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Haberberger JF, Pegram W, Britt N, Schiavone K, Severson E, Sharaf R, Albacker LA, Williams E, Lechpammer M, Hemmerich A, Lin D, Huang RSP, Hiemenz M, Elvin J, Graf R, Lesser G, Kram D, Strowd R, Bi WL, Ramkissoon LA, Cohen MB, Reddy P, Creeden J, Ross JS, Alexander BM, Ramkissoon SH. A Retrospective Genomic Landscape of 661 Young Adult Glioblastomas Diagnosed Using 2016 WHO Guidelines for Central Nervous System Tumors. Oncologist 2024; 29:e47-e58. [PMID: 37619245 PMCID: PMC10769808 DOI: 10.1093/oncolo/oyad224] [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: 08/01/2022] [Accepted: 05/21/2023] [Indexed: 08/26/2023] Open
Abstract
The authors present a cohort of 661 young adult glioblastomas diagnosed using 2016 WHO World Health Organization Classification of Tumors of the Central Nervous System, utilizing comprehensive genomic profiling (CGP) to explore their genomic landscape and assess their relationship to currently defined disease entities. This analysis explored variants with evidence of pathogenic function, common copy number variants (CNVs), and several novel fusion events not described in literature. Tumor mutational burden (TMB) mutational signatures, anatomic location, and tumor recurrence are further explored. Using data collected from CGP, unsupervised machine-learning techniques were leveraged to identify 10 genomic classes in previously assigned young adult glioblastomas. The authors relate these molecular classes to current World Health Organization guidelines and reference current literature to give therapeutic and prognostic descriptions where possible.
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Affiliation(s)
| | - Worthy Pegram
- Pathology Department, Foundation Medicine, Morrisville, NC, USA
| | - Nicholas Britt
- Pathology Department, Foundation Medicine, Morrisville, NC, USA
| | | | - Eric Severson
- Pathology Department, Foundation Medicine, Morrisville, NC, USA
| | - Radwa Sharaf
- Pathology Department, Foundation Medicine, Cambridge, MA, USA
| | - Lee A Albacker
- Pathology Department, Foundation Medicine, Cambridge, MA, USA
| | - Erik Williams
- Pathology Department, Foundation Medicine, Cambridge, MA, USA
| | | | | | - Douglas Lin
- Pathology Department, Foundation Medicine, Morrisville, NC, USA
| | | | - Matthew Hiemenz
- Pathology Department, Foundation Medicine, Cambridge, MA, USA
| | - Julia Elvin
- Pathology Department, Foundation Medicine, Cambridge, MA, USA
| | - Ryon Graf
- Pathology Department, Foundation Medicine, Cambridge, MA, USA
| | - Glenn Lesser
- Pathology Department, Section on Hematology-Oncology, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - David Kram
- Pathology Department, Section on Hematology-Oncology, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Roy Strowd
- Pathology Department, Section on Hematology-Oncology, Wake Forest School of Medicine, Winston Salem, NC, USA
| | - Wenya Linda Bi
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA, USA
| | - Lori A Ramkissoon
- Pathology Department, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Michael B Cohen
- Wake Forest Comprehensive Cancer Center and Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Prasanth Reddy
- Pathology Department, Foundation Medicine, Cambridge, MA, USA
| | - James Creeden
- Pathology Department, Foundation Medicine, Cambridge, MA, USA
| | - Jeffrey S Ross
- Pathology Department, Foundation Medicine, Cambridge, MA, USA
- Pathology Department, SUNY Upstate Medical University, Syracuse, NY, USA
| | | | - Shakti H Ramkissoon
- Pathology Department, Foundation Medicine, Morrisville, NC, USA
- Wake Forest Comprehensive Cancer Center and Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC, USA
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2
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Mohammadi A, Etemad B, Zhang X, Li Y, Bedwell GJ, Sharaf R, Kittilson A, Melberg M, Crain CR, Traunbauer AK, Wong C, Fajnzylber J, Worrall DP, Rosenthal A, Jordan H, Jilg N, Kaseke C, Giguel F, Lian X, Deo R, Gillespie E, Chishti R, Abrha S, Adams T, Siagian A, Dorazio D, Anderson PL, Deeks SG, Lederman MM, Yawetz S, Kuritzkes DR, Lichterfeld MD, Sieg S, Tsibris A, Carrington M, Brumme ZL, Castillo-Mancilla JR, Engelman AN, Gaiha GD, Li JZ. Viral and host mediators of non-suppressible HIV-1 viremia. Nat Med 2023; 29:3212-3223. [PMID: 37957382 PMCID: PMC10719098 DOI: 10.1038/s41591-023-02611-1] [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: 03/07/2023] [Accepted: 09/25/2023] [Indexed: 11/15/2023]
Abstract
Non-suppressible HIV-1 viremia (NSV) is defined as persistent low-level viremia on antiretroviral therapy (ART) without evidence of ART non-adherence or significant drug resistance. Unraveling the mechanisms behind NSV would broaden our understanding of HIV-1 persistence. Here we analyzed plasma virus sequences in eight ART-treated individuals with NSV (88% male) and show that they are composed of large clones without evidence of viral evolution over time in those with longitudinal samples. We defined proviruses that match plasma HIV-1 RNA sequences as 'producer proviruses', and those that did not as 'non-producer proviruses'. Non-suppressible viremia arose from expanded clones of producer proviruses that were significantly larger than the genome-intact proviral reservoir of ART-suppressed individuals. Integration sites of producer proviruses were enriched in proximity to the activating H3K36me3 epigenetic mark. CD4+ T cells from participants with NSV demonstrated upregulation of anti-apoptotic genes and downregulation of pro-apoptotic and type I/II interferon-related pathways. Furthermore, participants with NSV showed significantly lower HIV-specific CD8+ T cell responses compared with untreated viremic controllers with similar viral loads. We identified potential critical host and viral mediators of NSV that may represent targets to disrupt HIV-1 persistence.
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Affiliation(s)
- Abbas Mohammadi
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Valley Health System, Las Vegas, NV, USA
| | - Behzad Etemad
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xin Zhang
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Beijing Friendship Hospital Pinggu Campus, Capital Medical University, Beijing, China
| | - Yijia Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- University of Pittsburgh, Pittsburgh, PA, USA
| | - Gregory J Bedwell
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Radwa Sharaf
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Autumn Kittilson
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Meghan Melberg
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Charles R Crain
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Anna K Traunbauer
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Colline Wong
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jesse Fajnzylber
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Alex Rosenthal
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hannah Jordan
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Nikolaus Jilg
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Clarety Kaseke
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Francoise Giguel
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Rinki Deo
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Rida Chishti
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sara Abrha
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Taylor Adams
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Abigail Siagian
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Dominic Dorazio
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Peter L Anderson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, CA, USA
| | - Michael M Lederman
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Sigal Yawetz
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Mathias D Lichterfeld
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Scott Sieg
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Athe Tsibris
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Jose R Castillo-Mancilla
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alan N Engelman
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Gaurav D Gaiha
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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Tang TY, Nichetti F, Kaplan B, Lonardi S, Pietrantonio F, Salvatore L, Vivaldi C, Rimassa L, de Braud F, Rizzato MD, Pavlick D, Chu R, Danner De Armas A, Sharaf R, Sokol E, Rodon Ahnert J, Ross JS, Javle M, Niger M. Comparative Genomic Analysis and Clinical Outcomes of BRAF-mutated Advanced Biliary Tract Cancers. Clin Cancer Res 2023; 29:4853-4862. [PMID: 37773629 DOI: 10.1158/1078-0432.ccr-23-1926] [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: 07/05/2023] [Revised: 09/06/2023] [Accepted: 09/26/2023] [Indexed: 10/01/2023]
Abstract
PURPOSE BRAF mutations are rare in biliary tract cancers (BTC), but are of interest given the recent developments in targeted therapy for BTC. We investigated the clinical outcomes in a cohort of BRAF-mutant advanced BTC treated with first-line chemotherapy. Furthermore, we investigated the genomic landscape of BRAF class I, II, and III mutations in the intrahepatic cholangiocarcinoma (iCCA) subgroup of BTC. EXPERIMENTAL DESIGN We analyzed two nonoverlapping cohorts. We examined the genomic landscape of BRAF-mutated iCCA in a "genomic cohort" [187 class I, 82 class II, 113 class III BRAF mutants and 8,026 wildtype (WT)]. We also analyzed median progression-free survival (PFS) and overall survival (OS) on first-line chemotherapy in a separate multi-institutional "clinical cohort" of patients with BTC (including iCCA and extrahepatic cholangiocarcinoma (eCCA) and gallbladder cancer; 41 class I, 32 class II+III BRAF mutants and 1,042 WT). RESULTS In the entire BTC clinical cohort, the median PFS was shorter for class I [HR, 2.11 (P < 0.001)] and class II+III [HR, 1.72 (P = 0.007)] as compared with BRAF WT. OS was also shorter in class I [HR, 2.04 (P = 0.011)] and class II+III [HR, 1.86 (P = 0.002)] as compared with BRAF WT. In the iCCA subgroup, class I alterations were mutually exclusive with FGFR2, IDH1/2, ERBB2, and KRAS mutations. Class II+III mutations appear to be mutually exclusive with FGFR2 and KRAS. CONCLUSIONS In BTC, all classes of BRAF mutations are associated with a worse prognosis. BRAF mutations occur in 5% of iCCA subgroup and may be mutually exclusive with other targetable mutations.
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Affiliation(s)
- Tin-Yun Tang
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Federico Nichetti
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Computational Oncology, Molecular Diagnostics Program, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ben Kaplan
- Foundation Medicine, Cambridge, Massachusetts
| | - Sara Lonardi
- Department of Oncology, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Filippo Pietrantonio
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Lisa Salvatore
- Oncologia Medica, Comprehensive Cancer Center, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS, Rome, Italy
| | - Caterina Vivaldi
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Lorenza Rimassa
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- Medical Oncology and Hematology Unit, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Filippo de Braud
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Mario Domenico Rizzato
- Department of Oncology, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
| | | | - Randy Chu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anaemy Danner De Armas
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Ethan Sokol
- Foundation Medicine, Cambridge, Massachusetts
| | - Jordi Rodon Ahnert
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeffrey S Ross
- Foundation Medicine, Cambridge, Massachusetts
- Departments of Pathology, Urology and Medicine (Oncology), Upstate Medical University, Syracuse, New York
| | - Milind Javle
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Monica Niger
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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4
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Sharaf R, Jin DX, Grady J, Napier C, Ebot E, Frampton GM, Albacker LA, Thomas DM, Montesion M. A pan-sarcoma landscape of telomeric content shows that alterations in RAD51B and GID4 are associated with higher telomeric content. NPJ Genom Med 2023; 8:26. [PMID: 37709802 PMCID: PMC10502097 DOI: 10.1038/s41525-023-00369-6] [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: 05/17/2023] [Accepted: 08/18/2023] [Indexed: 09/16/2023] Open
Abstract
Tumor cells need to activate a telomere maintenance mechanism, enabling limitless replication. The bulk of evidence supports that sarcomas predominantly use alternative lengthening of telomeres (ALT) mechanism, commonly associated with alterations in ATRX and DAXX. In our dataset, only 12.3% of sarcomas harbored alterations in these genes. Thus, we checked for the presence of other genomic determinants of high telomeric content in sarcomas. Our dataset consisted of 13555 sarcoma samples, sequenced as a part of routine clinical care on the FoundationOne®Heme platform. We observed a median telomeric content of 622.3 telomeric reads per GC-matched million reads (TRPM) across all samples. In agreement with previous studies, telomeric content was significantly higher in ATRX altered and POT1 altered sarcomas. We further observed that sarcomas with alterations in RAD51B or GID4 were enriched in samples with high telomeric content, specifically within uterus leiomyosarcoma for RAD51B and soft tissue sarcoma (not otherwise specified, nos) for GID4, Furthermore, RAD51B and POT1 alterations were mutually exclusive with ATRX and DAXX alterations, suggestive of functional redundancy. Our results propose a role played by RAD51B and GID4 in telomere elongation in sarcomas and open research opportunities for agents aimed at targeting this critical pathway in tumorigenesis.
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Affiliation(s)
| | | | - John Grady
- Omico Australian Genomic Cancer Medicine, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, Australia
| | - Christine Napier
- Omico Australian Genomic Cancer Medicine, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, Australia
| | - Ericka Ebot
- Foundation Medicine Inc., Cambridge, MA, USA
| | | | | | - David M Thomas
- Omico Australian Genomic Cancer Medicine, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, Australia
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5
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Moore JA, Chen KT, Madison R, Newberg JY, Fleischmann Z, Wang S, Sharaf R, Murugesan K, Fendler BJ, Hughes J, Schrock AB, Hegde PS, Oxnard GR, Fabrizio D, Frampton GM, Antonarakis ES, Sokol ES, Jin DX. Pan-Cancer Analysis of Copy-Number Features Identifies Recurrent Signatures and a Homologous Recombination Deficiency Biomarker to Predict Poly (ADP-Ribose) Polymerase Inhibitor Response. JCO Precis Oncol 2023; 7:e2300093. [PMID: 37769224 DOI: 10.1200/po.23.00093] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/21/2023] [Accepted: 07/21/2023] [Indexed: 09/30/2023] Open
Abstract
PURPOSE Copy-number (CN) features reveal the molecular state of cancers and may have predictive and prognostic value in the treatment of cancer. We sought to apply published CN analysis methods to a large pan-cancer data set and characterize ubiquitous CN signatures across tumor types, including potential utility for treatment selection. METHODS We analyzed the landscape of CN features in 260,333 pan-cancer samples. We examined the association of 10 signatures with genomic alterations and clinical characteristics and trained a machine learning classifier using CN and insertion and deletion features to detect homologous recombination deficiency signature (HRDsig) positivity. Clinical outcomes were assessed using a real-world clinicogenomic database (CGDB) of comprehensive genomic profiling linked to deidentified, electronic health record-derived clinical data. RESULTS CN signatures were prevalent across cancer types and associated with diverse processes including focal tandem duplications, seismic amplifications, genome-wide loss of heterozygosity (gLOH), and HRD. Our novel HRDsig outperformed gLOH in predicting BRCAness and effectively distinguished biallelic BRCA and homologous recombination-repair wild-type (HRRwt) samples pan-tumor, demonstrating high sensitivity to detect biallelic BRCA in ovarian (93%) and other HRD-associated cancers (80%-87%). Pan-tumor prevalence of HRDsig was 6.4%. HRRwt cases represented a significant fraction of the HRDsig-positive cohort, likely reflecting a population with nongenomic mechanisms of HRD. In ovarian and prostate CGDBs, HRDsig identified more patients than gLOH and had predictive value for poly (ADP-ribose) polymerase inhibitor (PARPi) benefit. CONCLUSION Tumor CN profiles are informative, revealing diverse processes active in cancer. We describe the landscape of 10 CN signatures in a large pan-cancer cohort, including two associated with HRD. We trained a machine learning-based HRDsig that robustly identified BRCAness and associated with biallelic BRCA pan-tumor, and was predictive of PARPi benefit in real-world ovarian and prostate data sets.
