ subsequent therapy and treatment response were extracted from the medical record to determine clinical benefit rate from NGS-directed therapy at 6 months and exceptional responses lasting 12 months or longer. Results During the study period, NGS was attempted on tumors from 1138 patients and was successful in 1015 (89.2%) (MET1000 cohort) (538 men [53.0%]; mean [SD] age, 57.7 [13.3] years). Potentially clinically actionable genomic alterations were discovered in 817 patients (80.5%). Of these, 132 patients (16.2%) received sequencing-directed therapy, and 49 had clinical benefit (37.1%). Exceptional responses were observed in 26 patients (19.7% of treated patients). Pathogenic germline variants (PGVs) were identified in 160 patients (15.8% of cohort), including 49 PGVs (4.8% of cohort) with therapeutic relevance. For 55 patients with carcinoma of unknown primary origin, NGS identified the primary site in 28 (50.9%), and sequencing-directed therapy in 13 patients resulted in clinical benefit in 7 instances (53.8%), including 5 exceptional responses. Conclusions and Relevance The high rate of therapeutically relevant PGVs identified across diverse cancer types supports a recommendation for directed germline testing in all patients with advanced cancer. The high frequency of therapeutically relevant somatic and germline findings in patients with carcinoma of unknown primary origin and other rare cancers supports the use of comprehensive NGS profiling as a component of standard of care for these disease entities.
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Affiliation(s)
- Erin F Cobain
- Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Yi-Mi Wu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor.,Department of Pathology, University of Michigan, Ann Arbor
| | - Pankaj Vats
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor
| | - Rashmi Chugh
- Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Francis Worden
- Department of Internal Medicine, University of Michigan, Ann Arbor
| | - David C Smith
- Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Scott M Schuetze
- Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Mark M Zalupski
- Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Vaibhav Sahai
- Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Ajjai Alva
- Department of Internal Medicine, University of Michigan, Ann Arbor.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor
| | - Anne F Schott
- Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Megan E V Caram
- Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Daniel F Hayes
- Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Elena M Stoffel
- Department of Internal Medicine, University of Michigan, Ann Arbor
| | | | - Chandan Kumar-Sinha
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor.,Department of Pathology, University of Michigan, Ann Arbor
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor
| | - Rui Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor
| | - David Lucas
- Department of Pathology, University of Michigan, Ann Arbor
| | - Yu Ning
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor
| | - Erica Rabban
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor
| | - Janice Bell
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor
| | | | - Aaron M Udager
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor.,Department of Pathology, University of Michigan, Ann Arbor
| | - Marcin Cieslik
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor.,Department of Pathology, University of Michigan, Ann Arbor
| | - Robert J Lonigro
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor
| | - Lakshmi P Kunju
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor.,Department of Pathology, University of Michigan, Ann Arbor
| | - Dan R Robinson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor.,Department of Pathology, University of Michigan, Ann Arbor
| | - Moshe Talpaz
- Department of Internal Medicine, University of Michigan, Ann Arbor.,Rogel Cancer Center, University of Michigan, Ann Arbor
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor.,Department of Pathology, University of Michigan, Ann Arbor.,Rogel Cancer Center, University of Michigan, Ann Arbor.,Department of Urology, University of Michigan, Ann Arbor.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor
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3
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Hertz DL, Glatz A, Pasternak AL, Lonigro RJ, Vats P, Wu YM, Anderson B, Rabban E, Mora E, Frank K, Robinson DR, Mody RJ, Chinnaiyan A. Integration of Germline Pharmacogenetics Into a Tumor Sequencing Program. JCO Precis Oncol 2018; 2:PO.18.00011. [PMID: 32832831 PMCID: PMC7434089 DOI: 10.1200/po.18.00011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Evidence-based guidelines inform treatment decisions for patients for whom germline genetic information is available. Our real-time tumor sequencing program, which makes precision treatment decisions for patients with cancer, produces matched germline information, providing a unique opportunity to efficiently implement pharmacogenetics and benefit patients. METHODS The germline