1
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Mata DA, Lee JK, Shanmugam V, Marcus CB, Schrock AB, Williams EA, Ritterhouse LL, Hickman RA, Janovitz T, Patel NR, Kroger BR, Ross JS, Mirza KM, Oxnard GR, Vergilio JA, Elvin JA, Benhamida JK, Decker B, Xu ML. Liquid biopsy-based circulating tumour (ct)DNA analysis of a spectrum of myeloid and lymphoid malignancies yields clinically actionable results. Histopathology 2024; 84:1224-1237. [PMID: 38422618 DOI: 10.1111/his.15168] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024]
Abstract
AIMS Liquid biopsy (LBx)-based next-generation sequencing (NGS) of circulating tumour DNA (ctDNA) can facilitate molecular profiling of haematopoietic neoplasms (HNs), particularly when tissue-based NGS is infeasible. METHODS AND RESULTS We studied HN LBx samples tested with FoundationOne Liquid CDx, FoundationOne Liquid, or FoundationACT between July 2016 and March 2022. We identified 271 samples: 89 non-Hodgkin lymphoma (NHL), 43 plasma-cell neoplasm (PCN), 41 histiocytoses, 27 myelodysplastic syndrome (MDS), 25 diffuse large B-cell lymphoma (DLBCL), 22 myeloproliferative neoplasm (MPN), 14 Hodgkin lymphoma (HL), and 10 acute myeloid leukaemia (AML). Among 73.4% with detectable pathogenic alterations, median maximum somatic allele frequency (MSAF) was 16.6%, with AML (36.2%), MDS (19.7%), and MPN (44.5%) having higher MSAFs than DLBCL (3.9%), NHL (8.4%), HL (1.5%), PCN (2.8%), and histiocytoses (1.8%) (P = 0.001). LBx detected characteristic alterations across HNs, including in TP53, KRAS, MYD88, and BTK in NHLs; TP53, KRAS, NRAS, and BRAF in PCNs; IGH in DLBCL; TP53, ATM, and PDCD1LG2 in HL; BRAF and MAP2K1 in histiocytoses; TP53, SF3B1, DNMT3A, TET2, and ASXL1 in MDS; JAK2 in MPNs; and FLT3, IDH2, and NPM1 in AML. Among 24 samples, the positive percent agreement by LBx was 75.7% for variants present in paired buffy coat, marrow, or tissues. Also, 75.0% of pairs exhibited alterations only present on LBx. These were predominantly subclonal (clonal fraction of 3.8%), reflecting the analytical sensitivity of LBx. CONCLUSION These data demonstrate that LBx can detect relevant genomic alterations across HNs, including at low clonal fractions, suggesting a potential clinical utility for identifying residual or emerging therapy-resistant clones that may be undetectable in site-specific tissue biopsies.
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Affiliation(s)
| | | | - Vignesh Shanmugam
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Erik A Williams
- Foundation Medicine, Inc., Cambridge, MA, USA
- Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | | | | | | | - Benjamin R Kroger
- Division of Hematology/Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, MA, USA
- Departments of Pathology, Urology, and Medicine (Oncology), State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Kamran M Mirza
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | | | | | | | - Jamal K Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Mina L Xu
- Department of Pathology, Yale New-Haven Hospital, Yale School of Medicine, New Haven, CT, USA
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2
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Scott JA, Lennerz J, Johnson ML, Gordan LN, Dumanois RH, Quagliata L, Ritterhouse LL, Cappuzzo F, Wang B, Xue M, Vasudevan A, Varughese P, Vaidya V, Gart M, Dorrow N, Gierman HJ, Choksi RJ. Compromised Outcomes in Stage IV Non-Small-Cell Lung Cancer With Actionable Mutations Initially Treated Without Tyrosine Kinase Inhibitors: A Retrospective Analysis of Real-World Data. JCO Oncol Pract 2024; 20:145-153. [PMID: 37556776 PMCID: PMC10827288 DOI: 10.1200/op.22.00611] [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: 08/31/2022] [Revised: 05/24/2023] [Accepted: 06/29/2023] [Indexed: 08/11/2023] Open
Abstract
PURPOSE Identification and targeting of actionable oncogenic drivers (AODs) in advanced non-small-cell lung cancer (NSCLC) has dramatically improved outcomes. However, genomic testing uptake is variable and hampered by factors including slow turnaround time, frequently resulting in initial non-tyrosine kinase inhibitor (TKI) treatment. We investigate how this behavior affects outcomes. METHODS This retrospective analysis of real-world, deidentified data from the Integra Connect Database included adults with stage IV NSCLC newly diagnosed from January 1, 2018, to December 31, 2020, with mutations of EGFR, ALK, ROS1, BRAF, MET, RET, ERBB2, or NTRK. Outcomes were reported as time to next treatment or death (TTNT) and overall survival (OS). RESULTS Five hundred ten patients harboring AODs were identified and grouped as follows: group A (n = 379) were treated after the AOD was reported and served as the comparator. One hundred thirty-one patients treated before their AOD report were divided into group B (n = 47) who were initially started on chemotherapy and/or checkpoint inhibitor but switched to appropriate TKI within 35 days and group C (n = 84) who were also started empirically on non-TKI and did not switch within 35 days. Survival (OS) was significantly superior in group A compared with group C; TTNT was significantly superior in group A compared with groups B and C. CONCLUSION For patients harboring AODs in advanced NSCLC, initial treatment before receipt of genomic test results yields significantly inferior outcomes and should be avoided. Molecular profiling panels with rapid turnaround times are essential to optimize patient outcomes and should be standard of care.
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Affiliation(s)
| | - Jochen Lennerz
- Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | | | - Lucio N. Gordan
- Research Institute, Florida Cancer Specialists, Fort Myers, FL
| | | | | | | | - Federico Cappuzzo
- Division of Medical Oncology 2, IRCCS Regina Elena National Cancer Institute, Roma, Italy
| | | | - Mei Xue
- Integra Connect, West Palm Beach, FL
| | | | | | - Varun Vaidya
- Department of Pharmacy Practice, The University of Toledo, Toledo, OH
| | - Mike Gart
- Integra Connect, West Palm Beach, FL
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3
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Weissinger SE, Georgantas NZ, Thierauf JC, Pellerin R, Gardecki E, Kühlinger S, Ritterhouse LL, Möller P, Lennerz JK. Slide-to-Slide Tissue Transfer and Array Assembly From Limited Samples for Comprehensive Molecular Profiling. J Transl Med 2023; 103:100062. [PMID: 36801639 PMCID: PMC10198954 DOI: 10.1016/j.labinv.2023.100062] [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: 10/12/2022] [Revised: 12/28/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023] Open
Abstract
Tissue microarrays (TMA) have become an important tool in high-throughput molecular profiling of tissue samples in the translational research setting. Unfortunately, high-throughput profiling in small biopsy specimens or rare tumor samples (eg, orphan diseases or unusual tumors) is often precluded owing to limited amounts of tissue. To overcome these challenges, we devised a method that allows tissue transfer and construction of TMAs from individual 2- to 5-μm sections for subsequent molecular profiling. We named the technique slide-to-slide (STS) transfer, and it requires a series of chemical exposures (so-called xylene-methacrylate exchange) in combination with rehydrated lifting, microdissection of donor tissues into multiple small tissue fragments (methacrylate-tissue tiles), and subsequent remounting on separate recipient slides (STS array slide). We developed the STS technique by assessing the efficacy and analytical performance using the following key metrics: (a) dropout rate, (b) transfer efficacy, (c) success rates using different antigen-retrieval methods, (d) success rates of immunohistochemical stains, (e) fluorescent in situ hybridization success rates, and (f) DNA and (g) RNA extraction yields from single slides, which all functioned appropriately. The dropout rate ranged from 0.7% to 6.2%; however, we applied the same STS technique successfully to fill these dropouts ("rescue" transfer). Hematoxylin and eosin assessment of donor slides confirmed a transfer efficacy of >93%, depending on the size of the tissue (range, 76%-100%). Fluorescent in situ hybridization success rates and nucleic acid yields were comparable with those of traditional workflows. In this study, we present a quick, reliable, and cost-effective method that offers the key advantages of TMAs and other molecular techniques-even when tissue is sparse. The perspectives of this technology in biomedical sciences and clinical practice are promising, given that it allows laboratories to create more data with less tissue.
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Affiliation(s)
- Stephanie E Weissinger
- Institute of Pathology, Alb Fils Clinics GmbH, Göppingen, Germany; Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | - N Zeke Georgantas
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts
| | - Julia C Thierauf
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts
| | - Rebecca Pellerin
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts
| | - Emma Gardecki
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts
| | | | - Lauren L Ritterhouse
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts
| | - Peter Möller
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | - Jochen K Lennerz
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts.
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4
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Lennerz JK, Salgado R, Kim GE, Sirintrapun SJ, Thierauf JC, Singh A, Indave I, Bard A, Weissinger SE, Heher YK, de Baca ME, Cree IA, Bennett S, Carobene A, Ozben T, Ritterhouse LL. Diagnostic quality model (DQM): an integrated framework for the assessment of diagnostic quality when using AI/ML. Clin Chem Lab Med 2023; 61:544-557. [PMID: 36696602 DOI: 10.1515/cclm-2022-1151] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/13/2023] [Indexed: 01/26/2023]
Abstract
BACKGROUND Laboratory medicine has reached the era where promises of artificial intelligence and machine learning (AI/ML) seem palpable. Currently, the primary responsibility for risk-benefit assessment in clinical practice resides with the medical director. Unfortunately, there is no tool or concept that enables diagnostic quality assessment for the various potential AI/ML applications. Specifically, we noted that an operational definition of laboratory diagnostic quality - for the specific purpose of assessing AI/ML improvements - is currently missing. METHODS A session at the 3rd Strategic Conference of the European Federation of Laboratory Medicine in 2022 on "AI in the Laboratory of the Future" prompted an expert roundtable discussion. Here we present a conceptual diagnostic quality framework for the specific purpose of assessing AI/ML implementations. RESULTS The presented framework is termed diagnostic quality model (DQM) and distinguishes AI/ML improvements at the test, procedure, laboratory, or healthcare ecosystem level. The operational definition illustrates the nested relationship among these levels. The model can help to define relevant objectives for implementation and how levels come together to form coherent diagnostics. The affected levels are referred to as scope and we provide a rubric to quantify AI/ML improvements while complying with existing, mandated regulatory standards. We present 4 relevant clinical scenarios including multi-modal diagnostics and compare the model to existing quality management systems. CONCLUSIONS A diagnostic quality model is essential to navigate the complexities of clinical AI/ML implementations. The presented diagnostic quality framework can help to specify and communicate the key implications of AI/ML solutions in laboratory diagnostics.
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Affiliation(s)
- Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital/Harvard Medical, Boston, MA, USA
| | - Roberto Salgado
- Department of Pathology, GZA-ZNA Hospitals, Antwerp, Belgium
- Division of Research, Peter Mac Callum Cancer Centre, Melbourne, Australia
| | - Grace E Kim
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | | | - Julia C Thierauf
- Department of Pathology, Massachusetts General Hospital/Harvard Medical, Boston, MA, USA
- Department of Otorhinolaryngology, Head and Neck Surgery, German Cancer Research Center (DKFZ), Heidelberg University Hospital and Research Group Molecular Mechanisms of Head and Neck Tumors, Heidelberg, Germany
| | - Ankit Singh
- Department of Pathology, Massachusetts General Hospital/Harvard Medical, Boston, MA, USA
| | - Iciar Indave
- European Monitoring Centre for Drugs and Drug Addiction (EMCDDA), Lisbon, Portugal
| | - Adam Bard
- Department of Pathology, Massachusetts General Hospital/Harvard Medical, Boston, MA, USA
| | | | - Yael K Heher
- Department of Pathology, Massachusetts General Hospital/Harvard Medical, Boston, MA, USA
| | | | - Ian A Cree
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
| | - Shannon Bennett
- Department of Laboratory Medicine and Pathology (DLMP), Mayo Clinic, Rochester, MN, USA
| | - Anna Carobene
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Tomris Ozben
- Medical Faculty, Dept. of Clinical Biochemistry, Akdeniz University, Antalya, Türkiye
- Medical Faculty, Clinical and Experimental Medicine, Ph.D. Program, University of Modena and Reggio Emilia, Modena, Italy
| | - Lauren L Ritterhouse
- Department of Pathology, Massachusetts General Hospital/Harvard Medical, Boston, MA, USA
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5
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Boulanger MC, Temel JS, Mino-Kenudson M, Ritterhouse LL, Dagogo-Jack I. Primary Resistance to Larotrectinib in a Patient with Squamous Non-Small Cell Lung Cancer with Subclonal NTRK1 Fusion: Case Report. JTO Clin Res Rep 2023; 4:100501. [PMID: 37095749 PMCID: PMC10122012 DOI: 10.1016/j.jtocrr.2023.100501] [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] [Received: 11/13/2022] [Revised: 02/13/2023] [Accepted: 03/12/2023] [Indexed: 03/19/2023] Open
Abstract
The NTRK genes encode the TRK proteins. NTRK fusions lead to constitutively active, ligand-independent downstream signaling. NTRK fusions are implicated in up to 1% of all solid tumors and 0.2% of NSCLC. Larotrectinib, a highly selective small molecule inhibitor of all three TRK proteins, has a response rate of 75% across a wide range of solid tumors. Mechanisms of primary resistance to larotrectinib are not well understood. We report a case of a 75-year-old male with minimal smoking history with NTRK fusion-positive metastatic squamous NSCLC with primary resistance to larotrectinib. We suggest subclonal NTRK fusion as a possible mechanism contributing to primary resistance to larotrectinib.
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Affiliation(s)
- Mary C. Boulanger
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Jennifer S. Temel
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Ibiayi Dagogo-Jack
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Corresponding author. Address for correspondence: Ibiayi Dagogo-Jack, MD, Department of Medicine, Massachusetts General Hospital Cancer Center, 55 Fruit Street, Yawkey 7B, Boston, MA 02114.
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6
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Brett JO, Ritterhouse LL, Newman ET, Irwin KE, Dawson M, Ryan LY, Spring LM, Rivera MN, Lennerz JK, Dias-Santagata D, Ellisen LW, Bardia A, Wander SA. Clinical Implications and Treatment Strategies for ESR1 Fusions in Hormone Receptor-Positive Metastatic Breast Cancer: A Case Series. Oncologist 2022; 28:172-179. [PMID: 36493359 PMCID: PMC9907034 DOI: 10.1093/oncolo/oyac248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 10/25/2022] [Indexed: 12/14/2022] Open
Abstract
In hormone receptor-positive metastatic breast cancer (HR+ MBC), endocrine resistance is commonly due to genetic alterations of ESR1, the gene encoding estrogen receptor alpha (ERα). While ESR1 point mutations (ESR1-MUT) cause acquired resistance to aromatase inhibition (AI) through constitutive activation, far less is known about the molecular functions and clinical consequences of ESR1 fusions (ESR1-FUS). This case series discusses 4 patients with HR+ MBC with ESR1-FUS in the context of the existing ESR1-FUS literature. We consider therapeutic strategies and raise the hypothesis that CDK4/6 inhibition (CDK4/6i) may be effective against ESR1-FUS with functional ligand-binding domain swaps. These cases highlight the importance of screening for ESR1-FUS in patients with HR+ MBC while continuing investigation of precision treatments for these genomic rearrangements.