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6
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Sivakumar S, Moore JA, Montesion M, Sharaf R, Lin DI, Colón CI, Fleishmann Z, Ebot EM, Newberg JY, Mills JM, Hegde PS, Pan Q, Dowlati A, Frampton GM, Sage J, Lovly CM. Integrative Analysis of a Large Real-World Cohort of Small Cell Lung Cancer Identifies Distinct Genetic Subtypes and Insights into Histologic Transformation. Cancer Discov 2023; 13:1572-1591. [PMID: 37062002 PMCID: PMC10326603 DOI: 10.1158/2159-8290.cd-22-0620] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 03/08/2023] [Accepted: 04/06/2023] [Indexed: 04/17/2023]
Abstract
Small cell lung cancer (SCLC) is a recalcitrant neuroendocrine carcinoma with dismal survival outcomes. A major barrier in the field has been the relative paucity of human tumors studied. Here we provide an integrated analysis of 3,600 "real-world" SCLC cases. This large cohort allowed us to identify new recurrent alterations and genetic subtypes, including STK11-mutant tumors (1.7%) and TP53/RB1 wild-type tumors (5.5%), as well as rare cases that were human papillomavirus-positive. In our cohort, gene amplifications on 4q12 are associated with increased overall survival, whereas CCNE1 amplification is associated with decreased overall survival. We also identify more frequent alterations in the PTEN pathway in brain metastases. Finally, profiling cases of SCLC containing oncogenic drivers typically associated with NSCLC demonstrates that SCLC transformation may occur across multiple distinct molecular cohorts of NSCLC. These novel and unsuspected genetic features of SCLC may help personalize treatment approaches for this fatal form of cancer. SIGNIFICANCE Minimal changes in therapy and survival outcomes have occurred in SCLC for the past four decades. The identification of new genetic subtypes and novel recurrent mutations as well as an improved understanding of the mechanisms of transformation to SCLC from NSCLC may guide the development of personalized therapies for subsets of patients with SCLC. This article is highlighted in the In This Issue feature, p. 1501.
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Affiliation(s)
| | - Jay A. Moore
- Foundation Medicine, Inc., Cambridge, Massachusetts
| | | | - Radwa Sharaf
- Foundation Medicine, Inc., Cambridge, Massachusetts
| | | | - Caterina I. Colón
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California
| | | | | | | | | | | | - Quintin Pan
- University Hospitals Seidman Cancer Center and Case Western Reserve University, Cleveland, Ohio
| | - Afshin Dowlati
- University Hospitals Seidman Cancer Center and Case Western Reserve University, Cleveland, Ohio
| | | | - Julien Sage
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California
| | - Christine M. Lovly
- Division of Hematology-Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
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7
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Esmaeilzadeh E, Etemad B, Lavine CL, Garneau L, Li Y, Regan J, Wong C, Sharaf R, Connick E, Volberding P, Sagar M, Seaman MS, Li JZ. Autologous neutralizing antibodies increase with early antiretroviral therapy and shape HIV rebound after treatment interruption. Sci Transl Med 2023; 15:eabq4490. [PMID: 37163616 PMCID: PMC10576978 DOI: 10.1126/scitranslmed.abq4490] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 04/10/2023] [Indexed: 05/12/2023]
Abstract
Early initiation of antiretroviral therapy (ART) alters viral rebound kinetics after analytic treatment interruption (ATI) and may play a role in promoting HIV-1 remission. Autologous neutralizing antibodies (aNAbs) represent a key adaptive immune response in people living with HIV-1. We aimed to investigate the role of aNAbs in shaping post-ATI HIV-1 rebound variants. We performed single-genome amplification of HIV-1 env from pre-ART and post-ATI plasma samples of 12 individuals who initiated ART early after infection. aNAb activity was quantified using pseudoviruses derived from the most common plasma variant, and the serum dilution that inhibited 50% of viral infections was determined. aNAb responses matured while participants were on suppressive ART, because on-ART plasma and purified immunoglobulin G (IgG) demonstrated improved neutralizing activity against pre-ART HIV-1 strains when compared with pre-ART plasma or purified IgG. Post-ATI aNAb responses exerted selective pressure on the rebounding viruses, because the post-ATI HIV-1 strains were more resistant to post-ATI plasma neutralization compared with the pre-ART virus. Several pre-ATI features distinguished post-treatment controllers from noncontrollers, including an infecting HIV-1 sequence that was more similar to consensus HIV-1 subtype B, more restricted proviral diversity, and a stronger aNAb response. Post-treatment control was also associated with the evolution of distinct N-glycosylation profiles in the HIV-1 envelope. In summary, aNAb responses appeared to mature after early initiation of ART and applied selective pressure on rebounding viruses. The combination of aNAb activity with select HIV-1 sequence and reservoir features identified individuals with a greater chance of post-treatment control.
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Affiliation(s)
| | - Behzad Etemad
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Lauren Garneau
- Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Yijia Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - James Regan
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Colline Wong
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Radwa Sharaf
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Paul Volberding
- University of California, San Francisco, San Francisco, CA 94158, USA
| | - Manish Sagar
- Boston University Chobanian and Avedesian School of Medicine, Boston, MA 02118, USA
| | | | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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8
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Keller RB, Haberberger J, Janovitz T, Schrock AB, Tukachinsky H, Zhong L, Mata DA, Lopez LV, Fleischmann Z, Sharaf R, Sokol ES, Frampton GM, Patel NR, Lin DI, Oxnard GR, Williams EA, Elvin JA, Decker B. Abstract 305: POLE-specific variant classification strategy is critical for identifying patients who may benefit from immunotherapy. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-305] [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: 04/07/2023]
Abstract
Abstract
BACKGROUND: Pathogenic POLE exonuclease domain mutations (pPOLE) undermine mismatch error correction during DNA replication, causing somatic ultramutation and response to immunotherapy. We examined the pan-cancer landscape of POLE mutations and applied a POLE-specific variant classification model.
METHODS: Comprehensive genomic profiling was performed during clinical care. Mutational signature calling was performed via decomposition using the 96-feature single-base substitution COSMIC reference signatures. A POLE-specific classification model encompassing mutation position in the exonuclease domain, TMB, presence of POLE signature, absence of other signatures, germline frequency, and other features was applied to identify pPOLE mutations causative of ultramutation.
RESULTS: POLE mutation status was evaluated in 458,437 samples (425,520 tissue biopsies (TB) and 32,917 liquid biopsies (LB)). One or more POLE alterations, including pathogenic alterations and variants of unknown significance (VUS), were detected in 3.8% of samples. 19,470 total alterations were identified, 84.8% of which were missense substitutions. Application of the POLE-specific classification model identified 35 unique pathogenic variants, many of which were VUS prior to this study. 749 samples harbored a pPOLE, more than half (56.6%) of which were either p.P286R (n=245) or p.V411L (n=179). pPOLE were found in 1.4% (199/13,688) of endometrial cancers (EC) and 0.5% (270/55,981) of colorectal cancers (CRC) and were rarer in a long tail of other malignancies. The overall pPOLE rate was significantly lower in LB than TB (0.02% vs 0.17%, P<0.001) in the context of different clinical ordering patterns for EC (0.9% of LB cohort vs 3.1% of TB cohort; P<0.001) and CRC (7.5% of LB cohort vs 12.6% of TB cohort; P<0.001). Median TB TMB for pPOLE+ samples was 157.5 mut/mb, compared to 3.5 for the cohort overall (P<0.001). Similarly in LB, median pPOLE+ bTMB was 165.6 vs 2.5 overall (P<0.001). MSI-H or an MMR-associated signature was found in 17.5% of samples with pPOLE, most commonly in neurologic malignancies (75%, 27/36). Median TMB of samples with both pPOLE and MMRD was 2.4-fold higher than those with pPOLE alone (337.6 vs 139.4; P<0.001). Notably, 6.8% of pPOLE+ cases had TMB<10, which was associated median pPOLE VAF of 3.5%, compared with 25.7% among pPOLE samples with TMB≥10 (P<0.001). This pattern suggests that TMB is underestimated when tumor purity is near the limit of detection for the assay.
CONCLUSIONS: pPOLE were seen in both TB and LB across cancer types. The high rate of passenger mutations underscores the utility of this POLE-specific variant classification model. Because TMB can be underestimated when tumor purity is near the limit of detection for the assay, accurate detection and classification of pPOLE is critical for identifying patients who may benefit from immunotherapy.
Citation Format: Rachel B. Keller, James Haberberger, Tyler Janovitz, Alexa B. Schrock, Hanna Tukachinsky, Lei Zhong, Douglas A. Mata, Lyle V. Lopez, Zoe Fleischmann, Radwa Sharaf, Ethan S. Sokol, Garrett M. Frampton, Nimesh R. Patel, Douglas I. Lin, Geoff R. Oxnard, Erik A. Williams, Julia A. Elvin, Brennan Decker. POLE-specific variant classification strategy is critical for identifying patients who may benefit from immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 305.
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Affiliation(s)
| | | | | | | | | | - Lei Zhong
- 1Foundation Medicine, Inc., Cambridge, MA
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Mohammadi A, Etemad B, Zhang X, Li Y, Bedwell GJ, Sharaf R, Kittilson A, Melberg M, Wong C, Fajnzylber J, Worrall DP, Rosenthal A, Jordan H, Jilg N, Kaseke C, Giguel F, Lian X, Deo R, Gillespie E, Chishti R, Abrha S, Adams T, Siagian A, Anderson PL, Deeks SG, Lederman MM, Yawetz S, Kuritzkes DR, Lichterfeld MD, Tsibris A, Carrington M, Brumme ZL, Castillo-Mancilla JR, Engelman AN, Gaiha GD, Li JZ. Viral and Host Mediators of Non-Suppressible HIV-1 Viremia. medRxiv 2023:2023.03.30.23287124. [PMID: 37034605 PMCID: PMC10081408 DOI: 10.1101/2023.03.30.23287124] [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] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Non-suppressible HIV-1 viremia (NSV) can occur in persons with HIV despite adherence to combination antiretroviral therapy (ART) and in the absence of significant drug resistance. Here, we show that plasma NSV sequences are comprised primarily of large clones without evidence of viral evolution over time. We defined proviruses that contribute to plasma viremia as "producer", and those that did not as "non-producer". Compared to ART-suppressed individuals, NSV participants had a significantly larger producer reservoir. Producer proviruses were enriched in chromosome 19 and in proximity to the activating H3K36me3 epigenetic mark. CD4+ cells from NSV participants demonstrated upregulation of anti-apoptotic genes and downregulation of pro-apoptotic and type I/II interferon-related pathways. Furthermore, NSV participants showed no elevation in HIV-specific CD8+ cell responses and producer proviruses were enriched for HLA escape mutations. We identified critical host and viral mediators of NSV that represent potential targets to disrupt HIV persistence and promote viral silencing.