genetic database from the Michigan Oncology Sequencing (MI-Oncoseq) program was searched for 21 clinically actionable polymorphisms in five cancer-relevant genes: TPMT, DPYD, CYP2C19, CYP3A5, and UGT1A1. Residual germ line DNA was sent to an external Clinical Laboratory Improvement Amendments-approved laboratory for confirmatory genotyping. The medical records of MI-Oncoseq patients with actionable phenotypes were searched for receipt of relevant drugs and to determine whether having genetic information at the time of treatment would have led to a treatment recommendation. RESULTS All nine variants in TPMT, DPYD, and CYP2C19 that were detected in MI-Oncoseq were confirmed by external genotyping. Genotype determinations could not be made for CYP3A5*3, UGT1A1*28, or UGT1A1*80. On the basis of retrospective assessment of 115 adult and pediatric patient records, 4.3% (n = 5) had a potentially clinically actionable phenotype for TPMT, DPYD, or CYP2C19 and received a relevant medication. After accounting for differences in adult and pediatric recommendations, three of these patients could have received a treatment recommendation at the time of prescribing. CONCLUSION Germline genotype determinations for TPMT, DPYD, and CYP2C19 can be used to make evidence-based treatment recommendations in MI-Oncoseq patients. Although the proportion of patients for whom recommendations can be made is small, this added value to MI-Oncoseq and patient care comes at no additional genotyping cost. Pharmacogenetic assessment should be integrated into tumor sequencing programs that genotype matched germline DNA; however, the complexity and additional cost of implementing pharmacogenetics remain challenging.
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Affiliation(s)
- Daniel L. Hertz
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Andrew Glatz
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Amy L. Pasternak
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Robert J. Lonigro
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Pankaj Vats
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Yi-Mi Wu
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Bailey Anderson
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Erica Rabban
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Erika Mora
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Kevin Frank
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Dan R. Robinson
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Rajen J. Mody
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
| | - Arul Chinnaiyan
- Daniel L. Hertz, Andrew Glatz, Amy L. Pasternak, and Erika Mora, University of Michigan College of Pharmacy; Robert J. Lonigro, Pankaj Vats, Yi-Mi Wu, Bailey Anderson, Erica Rabban, Kevin Frank, Dan R. Robinson, Rajen J. Mody, and Arul Chinnaiyan, Michigan Medicine, Ann Arbor, MI
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4
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Connelly JA, Mody RJ, Wu YM, Robinson DR, Lonigro RJ, Vats P, Rabban E, Anderson B, Walkovich K. Identification of novel MECOM gene fusion and personalized therapeutic targets through integrative clinical sequencing in secondary acute myeloid leukemia in a patient with severe congenital neutropenia: a case report and literature review. Cold Spring Harb Mol Case Stud 2018; 4:a002204. [PMID: 29572239 PMCID: PMC5880254 DOI: 10.1101/mcs.a002204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 06/30/2017] [Accepted: 01/17/2018] [Indexed: 12/25/2022] Open
Abstract
Severe congenital neutropenia (SCN) is a rare hematologic disorder characterized by defective myelopoiesis and a high incidence of malignant transformation to myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). SCN patients who develop MDS/AML have excessive toxicities to traditional chemotherapy, and safer therapies are needed to improve overall survival in this population. In this report, we outline the use of a prospective integrative clinical sequencing trial (PEDS-MIONCOSEQ) in a patient with SCN and AML to help identify oncogenic targets for less toxic agents. Integrative sequencing identified two somatic cis-mutations in the colony stimulating factor 3 receptor (CSF3R) gene, a p.T640N mutation in the transmembrane region and a p.Q768* truncation mutation in the cytoplasmic domain. A somatic mutation p.H105Y, in the runt homology domain (RHD) of runt-related transcription factor 1 (RUNX1), was also identified. In addition, sequencing discovered a unique in-frame EIF4A2-MECOM (MDS1 and ectopic viral integration site 1 complex) chromosomal translocation with high MECOM expression. His mutations in CSF3R served as potential targets for tyrosine kinase inhibition and therefore provided an avenue to avoid more harmful therapy. This study highlights the utility of integrative clinical sequencing in SCN patients who develop leukemia and outlines a strategy on how to approach these patients in a future clinical sequencing trial to improve historically poor outcomes. A thorough review of leukemia in SCN and the role of CSF3R mutations in oncologic therapy are provided to support a new strategy on how to approach MDS/AML in SCN.