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Affiliation(s)
- Jamie O Brett
- Massachusetts General Hospital Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Lauren L Ritterhouse
- Massachusetts General Hospital Department of Pathology, Center for Integrated Diagnostics, Harvard Medical School, Boston, MA, USA,Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Erik T Newman
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA,Massachusetts General Hospital Department of Orthopedic Surgery, Harvard Medical School, Boston, MA, USA
| | - Kelly E Irwin
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA,Massachusetts General Hospital Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Megan Dawson
- Massachusetts General Hospital Department of Psychiatry, Harvard Medical School, Boston, MA, USA,University of Michigan Department of Psychiatry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lianne Y Ryan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Laura M Spring
- Massachusetts General Hospital Department of Medicine, Harvard Medical School, Boston, MA, USA,Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Miguel N Rivera
- Massachusetts General Hospital Department of Pathology, Center for Integrated Diagnostics, Harvard Medical School, Boston, MA, USA,Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Jochen K Lennerz
- Massachusetts General Hospital Department of Pathology, Center for Integrated Diagnostics, Harvard Medical School, Boston, MA, USA,Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Dora Dias-Santagata
- Massachusetts General Hospital Department of Pathology, Center for Integrated Diagnostics, Harvard Medical School, Boston, MA, USA
| | - Leif W Ellisen
- Massachusetts General Hospital Department of Medicine, Harvard Medical School, Boston, MA, USA,Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Aditya Bardia
- Massachusetts General Hospital Department of Medicine, Harvard Medical School, Boston, MA, USA,Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Seth A Wander
- Corresponding author: Seth A. Wander, MD, PhD, Massachusetts General Hospital Cancer Center, Harvard Medical School, 55 Fruit Street, Boston, MA 02114, USA. Tel: +1 617 726 6500; E-mail:
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7
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Dias-Santagata D, Heist RS, Bard AZ, da Silva AFL, Dagogo-Jack I, Nardi V, Ritterhouse LL, Spring LM, Jessop N, Farahani AA, Mino-Kenudson M, Allen J, Goyal L, Parikh A, Misdraji J, Shankar G, Jordan JT, Martinez-Lage M, Frosch M, Graubert T, Fathi AT, Hobbs GS, Hasserjian RP, Raje N, Abramson J, Schwartz JH, Sullivan RJ, Miller D, Hoang MP, Isakoff S, Ly A, Bouberhan S, Watkins J, Oliva E, Wirth L, Sadow PM, Faquin W, Cote GM, Hung YP, Gao X, Wu CL, Garg S, Rivera M, Le LP, John Iafrate A, Juric D, Hochberg EP, Clark J, Bardia A, Lennerz JK. Implementation and Clinical Adoption of Precision Oncology Workflows Across a Healthcare Network. Oncologist 2022; 27:930-939. [PMID: 35852437 PMCID: PMC9632318 DOI: 10.1093/oncolo/oyac134] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/17/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Precision oncology relies on molecular diagnostics, and the value-proposition of modern healthcare networks promises a higher standard of care across partner sites. We present the results of a clinical pilot to standardize precision oncology workflows. METHODS Workflows are defined as the development, roll-out, and updating of disease-specific molecular order sets. We tracked the timeline, composition, and effort of consensus meetings to define the combination of molecular tests. To assess clinical impact, we examined order set adoption over a two-year period (before and after roll-out) across all gastrointestinal and hepatopancreatobiliary (GI) malignancies, and by provider location within the network. RESULTS Development of 12 disease center-specific order sets took ~9 months, and the average number of tests per indication changed from 2.9 to 2.8 (P = .74). After roll-out, we identified significant increases in requests for GI patients (17%; P < .001), compliance with testing recommendations (9%; P < .001), and the fraction of "abnormal" results (6%; P < .001). Of 1088 GI patients, only 3 received targeted agents based on findings derived from non-recommended orders (1 before and 2 after roll-out); indicating that our practice did not negatively affect patient treatments. Preliminary analysis showed 99% compliance by providers in network sites, confirming the adoption of the order sets across the network. CONCLUSION Our study details the effort of establishing precision oncology workflows, the adoption pattern, and the absence of harm from the reduction of non-recommended orders. Establishing a modifiable communication tool for molecular testing is an essential component to optimize patient care via precision oncology.
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Affiliation(s)
- Dora Dias-Santagata
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Rebecca S Heist
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Adam Z Bard
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Ibiayi Dagogo-Jack
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lauren L Ritterhouse
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Laura M Spring
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Nicholas Jessop
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Alexander A Farahani
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jill Allen
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Lipika Goyal
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Aparna Parikh
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Joseph Misdraji
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Present affiliation: Department of Pathology, Yale University, New Haven, CT, USA
| | - Ganesh Shankar
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Justin T Jordan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Maria Martinez-Lage
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Matthew Frosch
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Timothy Graubert
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Amir T Fathi
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Gabriela S Hobbs
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Robert P Hasserjian
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Noopur Raje
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Jeremy Abramson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Joel H Schwartz
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Ryan J Sullivan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - David Miller
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Mai P Hoang
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Steven Isakoff
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Amy Ly
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sara Bouberhan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Jaclyn Watkins
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Esther Oliva
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lori Wirth
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Peter M Sadow
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - William Faquin
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Gregory M Cote
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Yin P Hung
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xin Gao
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Chin-Lee Wu
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Salil Garg
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Miguel Rivera
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Long P Le
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Dejan Juric
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Ephraim P Hochberg
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Jeffrey Clark
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Aditya Bardia
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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8
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Roy-Chowdhuri S, Davies KD, Ritterhouse LL, Snow AN. ERBB2 (HER2) Alterations in Colorectal Cancer. J Mol Diagn 2022; 24:1064-1066. [DOI: 10.1016/j.jmoldx.2022.07.001] [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] [Received: 05/25/2022] [Revised: 06/03/2022] [Accepted: 07/19/2022] [Indexed: 10/15/2022] Open
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9
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Ritterhouse LL, Gogakos T. Molecular Biomarkers of Response to Cancer Immunotherapy. Clin Lab Med 2022; 42:469-484. [DOI: 10.1016/j.cll.2022.05.004] [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: 11/28/2022]
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Brett JO, Weipert CM, Ritterhouse LL, Zhang N, Yu J, Ryan LY, Spring LM, Rivera MN, Lennerz JK, Dias-Santagata D, Ellisen LW, Bardia A, Wander SA. Abstract 5248: CDK4/6 inhibition (CDK4/6i) is effective in the real-world setting for hormone receptor-positive metastatic breast cancer (HR+ MBC) with ESR1 mutations and fusions. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-5248] [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 For HR+ MBC, ESR1 point mutations (ESR1-MUT) are a common mechanism of acquired resistance to aromatase inhibition (AI); ESR1 fusions (ESR1-FUS) are rare and promote intrinsic resistance to ER-targeting drugs. Retrospective analyses of CDK4/6i trials suggest ESR1-MUT does not cause CDK4/6i resistance, but whether CDK4/6i is effective for ESR1-MUT, or for ESR1-FUS, in the real-world setting is unknown.
Methods Real-world evidence was sourced from the GuardantInform database of commercial payer claims and ctDNA tests from 170,000+ individuals. Patients with MBC who started CDK4/6i within 30 days of ctDNA testing were categorized as ESR1-MUT vs. ESR1-WT and analyzed for time-to-next-treatment (TTNT). Separately, cases with ESR1-FUS detected by tissue RNA-Seq were extracted from a clinicopathologic database at an academic cancer center.
Results There was no significant difference in TTNT on CDK4/6i for ESR1-MUT vs. ESR1-WT. As expected, ESR1-MUT had shorter overall survival (OS), even after adjustment for age, CDK4/6i drug, and prior treatment (HR 0.58 (0.42-0.82), p=0.002, multivariable Cox). Endocrine partner analysis was limited by lack of clinical annotation to 27% of cases: AI was given to 55% of ESR1-WT and 25% of ESR1-MUT; fulvestrant was given to 39% of ESR1-WT and 68% of ESR1-MUT. Additional stratified analyses will be presented.
In the clinicopathologic database, we identified 4 ESR1-FUS cases, and all received CDK4/6i. Progression-free survival durations on CDK4/6i were 4, 10, 11, and 33+ months.
Conclusions Using real-world evidence, we demonstrate that CDK4/6i is effective in both ESR1-MUT and ESR1-WT HR+ MBC, supporting the use of CDK4/6i in this setting. CDK4/6i may be additionally beneficial for patients with ESR1-FUS. Future directions include expanding the ESR1-FUS cohort and deciphering the heterogeneity of CDK4/6i responses in this patient population.
ESR1-WT ESR1-MUT p-value n=612 n=145 TTNT, median days (95% CI) 99 (85-121) 102 (85-152) 0.84 (log-rank) OS, median years (95% CI) 5.1 (4.5-NA) 2.2 (2.0-NA) <0.0001 (log-rank) CDK4/6i drug palbociclib: 71.1% ribociclib: 9.8% abemaciclib: 19.1% palbociclib: 60% ribociclib: 5.5% abemaciclib: 34.5% 0.038 (chi-square) Prior lines of treatment 0: 21.2% 1: 26.1% 2: 18.6% 3+: 34.0% median: 2 0: 15.9% 1: 22.8% 2: 17.2% 3+: 44.1% median: 2 0.013 (Mann-Whitney U)
Citation Format: Jamie O. Brett, Caroline M. Weipert, Lauren L. Ritterhouse, Nicole Zhang, Junhua Yu, Lianne Y. Ryan, Laura M. Spring, Miguel N. Rivera, Jochen K. Lennerz, Dora Dias-Santagata, Leif W. Ellisen, Aditya Bardia, Seth A. Wander. CDK4/6 inhibition (CDK4/6i) is effective in the real-world setting for hormone receptor-positive metastatic breast cancer (HR+ MBC) with ESR1 mutations and fusions [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 5248.
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Dagogo-Jack I, Madison RW, Lennerz JK, Chen KT, Hopkins JF, Schrock AB, Ritterhouse LL, Lester A, Wharton KA, Mino-Kenudson M, Danziger N, Hung YP, Mata DA, Ross JS. Molecular Characterization of Mesothelioma: Impact of Histologic Type and Site of Origin on Molecular Landscape. JCO Precis Oncol 2022; 6:e2100422. [PMID: 35704798 DOI: 10.1200/po.21.00422] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Mesothelioma is an aggressive malignancy with heterogeneous outcomes that are partly driven by the differential efficacy of existing therapies across histologic types and sites of origin. Large-scale molecular analysis of mesothelioma and its subtypes has the potential to inform future therapeutic strategies. MATERIALS AND METHODS We analyzed 1,294 mesotheliomas {980 pleural (malignant pleural mesothelioma [MPM]) and 314 peritoneal (malignant peritoneal mesothelioma [MPeM])} using next-generation sequencing, determined programmed death ligand-1 (PD-L1) expression and histology in a subset of cases, and assessed MTAP/CDKN2A copy-number status by fluorescence in situ hybridization and T-cell infiltration in an independent cohort. RESULTS The molecular landscape of MPM was characterized by inactivating alterations in CDKN2A (49%), BAP1 (44%), CDKN2B (42%), MTAP (34%), and NF2 (33%). Compared with epithelioid MPM, nonepithelioid (ie, biphasic and sarcomatoid) MPM had identical tumor mutational burden (median 1.25 mut/Mb, P = .63), more commonly expressed PD-L1 (74% v 51%, P = .02), and was more likely to harbor MTAP, CDKN2A, and CDKN2B copy loss (P < .05). Fluorescence in situ hybridization confirmed that homozygous MTAP loss was enriched in nonepithelioid MPM. Relative to MPM, MPeM had comparable tumor mutational burden and PD-L1 expression. The molecular profile of MPeM was similar to MPM, with the distinction that PBRM1 alterations occurred at higher frequency (16% v 7%, P < .01). ALK rearrangements were only observed in MPeM. CONCLUSION Regardless of histology and location, the molecular landscape of mesothelioma primarily consists of inactivating alterations in tumor suppressor genes, with enrichment of certain alterations in distinct subsets (eg, MTAP loss in nonepithelioid tumors). Given the limited efficacy of current therapies for this disease, novel approaches targeting recurring alterations should be explored.
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Affiliation(s)
- Ibiayi Dagogo-Jack
- Department of Medicine, Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA
| | | | - Jochen K Lennerz
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital, Boston, MA
| | | | | | | | - Lauren L Ritterhouse
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital, Boston, MA
| | | | | | | | | | - Yin P Hung
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | | | - Jeffrey S Ross
- Foundation Medicine Inc, Cambridge, MA.,Departments of Pathology, Urology and Oncology, Upstate Medical University, Syracuse, NY
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Davies KD, Ritterhouse LL, Snow AN, Sidiropoulos N. MET Exon 14 Skipping Mutations: Essential Considerations for Current Management of Non-Small Cell Lung Cancer. J Mol Diagn 2022; 24:841-843. [PMID: 35550186 DOI: 10.1016/j.jmoldx.2022.04.005] [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] [Received: 10/14/2021] [Revised: 04/05/2022] [Accepted: 04/25/2022] [Indexed: 10/18/2022] Open
Affiliation(s)
- Kurtis D Davies
- Emerging and Evolving Biomarker Content Committee, A Working Group of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Colorado-Anschutz Medical Campus, Denver, Colorado
| | - Lauren L Ritterhouse
- Emerging and Evolving Biomarker Content Committee, A Working Group of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Anthony N Snow
- Emerging and Evolving Biomarker Content Committee, A Working Group of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - Nikoletta Sidiropoulos
- Department of Pathology and Laboratory Medicine, University of Vermont Medical Center, Burlington, Vermont; The Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont.
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13
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Thierauf JC, Farahani AA, Indave BI, Bard AZ, White VA, Smith CR, Marble H, Hyrcza MD, Chan JKC, Bishop J, Shi Q, Ely K, Agaimy A, Martinez-Lage M, Nose V, Rivera M, Nardi V, Dias-Santagata D, Garg S, Sadow P, Le LP, Faquin W, Ritterhouse LL, Cree IA, Iafrate AJ, Lennerz JK. Diagnostic Value of MAML2 Rearrangements in Mucoepidermoid Carcinoma. Int J Mol Sci 2022; 23:4322. [PMID: 35457138 PMCID: PMC9026998 DOI: 10.3390/ijms23084322] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/10/2022] [Accepted: 04/11/2022] [Indexed: 02/04/2023] Open
Abstract
Mucoepidermoid carcinoma (MEC) is often seen in salivary glands and can harbor MAML2 translocations (MAML2+). The translocation status has diagnostic utility as an objective confirmation of the MEC diagnosis, for example, when distinction from the more aggressive adenosquamous carcinoma (ASC) is not straightforward. To assess the diagnostic relevance of MAML2, we examined our 5-year experience in prospective testing of 8106 solid tumors using RNA-seq panel testing in combinations with a two-round Delphi-based scenario survey. The prevalence of MAML2+ across all tumors was 0.28% (n = 23/8106) and the majority of MAML2+ cases were found in head and neck tumors (78.3%), where the overall prevalence was 5.9% (n = 18/307). The sensitivity of MAML2 for MEC was 60% and most cases (80%) were submitted for diagnostic confirmation; in 24% of cases, the MAML2 results changed the working diagnosis. An independent survey of 15 experts showed relative importance indexes of 0.8 and 0.65 for "confirmatory MAML2 testing" in suspected MEC and ASC, respectively. Real-world evidence confirmed that the added value of MAML2 is a composite of an imperfect confirmation test for MEC and a highly specific exclusion tool for the diagnosis of ASC. Real-world evidence can help move a rare molecular-genetic biomarker from an emerging tool to the clinic.