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Affiliation(s)
- Abbas Mohammadi
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Behzad Etemad
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Xin Zhang
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Yijia Li
- University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Radwa Sharaf
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Autumn Kittilson
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Meghan Melberg
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Colline Wong
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Jesse Fajnzylber
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Alex Rosenthal
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Hannah Jordan
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Nikolaus Jilg
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Clarety Kaseke
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Francoise Giguel
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaodong Lian
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Rinki Deo
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Rida Chishti
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sara Abrha
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Taylor Adams
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Abigail Siagian
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Peter L. Anderson
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Steven G. Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, CA, USA
| | - Michael M. Lederman
- Center for AIDS Research, Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Sigal Yawetz
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Mathias D. Lichterfeld
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Athe Tsibris
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, Canada
| | - Jose R. Castillo-Mancilla
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Alan N. Engelman
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Gaurav D. Gaiha
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jonathan Z. Li
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
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Tang TY, Danner De Armas A, Ross JS, Pavlick DC, Sharaf R, Kaplan BG, Sokol E, Rodon Ahnert J, Javle MM. Landscape of BRAF mutation classes in intrahepatic cholangiocarcinoma. J Clin Oncol 2023. [DOI: 10.1200/jco.2023.41.4_suppl.599] [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: 01/25/2023] Open
Abstract
599 Background: Genomic alterations (GA) in BRAF are categorized as Class I, II, or III mutations (muts) and are oncogenic drivers in intrahepatic cholangiocarcinoma (iCCA). Class I muts, such as BRAF V600, directly increase monomeric kinase activity at high levels to drive oncogenic ERK signaling. In comparison, BRAF Class II muts require homodimerization to increase kinase activity to an intermediate level and Class III muts have low kinase activity or are kinase-dead. There is emerging evidence that BRAF mut iCCA as a group are unique from BRAF wildtype (wt) iCCA and furthermore that BRAF Class II and III muts as a group are distinct from BRAF Class I muts. Methods: 8,069 iCCA underwent comprehensive genomic profiling (CGP) using an FDA-approved clinical-grade hybrid capture-based system to determine all classes of GA, MSI status and TMB. PD-L1 expression was measured using the Dako 22C3 TPS system (0% = negative, 1-49% low positive and > 50% = high positive). Genomic ancestry analysis was performed using patient SNPs. Cohorts compared with false discovery rate corrected using Bonferroni adjustment. Results: 7701 (95.4%) of iCCA were BRAF WT and 368 (4.6%) were BRAF mut with 186 (50.5%) Class I, 77 (20.9%) Class II and 105 (28.5%) Class III. BRAF muts (all classes) compared to BRAF wt have higher proportions of East Asians (7.0% v 4.7%, p=.04,) and GA in CDKN2A (45% v 30%, p<.001), CDKN2B (38% v 21%, p<.001), MTAP loss (28% v 15%, p<.001) and PD-L1 low positive (34% v 24%, p=.03); BRAF muts vs BRAF wt have lower proportions of African patients (3.0% v 7.9%, p<.001), GA in BAP1 (10% v 14%, p=.03), ERBB2 (2.4% v 5.0%, p=.03), FGFR2 (1.1% v 12%, p<.001), IDH2 (1.9% v 4.1%, p=.03), KRAS (4.9% v 21%, p<.001), MDM2 (1.4% v 4.4%, p=.002), MYC (2.4% v 4.7%, p=.04), NF1 (0.8%, 2.8%, p=.02), PBRM1 (5.7% v 11%, p<.001), TP53 (25% v 34%, p<.001), and gLOH-high (11% v 20%, p=.002). BRAF Class II+III muts versus BRAF Class I muts have higher mean age (66 v 59, p<.001), GA/tumor (5.1 v 4.2, p=.002), proportion of East Asians (10% v 3.7%, p=.01), GA in ARID1A (32% v 8.6%, p<.001), BAP1 (16% v 4.8%, p<.001), IDH1 (19% v 2.7%, p<.001), IDH2 (3.8% v 0%, p=.007), KRAS (8.2% v 1.6%, p=.003), MDM2 (2.7% v 0%, p=.03), PBRM1 (9.3% v 2.2%, p=.003), SMAD4 (14% v 1.6%, p<.001), TP53 (31% v 19%, p=.009), Mean TMB (3.6 v 2.1, P=.03), and TMB≥10 (6.0% v 1.6%, p=.03); BRAF Class II+III muts versus BRAF class I muts have lower proportion of Europeans (73% v 84%, p=.01), GA in CKN2A (34% v 56%, p<.001), CDKN2B (25% v 49%, p<.001), MTAP loss (20% v 37%, p=.003), and TERT (0.6% v 15%, p<.001). There were no differences across in COSMIC trinucleotide signatures across BRAF mut versus BRAF wt and BRAF II+III versus BRAF I. Conclusions: CGP reveals significant differences in patient characteristics and GA between BRAF mut and BRAF wt iCCA. Additional differences emerge when BRAF II+III are compared to BRAF I. These differences should be accounted for in the clinical trials setting with iCCA BRAF mut patients.
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Affiliation(s)
| | | | | | | | | | | | | | - Jordi Rodon Ahnert
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
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Eluri M, Danner De Armas A, Ross JS, Sharaf R, Pavlick DC, Chatterjee D, Javle MM. Clinical and mutational profiles of microsatellite instability (MSI-H) in intrahepatic cholangiocarcinoma (iCCA). J Clin Oncol 2023. [DOI: 10.1200/jco.2023.41.4_suppl.607] [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: 01/25/2023] Open
Abstract
607 Background: Microsatellite instability (MSI-H) and increased tumor mutation burden (TMB) have been associated with clinical benefit from immunotherapy. A small subset of patients with intrahepatic cholangiocarcinoma (iCCA) have microsatellite instability (MSI-H). Understanding their clinical outcomes and genomic landscape has been limited. These patients may derive clinical benefit from immunotherapy compared to chemotherapy. Methods: 7565 cases of iCCA underwent comprehensive genomic profiling of 324 genes (FoundationOne CDx). Prevalence of genomic alterations in cases with MSI-H were compared with MSI-low and MSS iCCA using Fischer’s exact test with Bonferonni correction. Clinical and pathological data were collected by retrospective chart review for patients with MSI-H/dMMR iCCA. Results: Among 7565 iCCA cases identified, 137 (1.8%) were MSI-H. Compared to MSS/MSI-low cases, MSS-H patients were more likely to be male and have Lynch syndrome. Median TMB was 21.7 (muts/Mb). MSI-H cases were enriched for genomic alterations (GA) in APC (13.9%), TP53 (59.9%), ARID1A (13.9%), and PRBM1 (37.2%). MSI-H cases had lower frequencies of previously identified, actionable iCCA drivers such as FGFR2 fusions (0% v 9%, p=NS), IDH1 (3.7% v 14.5%, p<0.0001) and IDH2 (0% v 4.1%, p=0.007). Compared to MSS/MSI-low, MSI-H cases had higher GA in PIK3CA (16.8% v 6.6%, p=<0.0001), PTEN (10.9% v 2.8%, p=<0.0001), and BRCA2 (10.2% v 2%, p=<0.0001). MSI-H cases had lower GA in CDKN2A (24.1% v 30.9%, p=0.09) and MTAP loss (3.4% v. 15.5%, p<0.0001). Five patients were identified with dMMR/MSI-H iCCA out of 974 patients at a single institution (0.5%). Median age at diagnosis was 53 years (range 46-70) and 83% were male (n=4). Two patients had resectable disease at time of diagnosis. TMB range was 20-29 (muts/Mb). Patients had 4-6 co-mutations on average with the most common GA being TP53, ARID1A and CDKN2A. One patient had Lynch syndrome with germline alteration of MLH1 gene and one patient had a germline BRCA mutation. One patient was noted to have FGFR2 rearrangement. Gemcitabine/Cisplatin was given to 3 of 6 patients as first-line (1L) therapy, with median progression free survival of 4 months. One hundred percent of patients received immunotherapy (IO) as first or second-line (2L) therapies. Patients receiving IO in the 1L had responses ranging from 4 to 9 months. Three patients have ongoing responses. Median overall survival ranged from 12 months to >18 months. Two patients presented with CNS involvement and did not respond to immunotherapy-based regimens. Conclusions: MSI-H represents a small subset of patients with iCCA. High-TMB noted amongst MSI-H iCCA. Currently, MSI testing is not universally performed and may be necessary to identify and best treat these patients. These findings support the development of personalized immunotherapy treatment strategies for this distinct patient population.
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Sharaf R, Jin D, Grady J, Frampton G, Albacker L, Thomas D, Montesion M. 1487MO A pan-sarcoma investigation of genetic alterations associated with high telomeric content. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Sharaf R, Frampton GM, Albacker LA. Mutations in the TERC template sequence can be incorporated into the telomeres of human tumors. PLoS One 2022; 17:e0272707. [PMID: 36006930 PMCID: PMC9409504 DOI: 10.1371/journal.pone.0272707] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/25/2022] [Indexed: 11/29/2022] Open
Abstract
Telomerase-mediated lengthening is a mechanism by which some cancer cells avoid senescence-mediated cell cycle arrest due to shortened telomeres. By reverse transcribing an RNA template, encoded by TERC, the enzyme telomerase synthesizes the elongation of telomeric DNA using the 3’ end of the chromosome as a primer. TERC harbors a highly conserved template region consisting of 11 nucleotides spanning hg19 coordinates chr3:169482793–169482803. In human cell lines, when TERC was mutated to alter its template region, telomerase generated the predicted mutant telomeric repeats. However, it is unknown if this can occur in human clinical samples. Here, we report on the rare occurrence of two tumor samples where TERC template mutations were reflected in telomeric repeats.
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Affiliation(s)
- Radwa Sharaf
- Foundation Medicine Inc., Cambridge, MA, United States of America
| | | | - Lee A. Albacker
- Foundation Medicine Inc., Cambridge, MA, United States of America
- * E-mail:
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Chen KT, Sharaf R, Frampton G, Albacker L, Ebot E. Abstract 1243: Identification of aneuploidy biomarkers associated with response to first-line treatment of metastatic pancreatic cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1243] [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: NCCN guidelines for first-line treatment of patients with metastatic pancreatic cancer includes either FOLFIRINOX or gemcitabine plus paclitaxel; however, these two treatment regimens have not been compared in a randomized clinical trial. In this study, we investigated genomic predictors of treatment response to guide this treatment decision.
Methods: We selected 1,250 patients with metastatic pancreatic cancer who were treated with first-line FOLFIRINOX (FOLF, n = 588) or gemcitabine plus paclitaxel (G+P, n = 662) within the nationwide de-identified Flatiron Health-Foundation Medicine clinico-genomic database (CGDB). The de-identified data originated from approximately 280 US cancer clinics (~800 sites of care). Comprehensive genomic profiling was performed by Foundation Medicine on tumor samples from each patient as part of the standard of care. Gain/loss status as well as loss of heterozygosity (LOH) status of each chromosome arm was assessed using a custom research-use only algorithm that utilizes copy number model calls for each segment and SNP MAF information from sequencing data. Univariable Cox proportional hazards regression was used to identify chromosome arm-level aneuploidies associated with survival in patients treated with first-line FOLF or G+P. In each treatment cohort, a multivariable Cox model was built using the bidirectional stepwise regression procedure to select aneuploidy features associated with survival. A binary risk score was calculated based on the linear predictor of the multivariable Cox model and categorized as high vs low using a median threshold.
Results: Among the FOLF-treated cohort, we identified six aneuploidy features associated with survival (Bonferroni adjusted p < 0.05). FOLF-treated patients with a low FOLF risk score had better survival compared to those with a high FOLF risk score (HR: 0.46, 95%CI: 0.34-0.61, p = <0.001). This association was not observed among G+P-treated patients (HR: 0.86, 95%CI: 0.66-1.11, p = 0.25). Among the G+P treated cohort; eight aneuploidy features were associated with survival (Bonferroni adjusted p < 0.05). G+P-treated patients with a low G+P risk score had better survival compared to patients with a high G+P risk score (HR: 0.43, 95%CI: 0.33-0.57, p = <0.001). This association was not observed among FOLF-treated patients (HR: 0.86, 95%CI: 0.66-1.12, p = 0.25). These findings remained after adjusting for clinical features including surgery and ECOG performance status (HRG+P: 0.52, p = <0.001; HRFOLF: 0.5, p = <0.001).
Conclusions: In metastatic pancreatic cancer, we found different chromosome arm-level aneuploidies were associated with survival for FOLF and G+P regimens which suggests an aneuploidy-based risk score may have utility in choosing first-line treatment.
Citation Format: Kuei-Ting Chen, Radwa Sharaf, Garrett Frampton, Lee Albacker, Ericka Ebot. Identification of aneuploidy biomarkers associated with response to first-line treatment of metastatic pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1243.
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Feng Z, Pignon JC, Sharaf R, Romanov N, Doudement J, Albacker LA, Kurata N, Smith NR, Matsushita N, Scheuenpflug J. Abstract 5737: Precision oncology driven real world clinical genomics data mining of MET alterations, TMB, and PDL-1 to empower indication agnostic patient enrollment and combination strategies. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-5737] [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: Following MET inhibitor and checkpoint inhibitor approvals, it is essential to identify cancer indications that harbor molecular alterations of interest and a thorough real-world molecular genomics based characterization of those tumors would allow to expand cancer specific indications that might benefit from MET and checkpoint inhibitors and shed light on exploring clinically efficacious combo strategies. Importantly, such an approach provides the end-to-end solutions that shall significantly contribute to clinical translation and/or back translation strategies for innovative cancer therapies.
Methods: We systemically interrogated FoundationInsights®, a dataset of real-world molecular genomic tumor profiling from North American patients, and investigated the prevalence of MET amplifications, METex14 skipping and MET fusions prevalence in 62110 unique patient samples across five indications (lung adenocarcinoma [LUAD], esophageal/gastroesophageal-junction/stomach adenocarcinoma [Eso/GEJ/Sto], papillary renal cell carcinoma, hepatocellular carcinoma [HCC] and glioblastoma). MET alteration prevalence was further categorized based on tumor cell PD-L1 IHC status (22C3 pharmDx) and TMB status. Additionally, comprehensive text mining from clinicaltrials.gov and landscape overview were conducted.
Results: MET amplification was the most frequent MET alteration examined with a prevalence ranging from 1.4% in HCC to 4.8% in Eso/GEJ/Sto. In HCC and LUAD, MET amplification prevalence was higher in tumors with high TMB (≥10 mutations/megabase, P<0.05). In Eso/GEJ/Sto and LUAD, MET amplification occurrence was higher in PD-L1-high tumor vs. PD-L1-low or PD-L1-neg tumors (P<0.05). METex14 skipping mutations were observed in LUAD (2.3%), rarely in the other five tumor types analyzed (≤0.1%). Lastly in LUAD, METex14 skipping mutations were more frequent in PD-L1 high tumors but not those with high TMB (P<0.05). Text mining results indicate that- while most trials use MET amplification for patient stratification- there is a distinct tendency for MET inhibitor trials to increasingly include METex14 skipping as a major selection criterion as well.
Conclusions: Real world genomics corroborated MET amplification as a predominant MET alteration across various indication. The potential clinical benefit to combine MET inhibitors with PD-1/PD-L1 blockades in specific indications and specific subsets of patients is further recognized. Collectively, the comprehensive molecular profiling & text mining approaches will continue to guide application of precision medicine in clinical trial design based on appropriate biomarker selection.
Citation Format: Zheng Feng, Jean-Christophe Pignon, Radwa Sharaf, Natalie Romanov, Julien Doudement, Lee A. Albacker, Noriaki Kurata, Neil R. Smith, Nobutoshi Matsushita, Juergen Scheuenpflug. Precision oncology driven real world clinical genomics data mining of MET alterations, TMB, and PDL-1 to empower indication agnostic patient enrollment and combination strategies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5737.