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MESH Headings
- Adolescent
- Alleles
- Biomarkers
- Biopsy
- Bone Marrow/pathology
- Congenital Bone Marrow Failure Syndromes
- Gene Expression Profiling
- Genotype
- Humans
- In Situ Hybridization, Fluorescence
- Karyotype
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/etiology
- Leukemia, Myeloid, Acute/therapy
- MDS1 and EVI1 Complex Locus Protein/genetics
- Male
- Neoplasms, Second Primary/diagnosis
- Neoplasms, Second Primary/etiology
- Neoplasms, Second Primary/therapy
- Neutropenia/complications
- Neutropenia/congenital
- Neutropenia/therapy
- Oncogene Proteins, Fusion/genetics
- Transcriptome
- Exome Sequencing
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Affiliation(s)
- James A Connelly
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee 37232-6310, USA
| | - Rajen J Mody
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
| | - Yi-Mi Wu
- Michigan Center for Translational Pathology, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
| | - Dan R Robinson
- Michigan Center for Translational Pathology, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
| | - Robert J Lonigro
- Michigan Center for Translational Pathology, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
| | - Pankaj Vats
- Michigan Center for Translational Pathology, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
| | - Erica Rabban
- Michigan Center for Translational Pathology, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
| | - Bailey Anderson
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
| | - Kelly Walkovich
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
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5
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Cobain EF, Robinson DR, Wu YM, Lonigro R, Vats P, Rabban E, Kumar-Sinha C, Schott AF, Smerage JB, Morikawa A, Burness ML, Van Poznak CH, Griggs J, Wicha M, Hayes DF, Chinnaiyan AM. Abstract P2-09-26: Frequency and mechanisms of elevated somatic mutation burden in metastatic breast cancer and response to immune checkpoint blockade. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p2-09-26] [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
Background: Immune checkpoint blockade (ICB) is effective in the treatment of various malignancies. Thus far, however, results in breast cancer have been mixed. Elevated tumor mutational load, and subsequent increased likelihood of forming immunogenic neoantigens, has been correlated with response to ICB. Mutational load observed in breast cancers varies widely. However, most studies have assessed mutational load using primary tumors. Few studies have explored the frequency of high mutational load, molecular mechanisms accounting for this phenomenon, and its potential impact on response to ICB in metastatic breast cancer (MBC).
Methods: From 2011-2016, 124 patients (pts) with MBC of varying subtypes underwent research biopsy of their metastatic disease for whole genome, exome and transcriptome sequencing of tumor and matched normal sample through the Michigan Oncology Sequencing Center (Mi-OncoSeq). Those pts with elevated somatic mutation load were defined as having greater than 10 mutations per megabase of targeted sequencing and mutational signatures accounting for high mutation load were noted. Pts treated subsequently with ICB were followed to assess response.
Results: Twelve MBC pts had high mutation load (10% of cohort). Eight pts had estrogen receptor (ER) positive MBC and 4 pts had metastatic triple negative breast cancer (TNBC). In 5 cases, a clear mutational signature accounting for high mutation load was evident. Two TNBC cases harbored an APOBEC mutational signature in addition to 1 TNBC and 2 ER positive tumors displaying a microsatellite instability signature (MSI-H). Among the tumors with MSI-H signature, 1 case was associated with a pathogenic germline alteration in MLH1. Two pts were subsequently treated with ICB on a clinical trial. One pt came off study after 3 months due to progressive brain metastases and another had partial response to therapy lasting 7 months.
Conclusions: Elevated somatic mutation burden in MBC is observed in approximately 10% of pts, and is detected in both ER positive and TNBC. Since high mutation burden has been associated with increased likelihood of response to ICB, identification of this genomic feature could have important therapeutic implications for MBC pts.
