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Sholl LM, Awad M, Basu Roy U, Beasley MB, Cartun RW, Hwang DM, Kalemkerian G, Lopez-Rios F, Mino-Kenudson M, Paintal A, Reid K, Ritterhouse L, Souter LA, Swanson PE, Ventura CB, Furtado LV. Programmed Death Ligand-1 and Tumor Mutation Burden Testing of Patients With Lung Cancer for Selection of Immune Checkpoint Inhibitor Therapies: Guideline From the College of American Pathologists, Association for Molecular Pathology, International Association for the Study of Lung Cancer, Pulmonary Pathology Society, and LUNGevity Foundation. Arch Pathol Lab Med 2024:499926. [PMID: 38625026 DOI: 10.5858/arpa.2023-0536-cp] [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] [Accepted: 02/29/2024] [Indexed: 04/17/2024]
Abstract
CONTEXT.— Rapid advancements in the understanding and manipulation of tumor-immune interactions have led to the approval of immune therapies for patients with non-small cell lung cancer. Certain immune checkpoint inhibitor therapies require the use of companion diagnostics, but methodologic variability has led to uncertainty around test selection and implementation in practice. OBJECTIVE.— To develop evidence-based guideline recommendations for the testing of immunotherapy/immunomodulatory biomarkers, including programmed death ligand-1 (PD-L1) and tumor mutation burden (TMB), in patients with lung cancer. DESIGN.— The College of American Pathologists convened a panel of experts in non-small cell lung cancer and biomarker testing to develop evidence-based recommendations in accordance with the standards for trustworthy clinical practice guidelines established by the National Academy of Medicine. A systematic literature review was conducted to address 8 key questions. Using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach, recommendations were created from the available evidence, certainty of that evidence, and key judgments as defined in the GRADE Evidence to Decision framework. RESULTS.— Six recommendation statements were developed. CONCLUSIONS.— This guideline summarizes the current understanding and hurdles associated with the use of PD-L1 expression and TMB testing for immune checkpoint inhibitor therapy selection in patients with advanced non-small cell lung cancer and presents evidence-based recommendations for PD-L1 and TMB testing in the clinical setting.
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Affiliation(s)
- Lynette M Sholl
- From the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Sholl)
| | - Mark Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts (Awad)
| | - Upal Basu Roy
- Translational Science Research Program, LUNGevity Foundation, Chicago, Illinois (Basu Roy)
| | - Mary Beth Beasley
- the Department of Anatomic Pathology and Clinical Pathology, Mt. Sinai Medical Center, New York, New York (Beasley)
| | - Richard Walter Cartun
- the Department of Anatomic Pathology, Hartford Hospital, Hartford, Connecticut (Cartun)
| | - David M Hwang
- the Department of Laboratory Medicine & Pathobiology, Sunnybrook Health Science Centre, Toronto, Ontario, Canada (Hwang)
| | - Gregory Kalemkerian
- the Department of Medical Oncology and Internal Medicine, University of Michigan Health, Ann Arbor (Kalemkerian)
| | - Fernando Lopez-Rios
- Pathology Department, Hospital Universitario 12 de Octubre, Madrid, Spain (Lopez-Rios)
| | - Mari Mino-Kenudson
- the Department of Pathology, Massachusetts General Hospital, Boston (Mino-Kenudson)
| | - Ajit Paintal
- the Department of Pathology, NorthShore University Health System, Evanston, Illinois (Paintal)
| | - Kearin Reid
- Governance (Reid) and the Pathology and Laboratory Quality Center for Evidence-based Guidelines (Ventura), College of American Pathologists, Northfield, Illinois
| | - Lauren Ritterhouse
- the Department of Pathology, Foundation Medicine, Cambridge, Massachusetts (Ritterhouse)
| | | | - Paul E Swanson
- the Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle (Swanson)
| | - Christina B Ventura
- Governance (Reid) and the Pathology and Laboratory Quality Center for Evidence-based Guidelines (Ventura), College of American Pathologists, Northfield, Illinois
| | - Larissa V Furtado
- the Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee (Furtado)
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Ricciuti B, Lamberti G, Puchala SR, Mahadevan NR, Lin JR, Alessi JV, Chowdhury A, Li YY, Wang X, Spurr L, Pecci F, Di Federico A, Venkatraman D, Barrichello AP, Gandhi M, Vaz VR, Pangilinan AJ, Haradon D, Lee E, Gupta H, Pfaff KL, Welsh EL, Nishino M, Cherniack AD, Johnson BE, Weirather JL, Dryg ID, Rodig SJ, Sholl LM, Sorger P, Santagata S, Umeton R, Awad MM. Genomic and Immunophenotypic Landscape of Acquired Resistance to PD-(L)1 Blockade in Non-Small-Cell Lung Cancer. J Clin Oncol 2024; 42:1311-1321. [PMID: 38207230 DOI: 10.1200/jco.23.00580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 08/27/2023] [Accepted: 10/24/2023] [Indexed: 01/13/2024] Open