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Affiliation(s)
- Zheng Feng
- 1EMD Serono R&D Institute, Billerica, MA
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Maharaj S, Sharaf R, Redman RA, Rojan A. Chromosome 20q and 13q gain in metastatic colorectal cancer: Prognostic significance and genomic correlates. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.e15553] [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
e15553 Background: Chromosome 13q and 20q gain are major molecular events in adenoma-carcinoma progression and metastasis. The prognostic significance and correlates of 13q and 20q gain in metastatic colorectal cancer (CRC) have not been established. Methods: A total of 108 cases were selected at the University of Louisville. We ran a custom research-use only algorithm to assess whole arm chr13q and chr20q gain from next generation sequencing data of CRC samples. The algorithm utilized the coverage data of baited regions of the genome to model the copy number of each segment. A gain call was made if > 50% of the chromosome arm was gained. Tumors were noted as left-sided colon, right-sided colon, or rectal cancers. Data on demographics, treatment and Kaplan-Meier survival were analyzed. Results: The prevalence of 13q gain was 58% and 20q gain was detected in 61% of cases. Concurrent 13q and 20q gains were frequent, with 49% prevalence. The only 2 MSI-High samples were negative for 13q or 20q gain. Tumors with 13q and 20q gain were significantly more likely to have mutations in TP53 and APC (Table). Rectal tumors were significantly enriched for 13q gain ( p= 0.020) and 20q gain ( p= 0.007). Examining survival by tumor location, 13q gain conferred significantly worse outcome for rectal cancers ( p= 0.007), as did 20q gain ( p= 0.037). Conclusions: With median follow up of over 3 years, 13q and 20q gains were significantly associated with worse prognosis in rectal cancers. The data indicate that 13q/20q gain and associated molecular signature are important prognostic markers in CRC.[Table: see text]
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Sharaf R, Montesion M, Hopkins JF, Song J, Frampton GM, Albacker LA. A pan-cancer landscape of telomeric content shows that RAD21 and HGF alterations are associated with longer telomeres. Genome Med 2022; 14:25. [PMID: 35227290 PMCID: PMC8883689 DOI: 10.1186/s13073-022-01029-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 08/04/2021] [Accepted: 02/11/2022] [Indexed: 01/02/2023] Open
Abstract
Background Cancer cells can proliferate indefinitely through telomere maintenance mechanisms. These mechanisms include telomerase-dependent elongation, mediated by TERT activation, and alternative lengthening of telomeres (ALT), linked to loss of ATRX or DAXX. Methods We analyzed the telomeric content of 89,959 tumor samples within the Foundation Medicine dataset and investigated the genomic determinants of high telomeric content, linking them to clinical outcomes, when available. Results Telomeric content varied widely by disease type with leiomyosarcoma having the highest and Merkel cell carcinoma having the lowest telomeric content. In agreement with previous studies, telomeric content was significantly higher in samples with alterations in TERC, ATRX, and DAXX. We further identified that amplifications in two genes, RAD21 and HGF, were enriched in samples with high telomeric content, which was confirmed using the PCAWG/ICGC dataset. We identified the minimal amplified region associated with high telomeric content for RAD21 (8q23.1–8q24.12), which excludes MYC, and for HGF (7q21.11). Our results demonstrated that RAD21 and HGF exerted an additive telomere lengthening effect on samples with existing alterations in canonical genes previously associated with telomere elongation. Furthermore, patients with breast cancer who harbor RAD21 alterations had poor median overall survival and trended towards higher levels of Ki-67 staining. Conclusions This study highlights the importance of the role played by RAD21 (8q23.1–8q24.12) and HGF (7q21.11) in the lengthening of telomeres, supporting unlimited replication in tumors. These findings open avenues for work aimed at targeting this crucial pathway in tumorigenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01029-7.
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Affiliation(s)
- Radwa Sharaf
- Foundation Medicine Inc, 150 Second Street, Cambridge, MA, 02141, USA
| | - Meagan Montesion
- Foundation Medicine Inc, 150 Second Street, Cambridge, MA, 02141, USA
| | - Julia F Hopkins
- Foundation Medicine Inc, 150 Second Street, Cambridge, MA, 02141, USA
| | - Jiarong Song
- Foundation Medicine Inc, 150 Second Street, Cambridge, MA, 02141, USA
| | | | - Lee A Albacker
- Foundation Medicine Inc, 150 Second Street, Cambridge, MA, 02141, USA.
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Fajnzylber J, Sharaf R, Hutchinson JN, Aga E, Bosch RJ, Hartogensis W, Jacobson JM, Connick E, Volberding P, Skiest DJ, Margolis D, Sneller MC, Little SJ, Gulick RM, Mellors JW, Gandhi RT, Schooley RT, Henry K, Tebas P, Deeks S, Chun TW, Collier AC, Hecht FM, Li JZ. Frequency of post treatment control varies by antiretroviral therapy restart and viral load criteria. AIDS 2021; 35:2225-2227. [PMID: 34127579 PMCID: PMC8490281 DOI: 10.1097/qad.0000000000002978] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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] [Indexed: 11/26/2022]
Abstract
Clinical trials including an analytical treatment interruption (ATI) are vital for evaluating the efficacy of novel strategies for HIV remissions. We briefly describe an interactive tool for predicting viral rebound timing in ATI trials and the impact of posttreatment controller (PTC) definitions on PTC frequency estimates. A 4-week viral load threshold of 1000 cps/ml provides both high specificity and sensitivity for PTC detection. PTC frequency varies greatly based on the definition of a PTC.
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Affiliation(s)
| | - Radwa Sharaf
- Brigham and Women's Hospital, Harvard Medical School
| | | | - Evgenia Aga
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Ronald J Bosch
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | | | | | | | - Paul Volberding
- University of California, San Francisco, San Francisco, California
| | - Daniel J Skiest
- University of Massachusetts-Baystate, Springfield, Massachusetts
| | - David Margolis
- University of North Carolina, Chapel Hill, North Carolina
| | - Michael C Sneller
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - Susan J Little
- University of Caliornia, San Diego, San Diego, California
| | | | | | - Rajesh T Gandhi
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Keith Henry
- University of Minnesota, Minneapolis, Minnesota
| | - Pablo Tebas
- University of Pennsylvania, Philadelphia, Pennsylvania
| | - Steve Deeks
- University of California, San Francisco, San Francisco, California
| | - Tae-Wook Chun
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | | | | | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School
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Negrao M, Schmidt S, Sui D, Sharaf R, Kemp H, Lewis W, Bristow C, Frampton G, Lee J, Heymach J, Gibbons D, Albacker L, Skoulidis F. MA09.07 Genomic Landscape and Clinical Outcomes With Immune Checkpoint Inhibitors in NF1-Mutant NSCLC. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.08.157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Murugesan K, Sharaf R, Montesion M, Moore JA, Pao J, Pavlick DC, Frampton GM, Upadhyay VA, Alexander BM, Miller VA, Javle MM, Bekaii Saab TS, Albacker LA, Ross JS, Ali SM. Genomic Profiling of Combined Hepatocellular Cholangiocarcinoma Reveals Genomics Similar to Either Hepatocellular Carcinoma or Cholangiocarcinoma. JCO Precis Oncol 2021; 5:PO.20.00397. [PMID: 34476330 PMCID: PMC8384404 DOI: 10.1200/po.20.00397] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 03/05/2021] [Accepted: 06/11/2021] [Indexed: 01/07/2023] Open
Abstract
PURPOSE Combined hepatocellular cholangiocarcinoma (cHCC-CCA) is a rare, aggressive primary liver carcinoma, with morphologic features of both hepatocellular carcinomas (HCC) and liver cholangiocarcinomas (CCA). METHODS The genomic profiles of 4,975 CCA, 1,470 HCC, and 73 cHCC-CCA cases arising from comprehensive genomic profiling in the course of clinical care were reviewed for genomic alterations (GA), tumor mutational burden, microsatellite instability status, genomic loss of heterozygosity, chromosomal aneuploidy, genomic ancestry, and hepatitis B virus status. RESULTS In cHCC-CCA, GA were most common in TP53 (65.8%), TERT (49.3%), and PTEN (9.6%), and 24.6% cHCC-CCA harbored potentially targetable GA. Other GA were predominantly associated with either HCC or CCA, including, but not limited to, TERT, FGFR2, IDH1, and presence of hepatitis B virus. On the basis of these features, a machine learning (ML) model was trained to classify a cHCC-CCA case as CCA-like or HCC-like. Of cHCC-CCA cases, 16% (12/73) were ML-classified as CCA-like and 58% (42/73) cHCC-CCA were ML-classified as HCC-like. The ML model classified more than 70% of cHCC-CCA as CCA-like or HCC-like on the basis of genomic profiles, without additional clinico-pathologic input. CONCLUSION These findings demonstrate the use of ML for classification as based on a targeted exome panel used during routine clinical care. Classification of cHCC-CCA by genomic features alone creates insights into the biology of the disease and warrants further investigation for relevance to clinical care.
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Affiliation(s)
| | | | | | | | - James Pao
- Foundation Medicine Inc, Cambridge, MA
| | | | | | - Vivek A Upadhyay
- Foundation Medicine Inc, Cambridge, MA.,Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
| | | | | | - Milind M Javle
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Jeffrey S Ross
- Foundation Medicine Inc, Cambridge, MA.,Department of Pathology, State University of New York Upstate Medical University, Syracuse, NY
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21
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Wong J, Kuplast-Barr K, Abo RP, Kulkarni AS, Nieman LT, Neyaz A, Xu KH, Sharaf R, Albacker LA, Ting DT, Keilhack H, McEachern KA. Abstract 381: Elevated PARP7 expression in select cancers identifies a target population for RBN-2397 therapy. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-381] [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
PARP7 (TIPARP) is a monoPARP which catalyzes the transfer of single units of ADP-ribose onto substrates to change their function. Its expression is upregulated during cellular stress, including viral infection or through the activation of the aryl hydrocarbon receptor after exposure to cigarette smoke. We and others have shown that PARP7 activity suppresses the Type I interferon (IFN) response following activation by cytosolic nucleic acid sensing pathways. RBN-2397 is a first-in class PARP7 inhibitor, which induces cancer cell autonomous and immune stimulatory effects in preclinical models through enhanced Type I IFN signaling in cancer cells. Here we describe the presence of PARP7 genomic amplification with corresponding increased mRNA expression across select cancers. Elevated PARP7 expression or amplification may identify cancer patients that could derive benefit from treatment with RBN-2397.
In characterizing PARP7 copy number and mRNA expression from The Cancer Genome Atlas (TCGA) database, we found the presence of PARP7 copy number amplification in a subset of tumor types, particularly those of squamous histology, as well as ovarian cancer that corresponded to higher mRNA expression levels. High PARP7 expression correlated with poor survival in squamous cancers, while it had no effect on survival in ovarian cancer. Interestingly, tumor types with high PARP7 expression also expressed higher levels of baseline interferon stimulated genes (ISGs). This parallels our findings that cancer cell lines with higher ISGs at baseline are more responsive to PARP7 inhibition.
To explore PARP7 copy number variations (CNVs) in advanced cancer patients, we queried the FoundationCore® (Foundation Medicine, Inc) database. Similar to TCGA, squamous cancers as well as ovarian, breast, and pancreatic ductal adenocarcinoma (PDAC) were among the tumor types with PARP7 amplifications. Moreover, PARP7 was found to be amplified both on the background of chromosome 3q arm-level amplifications as well as focally.
Congruent to our analysis of PARP7 amplifications, we evaluated PARP7 mRNA expression in both squamous and non-squamous non-small cell lung carcinoma (NSCLC), breast cancer, and PDAC primary tumor samples. Using a validated RNAscope ISH probe set, we analyzed over 1,000 patient samples and found that PARP7 was more highly expressed in tumor cells relative to corresponding normal tissues. Overall, there were varying levels of PARP7 expression across samples with higher expression levels of PARP7 in tumor cells, compared to stroma, across all cancers examined.
Our analyses describing the presence of PARP7 amplifications as well as high expression levels in several tumor types including NSCLC, breast, and PDAC provides evidence for the therapeutic relevance of PARP7 inhibition and highlights potential patient selection strategies to identify those patients more likely to benefit from RBN-2397 treatment.
Citation Format: Jodie Wong, Kristy Kuplast-Barr, Ryan P. Abo, Anupriya S. Kulkarni, Linda T. Nieman, Azfar Neyaz, Katherine H. Xu, Radwa Sharaf, Lee A. Albacker, David T. Ting, Heike Keilhack, Kristen A. McEachern. Elevated PARP7 expression in select cancers identifies a target population for RBN-2397 therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 381.
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Affiliation(s)
- Jodie Wong
- 1Ribon Therapeutics, Inc., Cambridge, MA
| | | | | | | | | | - Azfar Neyaz
- 2Massachusetts General Hospital Cancer Center, Boston, MA
| | | | | | | | - David T. Ting
- 2Massachusetts General Hospital Cancer Center, Boston, MA
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Sharaf R, Pavlick DC, Frampton GM, Cooper M, Jenkins J, Danziger N, Haberberger J, Alexander BM, Cloughesy T, Yong WH, Liau LM, Nghiemphu PL, Ji M, Lai A, Ramkissoon SH, Albacker LA. Erratum to: FoundationOne CDx testing accurately determines whole arm 1p19q codeletion status in gliomas. Neurooncol Adv 2021; 3:vdab059. [PMID: 34169283 PMCID: PMC8218850 DOI: 10.1093/noajnl/vdab059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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23
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Sharaf R, Pavlick DC, Frampton GM, Cooper M, Jenkins J, Danziger N, Haberberger J, Alexander BM, Cloughesy T, Yong WH, Liau LM, Nghiemphu PL, Ji M, Lai A, Ramkissoon SH, Albacker LA. FoundationOne CDx testing accurately determines whole arm 1p19q codeletion status in gliomas. Neurooncol Adv 2021; 3:vdab017. [PMID: 33778493 PMCID: PMC7986056 DOI: 10.1093/noajnl/vdab017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Molecular profiling of gliomas is vital to ensure diagnostic accuracy, inform prognosis, and identify clinical trial options for primary and recurrent tumors. This study aimed to determine the accuracy of reporting the whole arm 1p19q codeletion status from the FoundationOne platform. METHODS Testing was performed on glioma samples as part of clinical care and analyzed up to 395 cancer-associated genes (including IDH1/2). The whole arm 1p19q codeletion status was predicted from the same assay using a custom research-use only algorithm, which was validated using 463 glioma samples with available fluorescence in-situ hybridization (FISH) data. For 519 patients with available outcomes data, progression-free and overall survival were assessed based on whole arm 1p19q codeletion status derived from sequencing data. RESULTS Concordance between 1p19q status based on FISH and our algorithm was 96.7% (449/463) with a positive predictive value (PPV) of 100% and a positive percent agreement (PPA) of 91.0%. All discordant samples were positive for codeletion by FISH and harbored genomic alterations inconsistent with oligodendrogliomas. Median overall survival was 168 months for the IDH1/2 mutant, codeleted group, and 122 months for IDH1/2 mutant-only (hazard ratio (HR): 0.42; P < .05). CONCLUSIONS 1p19q codeletion status derived from FoundationOne testing is highly concordant with FISH results. Genomic profiling may be a reliable substitute for traditional FISH testing while also providing IDH1/2 status.