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Affiliation(s)
- Julia C. Thierauf
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital and Research Group Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Alex A. Farahani
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
| | - B. Iciar Indave
- International Agency for Research on Cancer (IARC), World Health Organization, 69372 Lyon, France; (B.I.I.); (V.A.W.); (I.A.C.)
| | - Adam Z. Bard
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
| | - Valerie A. White
- International Agency for Research on Cancer (IARC), World Health Organization, 69372 Lyon, France; (B.I.I.); (V.A.W.); (I.A.C.)
| | - Cameron R. Smith
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (C.R.S.); (M.M.-L.); (V.N.); (P.S.); (W.F.)
| | - Hetal Marble
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
| | - Martin D. Hyrcza
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB 2500, Canada;
| | - John K. C. Chan
- Department of Pathology, Queen Elizabeth Hospital, Kowloon, Hong Kong, China;
| | - Justin Bishop
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
| | - Qiuying Shi
- Department of Pathology, Emory University Hospital, Atlanta, GA 30322, USA;
| | - Kim Ely
- Department of Pathology, Vanderbilt University Medical Center, Nashville, TN 37232, USA;
| | - Abbas Agaimy
- Institute of Pathology, Friedrich Alexander University Erlangen-Nürnberg, University Hospital, 91054 Erlangen, Germany;
| | - Maria Martinez-Lage
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (C.R.S.); (M.M.-L.); (V.N.); (P.S.); (W.F.)
| | - Vania Nose
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (C.R.S.); (M.M.-L.); (V.N.); (P.S.); (W.F.)
| | - Miguel Rivera
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (C.R.S.); (M.M.-L.); (V.N.); (P.S.); (W.F.)
| | - Valentina Nardi
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
| | - Dora Dias-Santagata
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
| | - Salil Garg
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
| | - Peter Sadow
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (C.R.S.); (M.M.-L.); (V.N.); (P.S.); (W.F.)
| | - Long P. Le
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (C.R.S.); (M.M.-L.); (V.N.); (P.S.); (W.F.)
| | - William Faquin
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (C.R.S.); (M.M.-L.); (V.N.); (P.S.); (W.F.)
| | - Lauren L. Ritterhouse
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
| | - Ian A. Cree
- International Agency for Research on Cancer (IARC), World Health Organization, 69372 Lyon, France; (B.I.I.); (V.A.W.); (I.A.C.)
| | - A. John Iafrate
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (C.R.S.); (M.M.-L.); (V.N.); (P.S.); (W.F.)
| | - Jochen K. Lennerz
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; (J.C.T.); (A.A.F.); (A.Z.B.); (H.M.); (M.R.); (V.N.); (D.D.-S.); (S.G.); (L.P.L.); (L.L.R.); (A.J.I.)
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Bennett JA, Ordulu Z, Pinto A, Wanjari P, Antonescu CR, Ritterhouse LL, Oliva E. Uterine PEComas: correlation between melanocytic marker expression and TSC alterations/TFE3 fusions. Mod Pathol 2022; 35:515-523. [PMID: 34131293 PMCID: PMC8671557 DOI: 10.1038/s41379-021-00855-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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: 04/21/2021] [Revised: 05/19/2021] [Accepted: 06/01/2021] [Indexed: 11/09/2022]
Abstract
Uterine PEComas often present a diagnostic challenge as they share morphological and immunohistochemical features with smooth muscle tumors. Herein we evaluated a series of 19 uterine PEComas to compare the degree of melanocytic marker expression with their molecular profile. Patients ranged from 32-77 (median 48) years, with six tumors classified as malignant based on the modified gynecologic-specific prognostic algorithm. All patients with malignant PEComas were alive with disease or dead of disease at last follow-up, while all those of uncertain malignant potential were alive and well (median follow-up, 47 months).Seventeen of 19 (89%) PEComas harbored either a TSC1 or TSC2 alteration. One of the two remaining tumors showed a TFE3 rearrangement, but the other lacked alterations in all genes evaluated. All showed at least focal (usually strong) positivity for HMB-45, with 15/19 (79%) having >50% expression, while the tumor lacking TSC or TFE3 alterations was strongly positive in 10% of cells. Melan-A and MiTF were each positive in 15/19 (79%) tumors, but staining extent and intensity were much more variable than HMB-45. Five of six (83%) malignant PEComas also harbored alterations in TP53, ATRX, or RB1, findings not identified in any tumors of uncertain malignant potential. One malignant PEComa was microsatellite-unstable/mismatch repair protein-deficient.In summary, TSC alterations/TFE3 fusions and diffuse (>50%) HMB-45 expression are characteristic of uterine PEComas. In morphologically ambiguous mesenchymal neoplasms with myomelanocytic differentiation, especially those with metastatic or recurrent disease, next-generation sequencing is recommended to evaluate for TSC alterations; as such, patients can be eligible for targeted therapy.
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Affiliation(s)
| | - Zehra Ordulu
- Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | | | | | | | | | - Esther Oliva
- Massachusetts General Hospital and Harvard Medical School, Boston, MA
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15
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Ritterhouse LL, Sholl LM. Neurotrophin Receptor Kinase: Updated Perspectives, Laboratory Considerations, and Clinical Implications. J Mol Diagn 2021; 24:107-108. [PMID: 34838777 DOI: 10.1016/j.jmoldx.2021.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/27/2021] [Accepted: 11/10/2021] [Indexed: 11/28/2022] Open
Affiliation(s)
- Lauren L Ritterhouse
- Emerging and Evolving Biomarker Content Committee, a working group of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Lynette M Sholl
- Emerging and Evolving Biomarker Content Committee, a working group of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.
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16
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Ordulu Z, Watkins J, Ritterhouse LL. Molecular Pathology of Ovarian Epithelial Neoplasms: Predictive, Prognostic, and Emerging Biomarkers. Surg Pathol Clin 2021; 14:415-428. [PMID: 34373093 DOI: 10.1016/j.path.2021.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This review focuses on the diagnostic, prognostic, and predictive molecular biomarkers in ovarian epithelial neoplasms in the context of their morphologic classifications. Currently, most clinically actionable molecular findings are reported in high-grade serous carcinomas; however, the data on less common tumor types are rapidly accelerating. Overall, the advances in genomic knowledge over the last decade highlight the significance of integrating molecular findings with morphology in ovarian epithelial tumors for a wide-range of clinical applications, from assistance in diagnosis to predicting response to therapy.
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Affiliation(s)
- Zehra Ordulu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02124, USA
| | - Jaclyn Watkins
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02124, USA
| | - Lauren L Ritterhouse
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02124, USA.
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17
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Bennett JA, Young RH, Howitt BE, Croce S, Wanjari P, Zhen C, Da Cruz Paula A, Meserve E, Kenneth Schoolmeester J, Westbom-Fremer S, Benzi E, Patil NM, Kooreman L, El-Bahrawy M, Zannoni GF, Krausz T, Glenn McCluggage W, Weigelt B, Ritterhouse LL, Oliva E. A Distinctive Adnexal (Usually Paratubal) Neoplasm Often Associated With Peutz-Jeghers Syndrome and Characterized by STK11 Alterations (STK11 Adnexal Tumor): A Report of 22 Cases. Am J Surg Pathol 2021; 45:1061-1074. [PMID: 33534223 PMCID: PMC8277663 DOI: 10.1097/pas.0000000000001677] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We describe 22 examples of a novel, usually paratubal, adnexal tumor associated with Peutz-Jeghers syndrome in nearly 50% of cases that harbored STK11 alterations in all tested (n=21). The patients ranged from 17 to 66 years (median=39 y) and the tumors from 4.5 to 25.5 cm (median=11 cm). Most (n=18) were paratubal, with metastases noted in 11/22 (50%) and recurrences in 12/15 (80%). Morphologically, they were characterized by interanastomosing cords and trabeculae of predominantly epithelioid cells, set in a variably prominent myxoid to focally edematous stroma, that often merged to form tubular, cystic, cribriform, and microacinar formations, reminiscent of salivary gland-type tumors. The tumor cells were uniformly atypical, often with prominent nucleoli and a variable mitotic index (median=9/10 HPFs). The tumors were usually positive to a variable extent for epithelial (CAM5.2, AE1/AE3, cytokeratin 7), sex cord (calretinin, inhibin, WT1), and mesothelial (calretinin, D2-40) markers, as well as hormone receptors. PAX8, SF1, and GATA-3 were rarely positive, while claudin-4, FOXL2, and TTF-1 were consistently negative. All sequenced tumors (n=21) harbored alterations in STK11, often with a loss of heterozygosity event. There were no other recurrently mutated genes. Recurrent copy number alterations included loss of 1p and 11q, and gain of 1q, 15q, and 15p. Despite an extensive morphologic, immunohistochemical, and molecular evaluation, we are unable to determine with certainty the histogenesis of this unique tumor. Wolffian, sex cord stromal, epithelial, and mesothelial origins were considered. We propose the term STK11 adnexal tumor to describe this novel entity and emphasize the importance of genetic counseling in these patients as a significant number of neoplasms occur in association with Peutz-Jeghers syndrome.
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Affiliation(s)
| | - Robert H. Young
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Sabrina Croce
- Institut Bergonié, Comprehensive Cancer Center, Bordeaux, France
| | | | - Chaojie Zhen
- University of Chicago Medical Center, Chicago, IL, USA
| | | | | | | | | | | | | | - Loes Kooreman
- Maastricht University Medical Center+, Maastricht, the Netherlands
| | | | | | - Thomas Krausz
- University of Chicago Medical Center, Chicago, IL, USA
| | | | - Britta Weigelt
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Esther Oliva
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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Trombetta BA, Kandigian SE, Kitchen RR, Grauwet K, Webb PK, Miller GA, Jennings CG, Jain S, Miller S, Kuo Y, Sweeney T, Gilboa T, Norman M, Simmons DP, Ramirez CE, Bedard M, Fink C, Ko J, De León Peralta EJ, Watts G, Gomez-Rivas E, Davis V, Barilla RM, Wang J, Cunin P, Bates S, Morrison-Smith C, Nicholson B, Wong E, El-Mufti L, Kann M, Bolling A, Fortin B, Ventresca H, Zhou W, Pardo S, Kwock M, Hazra A, Cheng L, Ahmad QR, Toombs JA, Larson R, Pleskow H, Luo NM, Samaha C, Pandya UM, De Silva P, Zhou S, Ganhadeiro Z, Yohannes S, Gay R, Slavik J, Mukerji SS, Jarolim P, Walt DR, Carlyle BC, Ritterhouse LL, Suliman S. Correction to: Evaluation of serological lateral flow assays for severe acute respiratory syndrome coronavirus-2. BMC Infect Dis 2021; 21:628. [PMID: 34210278 PMCID: PMC8246132 DOI: 10.1186/s12879-021-06333-y] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Bianca A Trombetta
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Boston, MA, USA
| | - Savannah E Kandigian
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Boston, MA, USA
| | - Robert R Kitchen
- Department of Medicine, Harvard Medical School, Boston, MA, USA.,Mass General Brigham Innovation, Boston, MA, USA
| | - Korneel Grauwet
- Cardiology Division, Massachusetts General Hospital, Charlestown, MA, USA
| | - Pia Kivisäkk Webb
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | - Charles G Jennings
- Cardiology Division, Massachusetts General Hospital, Charlestown, MA, USA.,Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sejal Jain
- Department of Medical Oncology and Center for Cancer-Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Samara Miller
- Department of Medicine, Harvard Medical School, Boston, MA, USA.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA.,Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Yikai Kuo
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Boston, MA, USA.,Cardiology Division, Massachusetts General Hospital, Charlestown, MA, USA
| | - Thadryan Sweeney
- Cardiology Division, Massachusetts General Hospital, Charlestown, MA, USA
| | - Tal Gilboa
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Maia Norman
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
| | - Daimon P Simmons
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Christopher E Ramirez
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Boston, MA, USA
| | - Melissa Bedard
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Catherine Fink
- Medical Diagnostic Technology Evaluation, LLC, Carlisle, MA, USA
| | - Jina Ko
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Esmarline J De León Peralta
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.,Wellman Center for Photomedicine, Massachusetts General Research Institute, Boston, MA, USA.,Department of Dermatology, Massachusetts General Hospital, Boston, MA, USA
| | - Gerald Watts
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Emma Gomez-Rivas
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Vannessa Davis
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rocky M Barilla
- Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Jianing Wang
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Pierre Cunin
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Samuel Bates
- Functional Genomics Laboratory, Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Chevaun Morrison-Smith
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Benjamin Nicholson
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Edmond Wong
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Leena El-Mufti
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Boston, MA, USA
| | - Michael Kann
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Anna Bolling
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Boston, MA, USA
| | - Brooke Fortin
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Boston, MA, USA
| | - Hayden Ventresca
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Wen Zhou
- Division of Nephrology and Endocrine Unit Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Santiago Pardo
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Boston, MA, USA
| | - Megan Kwock
- Cancer Center Protocol Office, Massachusetts General Hospital, Boston, MA, USA
| | - Aditi Hazra
- Department of Medicine, Harvard Medical School, Boston, MA, USA.,Division of Preventative Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Leo Cheng
- Radiology and pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Q Rushdy Ahmad
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - James A Toombs
- Brigham Research Institute, Brigham and Women's Hospital, Boston, MA, USA
| | - Rebecca Larson
- Immunology Program, Harvard Medical School, Boston, MA, USA.,Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Haley Pleskow
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA.,Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Unnati M Pandya
- Department of Medicine, Harvard Medical School, Boston, MA, USA.,Vincent Center for Reproductive Biology, Department of Obstetrics and Gynecology, Massachusetts General Hospital, Boston, MA, USA
| | - Pushpamali De Silva
- Wellman Center for Photomedicine, Massachusetts General Research Institute, Boston, MA, USA
| | - Sally Zhou
- Department of Biology, Northeastern University, Boston, MA, USA.,College of Science, Northeastern University, Boston, MA, USA
| | - Zakary Ganhadeiro
- Department of Biology, Northeastern University, Boston, MA, USA.,College of Science, Northeastern University, Boston, MA, USA
| | - Sara Yohannes
- Brigham Research Institute, Brigham and Women's Hospital, Boston, MA, USA
| | - Rakiesha Gay
- Brigham Research Institute, Brigham and Women's Hospital, Boston, MA, USA.,College of Science, Northeastern University, Boston, MA, USA
| | - Jacqueline Slavik
- Brigham Research Institute, Brigham and Women's Hospital, Boston, MA, USA
| | - Shibani S Mukerji
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Boston, MA, USA
| | - Petr Jarolim
- Department of Pathology, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - David R Walt
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Mass General Brigham COVID Center for Innovation, Diagnostics Accelerator, Boston, MA, USA
| | - Becky C Carlyle
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Lauren L Ritterhouse
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.,Mass General Brigham COVID Center for Innovation, Diagnostics Accelerator, Boston, MA, USA
| | - Sara Suliman
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA. .,Mass General Brigham COVID Center for Innovation, Diagnostics Accelerator, Boston, MA, USA.
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19
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Trombetta BA, Kandigian SE, Kitchen RR, Grauwet K, Webb PK, Miller GA, Jennings CG, Jain S, Miller S, Kuo Y, Sweeney T, Gilboa T, Norman M, Simmons DP, Ramirez CE, Bedard M, Fink C, Ko J, De León Peralta EJ, Watts G, Gomez-Rivas E, Davis V, Barilla RM, Wang J, Cunin P, Bates S, Morrison-Smith C, Nicholson B, Wong E, El-Mufti L, Kann M, Bolling A, Fortin B, Ventresca H, Zhou W, Pardo S, Kwock M, Hazra A, Cheng L, Ahmad QR, Toombs JA, Larson R, Pleskow H, Luo NM, Samaha C, Pandya UM, De Silva P, Zhou S, Ganhadeiro Z, Yohannes S, Gay R, Slavik J, Mukerji SS, Jarolim P, Walt DR, Carlyle BC, Ritterhouse LL, Suliman S. Evaluation of serological lateral flow assays for severe acute respiratory syndrome coronavirus-2. BMC Infect Dis 2021; 21:580. [PMID: 34134647 PMCID: PMC8206878 DOI: 10.1186/s12879-021-06257-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 02/08/2021] [Accepted: 05/25/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND COVID-19 has resulted in significant morbidity and mortality worldwide. Lateral flow assays can detect anti-Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) antibodies to monitor transmission. However, standardized evaluation of their accuracy and tools to aid in interpreting results are needed. METHODS We evaluated 20 IgG and IgM assays selected from available tests in April 2020. We evaluated the assays' performance using 56 pre-pandemic negative and 56 SARS-CoV-2-positive plasma samples, collected 10-40 days after symptom onset, confirmed by a molecular test and analyzed by an ultra-sensitive immunoassay. Finally, we developed a user-friendly web app to extrapolate the positive predictive values based on their accuracy and local prevalence. RESULTS Combined IgG + IgM sensitivities ranged from 33.9 to 94.6%, while combined specificities ranged from 92.6 to 100%. The highest sensitivities were detected in Lumiquick for IgG (98.2%), BioHit for both IgM (96.4%), and combined IgG + IgM sensitivity (94.6%). Furthermore, 11 LFAs and 8 LFAs showed perfect specificity for IgG and IgM, respectively, with 15 LFAs showing perfect combined IgG + IgM specificity. Lumiquick had the lowest estimated limit-of-detection (LOD) (0.1 μg/mL), followed by a similar LOD of 1.5 μg/mL for CareHealth, Cellex, KHB, and Vivachek. CONCLUSION We provide a public resource of the accuracy of select lateral flow assays with potential for home testing. The cost-effectiveness, scalable manufacturing process, and suitability for self-testing makes LFAs an attractive option for monitoring disease prevalence and assessing vaccine responsiveness. Our web tool provides an easy-to-use interface to demonstrate the impact of prevalence and test accuracy on the positive predictive values.