Abstract
PURPOSE Although immune checkpoint inhibitors (ICI) have extended survival in patients with non-small-cell lung cancer (NSCLC), acquired resistance (AR) to ICI frequently develops after an initial benefit. However, the mechanisms of AR to ICI in NSCLC are largely unknown. METHODS Comprehensive tumor genomic profiling, machine learning-based assessment of tumor-infiltrating lymphocytes, multiplexed immunofluorescence, and/or HLA-I immunohistochemistry (IHC) were performed on matched pre- and post-ICI tumor biopsies from patients with NSCLC treated with ICI at the Dana-Farber Cancer Institute who developed AR to ICI. Two additional cohorts of patients with intervening chemotherapy or targeted therapies between biopsies were included as controls. RESULTS We performed comprehensive genomic profiling and immunophenotypic characterization on samples from 82 patients with NSCLC and matched pre- and post-ICI biopsies and compared findings with a control cohort of patients with non-ICI intervening therapies between biopsies (chemotherapy, N = 32; targeted therapies, N = 89; both, N = 17). Putative resistance mutations were identified in 27.8% of immunotherapy-treated cases and included acquired loss-of-function mutations in STK11, B2M, APC, MTOR, KEAP1, and JAK1/2; these acquired alterations were not observed in the control groups. Immunophenotyping of matched pre- and post-ICI samples demonstrated significant decreases in intratumoral lymphocytes, CD3e+ and CD8a+ T cells, and PD-L1-PD1 engagement, as well as increased distance between tumor cells and CD8+PD-1+ T cells. There was a significant decrease in HLA class I expression in the immunotherapy cohort at the time of AR compared with the chemotherapy (P = .005) and the targeted therapy (P = .01) cohorts. CONCLUSION These findings highlight the genomic and immunophenotypic heterogeneity of ICI resistance in NSCLC, which will need to be considered when developing novel therapeutic strategies aimed at overcoming resistance.
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Affiliation(s)
- Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Giuseppe Lamberti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Sreekar R Puchala
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA
| | | | - Jia-Ren Lin
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA
| | - Joao V Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Alexander Chowdhury
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA
| | - Yvonne Y Li
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Xinan Wang
- Harvard School of Public Health, Boston, MA
| | - Liam Spurr
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Federica Pecci
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Deepti Venkatraman
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Malini Gandhi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Victor R Vaz
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Andy J Pangilinan
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Danielle Haradon
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Elinton Lee
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Hersh Gupta
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA
| | - Kathleen L Pfaff
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Emma L Welsh
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Mizuki Nishino
- Department of Radiology, Brigham and Women's Hospital, Boston, MA
| | - Andrew D Cherniack
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA
| | - Bruce E Johnson
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Jason L Weirather
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Ian D Dryg
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Peter Sorger
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA
| | - Sandro Santagata
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA
| | - Renato Umeton
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA
| | - Mark M Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
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3
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Neil AJ, Chukwueke UN, Hoover N, Marris SRN, Rojas-Rudilla V, Manning DK, Mito JK, Cibas ES, Sholl LM. Validation of targeted next-generation sequencing of cell-free DNA from archival cerebrospinal fluid specimens for the detection of somatic variants in cancer involving the leptomeninges: Cytopathologic and radiographic correlation. Cancer Cytopathol 2024; 132:214-223. [PMID: 37812603 DOI: 10.1002/cncy.22768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/28/2023] [Accepted: 08/21/2023] [Indexed: 10/11/2023]