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Affiliation(s)
- Radwa Sharaf
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Dean C Pavlick
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Garrett M Frampton
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Maureen Cooper
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Jacqueline Jenkins
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Natalie Danziger
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - James Haberberger
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Brian M Alexander
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Timothy Cloughesy
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - William H Yong
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Linda M Liau
- Department of Neurosurgery, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Phioanh L Nghiemphu
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Matthew Ji
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Albert Lai
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Shakti H Ramkissoon
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
- Wake Forest Comprehensive Cancer Center and Department of Pathology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Lee A Albacker
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
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24
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Williams EA, Montesion M, Sharaf R, Corines J, Patel PJ, Gillespie BJ, Pavlick DC, Sokol ES, Alexander BM, Williams KJ, Elvin JA, Ross JS, Ramkissoon SH, Hemmerich AC, Tse JY, Mochel MC. CYLD-mutant cylindroma-like basaloid carcinoma of the anus: a genetically and morphologically distinct class of HPV-related anal carcinoma. Mod Pathol 2020; 33:2614-2625. [PMID: 32461623 PMCID: PMC7685972 DOI: 10.1038/s41379-020-0584-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 11/12/2022]
Abstract
Rare reports of anal carcinoma (AC) describe histologic resemblance to cutaneous cylindroma, but mutations in the tumor suppressor CYLD, the gene responsible for familial and sporadic cylindromas, have not been systematically investigated in AC. Here, we investigate CYLD-mutant AC, focusing on molecular correlates of distinct histopathology. Comprehensive genomic profiling (hybrid-capture-based DNA sequencing) was performed on 574 ACs, of which 75 unique cases (13%) harbored a CYLD mutation. Clinical data, pathology reports, and histopathology were reviewed for each CYLD-mutant case. The spectrum of CYLD mutations included truncating (n = 50; 67%), homozygous deletion (n = 10; 13%), missense (n = 16; 21%), and splice-site (n = 3; 4%) events. Compared with CYLD-wildtype AC (n = 499), CYLD-mutant ACs were significantly enriched for females (88% vs. 67%, p = 0.0001), slightly younger (median age 59 vs. 61 years, p = 0.047), and included near-universal detection of high-risk HPV sequences (97% vs. 88%, p = 0.014), predominantly HPV16 (96%). The CYLD-mutant cohort also showed significantly lower tumor mutational burden (TMB; median 2.6 vs. 5.2 mut/Mb, p < 0.00001) and less frequent alterations in PIK3CA (13% vs. 31%, p = 0.0015). On histopathologic examination, 73% of CYLD-mutant AC (55/75 cases) showed a striking cylindroma-like histomorphology, composed of aggregates of basaloid cells surrounded by thickened basement membranes and containing characteristic hyaline globules, while only 8% of CYLD-wildtype tumors (n = 34/409) contained cylindroma-like hyaline globules (p < 0.0001). CYLD-mutant carcinomas with cylindroma-like histomorphology (n = 55) showed significantly lower TMB compared with CYLD-mutant cases showing basaloid histology without the distinctive hyaline globules (n = 14) (median 1.7 vs. 4.4 mut/Mb, p = 0.0058). Only five CYLD-mutant cases (7%) showed nonbasaloid conventional squamous cell carcinoma histology (median TMB = 5.2 mut/Mb), and a single CYLD-mutant case showed transitional cell carcinoma-like histology. Within our cohort of ACs, CYLD mutations characterize a surprisingly large subset (13%), with distinct clinical and genomic features and, predominantly, a striking cylindroma-like histopathology, representing a genotype-phenotype correlation which may assist in classification of AC.
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Affiliation(s)
- Erik A Williams
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA.
| | - Meagan Montesion
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Radwa Sharaf
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - James Corines
- Department of Pathology, State University of New York Upstate Medical University, 766 Irving Avenue, Syracuse, NY, 13210, USA
| | - Parth J Patel
- Department of Surgery, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | | | - Dean C Pavlick
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Ethan S Sokol
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Brian M Alexander
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Kevin Jon Williams
- Department of Physiology and Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Julia A Elvin
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Jeffrey S Ross
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
- Department of Pathology, State University of New York Upstate Medical University, 766 Irving Avenue, Syracuse, NY, 13210, USA
| | - Shakti H Ramkissoon
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
- Wake Forest Comprehensive Cancer Center and Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | | | - Julie Y Tse
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
- Department of Pathology & Laboratory Medicine, Tufts University School of Medicine, 145 Harrison Ave, Boston, MA, 02111, USA
| | - Mark C Mochel
- Departments of Pathology and Dermatology, Virginia Commonwealth University School of Medicine, Richmond, VA, 23298, USA
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25
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Williams EA, Montesion M, Shah N, Sharaf R, Pavlick DC, Sokol ES, Alexander B, Venstrom J, Elvin JA, Ross JS, Williams KJ, Tse JY, Mochel MC. Melanoma with in-frame deletion of MAP2K1: a distinct molecular subtype of cutaneous melanoma mutually exclusive from BRAF, NRAS, and NF1 mutations. Mod Pathol 2020; 33:2397-2406. [PMID: 32483240 PMCID: PMC7685971 DOI: 10.1038/s41379-020-0581-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 11/12/2022]
Abstract
While the genomics of BRAF, NRAS, and other key genes influencing MAP kinase (MAPK) activity have been thoroughly characterized in melanoma, mutations in MAP2K1 (MEK1) have received significantly less attention and have consisted almost entirely of missense mutations considered secondary oncogenic drivers of melanoma. Here, we investigated melanomas with in-frame deletions of MAP2K1, alterations characterized as MAPK-activating in recent experimental models. Our case archive of clinical melanoma samples with comprehensive genomic profiling by a hybrid capture-based DNA sequencing platform was searched for MAP2K1 genetic alterations. Clinical data, pathology reports, and histopathology were reviewed for each case. From a cohort of 7119 advanced melanomas, 37 unique cases (0.5%) featured small in-frame deletions in MAP2K1. These included E102_I103del (n = 11 cases), P105_A106del (n = 8), Q58_E62del (n = 6), I103_K104del (n = 5), I99_K104del (n = 3), L98_I103del (n = 3), and E41_F53del (n = 1). All 37 were wild type for BRAF, NRAS, and NF1 genomic alterations ("triple wild-type"), representing 2.0% of triple wild-type melanomas overall (37/1882). Median age was 66 years and 49% were male. The majority arose from primary cutaneous sites (35/37; 95%) and demonstrated a UV signature when available (21/25; 84%). Tumor mutational burden was typical for cutaneous melanoma (median = 9.6 mut/Mb, range 0-35.7), and frequently mutated genes included TERTp (63%), CDKN2A (46%), TP53 (11%), PTEN (8%), APC (8%), and CTNNB1 (5%). Histopathology revealed a spectrum of appearances typical of melanoma. For comparison, we evaluated 221 cases with pathogenic missense single nucleotide variants in MAP2K1. The vast majority of melanomas with missense SNVs in MAP2K1 showed co-mutations in BRAF (58%), NF1 (23%), or NRAS (18%). In-frame deletions in MAP2K1, previously shown in experimental models to be strongly MAPK-activating, characterized a significant subset of triple wild-type melanoma (2.0%), suggesting a primary oncogenic role for these mutations. Comprehensive genomic profiling of melanomas enables detection of this alteration, which may have implications for potential therapeutic options.
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Affiliation(s)
- Erik A Williams
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA.
| | - Meagan Montesion
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Nikunj Shah
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Radwa Sharaf
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Dean C Pavlick
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Ethan S Sokol
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Brian Alexander
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Jeff Venstrom
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Julia A Elvin
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Jeffrey S Ross
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
- Department of Pathology, State University of New York Upstate Medical University, 766 Irving Avenue, Syracuse, NY, 13210, USA
| | - Kevin Jon Williams
- Department of Physiology, Department of Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Julie Y Tse
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
- Department of Pathology & Laboratory Medicine, Tufts University School of Medicine, 145 Harrison Ave, Boston, MA, 02111, USA
| | - Mark C Mochel
- Departments of Pathology and Dermatology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
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Sharaf R, Pavlick DC, Frampton GM, Cooper M, Jenkins J, Alexander B, Cloughesy T, Yong W, Liau L, Nghiemphu P, Ji M, Lai A, Albacker LA, Ramkissoon SH. PATH-16. COMPREHENSIVE GENOMIC PROFILING ACCURATELY DETERMINES 1p19q CODELETION STATUS IN GLIOMAS. Neuro Oncol 2020. [DOI: 10.1093/neuonc/noaa215.698] [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: 11/14/2022] Open
Abstract
Abstract
BACKGROUND
Genomic profiling of gliomas is vital to ensure diagnostic accuracy, inform prognosis, and identify therapeutic options for primary and recurrent tumors. The integration of genomic biomarkers into brain tumor classification has improved the diagnostic accuracy and led to the development of molecularly stratified clinical trials.
DESIGN
Comprehensive genomic profiling (CGP) was performed on FFPE material from 310 (162 FoundationOne® and 148 FoundationOne® CDx) samples of brain tumors with available 1p19q FISH results, initially diagnosed by submitting institutions based on histology. Via CGP, we analyzed tumors in up to 395 cancer-associated genes (including IDH1/2) and predicted 1p19q codeletion using a custom research-use only algorithm. Progression-free (PFS) and overall survival (OS) were determined for 519 patients based on computationally predicted 1p19q codeletion status.
RESULTS
For all samples, regardless of their IDH1/2 mutation status, concordance between 1p19q status based on FISH and our algorithm was 97.1%, (301/310), with a positive predictive value (PPV) of 100% (133/133) and sensitivity of 93.7% (133/142). All discordant samples were called as positive for codeletion by FISH and negative by our CGP-based algorithm. Discordant samples were either IDH1/2 wild-type (2) or IDH1/2, ATRX, and TP53 altered (7), consistent with the genomic profile of diffuse astrocytomas. For IDH1/2-mutated samples, concordance was 96.7% (238/246). In the clinical outcomes dataset, median PFS was 35 months for the codeletion group compared to 13 months for the non-codeletion group (hazard ratio (HR): 0.60; 95% CI: 0.40-0.88; p=0.009). Similarly, median OS was 160 and 34 months respectively for codeleted versus intact (HR: 0.46; 95% CI: 0.28-0.76; p=0.002).
CONCLUSIONS
1p19q codeletion status derived from CGP is highly concordant with FISH results suggesting that CGP-derived 1p19q codeletion status may be a reliable substitute for traditional FISH testing. Patients with CGP-derived 1p19q codeletion showed increased PFS and OS compared to non-codeleted counterparts.
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Affiliation(s)
| | | | | | | | | | | | | | - William Yong
- University of California Los Angeles, Los Angeles, CA, USA
| | - Linda Liau
- University of California Los Angeles, Los Angeles, CA, USA
| | | | - Matthew Ji
- University of California Los Angeles, Los Angeles, CA, USA
| | - Albert Lai
- University of California Los Angeles, Los Angeles, CA, USA
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Montesion M, Murugesan K, Jin DX, Sharaf R, Sanchez N, Guria A, Minker M, Li G, Fisher V, Sokol ES, Pavlick DC, Moore JA, Braly A, Singal G, Fabrizio D, Comment LA, Rizvi NA, Alexander BM, Frampton GM, Hegde PS, Albacker LA. Somatic HLA Class I Loss Is a Widespread Mechanism of Immune Evasion Which Refines the Use of Tumor Mutational Burden as a Biomarker of Checkpoint Inhibitor Response. Cancer Discov 2020; 11:282-292. [PMID: 33127846 DOI: 10.1158/2159-8290.cd-20-0672] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/14/2020] [Accepted: 10/27/2020] [Indexed: 11/16/2022]
Abstract
Neoantigen presentation arises as a result of tumor-specific mutations and is a critical component of immune surveillance that can be abrogated by somatic LOH of the human leukocyte antigen class I (HLA-I) locus. To understand the role of HLA-I LOH in oncogenesis and treatment, we utilized a pan-cancer genomic dataset of 83,644 patient samples, a small subset of which had treatment outcomes with immune checkpoint inhibitors (ICI). HLA-I LOH was common (17%) and unexpectedly had a nonlinear relationship with tumor mutational burden (TMB). HLA-I LOH was frequent at intermediate TMB, yet prevalence decreased above 30 mutations/megabase, suggesting highly mutated tumors require alternate immune evasion mechanisms. In ICI-treated patients with nonsquamous non-small cell lung cancer, HLA-I LOH was a significant negative predictor of overall survival. Survival prediction improved when combined with TMB, suggesting TMB with HLA-I LOH may better identify patients likely to benefit from ICIs. SIGNIFICANCE: This work shows the pan-cancer landscape of HLA-I LOH, revealing an unexpected "Goldilocks" relationship between HLA-I LOH and TMB, and demonstrates HLA-I LOH as a significant negative predictor of outcomes after ICI treatment. These data informed a combined predictor of outcomes after ICI and have implications for tumor vaccine development.This article is highlighted in the In This Issue feature, p. 211.