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Affiliation(s)
- Bianca A Trombetta
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Boston, MA, USA
| | - Savannah E Kandigian
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Boston, MA, USA
| | - Robert R Kitchen
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Mass General Brigham Innovation, Boston, MA, USA
| | - Korneel Grauwet
- Cardiology Division, Massachusetts General Hospital, Charlestown, MA, USA
| | - Pia Kivisäkk Webb
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | - Charles G Jennings
- Cardiology Division, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sejal Jain
- Department of Medical Oncology and Center for Cancer-Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Samara Miller
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Yikai Kuo
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Boston, MA, USA
- Cardiology Division, Massachusetts General Hospital, Charlestown, MA, USA
| | - Thadryan Sweeney
- Cardiology Division, Massachusetts General Hospital, Charlestown, MA, USA
| | - Tal Gilboa
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Maia Norman
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
| | - Daimon P Simmons
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Christopher E Ramirez
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Boston, MA, USA
| | - Melissa Bedard
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Catherine Fink
- Medical Diagnostic Technology Evaluation, LLC, Carlisle, MA, USA
| | - Jina Ko
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Esmarline J De León Peralta
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Wellman Center for Photomedicine, Massachusetts General Research Institute, Boston, MA, USA
- Department of Dermatology, Massachusetts General Hospital, Boston, MA, USA
| | - Gerald Watts
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Emma Gomez-Rivas
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Vannessa Davis
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rocky M Barilla
- Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Jianing Wang
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Pierre Cunin
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Samuel Bates
- Functional Genomics Laboratory, Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Chevaun Morrison-Smith
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Benjamin Nicholson
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Edmond Wong
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Leena El-Mufti
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Boston, MA, USA
| | - Michael Kann
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Anna Bolling
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Boston, MA, USA
| | - Brooke Fortin
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Boston, MA, USA
| | - Hayden Ventresca
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Wen Zhou
- Division of Nephrology and Endocrine Unit Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Santiago Pardo
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Boston, MA, USA
| | - Megan Kwock
- Cancer Center Protocol Office, Massachusetts General Hospital, Boston, MA, USA
| | - Aditi Hazra
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Preventative Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Leo Cheng
- Radiology and pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Q Rushdy Ahmad
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - James A Toombs
- Brigham Research Institute, Brigham and Women's Hospital, Boston, MA, USA
| | - Rebecca Larson
- Immunology Program, Harvard Medical School, Boston, MA, USA
- Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Haley Pleskow
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Unnati M Pandya
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Vincent Center for Reproductive Biology, Department of Obstetrics and Gynecology, Massachusetts General Hospital, Boston, MA, USA
| | - Pushpamali De Silva
- Wellman Center for Photomedicine, Massachusetts General Research Institute, Boston, MA, USA
| | - Sally Zhou
- Department of Biology, Northeastern University, Boston, MA, USA
- College of Science, Northeastern University, Boston, MA, USA
| | - Zakary Ganhadeiro
- Department of Biology, Northeastern University, Boston, MA, USA
- College of Science, Northeastern University, Boston, MA, USA
| | - Sara Yohannes
- Brigham Research Institute, Brigham and Women's Hospital, Boston, MA, USA
| | - Rakiesha Gay
- Brigham Research Institute, Brigham and Women's Hospital, Boston, MA, USA
- College of Science, Northeastern University, Boston, MA, USA
| | - Jacqueline Slavik
- Brigham Research Institute, Brigham and Women's Hospital, Boston, MA, USA
| | - Shibani S Mukerji
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Boston, MA, USA
| | - Petr Jarolim
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - David R Walt
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Mass General Brigham COVID Center for Innovation, Diagnostics Accelerator, Boston, MA, USA
| | - Becky C Carlyle
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Lauren L Ritterhouse
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Mass General Brigham COVID Center for Innovation, Diagnostics Accelerator, Boston, MA, USA
| | - Sara Suliman
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA.
- Mass General Brigham COVID Center for Innovation, Diagnostics Accelerator, Boston, MA, USA.
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20
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Anahtar MN, Shaw BM, Slater D, Byrne EH, Botti-Lodovico Y, Adams G, Schaffner SF, Eversley J, McGrath GEG, Gogakos T, Lennerz J, Marble HD, Ritterhouse LL, Batten JM, Georgantas NZ, Pellerin R, Signorelli S, Thierauf J, Kemball M, Happi C, Grant DS, Ndiaye D, Siddle KJ, Mehta SB, Harris JB, Ryan ET, Pierce VM, LaRocque RC, Lemieux JE, Sabeti PC, Rosenberg ES, Branda JA, Turbett SE. Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: a guide and case study in setting up an emergency-use, laboratory-developed molecular microbiological assay. J Clin Pathol 2021; 74:496-503. [PMID: 34049977 PMCID: PMC8311084 DOI: 10.1136/jclinpath-2020-207128] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/20/2021] [Accepted: 01/30/2021] [Indexed: 12/31/2022]
Abstract
Developing and deploying new diagnostic tests are difficult, but the need to do so in response to a rapidly emerging pandemic such as COVID-19 is crucially important. During a pandemic, laboratories play a key role in helping healthcare providers and public health authorities detect active infection, a task most commonly achieved using nucleic acid-based assays. While the landscape of diagnostics is rapidly evolving, PCR remains the gold-standard of nucleic acid-based diagnostic assays, in part due to its reliability, flexibility and wide deployment. To address a critical local shortage of testing capacity persisting during the COVID-19 outbreak, our hospital set up a molecular-based laboratory developed test (LDT) to accurately and safely diagnose SARS-CoV-2. We describe here the process of developing an emergency-use LDT, in the hope that our experience will be useful to other laboratories in future outbreaks and will help to lower barriers to establishing fast and accurate diagnostic testing in crisis conditions.
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Affiliation(s)
- Melis N Anahtar
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Bennett M Shaw
- Infectious Disease and Microbiome Program, Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Damien Slater
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Elizabeth H Byrne
- Infectious Disease and Microbiome Program, Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Yolanda Botti-Lodovico
- Infectious Disease and Microbiome Program, Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Gordon Adams
- Infectious Disease and Microbiome Program, Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Stephen F Schaffner
- Infectious Disease and Microbiome Program, Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Jacqueline Eversley
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Graham E G McGrath
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Tasos Gogakos
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jochen Lennerz
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Hetal Desai Marble
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Lauren L Ritterhouse
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Julie M Batten
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - N Zeke Georgantas
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Rebecca Pellerin
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Sylvia Signorelli
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Julia Thierauf
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Otorhinolaryngology, University Hospital Heidelberg, Heidelberg, Baden-Württemberg, Germany
| | - Molly Kemball
- Infectious Disease and Microbiome Program, Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Christian Happi
- Department of Biological Sciences, Redeemer's University, Ede, Osun, Nigeria.,African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun, Nigeria
| | - Donald S Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone.,College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Daouda Ndiaye
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun, Nigeria.,Department of Mycology and Pharmacology, Universite Cheikh Anta Diop, Dakar, Senegal
| | - Katherine J Siddle
- Infectious Disease and Microbiome Program, Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Samar B Mehta
- Infectious Disease and Microbiome Program, Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Jason B Harris
- Department of Pediatrics, Massachusetts General Hospital for Children, Boston, Massachusetts, USA
| | - Edward T Ryan
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Virginia M Pierce
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Pediatrics, Massachusetts General Hospital for Children, Boston, Massachusetts, USA
| | - Regina C LaRocque
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jacob E Lemieux
- Infectious Disease and Microbiome Program, Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA .,Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Pardis C Sabeti
- Infectious Disease and Microbiome Program, Eli and Edythe L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA .,Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Eric S Rosenberg
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - John A Branda
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Sarah E Turbett
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA .,Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
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21
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Shepherd DJ, Miller TE, Forst DA, Jones P, Nardi V, Martinez-Lage M, Stemmer-Rachamimov A, Gonzalez RG, Iafrate AJ, Ritterhouse LL. Mosaicism for Receptor Tyrosine Kinase Activation in a Glioblastoma Involving Both PDGFRA Amplification and NTRK2 Fusion. Oncologist 2021; 26:919-924. [PMID: 34041811 DOI: 10.1002/onco.13835] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/13/2021] [Indexed: 12/28/2022] Open
Abstract
Rearrangements involving the neurotrophic receptor tyrosine kinase (NTRK) gene family have been reported in diverse tumor types, and NTRK-targeted therapies have recently been approved. In this article, we report a case of a 26-year-old man with an NTRK2-rearranged isocitrate dehydrogenase-wild-type glioblastoma who showed a robust but temporary response to the NTRK inhibitor larotrectinib. Rebiopsy after disease progression showed elimination of the NTRK2-rearranged tumor cell clones, with secondary emergence of a PDGFRA-amplified subclone. Retrospective examination of the initial biopsy material confirmed rare cells harboring PDGFRA amplification. Although mosaic amplification of multiple receptor tyrosine kinase genes in glioblastoma has been previously described, mosaicism involving a fusion gene driver event has not. This case highlights the potential efficacy of NTRK-targeted treatment in glioblastoma and the implications of molecular heterogeneity in the setting of targeted therapy. KEY POINTS: This case highlights the efficacy of the NTRK inhibitor larotrectinib in treating NTRK-rearranged glioblastoma. This is the first case to demonstrate mosaicism in glioblastoma involving both a fusion gene and amplification for receptor tyrosine kinases. Intratumoral heterogeneity in glioblastoma has significant implications for tumor resistance to targeted therapies.
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Affiliation(s)
- Daniel J Shepherd
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tyler E Miller
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Deborah A Forst
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Pamela Jones
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Maria Martinez-Lage
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Anat Stemmer-Rachamimov
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ramon G Gonzalez
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lauren L Ritterhouse
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
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22
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Goldberg SA, Lennerz J, Klompas M, Mark E, Pierce VM, Thompson RW, Pu CT, Ritterhouse LL, Dighe A, Rosenberg ES, Grabowski DC. Presymptomatic Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Among Residents and Staff at a Skilled Nursing Facility: Results of Real-time Polymerase Chain Reaction and Serologic Testing. Clin Infect Dis 2021; 72:686-689. [PMID: 32667967 PMCID: PMC7454467 DOI: 10.1093/cid/ciaa991] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 07/10/2020] [Indexed: 01/10/2023] Open
Abstract
High rates of asymptomatic infection suggest benefits to routine testing in congregate care settings. SARS-CoV-2 screening was undertaken in a single nursing facility without a known case of COVID-19, demonstrating an 85% prevalence among residents and 37% among staff. Serology was not helpful in identifying infections.
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Affiliation(s)
- Scott A Goldberg
- Department of Emergency Medicine, Brigham & Women's Hospital, Boston, Massachusetts, USA
| | - Jochen Lennerz
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Michael Klompas
- Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, Massachusetts, USA.,Department of Medicine, Brigham & Women's Hospital, Boston, Massachusetts, USA
| | - Eden Mark
- Population Health Management, Partners HealthCare, Boston, Massachusetts, USA
| | - Virginia M Pierce
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Ryan W Thompson
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Charles T Pu
- Population Health Management, Partners HealthCare, Boston, Massachusetts, USA
| | - Lauren L Ritterhouse
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Anand Dighe
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Eric S Rosenberg
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
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23
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Abstract
Several subsets of non-small cell lung cancer (NSCLC) are defined by the presence of oncogenic rearrangements that result in constitutive activation of a chimeric fusion protein. In NSCLCs that harbor ALK or ROS1 rearrangements, aberrant signaling from these fusion proteins can be overcome by potent and selective tyrosine kinase inhibitors (TKIs). These targeted therapies can induce durable responses and significantly improve prognostic outcomes. Historically, analysis of tissue biopsies was the primary approach to identifying key activating rearrangements. In recent years, non-invasive genotyping of tumor-derived nucleic acids in the circulation has gained ground as a strategy for determining the genetic composition of NSCLCs at diagnosis and throughout the disease course based on prospective and retrospective studies validating the utility of plasma analysis in heterogeneous populations of patients with metastatic NSCLC. Notably, these practice-changing studies predominantly included patients with NSCLCs with oncogenic mutations. Compared to other types of molecular alterations such as mutations and insertions/deletions, oncogenic rearrangements are more complex as they incorporate a variety of fusion partners and diverse breakpoints. Because of this structural complexity, detecting oncogenic rearrangements with plasma assays is more challenging than identifying disease-defining point mutations. In this review, we discuss technical aspects of plasma genotyping strategies and summarize findings from studies exploring plasma genotyping (including ctDNA analysis and profiling of nucleic acids contained in other plasma components) in two rearrangement-driven NSCLC subsets (ALK-rearranged and ROS1-rearranged).
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Affiliation(s)
- Ibiayi Dagogo-Jack
- Department of Medicine and Cancer Center, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Lauren L Ritterhouse
- Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
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24
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Miller TE, Garcia Beltran WF, Bard AZ, Gogakos T, Anahtar MN, Astudillo MG, Yang D, Thierauf J, Fisch AS, Mahowald GK, Fitzpatrick MJ, Nardi V, Feldman J, Hauser BM, Caradonna TM, Marble HD, Ritterhouse LL, Turbett SE, Batten J, Georgantas NZ, Alter G, Schmidt AG, Harris JB, Gelfand JA, Poznansky MC, Bernstein BE, Louis DN, Dighe A, Charles RC, Ryan ET, Branda JA, Pierce VM, Murali MR, Iafrate AJ, Rosenberg ES, Lennerz JK. Clinical sensitivity and interpretation of PCR and serological COVID-19 diagnostics for patients presenting to the hospital. FASEB J 2020; 34:13877-13884. [PMID: 32856766 PMCID: PMC7461169 DOI: 10.1096/fj.202001700rr] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/04/2020] [Accepted: 08/07/2020] [Indexed: 12/15/2022]
Abstract
The diagnosis of COVID-19 requires integration of clinical and laboratory data. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic assays play a central role in diagnosis and have fixed technical performance metrics. Interpretation becomes challenging because the clinical sensitivity changes as the virus clears and the immune response emerges. Our goal was to examine the clinical sensitivity of two most common SARS-CoV-2 diagnostic test modalities, polymerase chain reaction (PCR) and serology, over the disease course to provide insight into their clinical interpretation in patients presenting to the hospital. We conducted a single-center, retrospective study. To derive clinical sensitivity of PCR, we identified 209 PCR-positive SARS-CoV-2 patients with multiple PCR test results (624 total PCR tests) and calculated daily sensitivity from date of symptom onset or first positive test. Clinical sensitivity of PCR decreased with days post symptom onset with >90% clinical sensitivity during the first 5 days after symptom onset, 70%-71% from Days 9 to 11, and 30% at Day 21. To calculate daily clinical sensitivity by serology, we utilized 157 PCR-positive patients with a total of 197 specimens tested by enzyme-linked immunosorbent assay for IgM, IgG, and IgA anti-SARS-CoV-2 antibodies. In contrast to PCR, serological sensitivity increased with days post symptom onset with >50% of patients seropositive by at least one antibody isotype after Day 7, >80% after Day 12, and 100% by Day 21. Taken together, PCR and serology are complimentary modalities that require time-dependent interpretation. Superimposition of sensitivities over time indicate that serology can function as a reliable diagnostic aid indicating recent or prior infection.