Abstract
BACKGROUND Leptomeningeal metastases occur across multiple solid and lymphoid cancers, and patients typically undergo cytopathologic assessment of cerebrospinal fluid (CSF) in this setting. For patients diagnosed with metastatic cancer, the detection of actionable somatic mutations in CSF can provide clinically valuable information for treatment without the need for additional tissue collection. METHODS The authors validated a targeted next-generation sequencing assay for the detection of somatic variants in cancer (OncoPanel) on cell-free DNA (cfDNA) isolated from archival CSF specimens in a cohort of 25 patients who had undergone molecular testing of a prior tumor specimen. RESULTS CSF storage time and volume had no impact on cfDNA concentration or mean target coverage of the assay. Previously identified somatic variants in CSF cfDNA were detected in 88%, 50%, and 27% of specimens diagnosed cytologically as positive, suspicious/atypical, and negative for malignancy, respectively. Somatic variants were identified in 81% of CSF specimens from patients who had leptomeningeal enhancement on magnetic resonance imaging compared with 31% from patients without such enhancement. CONCLUSIONS These data highlight the stability of cfDNA in CSF, which allows for cytopathologic evaluation before triage for next-generation sequencing assays. For a subset of cases in which clinical suspicion is high but cytologic or radiographic studies are inconclusive, the detection of pathogenic somatic variants in CSF cfDNA may aid in the diagnosis of leptomeningeal metastases.
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Affiliation(s)
- Alexander J Neil
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ugonma N Chukwueke
- Center for Neuro-Oncology, Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Nicholas Hoover
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sean R N Marris
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Vanesa Rojas-Rudilla
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Danielle K Manning
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeffrey K Mito
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Edmund S Cibas
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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4
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Boiarsky D, Gulhan DC, Savignano H, Lakshminarayanan G, McClure HM, Silver R, Hirsch MS, Sholl LM, Choudhury AD, Ananda G, Park PJ, Tewari AK, Berchuck JE. A Panel-Based Mutational Signature of Mismatch Repair Deficiency is Associated With Durable Response to Pembrolizumab in Metastatic Castration-Resistant Prostate Cancer. Clin Genitourin Cancer 2024; 22:558-568.e3. [PMID: 38342659 PMCID: PMC10939759 DOI: 10.1016/j.clgc.2024.01.011] [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: 12/06/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 02/13/2024]
Abstract
INTRODUCTION/BACKGROUND Immune checkpoint inhibitors (ICIs) have limited efficacy in prostate cancer (PCa). Better biomarkers are needed to predict responses to ICIs. We sought to demonstrate that a panel-based mutational signature identifies mismatch repair (MMR) deficient (MMRd) PCa and is a biomarker of response to pembrolizumab. PATIENTS AND METHODS Clinico-genomic data was obtained for 2664 patients with PCa sequenced at Dana-Farber Cancer Institute (DFCI) and Memorial Sloan Kettering (MSK). Clinical outcomes were collected for patients with metastatic castration-resistant PCa (mCRPC) treated with pembrolizumab at DFCI. SigMA was used to characterize tumors as MMRd or MMR proficient (MMRp). The concordance between MMRd with microsatellite instability (MSI-H) was assessed. Radiographic progression-free survival (rPFS) and overall survival (OS) were collected for patients treated with pembrolizumab. Event-time distributions were estimated using Kaplan-Meier methodology. RESULTS Across both cohorts, 100% (DFCI: 12/12; MSK: 43/43) of MSI-H tumors were MMRd. However, 14% (2/14) and 9.1% (6/66) of MMRd tumors in the DFCI and MSK cohorts respectively were microsatellite stable (MSS), and 26% (17/66) were MSI-indeterminate in the MSK cohort. Among patients treated with pembrolizumab, those with MMRd (n = 5) versus MMRp (n = 14) mCRPC experienced markedly improved rPFS (HR = 0.088, 95% CI: 0.011-0.70; P = .0064) and OS (HR = 0.11, 95% CI: 0.014-0.80; P = .010) from start of treatment. Four patients with MMRd experienced remissions of >= 2.5 years. CONCLUSION SigMA detects additional cases of MMRd as compared to MSI testing in PCa and identifies patients likely to experience durable response to pembrolizumab.