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Affiliation(s)
| | | | - Dexter X Jin
- Foundation Medicine, Inc., Cambridge, Massachusetts
| | - Radwa Sharaf
- Foundation Medicine, Inc., Cambridge, Massachusetts
| | - Nora Sanchez
- Foundation Medicine, Inc., Cambridge, Massachusetts
| | - Ameet Guria
- Foundation Medicine, Inc., Cambridge, Massachusetts
| | - Max Minker
- Foundation Medicine, Inc., Cambridge, Massachusetts
| | - Gerald Li
- Foundation Medicine, Inc., Cambridge, Massachusetts
| | | | | | | | - Jay A Moore
- Foundation Medicine, Inc., Cambridge, Massachusetts
| | - Alan Braly
- Foundation Medicine, Inc., Cambridge, Massachusetts
| | | | | | | | - Naiyer A Rizvi
- Columbia University Irving Medical Center, New York, New York
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Williams EA, Santagata S, Wakimoto H, Shankar GM, Barker FG, Sharaf R, Reddy A, Spear P, Alexander BM, Ross JS, Brastianos PK, Cahill DP, Ramkissoon SH, Juratli TA. Distinct genomic subclasses of high-grade/progressive meningiomas: NF2-associated, NF2-exclusive, and NF2-agnostic. Acta Neuropathol Commun 2020; 8:171. [PMID: 33087175 PMCID: PMC7580027 DOI: 10.1186/s40478-020-01040-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Genomic studies of high-grade/progressive meningiomas have reported a heterogeneous mutation spectrum, identifying few recurrently mutated genes. Most studies have been underpowered to detect genomic subclasses of aggressive meningiomas due to relatively small number of available samples. Here, we present a genomic survey of one of the largest multi-institutional cohorts of high-grade/progressive meningiomas to date. METHODS 850 high-grade/progressive meningiomas, including 441 WHO grade 2 and 176 WHO grade 3 meningiomas and 220 progressive WHO grade 1 meningiomas, were tested as part of a clinical testing program by hybridization capture of 406 cancer-related genes to detect base substitutions, indels, amplifications, deletions, and rearrangements. Information from pathology reports, histopathology review, and patient clinical data was assessed. RESULTS Genomic analyses converged to identify at least three distinct patterns of biologically-aggressive meningiomas. The first and most common contained NF2-mutant tumors (n = 426, 50%), was associated with male sex (64.4% %, p = 0.0001) and often harbored additional mutations in CDKN2A/B (24%), and the chromatin regulators ARID1A (9%), and KDM6A (6%). A second group (NF2-agnostic) featured TERT promoter (TERTp; n = 56) or TP53 mutations (n = 25) and were either NF2-mutant or wild-type, and displayed no association with either sex (p = 0.39). The remaining group generally lacked NF2 mutations, and accounted for 40% of the cases-with three subgroups. One consistent primarily of grade 3 lesions harboring alterations in chromatin regulators BAP1 (n = 22) or PBRM1 (n = 16). A second subgroup contained AKT1 (n = 26), PIK3CA (n = 14) and SMO (n = 7) mutant skull-based meningiomas, and a third mixed subgroup included 237 meningiomas with a heterogeneous spectrum of low frequency and non-recurrent alterations. CONCLUSIONS Our findings indicate that the patterns of genomic alterations in high-grade/progressive meningiomas commonly group into three different categories. The most common NF2-associated canonical group frequently harbored CDKN2A/B alterations, which is potentially amenable to targeted therapies. An NF2-agnostic group harbored frequent TERTp and TP53 mutations. The final subclass, distinct from the canonical NF2 mutant associated pathway, was partly characterized by BAP1/PBRM1 alterations (rhabdoid/papillary histology) or skull-base disease. Overall, these data increase our understanding of the pathobiology of high-grade/progressive meningiomas and can guide the design of clinical trials. IRB APPROVAL STATUS Reviewed and approved by Western IRB; Protocol No. 20152817.
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Kahn R, Chapman-Davis E, Krinsky H, Lipkin K, Anderson S, Tubito F, Pires M, Sharaf R, Blank S, Caputo T, Holcomb K, Frey M. Distress and anxiety associated with identifying germline cancer-associated mutations with cascade genetic testing. Gynecol Oncol 2020. [DOI: 10.1016/j.ygyno.2020.05.435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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30
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Kahn R, Krinsky H, Chervenak J, Anderson S, Lipkin K, Tubito F, Pires M, Blank S, Sharaf R, Chapman-Davis E, Caputo T, Holcomb K, Frey M. Cascade genetic testing: What are the quality of life implications for at-risk relatives undergoing genetic testing? Gynecol Oncol 2020. [DOI: 10.1016/j.ygyno.2020.05.434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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31
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Li X, Kahn R, Lackner A, Nelson BB, Krinsky H, Mei E, Badiner N, Holcomb K, Chapman-Davis E, Nitecki R, Rauh-Hain J, Sharaf R, Frey M. Cascade genetic testing for hereditary cancer syndromes: A systematic review and meta-analysis. Gynecol Oncol 2020. [DOI: 10.1016/j.ygyno.2020.05.431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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32
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Kahn R, Chapman-Davis E, Krinsky H, Anderson S, Caputo T, Tubito F, Pires M, Tkachuk K, Sharaf R, Offit K, Holcomb K, Lipkin K, Frey M. Barriers to uptake of oncologic cascade genetic testing: Results of a prospective cohort study. Gynecol Oncol 2020. [DOI: 10.1016/j.ygyno.2020.05.433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Lackner A, Li X, Kahn R, Baltich NB, Krinsky H, Mei E, Badiner N, Caputo T, Holcomb K, Chapman-Davis E, Nitecki R, Rauh-Hain J, Sharaf R, Frey M. Cascade testing für erbliche Tumorerkrankungen: Eine Meta-Analyse. Geburtshilfe Frauenheilkd 2020. [DOI: 10.1055/s-0040-1718159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
| | - X Li
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - R Kahn
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - Nelson B Baltich
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - H Krinsky
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - E Mei
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - N Badiner
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - T.A Caputo
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - K Holcomb
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - E Chapman-Davis
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - R Nitecki
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - J.A Rauh-Hain
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - R Sharaf
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
| | - M.K Frey
- New York Presbyterian Hospital – Weill Cornell, Gynecologic Oncology
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34
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Williams EA, Sharaf R, Decker B, Werth AJ, Toma H, Montesion M, Sokol ES, Pavlick DC, Shah N, Williams KJ, Venstrom JM, Alexander BM, Ross JS, Albacker LA, Lin DI, Ramkissoon SH, Elvin JA. CDKN2C-Null Leiomyosarcoma: A Novel, Genomically Distinct Class of TP53/ RB1-Wild-Type Tumor With Frequent CIC Genomic Alterations and 1p/19q-Codeletion. JCO Precis Oncol 2020; 4:PO.20.00040. [PMID: 33015533 PMCID: PMC7529542 DOI: 10.1200/po.20.00040] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2020] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Leiomyosarcoma (LMS) harbors frequent mutations in TP53 and RB1 but few actionable genomic alterations. Here, we searched for recurrent actionable genomic alterations in LMS that occur in the absence of common untreatable oncogenic drivers. METHODS Tissues from 276,645 unique advanced cancers, including 2,570 uterine and soft tissue LMS, were sequenced by hybrid-capture-based next-generation DNA and RNA sequencing/comprehensive genomic profiling of up to 406 genes. We characterized clinicopathologic features of relevant patient cases. RESULTS Overall, 77 LMS exhibited homozygous copy loss of CDKN2C at chromosome 1p32.3 (3.0% of LMS). Genomic alterations (GAs) in TP53, RB1, and ATRX were rare compared with the remainder of the LMS cohort (11.7% v 73.4%, 0% v 54.5%, 2.6% v 24.5%, respectively; all P < .0001). CDKN2C-null LMS patient cases were significantly enriched for GAs in CIC (40.3% v 1.4%) at 19q13.2, CDKN2A (46.8% v 7.0%), and RAD51B (16.9% v 1.7%; all P < .0001). Chromosome arm-level aneuploidy analysis of available LMS patient cases (n = 1,284) found that 81% (58 of 72) of CDKN2C-null LMS exhibited 1p/19q-codeletion, a significant enrichment compared with 5.1% in the remainder of the LMS cohort (P < .0001). In total, 99% of CDKN2C-null LMS were in women; the median age was 61 years at surgery (range, 36-81 years). Fifty-five patient cases were uterine primary, four were nonuterine, and the remaining 18 were of uncertain primary site. Sixty percent of cases showed at least focal epithelioid variant histology. Most patients had advanced-stage disease, with 62% of confirmed uterine primary LMS at International Federation of Gynecology and Obstetrics stage IVB. We further validated our findings in two publicly available datasets: The Cancer Genome Atlas and the Project GENIE initiative. CONCLUSION CDKN2C-null LMS defines a genomically distinct tumor that may have prognostic and/or therapeutic clinical implications, including possible use of specific cyclin-dependent kinase inhibitors.
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Affiliation(s)
| | | | - Brennan Decker
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Adrienne J. Werth
- Christiana Hospital, Department of Obstetrics and Gynecology, Newark, DE
| | - Helen Toma
- Christiana Hospital, Department of Obstetrics and Gynecology, Newark, DE
| | | | | | | | | | - Kevin Jon Williams
- Department of Physiology, Department of Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | | | | | - Jeffrey S. Ross
- Foundation Medicine, Cambridge, MA
- Department of Pathology, State University of New York Upstate Medical University, Syracuse, NY
| | | | | | - Shakti H. Ramkissoon
- Foundation Medicine, Cambridge, MA
- Wake Forest Comprehensive Cancer Center and Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC
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Williams EA, Shah N, Montesion M, Sharaf R, Pavlick DC, Sokol ES, Alexander BM, Venstrom JM, Elvin JA, Ross JS, Tse JY, Mochel MC. Melanomas with activating RAF1 fusions: clinical, histopathologic, and molecular profiles. Mod Pathol 2020; 33:1466-1474. [PMID: 32123303 PMCID: PMC7384985 DOI: 10.1038/s41379-020-0510-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/19/2020] [Accepted: 02/19/2020] [Indexed: 01/08/2023]
Abstract
A subset of melanomas is characterized by fusions involving genes that encode kinases. Melanomas with RAF1 fusions have been rarely reported, mostly in clinical literature. To investigate this distinctive group of melanomas, we searched for melanomas with activating structural variants in RAF1, utilizing our case archive of clinical samples with comprehensive genomic profiling (CGP) by a hybrid capture-based DNA sequencing platform. Clinical data, pathology reports, and histopathology were reviewed for each case. RAF1 breakpoints, fusion partners, and co-occurring genetic alterations were characterized. From a cohort of 7119 melanomas, 40 cases (0.6%) featured fusions that created activating structural variants in RAF1. Cases with activating RAF1 fusions had median age of 62 years, were 58% male, and consisted of 9 primary tumors and 31 metastases. Thirty-nine cases were cutaneous primary, while one case was mucosal (anal) primary. Primary cutaneous melanomas showed variable architectures, including wedge-shaped and nodular growth patterns. Cytomorphology was predominantly epithelioid, with only one case, a desmoplastic melanoma, consisting predominantly of spindle cells. RAF1 5' rearrangement partners were predominantly intrachromosomal (n = 18), and recurrent partners included MAP4 (n = 3), CTNNA1 (n = 2), LRCH3 (n = 2), GOLGA4 (n = 2), CTDSPL (n = 2), and PRKAR2A (n = 2), all 5' of the region encoding the kinase domain. RAF1 breakpoints occurred in intron 7 (n = 32), intron 9 (n = 4), intron 5 (n = 2), and intron 6 (n = 2). Ninety-eight percent (n = 39) were wild type for BRAF, NRAS, and NF1 genomic alterations (triple wild type). Activating RAF1 fusions were present in 2.1% of triple wild-type melanomas overall (39/1882). In melanomas with activating RAF1 fusions, frequently mutated genes included TERTp (62%), CDKN2A (60%), TP53 (13%), ARID2 (10%), and PTEN (10%). Activating RAF1 fusions characterize a significant subset of triple wild-type melanoma (2.1%) with frequent accompanying mutations in TERTp and CDKN2A. CGP of melanomas may improve tumor classification and inform potential therapeutic options, such as consideration of specific kinase inhibitors.