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Affiliation(s)
- Tyler E. Miller
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | | | - Adam Z. Bard
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Tasos Gogakos
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Melis N. Anahtar
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | | | - Diane Yang
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Julia Thierauf
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Adam S. Fisch
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Grace K. Mahowald
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Megan J. Fitzpatrick
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Valentina Nardi
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Jared Feldman
- Ragon Institute of MGH, MIT, and HarvardCambridgeMAUSA
| | | | | | - Hetal D. Marble
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Lauren L. Ritterhouse
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Sara E. Turbett
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
- Division of Infectious DiseasesDepartment of MedicineMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Julie Batten
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | | | - Galit Alter
- Ragon Institute of MGH, MIT, and HarvardCambridgeMAUSA
| | | | - Jason B. Harris
- Division of Infectious DiseasesDepartment of PediatricsMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Jeffrey A. Gelfand
- Division of Infectious DiseasesDepartment of MedicineMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Mark C. Poznansky
- Division of Infectious DiseasesDepartment of MedicineMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Bradley E. Bernstein
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - David N. Louis
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Anand Dighe
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Richelle C. Charles
- Division of Infectious DiseasesDepartment of MedicineMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Edward T. Ryan
- Division of Infectious DiseasesDepartment of MedicineMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - John A. Branda
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Virginia M. Pierce
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
- Division of Infectious DiseasesDepartment of PediatricsMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Mandakolathur R. Murali
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
- Division of Allergy and ImmunologyDepartment of MedicineMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - A. John Iafrate
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Eric S. Rosenberg
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
- Division of Infectious DiseasesDepartment of MedicineMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
| | - Jochen K. Lennerz
- Department of PathologyMassachusetts General Hospital/Harvard Medical SchoolBostonMAUSA
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25
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Anahtar MN, Shaw B, Slater D, Byrne E, Botti-Lodovico Y, Adams G, Schaffner S, Eversley J, McGrath G, Gogakos T, Lennerz J, Desai Marble H, Ritterhouse LL, Batten J, Georgantas NZ, Pellerin R, Signorelli S, Thierauf J, Kemball M, Happi C, Grant DS, Ndiaye D, Siddle KJ, Mehta SB, Harris J, Ryan ET, Pierce V, LaRocque R, Lemieux JE, Sabeti P, Rosenberg E, Branda J, Turbett SE. Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: A guide and case study in setting up an emergency-use, laboratory-developed molecular assay. medRxiv 2020. [PMID: 32909014 PMCID: PMC7480066 DOI: 10.1101/2020.08.26.20157297] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Developing and deploying new diagnostic tests is difficult, but the need to do so in response to a rapidly emerging pandemic such as COVID-19 is crucially important for an effective response. In the early stages of a pandemic, laboratories play a key role in helping health care providers and public health authorities detect active infection, a task most commonly achieved using nucleic acid-based assays. While the landscape of diagnostics is rapidly evolving, polymerase chain reaction (PCR) remains the gold-standard of nucleic acid-based diagnostic assays, in part due to its reliability, flexibility, and wide deployment. To address a critical local shortage of testing capacity persisting during the COVID-19 outbreak, our hospital set up a molecular based laboratory developed test (LDT) to accurately and safely diagnose SARS-CoV-2. We describe here the process of developing an emergency-use LDT, in the hope that our experience will be useful to other laboratories in future outbreaks and will help to lower barriers to fast and accurate diagnostic testing in crisis conditions.
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Affiliation(s)
- Melis N Anahtar
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts
| | - Bennett Shaw
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.,Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Damien Slater
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Elizabeth Byrne
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Yolanda Botti-Lodovico
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Gordon Adams
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.,Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Stephen Schaffner
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.,Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Jacqueline Eversley
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts
| | - Graham McGrath
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Tasos Gogakos
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts
| | - Jochen Lennerz
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts
| | - Hetal Desai Marble
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts
| | - Lauren L Ritterhouse
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts
| | - Julie Batten
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts
| | - N Zeke Georgantas
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts
| | - Rebecca Pellerin
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts
| | - Sylvia Signorelli
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts
| | - Julia Thierauf
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts.,Department of Otorhinolaryngology, Head and Neck Surgery, Experimental Head and Neck Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Molly Kemball
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.,Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Christian Happi
- Department of Biological Sciences, Redeemer's University, Ede, Osun State, Nigeria.,African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Donald S Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, 1 Combema Road, Kenema, Sierra Leone.,College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Daouda Ndiaye
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.,Université Cheikh Anta Diop, BP 5005, Dakar, Sénégal
| | - Katherine J Siddle
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.,Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Samar B Mehta
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.,Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jason Harris
- Department of Pediatrics, Massachusetts General Hospital for Children, Boston, MA, USA
| | - Edward T Ryan
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Virginia Pierce
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts.,Department of Pediatrics, Massachusetts General Hospital for Children, Boston, MA, USA
| | - Regina LaRocque
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Jacob E Lemieux
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.,Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Pardis Sabeti
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.,Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.,Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland.,Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - Eric Rosenberg
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts.,Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - John Branda
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts
| | - Sarah E Turbett
- Department of Pathology and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts.,Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
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26
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Parilla M, Ritterhouse LL. Beyond the Variants: Mutational Patterns in Next-Generation Sequencing Data for Cancer Precision Medicine. Front Cell Dev Biol 2020; 8:370. [PMID: 32509788 PMCID: PMC7248322 DOI: 10.3389/fcell.2020.00370] [Citation(s) in RCA: 2] [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: 11/23/2019] [Accepted: 04/24/2020] [Indexed: 12/12/2022] Open
Abstract
Massively parallel sequencing, also referred to as “next-generation sequencing” (NGS) provides not only information about simple, single nucleotide alterations, but it can also provide information on complex variations, such as insertions and deletions, copy number alterations, and structural variants. In addition to identifying individual alterations, genome-wide biomarkers can be discerned from somatic cancer NGS data, broadly termed mutational patterns and signatures. This review will focus on several of the most common genome-wide biomarkers such as tumor mutational burden, microsatellite instability, homologous recombination deficiency, and mutational signatures.
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Affiliation(s)
- Megan Parilla
- Department of Pathology, University of Chicago Medicine, Chicago, IL, United States
| | - Lauren L Ritterhouse
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
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27
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Trujillo JA, Luke JJ, Zha Y, Segal JP, Ritterhouse LL, Spranger S, Matijevich K, Gajewski TF. Secondary resistance to immunotherapy associated with β-catenin pathway activation or PTEN loss in metastatic melanoma. J Immunother Cancer 2019; 7:295. [PMID: 31703593 PMCID: PMC6839232 DOI: 10.1186/s40425-019-0780-0] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [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: 06/17/2019] [Accepted: 10/22/2019] [Indexed: 12/18/2022] Open
Abstract
Background While cancer immunotherapies including checkpoint blockade antibodies, adoptive T cell therapy, and even some vaccines have given rise to major clinical responses with durability in many cases, a subset of patients who initially respond subsequently develop secondary resistance to therapy. Tumor-intrinsic mechanisms of acquired immunotherapy resistance are incompletely understood. Methods Baseline and treatment-resistant tumors underwent molecular analysis via transcriptional profiling or genomic sequencing for oncogenic alterations and histologic analysis for T cell infiltration to investigate mechanisms contributing to T cell exclusion and acquired resistance to immunotherapy. Results We describe two patients with metastatic melanoma who initially showed a durable partial response to either a melanoma-peptide/interleukin-12 vaccine or combined anti-CTLA-4 + anti-PD-1 therapy, but subsequently developed new treatment-resistant metastases. In the first case, the recurrent tumor showed new robust tumor expression of β-catenin, whereas in the second case genomic sequencing revealed acquired PTEN loss. Both cases were associated with loss of T cell infiltration, and both pathways have been mechanistically linked to immune resistance preclinically. Conclusion Our results suggest that secondary resistance to immunotherapies can arise upon selection for new oncogenic variants that mediate T cell exclusion. To identify the spectrum of underlying mechanisms of therapeutic resistance, similar evaluation for the emergence of tumor-intrinsic alterations in resistant lesions should be done prospectively at the time of relapse in a range of additional patients developing secondary resistance.
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Affiliation(s)
- Jonathan A Trujillo
- Department of Medicine, University of Chicago, 5841 S. Maryland Ave, MC2115, Chicago, IL, 60637, USA
| | - Jason J Luke
- Department of Medicine, University of Chicago, 5841 S. Maryland Ave, MC2115, Chicago, IL, 60637, USA
| | - Yuanyuan Zha
- Department of Medicine, University of Chicago, 5841 S. Maryland Ave, MC2115, Chicago, IL, 60637, USA
| | - Jeremy P Segal
- Department of Pathology, University of Chicago, 5841 S. Maryland Ave, MC2115, Chicago, IL, 60637, USA
| | - Lauren L Ritterhouse
- Department of Pathology, University of Chicago, 5841 S. Maryland Ave, MC2115, Chicago, IL, 60637, USA
| | - Stefani Spranger
- Department of Pathology, University of Chicago, 5841 S. Maryland Ave, MC2115, Chicago, IL, 60637, USA.,Present address: Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Department of Biology at MIT, Cambridge, USA
| | - Karen Matijevich
- Department of Medicine, University of Chicago, 5841 S. Maryland Ave, MC2115, Chicago, IL, 60637, USA
| | - Thomas F Gajewski
- Department of Medicine, University of Chicago, 5841 S. Maryland Ave, MC2115, Chicago, IL, 60637, USA. .,Department of Pathology, University of Chicago, 5841 S. Maryland Ave, MC2115, Chicago, IL, 60637, USA.
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28
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Ritterhouse LL, Parilla M, Zhen CJ, Wurst MN, Puranik R, Henderson CM, Joudeh NZ, Hartley MJ, Haridas R, Wanjari P, Furtado LV, Kadri S, Segal JP. Clinical Validation and Implementation of a Measurable Residual Disease Assay for NPM1 in Acute Myeloid Leukemia by Error-Corrected Next-Generation Sequencing. Mol Diagn Ther 2019; 23:791-802. [DOI: 10.1007/s40291-019-00436-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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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29
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Balagopal V, Hantel A, Kadri S, Steinhardt G, Zhen CJ, Kang W, Wanjari P, Ritterhouse LL, Stock W, Segal JP. Measurable residual disease monitoring for patients with acute myeloid leukemia following hematopoietic cell transplantation using error corrected hybrid capture next generation sequencing. PLoS One 2019; 14:e0224097. [PMID: 31658273 PMCID: PMC6816574 DOI: 10.1371/journal.pone.0224097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 06/03/2019] [Accepted: 10/05/2019] [Indexed: 12/22/2022] Open
Abstract
Improved systems for detection of measurable residual disease (MRD) in acute myeloid leukemia (AML) are urgently needed, however attempts to utilize broad-scale next-generation sequencing (NGS) panels to perform multi-gene surveillance in AML post-induction have been stymied by persistent premalignant mutation-bearing clones. We hypothesized that this technology may be more suitable for evaluation of fully engrafted patients following hematopoietic cell transplantation (HCT). To address this question, we developed a hybrid-capture NGS panel utilizing unique molecular identifiers (UMIs) to detect variants at 0.1% VAF or below across 22 genes frequently mutated in myeloid disorders and applied it to a retrospective sample set of blood and bone marrow DNA samples previously evaluated as negative for disease via standard-of-care short tandem repeat (STR)-based engraftment testing and hematopathology analysis in our laboratory. Of 30 patients who demonstrated trackable mutations in the 22 genes at eventual relapse by standard NGS analysis, we were able to definitively detect relapse-associated mutations in 18/30 (60%) at previously disease-negative timepoints collected 20-100 days prior to relapse date. MRD was detected in both bone marrow (15/28, 53.6%) and peripheral blood samples (9/18, 50%), while showing excellent technical specificity in our sample set. We also confirmed the disappearance of all MRD signal with increasing time prior to relapse (>100 days), indicating true clinical specificity, even using genes commonly associated with clonal hematopoiesis of indeterminate potential (CHIP). This study highlights the efficacy of a highly sensitive, NGS panel-based approach to early detection of relapse in AML and supports the clinical validity of extending MRD analysis across many genes in the post-transplant setting.
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Affiliation(s)
- Vidya Balagopal
- Department of Pathology, Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois, United States of America
| | - Andrew Hantel
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, Chicago, Illinois, United States of America
| | - Sabah Kadri
- Department of Pathology, Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois, United States of America
| | - George Steinhardt
- Department of Pathology, Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois, United States of America
| | - Chao Jie Zhen
- Department of Pathology, Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois, United States of America
| | - Wenjun Kang
- Center for Research Informatics, The University of Chicago, Chicago, Illinois, United States of America
| | - Pankhuri Wanjari
- Department of Pathology, Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois, United States of America
| | - Lauren L. Ritterhouse
- Department of Pathology, Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois, United States of America
| | - Wendy Stock
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, Chicago, Illinois, United States of America
| | - Jeremy P. Segal
- Department of Pathology, Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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30
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de Jonge MM, Ritterhouse LL, de Kroon CD, Vreeswijk MPG, Segal JP, Puranik R, Hollema H, Rookus MA, van Asperen CJ, van Leeuwen FE, Smit VTHBM, Howitt BE, Bosse T. Germline BRCA-Associated Endometrial Carcinoma Is a Distinct Clinicopathologic Entity. Clin Cancer Res 2019; 25:7517-7526. [PMID: 31492746 DOI: 10.1158/1078-0432.ccr-19-0848] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/05/2019] [Accepted: 08/20/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Whether endometrial carcinoma (EC) should be considered part of the gBRCA1/2-associated hereditary breast and ovarian cancer (HBOC) syndrome is topic of debate. We sought to assess whether ECs occurring in gBRCA carriers are enriched for clinicopathologic and molecular characteristics, thereby supporting a causal relationship. EXPERIMENTAL DESIGN Thirty-eight gBRCA carriers that developed EC were selected from the nationwide cohort study on hereditary breast and ovarian cancer in the Netherlands (HEBON), and these were supplemented with four institutional cases. Tumor tissue was retrieved via PALGA (Dutch Pathology Registry). Nineteen morphologic features were scored and histotype was determined by three expert gynecologic pathologists, blinded for molecular analyses (UCM-OncoPlus Assay including 1213 genes). ECs with LOH of the gBRCA-wild-type allele (gBRCA/LOHpos) were defined "gBRCA-associated," those without LOH (gBRCA/LOHneg) were defined "sporadic." RESULTS LOH could be assessed for 40 ECs (30 gBRCA1, 10 gBRCA2), of which 60% were gBRCA/LOHpos. gBRCA/LOHpos ECs were more frequently of nonendometrioid (58%, P = 0.001) and grade 3 histology (79%, P < 0.001). All but two were in the TP53-mutated TCGA-subgroup (91.7%, P < 0.001). In contrast, gBRCA/LOHneg ECs were mainly grade 1 endometrioid EC (94%) and showed a more heterogeneous distribution of TCGA-molecular subgroups: POLE-mutated (6.3%), MSI-high (25%), NSMP (62.5%), and TP53-mutated (6.3%). CONCLUSIONS We provide novel evidence in favor of EC being part of the gBRCA-associated HBOC-syndrome. gBRCA-associated ECs are enriched for EC subtypes associated with unfavorable clinical outcome. These findings have profound therapeutic consequences as these patients may benefit from treatment strategies such as PARP inhibitors. In addition, it should influence counseling and surveillance of gBRCA carriers.
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Affiliation(s)
- Marthe M de Jonge
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Lauren L Ritterhouse
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Cornelis D de Kroon
- Department of Gynaecology, Leiden University Medical Center, Leiden, the Netherlands
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Jeremy P Segal
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | | | - Harry Hollema
- Department of Pathology, University Medical Center Groningen, Groningen, the Netherlands
| | - Matti A Rookus
- Department of Epidemiology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Flora E van Leeuwen
- Department of Epidemiology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Vincent T H B M Smit
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Brooke E Howitt
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Tjalling Bosse
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands.