Citation Format: Cobain EF, Robinson DR, Wu Y-M, Lonigro R, Vats P, Rabban E, Kumar-Sinha C, Schott AF, Smerage JB, Morikawa A, Burness ML, Van Poznak CH, Griggs J, Wicha M, Hayes DF, Chinnaiyan AM. Frequency and mechanisms of elevated somatic mutation burden in metastatic breast cancer and response to immune checkpoint blockade [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-09-26.
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Affiliation(s)
- EF Cobain
- University of Michigan, Ann Arbor, MI
| | | | - Y-M Wu
- University of Michigan, Ann Arbor, MI
| | - R Lonigro
- University of Michigan, Ann Arbor, MI
| | - P Vats
- University of Michigan, Ann Arbor, MI
| | - E Rabban
- University of Michigan, Ann Arbor, MI
| | | | - AF Schott
- University of Michigan, Ann Arbor, MI
| | | | | | | | | | - J Griggs
- University of Michigan, Ann Arbor, MI
| | - M Wicha
- University of Michigan, Ann Arbor, MI
| | - DF Hayes
- University of Michigan, Ann Arbor, MI
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6
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Cobain EF, Robinson DR, Wu YM, Everett J, Rabban E, Kumar C, Schuetze S, Alva AS, Chugh R, Worden FP, Zalupski M, Tomlins SA, Ramnath N, Schott AF, Stoffel EM, Smith DC, Kunju LP, Hayes DF, Talpaz M, Chinnaiyan AM. Clinical application of comprehensive next generation sequencing in the management of metastatic cancer in adults. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [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
101 Background: Next generation sequencing (NGS) platforms are frequently utilized in the care of patients (pts) with metastatic cancer to identify tumor genomic alterations that may serve as therapeutic targets. Biomarker driven clinical trials, such as NCI-Molecular Analysis for Therapy Choice (MATCH) and Targeted Agent and Profiling Utilization Registry (TAPUR) have augmented clinicians’ ability use this strategy in clinical practice. Methods: From 2011-2015 over 500 adult pts with metastatic solid tumors of diverse lineage underwent biopsy for whole exome and transcriptome sequencing of tumor and matched normal sample through the Michigan Oncology Sequencing Center (Mi-Oncoseq). Genomic alterations identified were reviewed at Precision Medicine Tumor Board and tiered according to their clinical relevance. Alterations were also classified as being identifiable or not identifiable by a commercially available NGS assay such as Oncomine Focus or FoundationOne. Results: Genomic alterations identified by Mi-Oncoseq provided rationale for enrollment in a clinical trial in 72% (n = 360) of cases. The percentage of pts who did receive therapy informed by NGS results increased over time (5% in 2012 versus 11% in 2015). 11% of pts (n = 55) had a pathogenic germline variant (PGV) conferring increased cancer risk identified, none of which were known prior to study entry. Numerous pts had clinically relevant molecular alterations identified by Mi-Oncoseq that would not have been identifiable utilizing targeted NGS assays, including PGVs and activating/deleterious gene fusions. Conclusions: Comprehensive NGS, including DNA and RNA sequencing, readily identifies potentially actionable alterations in the vast majority of pts beyond what is observed with use of targeted NGS platforms. Observed modest increase in utilization of NGS results to direct subsequent therapy over time is due to clinician employment of this strategy earlier in the therapeutic algorithm, increased availability of biomarker driven clinical trials and changes in physician referral patterns. Comprehensive NGS identified many unanticipated PGVs of clinical importance for pts and their families. Clinical trial information: HUM00067928.
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Affiliation(s)
| | | | - Yi-Mi Wu
- Pathology Department, University of Michigan, Ann Arbor, MI
| | | | - Erica Rabban
- University of Michigan Center for Translational Pathology, Ann Arbor, MI
| | | | | | - Ajjai Shivaram Alva
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | | | | | | | | | | | | | | | | | | | - Daniel F. Hayes
- University of Michigan Comprehensive Cancer Center, Ann Arbor, MI
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