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Affiliation(s)
- Erik A Williams
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA.
| | - Nikunj Shah
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Meagan Montesion
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Radwa Sharaf
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Dean C Pavlick
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Ethan S Sokol
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Brian M Alexander
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Jeff M Venstrom
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Julia A Elvin
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Jeffrey S Ross
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
- Department of Pathology, State University of New York Upstate Medical University, 766 Irving Avenue, Syracuse, NY, 13210, USA
| | - Julie Y Tse
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
- Department of Pathology & Laboratory Medicine, Tufts University School of Medicine, 145 Harrison Ave, Boston, MA, 02111, USA
| | - Mark C Mochel
- Departments of Pathology and Dermatology, Virginia Commonwealth University School of Medicine, 1200 East Marshall Street, Richmond, VA, 23298, USA
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36
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Williams EA, Werth AJ, Sharaf R, Montesion M, Sokol ES, Pavlick DC, McLaughlin-Drubin M, Erlich R, Toma H, Williams KJ, Venstrom JM, Alexander BM, Shah N, Danziger N, Hemmerich AC, Severson EA, Killian JK, Lin DI, Ross JS, Tse JY, Ramkissoon SH, Mochel MC, Elvin JA. Vulvar Squamous Cell Carcinoma: Comprehensive Genomic Profiling of HPV+ Versus HPV- Forms Reveals Distinct Sets of Potentially Actionable Molecular Targets. JCO Precis Oncol 2020; 4:1900406. [PMID: 32923875 PMCID: PMC7446361 DOI: 10.1200/po.19.00406] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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] [Accepted: 04/28/2020] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Vulvar squamous cell carcinoma (vSCC) encompasses two predominant variants: one associated with detectable high-risk strains of human papillomavirus (hrHPV) and a second form often occurring in the context of chronic dermatitis in postmenopausal women. Genomic assessment of a large-scale cohort of patients with aggressive vSCC may identify distinct mutational signatures. MATERIALS AND METHODS Tumor samples from a total of 280 patients with vSCC underwent hybridization capture with analysis of up to 406 cancer-related genes. Human papillomavirus (HPV) sequences were detected by de novo assembly of nonhuman sequencing reads and aligned to the RefSeq database. Immunohistochemistry for programmed death-ligand 1 (PD-L1) was assessed. RESULTS One hundred two of 280 vSCCs (36%) contained hrHPV sequences, predominantly HPV 16 (88%). The HPV-positive (HPV+) group was significantly younger (median age, 59 v 64 years; P = .001). Compared with HPV-negative (HPV–) vSCCs, HPV+ tumors showed more frequent pathogenic alterations in PIK3CA (31% v 16%; P = .004), PTEN (14% v 2%; P < .0001), EP300 (14% v 1%; P < .0001), STK11 (14% v 1%; P < .0001), AR (5% v 0%; P = .006), and FBXW7 (10% v 3%; P = .03). In contrast, HPV– vSCCs showed more alterations in TP53 (83% v 6%; P < .0001), TERTp (71% v 9%; P < .0001), CDKN2A (55% v 2%; P < .0001), CCND1 amplification (22% v 2%; P < .0001), FAT1 (25% v 4%; P < .0001), NOTCH1 (19% v 6%; P = .002), and EGFR amplification (11% v 0%; P < .0001), as well as a higher rate of 9p24.1 (PDL1/PDL2) amplification (5% v 1%) and PD-L1 immunohistochemistry high-positive tumor staining (33% v 9%; P = .04). CONCLUSION Comprehensive molecular profiles of vSCC vary considerably with hrHPV status and may inform patient selection into clinical trials. Sixty-one percent of HPV+ vSCCs had a pathogenic alteration in the PI3K/mTOR pathway, whereas HPV– vSCCs showed alterations in TP53, TERTp, CDKN2A, CCND1, and EGFR, and biomarkers associated with responsiveness to immunotherapy.
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Affiliation(s)
| | - Adrienne J Werth
- Department of Obstetrics and Gynecology, Christiana Hospital, Newark, DE
| | | | | | | | | | | | | | - Helen Toma
- Department of Obstetrics and Gynecology, Christiana Hospital, Newark, DE
| | - Kevin Jon Williams
- Lewis Katz School of Medicine at Temple University, Department of Physiology, Department of Medicine, Philadelphia, PA
| | | | | | | | | | | | | | | | | | - Jeffrey S Ross
- Foundation Medicine, Cambridge, MA.,Department of Pathology, State University of New York Upstate Medical University, Syracuse, NY
| | - Julie Y Tse
- Foundation Medicine, Cambridge, MA.,Department of Pathology and Laboratory Medicine, Tufts University School of Medicine, Boston, MA
| | - Shakti H Ramkissoon
- Foundation Medicine, Cambridge, MA.,Wake Forest Comprehensive Cancer Center and Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC
| | - Mark C Mochel
- Departments of Pathology and Dermatology, Virginia Commonwealth University School of Medicine, Richmond, VA
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Lackner A, Li X, Kahn R, Baltich Nelson B, Krinsky H, Mei E, Badiner N, Caputo TA, Holcomb K, Chapman-Davis E, Nitecki R, Rauh-Hain JA, Sharaf R, Frey MK. Cascade testing für erbliche Tumorerkrankungen: Eine Meta-Analyse. Geburtshilfe Frauenheilkd 2020. [DOI: 10.1055/s-0040-1713236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- A Lackner
- Universitätsklinik für Frauenheilkunde, Medizinische Universität Wien, Wien, Österreich
| | - X Li
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - R Kahn
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - B Baltich Nelson
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - H Krinsky
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - E Mei
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - N Badiner
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - T A Caputo
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - K Holcomb
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - E Chapman-Davis
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - R Nitecki
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - J A Rauh-Hain
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - R Sharaf
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
| | - M K Frey
- Division of Gynecologic Oncology, Weill Cornell Medicine, New York, NY, USA
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Touat M, Li YY, Boynton AN, Spurr LF, Iorgulescu JB, Bohrson CL, Cortes-Ciriano I, Birzu C, Geduldig JE, Pelton K, Lim-Fat MJ, Pal S, Ferrer-Luna R, Ramkissoon SH, Dubois F, Bellamy C, Currimjee N, Bonardi J, Qian K, Ho P, Malinowski S, Taquet L, Jones RE, Shetty A, Chow KH, Sharaf R, Pavlick D, Albacker LA, Younan N, Baldini C, Verreault M, Giry M, Guillerm E, Ammari S, Beuvon F, Mokhtari K, Alentorn A, Dehais C, Houillier C, Laigle-Donadey F, Psimaras D, Lee EQ, Nayak L, McFaline-Figueroa JR, Carpentier A, Cornu P, Capelle L, Mathon B, Barnholtz-Sloan JS, Chakravarti A, Bi WL, Chiocca EA, Fehnel KP, Alexandrescu S, Chi SN, Haas-Kogan D, Batchelor TT, Frampton GM, Alexander BM, Huang RY, Ligon AH, Coulet F, Delattre JY, Hoang-Xuan K, Meredith DM, Santagata S, Duval A, Sanson M, Cherniack AD, Wen PY, Reardon DA, Marabelle A, Park PJ, Idbaih A, Beroukhim R, Bandopadhayay P, Bielle F, Ligon KL. Mechanisms and therapeutic implications of hypermutation in gliomas. Nature 2020; 580:517-523. [PMID: 32322066 PMCID: PMC8235024 DOI: 10.1038/s41586-020-2209-9] [Citation(s) in RCA: 342] [Impact Index Per Article: 85.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 03/04/2020] [Indexed: 12/19/2022]
Abstract
A high tumour mutational burden (hypermutation) is observed in some gliomas1-5; however, the mechanisms by which hypermutation develops and whether it predicts the response to immunotherapy are poorly understood. Here we comprehensively analyse the molecular determinants of mutational burden and signatures in 10,294 gliomas. We delineate two main pathways to hypermutation: a de novo pathway associated with constitutional defects in DNA polymerase and mismatch repair (MMR) genes, and a more common post-treatment pathway, associated with acquired resistance driven by MMR defects in chemotherapy-sensitive gliomas that recur after treatment with the chemotherapy drug temozolomide. Experimentally, the mutational signature of post-treatment hypermutated gliomas was recapitulated by temozolomide-induced damage in cells with MMR deficiency. MMR-deficient gliomas were characterized by a lack of prominent T cell infiltrates, extensive intratumoral heterogeneity, poor patient survival and a low rate of response to PD-1 blockade. Moreover, although bulk analyses did not detect microsatellite instability in MMR-deficient gliomas, single-cell whole-genome sequencing analysis of post-treatment hypermutated glioma cells identified microsatellite mutations. These results show that chemotherapy can drive the acquisition of hypermutated populations without promoting a response to PD-1 blockade and supports the diagnostic use of mutational burden and signatures in cancer.
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Affiliation(s)
- Mehdi Touat
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France.
| | - Yvonne Y Li
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Adam N Boynton
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Liam F Spurr
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - J Bryan Iorgulescu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham & Women's Hospital, Boston, Harvard Medical School, MA, USA
| | - Craig L Bohrson
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Bioinformatics and Integrative Genomics PhD Program, Harvard Medical School, Boston, MA, USA
| | - Isidro Cortes-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Cristina Birzu
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Jack E Geduldig
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kristine Pelton
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Mary Jane Lim-Fat
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sangita Pal
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ruben Ferrer-Luna
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Foundation Medicine Inc., Cambridge, MA, USA
| | - Shakti H Ramkissoon
- Foundation Medicine Inc., Cambridge, MA, USA
- Wake Forest Comprehensive Cancer Center and Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Frank Dubois
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Charlotte Bellamy
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Naomi Currimjee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Juliana Bonardi
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Kenin Qian
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Patricia Ho
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Seth Malinowski
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Leon Taquet
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Robert E Jones
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Aniket Shetty
- Center for Patient Derived Models, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kin-Hoe Chow
- Center for Patient Derived Models, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | | | - Nadia Younan
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Capucine Baldini
- Drug Development Department (DITEP), INSERM U1015, Université Paris Saclay, Gustave Roussy, Villejuif, France
| | - Maïté Verreault
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Marine Giry
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Erell Guillerm
- Unité fonctionnelle d'Oncogénétique et Angiogénétique Moléculaire, Département de génétique, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France
| | - Samy Ammari
- Department of Diagnostic Radiology, Gustave Roussy, Villejuif, France
- IR4M (UMR8081), Université Paris-Sud, Centre National de la Recherche Scientifique, Orsay, France
| | - Frédéric Beuvon
- AP-HP, Université Paris Descartes, Hôpital Cochin, Service d'Anatomie et Cytologie Pathologiques, Paris, France
| | - Karima Mokhtari
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neuropathologie Laboratoire Escourolle, Paris, France
| | - Agusti Alentorn
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Caroline Dehais
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Caroline Houillier
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Florence Laigle-Donadey
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Dimitri Psimaras
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Eudocia Q Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lakshmi Nayak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - J Ricardo McFaline-Figueroa
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alexandre Carpentier
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurochirurgie, Paris, France
| | - Philippe Cornu
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurochirurgie, Paris, France
| | - Laurent Capelle
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurochirurgie, Paris, France
| | - Bertrand Mathon
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurochirurgie, Paris, France
| | - Jill S Barnholtz-Sloan
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Arnab Chakravarti
- Department of Radiation Oncology, Arthur G. James Hospital/Ohio State Comprehensive Cancer Center, Columbus, OH, USA
| | - Wenya Linda Bi
- Department of Neurosurgery, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - E Antonio Chiocca
- Department of Neurosurgery, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Katie Pricola Fehnel
- Department of Neurosurgery, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sanda Alexandrescu
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Susan N Chi
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Daphne Haas-Kogan
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Tracy T Batchelor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Brian M Alexander
- Foundation Medicine Inc., Cambridge, MA, USA
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Raymond Y Huang
- Department of Radiology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Azra H Ligon
- Department of Pathology, Brigham & Women's Hospital, Boston, Harvard Medical School, MA, USA
| | - Florence Coulet
- Unité fonctionnelle d'Oncogénétique et Angiogénétique Moléculaire, Département de génétique, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France
| | - Jean-Yves Delattre
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
- Onconeurotek Tumor Bank, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Khê Hoang-Xuan
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - David M Meredith
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham & Women's Hospital, Boston, Harvard Medical School, MA, USA
| | - Sandro Santagata
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham & Women's Hospital, Boston, Harvard Medical School, MA, USA
- Ludwig Center at Harvard Medical School, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Alex Duval
- Sorbonne Université, Inserm, UMR 938, Centre de Recherche Saint Antoine, Equipe Instabilité des Microsatellites et Cancer, Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France
| | - Marc Sanson
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
- Onconeurotek Tumor Bank, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Andrew D Cherniack
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Patrick Y Wen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - David A Reardon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Aurélien Marabelle
- Drug Development Department (DITEP), INSERM U1015, Université Paris Saclay, Gustave Roussy, Villejuif, France
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Ahmed Idbaih
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Rameen Beroukhim
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Pratiti Bandopadhayay
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| | - Franck Bielle
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neuropathologie Laboratoire Escourolle, Paris, France.
| | - Keith L Ligon
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Pathology, Brigham & Women's Hospital, Boston, Harvard Medical School, MA, USA.
- Center for Patient Derived Models, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
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Li J, Etemad B, Namazi G, Wen Y, Jilg N, Esmaeilzadeh E, Zhang X, Sharaf R, Brumme Z, Kearney M. HIV post-treatment control despite plasma viral evolution and dual infection. J Virus Erad 2019. [DOI: 10.1016/s2055-6640(20)30170-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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40
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Namazi G, Fajnzylber JM, Aga E, Bosch RJ, Acosta EP, Sharaf R, Hartogensis W, Jacobson JM, Connick E, Volberding P, Skiest D, Margolis D, Sneller MC, Little SJ, Gianella S, Smith DM, Kuritzkes DR, Gulick RM, Mellors JW, Mehraj V, Gandhi RT, Mitsuyasu R, Schooley RT, Henry K, Tebas P, Deeks SG, Chun TW, Collier AC, Routy JP, Hecht FM, Walker BD, Li JZ. The Control of HIV After Antiretroviral Medication Pause (CHAMP) Study: Posttreatment Controllers Identified From 14 Clinical Studies. J Infect Dis 2019; 218:1954-1963. [PMID: 30085241 DOI: 10.1093/infdis/jiy479] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 07/31/2018] [Indexed: 01/09/2023] Open
Abstract
Background HIV posttreatment controllers are rare individuals who start antiretroviral therapy (ART), but maintain HIV suppression after treatment interruption. The frequency of posttreatment control and posttreatment interruption viral dynamics have not been well characterized. Methods Posttreatment controllers were identified from 14 studies and defined as individuals who underwent treatment interruption with viral loads ≤400 copies/mL at two-thirds or more of time points for ≥24 weeks. Viral load and CD4+ cell dynamics were compared between posttreatment controllers and noncontrollers. Results Of the 67 posttreatment controllers identified, 38 initiated ART during early HIV infection. Posttreatment controllers were more frequently identified in those treated during early versus chronic infection (13% vs 4%, P < .001). In posttreatment controllers with weekly viral load monitoring, 45% had a peak posttreatment interruption viral load of ≥1000 copies/mL and 33% had a peak viral load ≥10000 copies/mL. Of posttreatment controllers, 55% maintained HIV control for 2 years, with approximately 20% maintaining control for ≥5 years. Conclusions Posttreatment control was more commonly identified amongst early treated individuals, frequently characterized by early transient viral rebound and heterogeneous durability of HIV remission. These results may provide mechanistic insights and have implications for the design of trials aimed at achieving HIV remission.