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Ritterhouse LL, Wu EY, Kim WG, Dillon DA, Hirsch MS, Sholl LM, Agoston AT, Setia N, Lauwers GY, Park DY, Srivastava A, Doyle LA. Loss of SMAD4 protein expression in gastrointestinal and extra-gastrointestinal carcinomas. Histopathology 2019; 75:546-551. [PMID: 31054158 DOI: 10.1111/his.13894] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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: 03/13/2019] [Accepted: 04/30/2019] [Indexed: 12/19/2022]
Abstract
AIMS SMAD4 (DPC4) is a tumour suppressor gene that is dysregulated in various tumour types, particularly pancreaticobiliary and gastrointestinal carcinomas. Corresponding loss of protein expression has been reported in approximately 50% of pancreatic and 25% of colonic adenocarcinomas. In the evaluation of carcinoma of unknown primary site, immunohistochemical loss of SMAD4 expression is often used to suggest pancreaticobiliary origin, but there are limited data on the spectrum of SMAD4 expression in carcinomas of other sites. This study evaluates the frequency of SMAD4 loss in a large cohort of carcinomas from diverse anatomical sites. METHODS AND RESULTS Immunohistochemistry for SMAD4 was performed on tissue microarrays or whole tissue sections of 1210 carcinomas from various organs: gastrointestinal tract, liver, pancreas/biliary tract, lung, breast, thyroid, kidney, ovary and uterus. Expression was considered lost when there was complete absence of staining in tumour cell nuclei, in the presence of intact staining in non-neoplastic cells. SMAD4 loss was seen in 58% of pancreatic adenocarcinomas, 27% of appendiceal adenocarcinomas, 19% of colorectal adenocarcinomas, 16% of cholangiocarcinomas, 10% of lung adenocarcinomas and <5% of oesophageal, breast, gastric and mucinous ovarian adenocarcinomas. All papillary thyroid, hepatocellular, non-mucinous ovarian, endometrial and renal cell carcinomas showed intact SMAD4 nuclear expression. CONCLUSION In addition to pancreaticobiliary, appendiceal and colonic tumours, SMAD4 loss is also seen in a small subset of other carcinomas, specifically breast, lung, oesophageal and gastric adenocarcinomas, all of which are typically CK7-positive, similar to pancreaticobiliary carcinoma. Awareness of SMAD4 loss in these other carcinoma types is helpful in the evaluation of carcinomas of unknown or uncertain primary site.
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Affiliation(s)
| | - Elizabeth Yiru Wu
- Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Woo Gyeong Kim
- Haeundae Paik Hospital, University of Inje College of Medicine, Busan, Korea
| | - Deborah A Dillon
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michelle S Hirsch
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lynette M Sholl
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Agoston T Agoston
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Do Youn Park
- Pusan National University Medical School, Busan, Korea
| | | | - Leona A Doyle
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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Patel SS, Pinkus GS, Ritterhouse LL, Segal JP, Dal Cin P, Restrepo T, Harris MH, Stone RM, Hasserjian RP, Weinberg OK. High NPM1 mutant allele burden at diagnosis correlates with minimal residual disease at first remission in de novo acute myeloid leukemia. Am J Hematol 2019; 94:921-928. [PMID: 31148220 DOI: 10.1002/ajh.25544] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 05/21/2019] [Accepted: 05/28/2019] [Indexed: 12/28/2022]
Abstract
Acute myeloid leukemia (AML) with mutated NPM1 is a newly recognized separate entity in the revised 2016 WHO classification, and is associated with a favorable prognosis. While previous studies have evaluated NPM1 in a binary fashion, we recently demonstrated a significant independent negative prognostic effect of high NPM1 mutant allele burden (VAF) at diagnosis in a cohort of de novo AML patients. Although the importance of minimal residual disease (MRD) monitoring in NPM1-mutated AML has been well characterized, the potential relationship between diagnostic allele burden and MRD is unknown. We retrospectively evaluated for MRD at first remission (CR1). We used either next-generation sequencing (NGS) [n = 71], and/or immunohistochemistry (IHC) for mutant NPM1 (NPM1c) [n = 60], in a subset of patients from our recently examined cohort. We identified a statistically significant positive correlation between the VAF at diagnosis, and at CR1 (Spearman r = 0.4, P = .006), and enrichment for MRD in high diagnostic VAF patients (P = .05), as previously defined. IHC-positivity also correlated significantly with a higher median diagnostic NPM1 VAF (0.42 vs 0.39, P = .02), and with the VAF at CR1 (Spearman r = 0.7, P = .003). In multivariable analyses, both high diagnostic VAF (P = .003) and MRD (P = .02) were independent predictors of shorter event-free survival (EFS). Our findings suggest a relationship between the NPM1 mutant allele burden at diagnosis, and the presence of MRD at first remission. Our findings support IHC as a potentially useful adjunctive tool for disease monitoring.
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Affiliation(s)
- Sanjay S. Patel
- Department of PathologyBrigham and Women's Hospital Boston Massachusetts
| | | | | | - Jeremy P. Segal
- Division of Genomic and Molecular PathologyUniversity of Chicago Chicago Illinois
| | - Paola Dal Cin
- Department of PathologyBrigham and Women's Hospital Boston Massachusetts
| | - Tamara Restrepo
- Department of PathologyBoston Children's Hospital Boston Massachusetts
| | - Marian H. Harris
- Department of PathologyBoston Children's Hospital Boston Massachusetts
| | - Richard M. Stone
- Department of Medical OncologyDana‐Farber Cancer Institute Boston Massachusetts
| | | | - Olga K. Weinberg
- Department of PathologyBrigham and Women's Hospital Boston Massachusetts
- Department of PathologyBoston Children's Hospital Boston Massachusetts
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Abstract
This commentary highlights the article by Blidner et al that describes a novel assay for detection of chimeric RNAs from gene fusions and exon-skipping events in non-small-cell lung cancer.
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Affiliation(s)
- Lauren L Ritterhouse
- Division of Genomic and Molecular Pathology, Department of Pathology, University of Chicago, Chicago, Illinois.
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Patil SA, Mujacic I, Ritterhouse LL, Segal JP, Kadri S. insiM. J Mol Diagn 2019; 21:19-26. [DOI: 10.1016/j.jmoldx.2018.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 07/16/2018] [Accepted: 08/14/2018] [Indexed: 12/25/2022] Open
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Kang W, Kadri S, Puranik R, Wurst MN, Patil SA, Mujacic I, Benhamed S, Niu N, Zhen CJ, Ameti B, Long BC, Galbo F, Montes D, Iracheta C, Gamboa VL, Lopez D, Yourshaw M, Lawrence CA, Aisner DL, Fitzpatrick C, McNerney ME, Wang YL, Andrade J, Volchenboum SL, Furtado LV, Ritterhouse LL, Segal JP. System for Informatics in the Molecular Pathology Laboratory: An Open-Source End-to-End Solution for Next-Generation Sequencing Clinical Data Management. J Mol Diagn 2018; 20:522-532. [PMID: 29698836 PMCID: PMC6039793 DOI: 10.1016/j.jmoldx.2018.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 12/20/2017] [Revised: 03/01/2018] [Accepted: 03/29/2018] [Indexed: 02/04/2023] Open
Abstract
Next-generation sequencing (NGS) diagnostic assays increasingly are becoming the standard of care in oncology practice. As the scale of an NGS laboratory grows, management of these assays requires organizing large amounts of information, including patient data, laboratory processes, genomic data, as well as variant interpretation and reporting. Although several Laboratory Information Systems and/or Laboratory Information Management Systems are commercially available, they may not meet all of the needs of a given laboratory, in addition to being frequently cost-prohibitive. Herein, we present the System for Informatics in the Molecular Pathology Laboratory (SIMPL), a free and open-source Laboratory Information System/Laboratory Information Management System for academic and nonprofit molecular pathology NGS laboratories, developed at the Genomic and Molecular Pathology Division at the University of Chicago Medicine. SIMPL was designed as a modular end-to-end information system to handle all stages of the NGS laboratory workload from test order to reporting. We describe the features of SIMPL, its clinical validation at University of Chicago Medicine, and its installation and testing within a different academic center laboratory (University of Colorado), and we propose a platform for future community co-development and interlaboratory data sharing.
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Affiliation(s)
- Wenjun Kang
- Center for Research Informatics, The University of Chicago, Chicago, Illinois
| | - Sabah Kadri
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Rutika Puranik
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Michelle N Wurst
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Sushant A Patil
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Ibro Mujacic
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Sonia Benhamed
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Nifang Niu
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Chao Jie Zhen
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Bekim Ameti
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Bradley C Long
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Filipo Galbo
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - David Montes
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Crystal Iracheta
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Venessa L Gamboa
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Daisy Lopez
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Michael Yourshaw
- Department of Pathology and Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Carolyn A Lawrence
- Department of Pathology and Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Dara L Aisner
- Department of Pathology and Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Carrie Fitzpatrick
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Megan E McNerney
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois; Department of Pediatrics, Biological Sciences Division, The University of Chicago, Chicago, Illinois; Comprehensive Cancer Center, The University of Chicago Medicine, Chicago, Illinois
| | - Y Lynn Wang
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Jorge Andrade
- Center for Research Informatics, The University of Chicago, Chicago, Illinois; Department of Pediatrics, Biological Sciences Division, The University of Chicago, Chicago, Illinois
| | - Samuel L Volchenboum
- Center for Research Informatics, The University of Chicago, Chicago, Illinois; Department of Pediatrics, Biological Sciences Division, The University of Chicago, Chicago, Illinois
| | - Larissa V Furtado
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Lauren L Ritterhouse
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Jeremy P Segal
- Division of Genomic and Molecular Pathology, Department of Pathology, The University of Chicago, Chicago, Illinois; Informatics Subdivision Leadership, Association for Molecular Pathology, Bethesda, Maryland.
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Abstract
This article focuses on the diagnostic, prognostic, and predictive molecular biomarkers in uterine malignancies, in the context of morphologic diagnoses. The histologic classification of endometrial carcinomas is reviewed first, followed by the description and molecular classification of endometrial epithelial malignancies in the context of histologic classification. Taken together, the molecular and histologic classifications help clinicians to approach troublesome areas encountered in clinical practice and evaluate the utility of molecular alterations in the diagnosis and subclassification of endometrial carcinomas. Putative prognostic markers are reviewed. The use of molecular alterations and surrogate immunohistochemistry as prognostic and predictive markers is also discussed.
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Affiliation(s)
- Lauren L Ritterhouse
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Brooke E Howitt
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA.
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Slight-Webb S, Lu R, Ritterhouse LL, Munroe ME, Maecker HT, Fathman CG, Utz PJ, Merrill JT, Guthridge JM, James JA. Autoantibody-Positive Healthy Individuals Display Unique Immune Profiles That May Regulate Autoimmunity. Arthritis Rheumatol 2017; 68:2492-502. [PMID: 27059145 PMCID: PMC5042816 DOI: 10.1002/art.39706] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [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: 09/25/2015] [Accepted: 03/29/2016] [Indexed: 01/07/2023]
Abstract
Objective Antinuclear antibodies (ANAs) are detected in ∼18% of females, yet autoimmune disease develops in only 5–8%. Immunologic differences between ANA‐positive healthy individuals and patients with systemic lupus erythematosus (SLE) may elucidate the regulatory mechanisms by which ANA‐positive individuals avoid transition to clinical autoimmune disease. Methods Healthy individuals (n = 790) were screened for autoantibodies specific for 11 antigens associated with lupus, systemic sclerosis, and Sjögren's syndrome. From this screening, 31 European American ANA‐positive healthy individuals were selected and demographically matched to ANA‐negative controls and SLE patients. Serum cytokine profiles, leukocyte subset frequency, and reactivity were analyzed by multiplex assays, immunophenotyping, and phosphospecific flow cytometry. Results Of 790 individuals screened, 57 (7%) were ANA‐positive. The majority of proinflammatory cytokines, including interferon‐γ (IFNγ), tumor necrosis factor, interleukin‐17 (IL‐17), and granulocyte colony‐stimulating factor, exhibited a stepwise increase in serum levels from ANA‐negative controls to ANA‐positive healthy individuals to SLE patients (P < 0.0001). IFNα, IFNβ, IL‐12p40, and stem cell factor/c‐Kit ligand were increased in SLE patients only (P < 0.05). B lymphocyte stimulator (BlyS) was elevated in SLE patients but decreased in ANA‐positive individuals (P < 0.001). Further, IL‐1 receptor antagonist (IL‐1Ra) was down‐regulated in SLE patients only (P < 0.0001). ANA‐positive individuals had increased frequencies of monocytes, memory B cells, and plasmablasts and increased levels of pSTAT‐1 and pSTAT‐3 following IFNα stimulation compared with ANA‐negative controls (P < 0.05). Conclusion ANA‐positive healthy individuals exhibit dysregulation in multiple immune pathways yet differ from SLE patients by the absence of elevated IFNs, BLyS, IL‐12p40, and stem cell factor/c‐Kit ligand. Further, severely decreased levels of IL‐1Ra in SLE patients compared with ANA‐positive individuals may contribute to disease development. These results highlight the importance of IFN‐related pathways and regulatory elements in SLE pathogenesis.
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Affiliation(s)
| | - Rufei Lu
- Oklahoma Medical Research Foundation, and University of Oklahoma Health Sciences Center, Oklahoma City
| | - Lauren L Ritterhouse
- Oklahoma Medical Research Foundation, and University of Oklahoma Health Sciences Center, Oklahoma City
| | | | | | | | - Paul J Utz
- Stanford University School of Medicine, Stanford, California
| | | | - Joel M Guthridge
- Oklahoma Medical Research Foundation, and University of Oklahoma Health Sciences Center, Oklahoma City
| | - Judith A James
- Oklahoma Medical Research Foundation, and University of Oklahoma Health Sciences Center, Oklahoma City.
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Lin JJ, Ritterhouse LL, Ali SM, Bailey M, Schrock AB, Gainor JF, Ferris LA, Mino-Kenudson M, Miller VA, Iafrate AJ, Lennerz JK, Shaw AT. ROS1 Fusions Rarely Overlap with Other Oncogenic Drivers in Non-Small Cell Lung Cancer. J Thorac Oncol 2017; 12:872-877. [PMID: 28088512 PMCID: PMC5403618 DOI: 10.1016/j.jtho.2017.01.004] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [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: 11/28/2016] [Revised: 12/26/2016] [Accepted: 01/02/2017] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Chromosomal rearrangements involving the gene ROS1 define a distinct molecular subset of NSCLCs with sensitivity to ROS1 inhibitors. Recent reports have suggested a significant overlap between ROS1 fusions and other oncogenic driver alterations, including mutations in EGFR and KRAS. METHODS We identified patients at our institution with ROS1-rearranged NSCLC who had undergone testing for genetic alterations in additional oncogenes, including EGFR, KRAS, and anaplastic lymphoma receptor tyrosine kinase gene (ALK). Clinicopathologic features and genetic testing results were reviewed. We also examined a separate database of ROS1-rearranged NSCLCs identified through the commercial FoundationOne assay (Foundation Medicine, Cambridge, MA). RESULTS Among 62 patients with ROS1-rearranged NSCLC evaluated at our institution, none harbored concurrent ALK fusions (0%) or EGFR activating mutations (0%). KRAS mutations were detected in two cases (3.2%), one of which harbored a concurrent noncanonical KRAS I24N mutation of unknown biological significance. In a separate ROS1 fluorescence in situ hybridization-positive case, targeted sequencing failed to confirm a ROS1 fusion but instead identified a KRAS G13D mutation. No concurrent mutations in B-Raf proto-oncogene, serine/threonine kinase gene (BRAF), erb-b2 receptor tyrosine kinase 2 gene (ERBB2), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha gene (PIK3CA), AKT/serine threonine kinase 1 gene (AKT1), or mitogen-activated protein kinase kinase 1 gene (MAP2K1) were detected. Analysis of an independent data set of 166 ROS1-rearranged NSCLCs identified by FoundationOne demonstrated rare cases with co-occurring driver mutations in EGFR (one of 166) and KRAS (three of 166) and no cases with co-occurring ROS1 and ALK rearrangements. CONCLUSIONS ROS1 rearrangements rarely overlap with alterations in EGFR, KRAS, ALK, or other targetable oncogenes in NSCLC.
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Affiliation(s)
- Jessica J Lin
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts; Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Siraj M Ali
- Foundation Medicine, Cambridge, Massachusetts
| | - Mark Bailey
- Foundation Medicine, Cambridge, Massachusetts
| | | | - Justin F Gainor
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts; Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Lorin A Ferris
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts; Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Anthony J Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Alice T Shaw
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts; Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts.
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Howitt BE, Strickland KC, Sholl LM, Rodig S, Ritterhouse LL, Chowdhury D, D'Andrea AD, Matulonis UA, Konstantinopoulos PA. Clear cell ovarian cancers with microsatellite instability: A unique subset of ovarian cancers with increased tumor-infiltrating lymphocytes and PD-1/PD-L1 expression. Oncoimmunology 2017; 6:e1277308. [PMID: 28344892 DOI: 10.1080/2162402x.2016.1277308] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [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: 11/23/2016] [Revised: 12/19/2016] [Accepted: 12/21/2016] [Indexed: 10/20/2022] Open
Abstract
Clear cell ovarian carcinoma (CCOC) represents a distinct histologic subtype of ovarian cancer associated with significantly worse prognosis across all stages and no effective therapeutic options. Here, we report a rare but clinically important cohort of CCOCs with microsatellite instability (MSI) (MSI-CCOCs), which are highly immunogenic and may thus be very responsive to immune checkpoint blockade. CCOCs with MSI exhibit a significantly higher number of CD8+ TILs, higher CD8+/CD4+ ratio, and higher PD-1+ TILs compared with microsatellite stable (MSS) CCOCs and compared with high grade serous ovarian cancers, which are the most common histologic subtype of ovarian cancer. Of note, PD-L1 expression in tumor cells or immune cells was noted in all cases of CCOCs with MSI. These observations open an alternative therapeutic avenue for a fraction of patients with CCOC and argue for the routine testing of CCOCs for MSI, a test that is not currently routinely performed.
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Affiliation(s)
- Brooke E Howitt
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School , Boston, MA, USA
| | - Kyle C Strickland
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School , Boston, MA, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School , Boston, MA, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School , Boston, MA, USA
| | - Lauren L Ritterhouse
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School , Boston, MA, USA
| | - Dipanjan Chowdhury
- Division of Genomic Stability and DNA Repair, Dana Farber Cancer Institute, Harvard Medical School , Boston, MA, USA
| | - Alan D D'Andrea
- Division of Genomic Stability and DNA Repair, Dana Farber Cancer Institute, Harvard Medical School , Boston, MA, USA
| | - Ursula A Matulonis
- Medical Gynecologic Oncology Program, Dana Farber Cancer Institute, Harvard Medical School , Boston, MA, USA
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Sholl LM, Do K, Shivdasani P, Cerami E, Dubuc AM, Kuo FC, Garcia EP, Jia Y, Davineni P, Abo RP, Pugh TJ, van Hummelen P, Thorner AR, Ducar M, Berger AH, Nishino M, Janeway KA, Church A, Harris M, Ritterhouse LL, Campbell JD, Rojas-Rudilla V, Ligon AH, Ramkissoon S, Cleary JM, Matulonis U, Oxnard GR, Chao R, Tassell V, Christensen J, Hahn WC, Kantoff PW, Kwiatkowski DJ, Johnson BE, Meyerson M, Garraway LA, Shapiro GI, Rollins BJ, Lindeman NI, MacConaill LE. Institutional implementation of clinical tumor profiling on an unselected cancer population. JCI Insight 2016; 1:e87062. [PMID: 27882345 DOI: 10.1172/jci.insight.87062] [Citation(s) in RCA: 326] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND. Comprehensive genomic profiling of a patient's cancer can be used to diagnose, monitor, and recommend treatment. Clinical implementation of tumor profiling in an enterprise-wide, unselected cancer patient population has yet to be reported. METHODS. We deployed a hybrid-capture and massively parallel sequencing assay (OncoPanel) for all adult and pediatric patients at our combined cancer centers. Results were categorized by pathologists based on actionability. We report the results for the first 3,727 patients tested. RESULTS. Our cohort consists of cancer patients unrestricted by disease site or stage. Across all consented patients, half had sufficient and available (>20% tumor) material for profiling; once specimens were received in the laboratory for pathology review, 73% were scored as adequate for genomic testing. When sufficient DNA was obtained, OncoPanel yielded a result in 96% of cases. 73% of patients harbored an actionable or informative alteration; only 19% of these represented a current standard of care for therapeutic stratification. The findings recapitulate those of previous studies of common cancers but also identify alterations, including in AXL and EGFR, associated with response to targeted therapies. In rare cancers, potentially actionable alterations suggest the utility of a "cancer-agnostic" approach in genomic profiling. Retrospective analyses uncovered contextual genomic features that may inform therapeutic response and examples where diagnoses revised by genomic profiling markedly changed clinical management. CONCLUSIONS. Broad sequencing-based testing deployed across an unselected cancer cohort is feasible. Genomic results may alter management in diverse scenarios; however, additional barriers must be overcome to enable precision cancer medicine on a large scale. FUNDING. This work was supported by DFCI, BWH, and the National Cancer Institute (5R33CA155554 and 5K23CA157631).
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Affiliation(s)
- Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Khanh Do
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Early Drug Discovery Center
| | - Priyanka Shivdasani
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Ethan Cerami
- Department of Biostatistics and Computational Biology, and
| | - Adrian M Dubuc
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Frank C Kuo
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Elizabeth P Garcia
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Yonghui Jia
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Phani Davineni
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Ryan P Abo
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Center for Cancer Genome Discovery, DFCI, Boston, Massachusetts, USA
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | | | - Aaron R Thorner
- Center for Cancer Genome Discovery, DFCI, Boston, Massachusetts, USA
| | - Matthew Ducar
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Center for Cancer Genome Discovery, DFCI, Boston, Massachusetts, USA
| | - Alice H Berger
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Mizuki Nishino
- Department of Radiology, DFCI and Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Katherine A Janeway
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts, USA
| | - Alanna Church
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Marian Harris
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Lauren L Ritterhouse
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Joshua D Campbell
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Vanesa Rojas-Rudilla
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Azra H Ligon
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Shakti Ramkissoon
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - James M Cleary
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Early Drug Discovery Center
| | - Ursula Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Geoffrey R Oxnard
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | | | | | | | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Center for Cancer Genome Discovery, DFCI, Boston, Massachusetts, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Lank Center for Genitourinary Oncology and
| | | | - David J Kwiatkowski
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Bruce E Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Matthew Meyerson
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Center for Cancer Genome Discovery, DFCI, Boston, Massachusetts, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Center for Cancer Precision Medicine, DFCI, Boston, Massachusetts, USA
| | - Geoffrey I Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Early Drug Discovery Center
| | - Barrett J Rollins
- Department of Medical Oncology, Dana-Farber Cancer Institute (DFCI), Boston, Massachusetts, USA; Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Laura E MacConaill
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Center for Cancer Genome Discovery, DFCI, Boston, Massachusetts, USA
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Ritterhouse LL, Nowak JA, Strickland KC, Garcia EP, Jia Y, Lindeman NI, Macconaill LE, Konstantinopoulos PA, Matulonis UA, Liu J, Berkowitz RS, Nucci MR, Crum CP, Sholl LM, Howitt BE. Morphologic correlates of molecular alterations in extrauterine Müllerian carcinomas. Mod Pathol 2016; 29:893-903. [PMID: 27150160 DOI: 10.1038/modpathol.2016.82] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 03/01/2016] [Accepted: 03/12/2016] [Indexed: 11/09/2022]
Abstract
Extrauterine high-grade serous carcinomas can exhibit various histologic patterns including (1) classic architecture that is papillary, micropapillary and infiltrative and (2) solid, endometrioid, and transitional (ie, SET) patterns. Although the SET pattern has been associated with germline BRCA mutations, potential molecular underpinnings have not been fully investigated. DNA was isolated from 174 carcinomas of the fallopian tube, ovary, or peritoneum. Targeted next-generation sequencing was performed and single-nucleotide and copy number variants were correlated with morphologic subtype. Overall, 79% of tumors were classified as high-grade serous carcinoma (n=138), and the most common mutations in high-grade serous carcinomas were TP53 (94%), BRCA1 (25%), BRCA2 (11%), and ATM (7%). Among chemotherapy-naive high-grade serous carcinomas, 40 cases exhibited classic morphology and 40 cases had non-classic morphology (SET or ambiguous features). Mutations in homologous recombination pathways were seen across all tumor histotypes. High-grade serous carcinomas with homologous recombination mutations were six times more likely to be associated with non-classic histology (P=0.002) and were significantly more likely to be platinum sensitive and have improved progression-free survival (PFS) (P=0.007 and P=0.004, respectively). In a multivariate analysis adjusted for age, homologous recombination mutation status and increased copy number variants were independently associated with improved PFS (P=0.008 and P=0.005, respectively). These findings underscore the potential significance of variant morphologic patterns and comprehensive genomic analysis in high-grade serous carcinomas with potential implications for pathogenesis, as well as response to targeted therapies.
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Affiliation(s)
- Lauren L Ritterhouse
- Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Jonathan A Nowak
- Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Kyle C Strickland
- Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Elizabeth P Garcia
- Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Yonghui Jia
- Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Laura E Macconaill
- Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | | | | | - Joyce Liu
- Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ross S Berkowitz
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Marisa R Nucci
- Women's and Perinatal Pathology Division, Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Christopher P Crum
- Women's and Perinatal Pathology Division, Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Brooke E Howitt
- Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.,Women's and Perinatal Pathology Division, Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
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Gainor JF, Dardaei L, Yoda S, Friboulet L, Leshchiner I, Katayama R, Dagogo-Jack I, Gadgeel S, Schultz K, Singh M, Chin E, Parks M, Lee D, DiCecca RH, Lockerman E, Huynh T, Logan J, Ritterhouse LL, Le LP, Muniappan A, Digumarthy S, Channick C, Keyes C, Getz G, Dias-Santagata D, Heist RS, Lennerz J, Sequist LV, Benes CH, Iafrate AJ, Mino-Kenudson M, Engelman JA, Shaw AT. Molecular Mechanisms of Resistance to First- and Second-Generation ALK Inhibitors in ALK-Rearranged Lung Cancer. Cancer Discov 2016; 6:1118-1133. [PMID: 27432227 DOI: 10.1158/2159-8290.cd-16-0596] [Citation(s) in RCA: 788] [Impact Index Per Article: 98.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 07/14/2016] [Indexed: 11/16/2022]
Abstract
Advanced, anaplastic lymphoma kinase (ALK)-positive lung cancer is currently treated with the first-generation ALK inhibitor crizotinib followed by more potent, second-generation ALK inhibitors (e.g., ceritinib and alectinib) upon progression. Second-generation inhibitors are generally effective even in the absence of crizotinib-resistant ALK mutations, likely reflecting incomplete inhibition of ALK by crizotinib in many cases. Herein, we analyzed 103 repeat biopsies from ALK-positive patients progressing on various ALK inhibitors. We find that each ALK inhibitor is associated with a distinct spectrum of ALK resistance mutations and that the frequency of one mutation, ALKG1202R, increases significantly after treatment with second-generation agents. To investigate strategies to overcome resistance to second-generation ALK inhibitors, we examine the activity of the third-generation ALK inhibitor lorlatinib in a series of ceritinib-resistant, patient-derived cell lines, and observe that the presence of ALK resistance mutations is highly predictive for sensitivity to lorlatinib, whereas those cell lines without ALK mutations are resistant. SIGNIFICANCE Secondary ALK mutations are a common resistance mechanism to second-generation ALK inhibitors and predict for sensitivity to the third-generation ALK inhibitor lorlatinib. These findings highlight the importance of repeat biopsies and genotyping following disease progression on targeted therapies, particularly second-generation ALK inhibitors. Cancer Discov; 6(10); 1118-33. ©2016 AACRSee related commentary by Qiao and Lovly, p. 1084This article is highlighted in the In This Issue feature, p. 1069.
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Affiliation(s)
- Justin F Gainor
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Leila Dardaei
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Satoshi Yoda
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Luc Friboulet
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts. Gustave Roussy Cancer Campus, Université Paris Saclay, INSERM U981, Paris, France
| | - Ignaty Leshchiner
- Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Ryohei Katayama
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts. Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Ibiayi Dagogo-Jack
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Shirish Gadgeel
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan
| | - Katherine Schultz
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Manrose Singh
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Emily Chin
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Melissa Parks
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Dana Lee
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Richard H DiCecca
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Elizabeth Lockerman
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Tiffany Huynh
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Jennifer Logan
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Long P Le
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Ashok Muniappan
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts
| | - Subba Digumarthy
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts
| | - Colleen Channick
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Colleen Keyes
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Gad Getz
- Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Dora Dias-Santagata
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Rebecca S Heist
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Jochen Lennerz
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Lecia V Sequist
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Cyril H Benes
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Jeffrey A Engelman
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts.
| | - Alice T Shaw
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts.
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Abstract
BACKGROUND Aberrations involving the ROS1 gene have not been reported in thyroid cancer. Here, a case of ROS1-associated thyroid cancer with unique and aggressive characteristics is presented. PATIENT FINDINGS A 24-year-old athlete presented with a 3.5 cm left paramedian upper neck mass. Open biopsy demonstrated a papillary thyroid carcinoma arising in the pyramidal lobe. Additional imaging revealed involvement of her cricothyroid membrane, thyroid laryngeal cartilage, and left vocal cord. Complete en bloc surgical resection of the thyroid with cricothyroid membrane and endolarynx was performed with negative surgical margins. Microscopically, the tumor was largely solid with microfollicular architecture with focal cytoplasmic clearing and nodular invasion with rare true papillae, extending posteriorly through the cricothyroid membrane into the deep soft tissue of the left anterior vocal cord (pT4a). Metastases were present in 5/11 lateral neck and pretracheal lymph nodes with a size up to 0.4 cm (pN1b) with perinodal lymphatic involvement. She was staged according to her age (<45 years) as stage I. The solid-variant histology and locally aggressive behavior triggered oncologic genotyping, which was performed using massive parallel sequencing and anchored multiplexed next-generation sequencing for gene fusion detection on formalin-fixed paraffin embedded tissue. Targeted genotyping did not reveal a panel-specific point mutation. However, gene fusion assessment demonstrated a gene fusion involving ROS1. Mapping of the fusion and sequence analysis identified CCDC30 as the ROS1 fusion partner. Sequence-based prediction of the fusion product revealed the coiled-coil domain 30 (CCDC30) gene fused to the N-terminal ROS1 kinase domain, with CCDC30 as the postulated driver of ROS1-kinase constitutive activation. ROS1 rearrangement was confirmed using fluorescent in situ hybridization as an orthogonal method. A review of all currently reported ROS1 fusions in >7000 samples (The Cancer Genome Atlas) showed no prior report of ROS1-CCDC30, ROS1 fusions, or presence of ROS1 aberrations in thyroid cancer. SUMMARY Herein, the first case of a ROS1 rearrangement in a papillary thyroid carcinoma with a locally aggressive presentation is reported. CONCLUSION A review of additional patients with solid-variant papillary thyroid carcinoma and similar clinical characteristics with undetermined tumor genetics is needed, especially in light of the availability of ROS1-targeted therapeutics.