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Affiliation(s)
- Golnaz Namazi
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jesse M Fajnzylber
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Evgenia Aga
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Ronald J Bosch
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | | | - Radwa Sharaf
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | | | | | | | | | | | - Michael C Sneller
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | | | | | | | - Daniel R Kuritzkes
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | | | - Vikram Mehraj
- McGill University Health Centre, Montreal, Quebec, Canada
| | - Rajesh T Gandhi
- Massachusetts General Hospital, Harvard Medical School, Boston
| | | | | | | | | | | | - Tae-Wook Chun
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | | | | | | | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge
| | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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41
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Einkauf KB, Lee GQ, Gao C, Sharaf R, Sun X, Hua S, Chen SM, Jiang C, Lian X, Chowdhury FZ, Rosenberg ES, Chun TW, Li JZ, Yu XG, Lichterfeld M. Intact HIV-1 proviruses accumulate at distinct chromosomal positions during prolonged antiretroviral therapy. J Clin Invest 2019; 129:988-998. [PMID: 30688658 DOI: 10.1172/jci124291] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [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: 08/16/2018] [Accepted: 12/04/2018] [Indexed: 12/16/2022] Open
Abstract
Chromosomal integration of genome-intact HIV-1 sequences into the host genome creates a reservoir of virally infected cells that persists throughout life, necessitating indefinite antiretroviral suppression therapy. During effective antiviral treatment, the majority of these proviruses remain transcriptionally silent, but mechanisms responsible for viral latency are insufficiently clear. Here, we used matched integration site and proviral sequencing (MIP-Seq), an experimental approach involving multiple displacement amplification of individual proviral species, followed by near-full-length HIV-1 next-generation sequencing and corresponding chromosomal integration site analysis to selectively map the chromosomal positions of intact and defective proviruses in 3 HIV-1-infected individuals undergoing long-term antiretroviral therapy. Simultaneously, chromatin accessibility and gene expression in autologous CD4+ T cells were analyzed by assays for transposase-accessible chromatin using sequencing (ATAC-Seq) and RNA-Seq. We observed that in comparison to proviruses with defective sequences, intact HIV-1 proviruses were enriched for non-genic chromosomal positions and more frequently showed an opposite orientation relative to host genes. In addition, intact HIV-1 proviruses were preferentially integrated in either relative proximity to or increased distance from active transcriptional start sites and to accessible chromatin regions. These studies strongly suggest selection of intact proviruses with features of deeper viral latency during prolonged antiretroviral therapy, and may be informative for targeting the genome-intact viral reservoir.
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Affiliation(s)
- Kevin B Einkauf
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Guinevere Q Lee
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Radwa Sharaf
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Xiaoming Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Stephane Hua
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Samantha My Chen
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Chenyang Jiang
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Xiaodong Lian
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Eric S Rosenberg
- Infectious Disease Division, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Tae-Wook Chun
- National Institute of Allergy and Infectious Diseases (NIAID), Bethesda, Maryland, USA
| | - Jonathan Z Li
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Xu G Yu
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Mathias Lichterfeld
- Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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42
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Sharaf R, Lee GQ, Sun X, Etemad B, Aboukhater LM, Hu Z, Brumme ZL, Aga E, Bosch RJ, Wen Y, Namazi G, Gao C, Acosta EP, Gandhi RT, Jacobson JM, Skiest D, Margolis DM, Mitsuyasu R, Volberding P, Connick E, Kuritzkes DR, Lederman MM, Yu XG, Lichterfeld M, Li JZ. HIV-1 proviral landscapes distinguish posttreatment controllers from noncontrollers. J Clin Invest 2018; 128:4074-4085. [PMID: 30024859 PMCID: PMC6118642 DOI: 10.1172/jci120549] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [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: 02/15/2018] [Accepted: 07/03/2018] [Indexed: 02/03/2023] Open
Abstract
HIV posttreatment controllers (PTCs) represent a natural model of sustained HIV remission, but they are rare and little is known about their viral reservoir. We obtained 1,450 proviral sequences after near-full-length amplification for 10 PTCs and 16 posttreatment noncontrollers (NCs). Before treatment interruption, the median intact and total reservoir size in PTCs was 7-fold lower than in NCs, but the proportion of intact, defective, and total clonally expanded proviral genomes was not significantly different between the 2 groups. Quantification of total but not intact proviral genome copies predicted sustained HIV remission as 81% of NCs, but none of the PTCs had a total proviral genome greater than 4 copies per million peripheral blood mononuclear cells (PBMCs). The results highlight the restricted intact and defective HIV reservoir in PTCs and suggest that total proviral genome burden could act as the first biomarker for identifying PTCs. Total and defective but not intact proviral copy numbers correlated with levels of cell-associated HIV RNA, activated NK cell percentages, and both HIV-specific CD4+ and CD8+ responses. These results support the concept that defective HIV genomes can lead to viral antigen production and interact with both the innate and adaptive immune systems.
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Affiliation(s)
- Radwa Sharaf
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Harvard PhD Program in Virology, Division of Medical Sciences, Harvard University, Boston, Massachusetts, USA
| | - Guinevere Q. Lee
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Xiaoming Sun
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Behzad Etemad
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Layla M. Aboukhater
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Zixin Hu
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Zabrina L. Brumme
- Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Evgenia Aga
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Ronald J. Bosch
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Ying Wen
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Golnaz Namazi
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ce Gao
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | | | - Rajesh T. Gandhi
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Daniel Skiest
- University of Massachusetts Medical School-Baystate, Springfield, Massachusetts, USA
| | | | | | - Paul Volberding
- Gladstone Center for AIDS Research, UCSF, San Francisco, California, USA
| | | | - Daniel R. Kuritzkes
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Xu G. Yu
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
- University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Mathias Lichterfeld
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Jonathan Z. Li
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Abstract
The introduction of multiphoton microscopy has dramatically broadened the scope of intravital imaging studies and has allowed researchers to validate and refine basic mechanistic concepts in many areas of biology within the context of physiologically relevant tissue microenvironments. This has also led to new insights into the behavior of immune cells at steady state, and how their behaviors are altered during an immune response. At the same time, advances in the humanized mouse model have allowed for in vivo studies of strictly human pathogens, such as HIV-1. Here, we describe in detail an intravital microscopy approach to visualize the dynamic behavior of HIV-infected T cells within the lymph nodes of live, anesthetized humanized mice.
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Affiliation(s)
- Radwa Sharaf
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy andImmunology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02129, USA
| | - Thorsten R Mempel
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy andImmunology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02129, USA
| | - Thomas T Murooka
- Departments of Immunology and Medical Microbiology, University of Manitoba, 750 McDermot Ave, Rm 433, Winnipeg, MB, Canada, R3E 0T5.
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44
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Schmueck-Henneresse M, Sharaf R, Vogt K, Weist BJD, Landwehr-Kenzel S, Fuehrer H, Jurisch A, Babel N, Rooney CM, Reinke P, Volk HD. Peripheral blood-derived virus-specific memory stem T cells mature to functional effector memory subsets with self-renewal potency. J Immunol 2015; 194:5559-67. [PMID: 25917088 DOI: 10.4049/jimmunol.1402090] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 03/27/2015] [Indexed: 12/31/2022]
Abstract
Memory T cells expressing stem cell-like properties have been described recently. The capacity of self-renewal and differentiation into various memory/effector subsets make them attractive for adoptive T cell therapy to combat severe virus infections and tumors. The very few reports on human memory stem T cells (T(SCM)) are restricted to analyses on polyclonal T cells, but extensive data on Ag-specific T(SCM )are missing. This might be due to their very low frequency limiting their enrichment and characterization. In this article, we provide functional and phenotypic data on human viral-specific T(SCM), defined as CD8(+)CD45RA(+)CCR7(+)CD127(+)CD95(+). Whereas <1% of total T cells express the T(SCM) phenotype, human CMV-specific T(SCM) can be detected at frequencies similar to those seen in other subsets, resulting in ∼ 1 /10,000 human CMV-specific T(SCM). A new virus-specific expansion protocol of sort-purified T(SCM) reveals both upregulation of various T cell subset markers and preservation of their stem cell phenotype in a significant proportion, indicating both self-renewal and differentiation potency of virus-specific T cells sharing their TCR repertoire. Furthermore, we describe a simplified culture protocol that allows fast expansion of virus-specific T(SCM) starting from a mixed naive T/T(SCM) pool of PBLs. Due to the clinical-grade compatibility, this might be the basis for novel cell therapeutic options in life-threatening courses of viral and tumor disease.
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Affiliation(s)
- Michael Schmueck-Henneresse
- Institute for Medical Immunology, Charité University Medicine Berlin, D-13353 Berlin, Germany; Renal and Transplant Research Unit, Department of Nephrology and Internal Intensive Care, Charité University Medicine Berlin, D-13353 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, D-13353 Berlin, Germany;
| | - Radwa Sharaf
- Institute for Medical Immunology, Charité University Medicine Berlin, D-13353 Berlin, Germany
| | - Katrin Vogt
- Institute for Medical Immunology, Charité University Medicine Berlin, D-13353 Berlin, Germany
| | - Benjamin J D Weist
- Renal and Transplant Research Unit, Department of Nephrology and Internal Intensive Care, Charité University Medicine Berlin, D-13353 Berlin, Germany
| | - Sybille Landwehr-Kenzel
- Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, D-13353 Berlin, Germany; Berlin-Brandenburg School for Regenerative Therapies, Charité University Medicine Berlin, D-13353 Berlin, Germany; Department for Pediatric Pulmonology and Immunology, Charité University Medicine Berlin, D-13353 Berlin, Germany
| | - Henrike Fuehrer
- Renal and Transplant Research Unit, Department of Nephrology and Internal Intensive Care, Charité University Medicine Berlin, D-13353 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, D-13353 Berlin, Germany
| | - Anke Jurisch
- Institute for Medical Immunology, Charité University Medicine Berlin, D-13353 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, D-13353 Berlin, Germany
| | - Nina Babel
- Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, D-13353 Berlin, Germany; Marien Hospital Herne, Ruhr University Bochum, D-44625 Herne, Germany; and
| | - Cliona M Rooney
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030
| | - Petra Reinke
- Renal and Transplant Research Unit, Department of Nephrology and Internal Intensive Care, Charité University Medicine Berlin, D-13353 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, D-13353 Berlin, Germany
| | - Hans-Dieter Volk
- Institute for Medical Immunology, Charité University Medicine Berlin, D-13353 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, D-13353 Berlin, Germany
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45
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Robbins RJ, Tuttle RM, Sonenberg M, Shaha A, Sharaf R, Robbins H, Fleisher M, Larson SM. Radioiodine ablation of thyroid remnants after preparation with recombinant human thyrotropin. Thyroid 2001; 11:865-9. [PMID: 11575856 DOI: 10.1089/105072501316973127] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Radioiodine ablation (RA) of normal thyroid remnants after thyroidectomy for differentiated thyroid carcinoma improves the sensitivity of subsequent radioiodine scans and serum thyroglobulin measurements for detection of residual thyroid carcinoma. Local cancer recurrences are also lower after RA. One standard preparation for RA involves rendering the patient hypothyroid in order to stimulate endogenous thyrotropin (TSH) secretion and sodium iodide symporter (NIS) activity. An alternative approach is to prescribe thyroxine after thyroidectomy and to stimulate NIS with exogenous recombinant human thyrotropin (rhTSH). This latter approach was used in 10 patients at our medical center. Complete resolution of all visible 131I thyroid bed uptake was achieved in all when follow-up scans were performed 5 to 13 months later. This approach has the potential to successfully ablate thyroid remnants without the need to induce hypothyroidism.
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Affiliation(s)
- R J Robbins
- Department of Medicine, Memorial Hospital for Cancer and Allied Diseases, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.
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46
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Ghosh S, Watanabe RM, Hauser ER, Valle T, Magnuson VL, Erdos MR, Langefeld CD, Balow J, Ally DS, Kohtamaki K, Chines P, Birznieks G, Kaleta HS, Musick A, Te C, Tannenbaum J, Eldridge W, Shapiro S, Martin C, Witt A, So A, Chang J, Shurtleff B, Porter R, Kudelko K, Unni A, Segal L, Sharaf R, Blaschak-Harvan J, Eriksson J, Tenkula T, Vidgren G, Ehnholm C, Tuomilehto-Wolf E, Hagopian W, Buchanan TA, Tuomilehto J, Bergman RN, Collins FS, Boehnke M. Type 2 diabetes: evidence for linkage on chromosome 20 in 716 Finnish affected sib pairs. Proc Natl Acad Sci U S A 1999; 96:2198-203. [PMID: 10051618 PMCID: PMC26760 DOI: 10.1073/pnas.96.5.2198] [Citation(s) in RCA: 170] [Impact Index Per Article: 6.8] [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] [Accepted: 12/31/1998] [Indexed: 12/22/2022] Open
Abstract
We are conducting a genome scan at an average resolution of 10 centimorgans (cM) for type 2 diabetes susceptibility genes in 716 affected sib pairs from 477 Finnish families. To date, our best evidence for linkage is on chromosome 20 with potentially separable peaks located on both the long and short arms. The unweighted multipoint maximum logarithm of odds score (MLS) was 3.08 on 20p (location, chi = 19.5 cM) under an additive model, whereas the weighted MLS was 2.06 on 20q (chi = 57 cM, recurrence risk,lambda(s) = 1. 25, P = 0.009). Weighted logarithm of odds scores of 2.00 (chi = 69.5 cM, P = 0.010) and 1.92 (chi = 18.5 cM, P = 0.013) were also observed. Ordered subset analyses based on sibships with extreme mean values of diabetes-related quantitative traits yielded sets of families who contributed disproportionately to the peaks. Two-hour glucose levels in offspring of diabetic individuals gave a MLS of 2. 12 (P = 0.0018) at 9.5 cM. Evidence from this and other studies suggests at least two diabetes-susceptibility genes on chromosome 20. We have also screened the gene for maturity-onset diabetes of the young 1, hepatic nuclear factor 4-a (HNF-4alpha) in 64 affected sibships with evidence for high chromosomal sharing at its location on chromosome 20q. We found no evidence that sequence changes in this gene accounted for the linkage results we observed.
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Affiliation(s)
- S Ghosh
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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