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Affiliation(s)
- Lauren L Ritterhouse
- 1 Department of Pathology, Massachusetts General Hospital/Harvard Medical School , Boston, Massachusetts
| | - Lori J Wirth
- 2 Department of Medicine, Massachusetts General Hospital/Harvard Medical School , Boston, Massachusetts
| | - Gregory W Randolph
- 3 Department of Surgery, Massachusetts General Hospital/Harvard Medical School , Boston, Massachusetts
- 4 Department of Otolaryngology, Massachusetts Eye and Ear Infirmary and Harvard Medical School , Boston, Massachusetts
| | - Peter M Sadow
- 1 Department of Pathology, Massachusetts General Hospital/Harvard Medical School , Boston, Massachusetts
- 4 Department of Otolaryngology, Massachusetts Eye and Ear Infirmary and Harvard Medical School , Boston, Massachusetts
| | - Douglas S Ross
- 2 Department of Medicine, Massachusetts General Hospital/Harvard Medical School , Boston, Massachusetts
| | - Whitney Liddy
- 4 Department of Otolaryngology, Massachusetts Eye and Ear Infirmary and Harvard Medical School , Boston, Massachusetts
| | - Jochen K Lennerz
- 1 Department of Pathology, Massachusetts General Hospital/Harvard Medical School , Boston, Massachusetts
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Howitt BE, Shukla SA, Sholl LM, Ritterhouse LL, Watkins JC, Rodig S, Stover E, Strickland KC, D'Andrea AD, Wu CJ, Matulonis UA, Konstantinopoulos PA. Association of Polymerase e-Mutated and Microsatellite-Instable Endometrial Cancers With Neoantigen Load, Number of Tumor-Infiltrating Lymphocytes, and Expression of PD-1 and PD-L1. JAMA Oncol 2016; 1:1319-23. [PMID: 26181000 DOI: 10.1001/jamaoncol.2015.2151] [Citation(s) in RCA: 449] [Impact Index Per Article: 56.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
IMPORTANCE Immune checkpoint inhibitor therapy has shown benefit in various cancers, but their potential in endometrial cancer (EC) is unknown. OBSERVATIONS Prediction of neoantigen load was performed using sequencing data from the Cancer Genome Atlas data set. Evaluation of tumor-infiltrating lymphocytes (TILs) and PD-1 and PD-L1 expression was performed in 63 patients with EC referred to our institution. The predicted median (range) neoantigen load (predicted neoepitopes per sample) was proportional to the mutational load: highest in ultramutated polymerase e (POLE) tumors (8342 [628-20 440]), less in hypermutated MSI (541 [146-8063]; P < .001), and lowest in microsatellite-stable tumors (70.5 [7-1877]; P < .001). The POLE and MSI ECs exhibited higher numbers of CD3+ (44.5 vs 21.8; P = .001) and CD8+ (32.8 vs 13.5; P < .001) TILs compared with microsatellite-stable tumors. PD-1 was overexpressed in TILs (81% vs 28%; P < .001) and peritumoral lymphocytes (90% vs 28%; P < .001) of POLE and MSI tumors. PD-L1 expression was infrequently noted in tumor cells but was common in intraepithelial immune cells and more frequent in POLE and MSI tumors (39% vs 13%; P = .02). CONCLUSIONS AND RELEVANCE Polymerase e-mutated and MSI ECs are associated with high neoantigen loads and number of TILs, which is counterbalanced by overexpression of PD-1 and PD-L1. Polymerase e-mutated and MSI EC tumors may be excellent candidates for PD-1-targeted immunotherapies.
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Affiliation(s)
- Brooke E Howitt
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Sachet A Shukla
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts3Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lauren L Ritterhouse
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jaclyn C Watkins
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Elizabeth Stover
- Medical Gynecologic Oncology Program, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Kyle C Strickland
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Alan D D'Andrea
- Division of Genomic Stability and DNA Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Catherine J Wu
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts3Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Ursula A Matulonis
- Medical Gynecologic Oncology Program, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
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46
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Strickland KC, Howitt BE, Shukla SA, Rodig S, Ritterhouse LL, Liu JF, Garber JE, Chowdhury D, Wu CJ, D'Andrea AD, Matulonis UA, Konstantinopoulos PA. Association and prognostic significance of BRCA1/2-mutation status with neoantigen load, number of tumor-infiltrating lymphocytes and expression of PD-1/PD-L1 in high grade serous ovarian cancer. Oncotarget 2016. [PMID: 26871470 DOI: 10.18632/oncotarget.7277] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Immune checkpoint inhibitors (e.g., anti-PD-1 and anti-PD-L1 antibodies) have demonstrated remarkable efficacy against hypermutated cancers such as melanomas and lung carcinomas. One explanation for this effect is that hypermutated lesions harbor more tumor-specific neoantigens that stimulate recruitment of an increased number of tumor-infiltrating lymphocytes (TILs), which is counterbalanced by overexpression of immune checkpoints such as PD-1 or PD-L1. Given that BRCA1/2-mutated high grade serous ovarian cancers (HGSOCs) exhibit a higher mutational load and a unique mutational signature with an elevated number of larger indels up to 50 bp, we hypothesized that they may also harbor more tumor-specific neoantigens, and, therefore, exhibit increased TILs and PD-1/PD-L1 expression. Here, we report significantly higher predicted neoantigens in BRCA1/2-mutated tumors compared to tumors without alterations in homologous recombination (HR) genes (HR-proficient tumors). Tumors with higher neoantigen load were associated with improved overall survival and higher expression of immune genes associated with tumor cytotoxicity such as genes of the TCR, the IFN-gamma and the TNFR pathways. Furthermore, immunohistochemistry studies demonstrated that BRCA1/2-mutated tumors exhibited significantly increased CD3+ and CD8+ TILs, as well as elevated expression of PD-1 and PD-L1 in tumor-associated immune cells compared to HR-proficient tumors. Survival analysis showed that both BRCA1/2-mutation status and number of TILs were independently associated with outcome. Of note, two distinct groups of HGSOCs, one with very poor prognosis (HR proficient with low number of TILs) and one with very good prognosis (BRCA1/2-mutated tumors with high number of TILs) were defined. These findings support a link between BRCA1/2-mutation status, immunogenicity and survival, and suggesting that BRCA1/2-mutated HGSOCs may be more sensitive to PD-1/PD-L1 inhibitors compared to HR-proficient HGSOCs.
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Affiliation(s)
- Kyle C Strickland
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brooke E Howitt
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sachet A Shukla
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lauren L Ritterhouse
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joyce F Liu
- Medical Gynecologic Oncology Program, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Judy E Garber
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Dipanjan Chowdhury
- Division of Genomic Stability and DNA Repair, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Catherine J Wu
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alan D D'Andrea
- Division of Genomic Stability and DNA Repair, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ursula A Matulonis
- Medical Gynecologic Oncology Program, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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47
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Strickland KC, Howitt BE, Shukla SA, Rodig S, Ritterhouse LL, Liu JF, Garber JE, Chowdhury D, Wu CJ, D'Andrea AD, Matulonis UA, Konstantinopoulos PA. Association and prognostic significance of BRCA1/2-mutation status with neoantigen load, number of tumor-infiltrating lymphocytes and expression of PD-1/PD-L1 in high grade serous ovarian cancer. Oncotarget 2016. [PMID: 26871470 DOI: 10.18632/oncotarget.7277]+[] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Immune checkpoint inhibitors (e.g., anti-PD-1 and anti-PD-L1 antibodies) have demonstrated remarkable efficacy against hypermutated cancers such as melanomas and lung carcinomas. One explanation for this effect is that hypermutated lesions harbor more tumor-specific neoantigens that stimulate recruitment of an increased number of tumor-infiltrating lymphocytes (TILs), which is counterbalanced by overexpression of immune checkpoints such as PD-1 or PD-L1. Given that BRCA1/2-mutated high grade serous ovarian cancers (HGSOCs) exhibit a higher mutational load and a unique mutational signature with an elevated number of larger indels up to 50 bp, we hypothesized that they may also harbor more tumor-specific neoantigens, and, therefore, exhibit increased TILs and PD-1/PD-L1 expression. Here, we report significantly higher predicted neoantigens in BRCA1/2-mutated tumors compared to tumors without alterations in homologous recombination (HR) genes (HR-proficient tumors). Tumors with higher neoantigen load were associated with improved overall survival and higher expression of immune genes associated with tumor cytotoxicity such as genes of the TCR, the IFN-gamma and the TNFR pathways. Furthermore, immunohistochemistry studies demonstrated that BRCA1/2-mutated tumors exhibited significantly increased CD3+ and CD8+ TILs, as well as elevated expression of PD-1 and PD-L1 in tumor-associated immune cells compared to HR-proficient tumors. Survival analysis showed that both BRCA1/2-mutation status and number of TILs were independently associated with outcome. Of note, two distinct groups of HGSOCs, one with very poor prognosis (HR proficient with low number of TILs) and one with very good prognosis (BRCA1/2-mutated tumors with high number of TILs) were defined. These findings support a link between BRCA1/2-mutation status, immunogenicity and survival, and suggesting that BRCA1/2-mutated HGSOCs may be more sensitive to PD-1/PD-L1 inhibitors compared to HR-proficient HGSOCs.
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Affiliation(s)
- Kyle C Strickland
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brooke E Howitt
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sachet A Shukla
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lauren L Ritterhouse
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joyce F Liu
- Medical Gynecologic Oncology Program, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Judy E Garber
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Dipanjan Chowdhury
- Division of Genomic Stability and DNA Repair, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Catherine J Wu
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alan D D'Andrea
- Division of Genomic Stability and DNA Repair, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ursula A Matulonis
- Medical Gynecologic Oncology Program, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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48
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Abstract
The significance of BRAF mutations in neoplasia was first recognized in 2002 when mutations were discovered in a broad range of cancers. Numerous subsequent studies expanded our understanding of BRAF V600E as a critical diagnostic, prognostic, and predictive biomarker in many cancers. Additionally, the advent of small-molecule inhibitors of BRAF V600E rendered assessment of BRAF mutation status essential in tumors such as melanoma. In clinical practice, evaluation of BRAF mutation status has routinely been performed by DNA-based assays utilizing polymerase chain reaction (PCR). However, molecular testing is not available at many hospitals since it is time-consuming, expensive, and requires expertise in molecular techniques. The first BRAF V600E-specific antibody was reported in 2011 (clone VE1). A purified version of this antibody as well as a second monoclonal antibody targeted to BRAF V600E is now commercially available. In this review, clinicopathologic characteristics associated with BRAF-mutant tumors will be highlighted, and the prognostic and predictive implications of a BRAF V600E mutation will be discussed with a focus on melanoma, thyroid carcinoma and colorectal carcinoma. Additionally, we will review the correlation between immunohistochemistry and molecular results and deliberate how BRAF immunohistochemistry might be utilized in the evaluation of these tumors.
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Affiliation(s)
- Lauren L Ritterhouse
- Department of Pathology, Brigham and Women׳s Hospital, Harvard Medical School, 75 Francis St, Boston, Massachusetts 02115
| | - Justine A Barletta
- Department of Pathology, Brigham and Women׳s Hospital, Harvard Medical School, 75 Francis St, Boston, Massachusetts 02115.
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Ritterhouse LL, Cykowski MD, Hassell LA, Slobodov G, Bane BL. Melanotic Xp11 translocation renal cancer: report of a case with a unique intratumoral sarcoid-like reaction. Diagn Pathol 2014; 9:81. [PMID: 24735727 PMCID: PMC4003493 DOI: 10.1186/1746-1596-9-81] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [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] [Received: 01/09/2014] [Accepted: 03/22/2014] [Indexed: 12/24/2022] Open
Abstract
Background Melanotic Xp11 translocation renal cancer is a rare tumor belonging to the family of microphthalmia-associated transcription factor (MiTF)/transcription factor E (TFE) neoplasms. This tumor family also includes alveolar soft part sarcoma, perivascular epithelioid cell neoplasms, Xp11 translocation renal cell carcinoma, and melanoma. To date, six confirmed melanotic Xp11 translocation cancers (five renal, one ovarian) have been reported in the literature. Case Report Here, we report the clinical, histologic, immunohistochemical, and molecular features of a unique melanotic Xp11 translocation renal cancer arising in a 34-year-old African-American female. Histologically, the tumor was composed of epithelioid tumor cells arranged in a nested pattern. The cells had clear to eosinophilic granular cytoplasm, vesicular nuclear chromatin, and prominent nucleoli. Multifocal intracytoplasmic deposits of granular brown melanin pigment were identified and confirmed by Fontana-Masson stain. An unusual histologic feature, not previously reported in melanotic Xp11 translocation renal cancer, was a sarcoid-like granulomatous reaction consisting of tight epithelioid granulomas with lymphocytic cuffing, numerous giant cells, and calcifications. Nuclear transcription factor E3 expression was identified by immunohistochemistry and TFE3 rearrangement was confirmed by fluorescence in situ hybridization. Additional immunohistochemical findings included immunoreactivity for HMB45, cathepsin K, and progesterone receptor; negative staining was seen with actin, desmin, cytokeratins, epithelial membrane antigen, CD10, vimentin, and PAX-8. The patient is currently free of disease, two years following initial clinicoradiologic presentation and twenty-two months following partial nephrectomy without additional therapy. Conclusion This report further expands the spectrum of morphologic and clinical findings previously described in melanotic Xp11 translocation renal cancer, a distinctive tumor showing overlapping features between Xp11 translocation renal cell carcinoma, melanoma, and perivascular epithelioid cell neoplasms. Virtual slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/7225796341180634
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Affiliation(s)
| | | | - Lewis A Hassell
- Department of Pathology, University of Oklahoma Health Sciences Center, BMSB 451 940 SL Young Blvd,, Oklahoma City, OK 73104, USA.
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Ritterhouse LL, Lu R, Shah HB, Robertson JM, Fife DA, Maecker HT, Du H, Fathman CG, Chakravarty EF, Scofield RH, Kamen DL, Guthridge JM, James JA. Vitamin d deficiency in a multiethnic healthy control cohort and altered immune response in vitamin D deficient European-American healthy controls. PLoS One 2014; 9:e94500. [PMID: 24727903 PMCID: PMC3984168 DOI: 10.1371/journal.pone.0094500] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [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: 10/21/2013] [Accepted: 03/17/2014] [Indexed: 01/08/2023] Open
Abstract
Objective In recent years, vitamin D has been shown to possess a wide range of immunomodulatory effects. Although there is extensive amount of research on vitamin D, we lack a comprehensive understanding of the prevalence of vitamin D deficiency or the mechanism by which vitamin D regulates the human immune system. This study examined the prevalence and correlates of vitamin D deficiency and the relationship between vitamin D and the immune system in healthy individuals. Methods Healthy individuals (n = 774) comprised of European-Americans (EA, n = 470), African–Americans (AA, n = 125), and Native Americans (NA, n = 179) were screened for 25-hydroxyvitamin D [25(OH)D] levels by ELISA. To identify the most noticeable effects of vitamin D on the immune system, 20 EA individuals with severely deficient (<11.3 ng/mL) and sufficient (>24.8 ng/mL) vitamin D levels were matched and selected for further analysis. Serum cytokine level measurement, immune cell phenotyping, and phosphoflow cytometry were performed. Results Vitamin D sufficiency was observed in 37.5% of the study cohort. By multivariate analysis, AA, NA, and females with a high body mass index (BMI, >30) demonstrate higher rates of vitamin D deficiency (p<0.05). Individuals with vitamin D deficiency had significantly higher levels of serum GM-CSF (p = 0.04), decreased circulating activated CD4+ (p = 0.04) and CD8+ T (p = 0.04) cell frequencies than individuals with sufficient vitamin D levels. Conclusion A large portion of healthy individuals have vitamin D deficiency. These individuals have altered T and B cell responses, indicating that the absence of sufficient vitamin D levels could result in undesirable cellular and molecular alterations ultimately contributing to immune dysregulation.
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Affiliation(s)
- Lauren L. Ritterhouse
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- Departments of Medicine and Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Rufei Lu
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- Departments of Medicine and Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Hemangi B. Shah
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Julie M. Robertson
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Dustin A. Fife
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Holden T. Maecker
- Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Hongwu Du
- Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Charles G. Fathman
- Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Eliza F. Chakravarty
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - R. Hal Scofield
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Diane L. Kamen
- Division of Rheumatology, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Joel M. Guthridge
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Judith A. James
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- Departments of Medicine and Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
- * E-mail:
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