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Affiliation(s)
| | - Doga C Gulhan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Hunter Savignano
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Heather M McClure
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Rebecca Silver
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Atish D Choudhury
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Guruprasad Ananda
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Alok K Tewari
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Jacob E Berchuck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.
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5
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Odintsov I, Sholl LM. Prognostic and predictive biomarkers in non-small cell lung carcinoma. Pathology 2024; 56:192-204. [PMID: 38199926 DOI: 10.1016/j.pathol.2023.11.006] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 01/12/2024]
Abstract
Lung cancer is the most common cause of cancer-related deaths globally, with the highest mortality rates among both men and women. Most lung cancers are diagnosed at late stages, necessitating systemic therapy. Modern clinical management of lung cancer relies heavily upon application of biomarkers, which guide the selection of systemic treatment. Here, we provide an overview of currently approved and emerging biomarkers of non-small cell lung cancer (NSCLC), including EGFR, ALK, ROS1, RET, NTRK1-3, KRAS, BRAF, MET, ERBB2/HER2, NRG1, PD-L1, TROP2, and CEACAM5. For practical purposes, we divide these biomarkers into genomic and protein markers, based on the tested substrate. We review the biology and epidemiology of the genomic and proteomic biomarkers, discuss optimal diagnostic assays for their detection, and highlight their contribution to the contemporary clinical management of NSCLC.
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Affiliation(s)
- Igor Odintsov
- 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.
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6
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Hariri LP, Beasley MB, Sholl LM, Wikenheiser-Brokamp KA. Speaking the Same Language: The Fleischner Society Glossary for Thoracic Imaging. Radiology 2024; 310:e240414. [PMID: 38530190 PMCID: PMC10982826 DOI: 10.1148/radiol.240414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 03/27/2024]
Affiliation(s)
- Lida P. Hariri
- From the Department of Pathology, Division of Pulmonary and Critical
Care Medicine, Massachusetts General Hospital, Harvard Medical School, 55 Fruit
St, Boston, MA 02114 (L.P.H.); Department of Pathology, the Icahn School of
Medicine at Mount Sinai, New York, NY (M.B.B.); Department of Pathology, Brigham
and Women’s Hospital, Harvard Medical School, Boston, Mass (L.M.S.);
Division of Pathology and Laboratory Medicine, Division of Pulmonary Medicine,
and Perinatal Institute Division of Pulmonary Biology, Cincinnati
Children’s Hospital Medical Center, Cincinnati, Ohio (K.A.W.B.); and
Department of Pathology and Laboratory Medicine, University of Cincinnati,
Cincinnati, Ohio (K.A.W.B.)
| | - Mary Beth Beasley
- From the Department of Pathology, Division of Pulmonary and Critical
Care Medicine, Massachusetts General Hospital, Harvard Medical School, 55 Fruit
St, Boston, MA 02114 (L.P.H.); Department of Pathology, the Icahn School of
Medicine at Mount Sinai, New York, NY (M.B.B.); Department of Pathology, Brigham
and Women’s Hospital, Harvard Medical School, Boston, Mass (L.M.S.);
Division of Pathology and Laboratory Medicine, Division of Pulmonary Medicine,
and Perinatal Institute Division of Pulmonary Biology, Cincinnati
Children’s Hospital Medical Center, Cincinnati, Ohio (K.A.W.B.); and
Department of Pathology and Laboratory Medicine, University of Cincinnati,
Cincinnati, Ohio (K.A.W.B.)
| | - Lynette M. Sholl
- From the Department of Pathology, Division of Pulmonary and Critical
Care Medicine, Massachusetts General Hospital, Harvard Medical School, 55 Fruit
St, Boston, MA 02114 (L.P.H.); Department of Pathology, the Icahn School of
Medicine at Mount Sinai, New York, NY (M.B.B.); Department of Pathology, Brigham
and Women’s Hospital, Harvard Medical School, Boston, Mass (L.M.S.);
Division of Pathology and Laboratory Medicine, Division of Pulmonary Medicine,
and Perinatal Institute Division of Pulmonary Biology, Cincinnati
Children’s Hospital Medical Center, Cincinnati, Ohio (K.A.W.B.); and
Department of Pathology and Laboratory Medicine, University of Cincinnati,
Cincinnati, Ohio (K.A.W.B.)
| | - Kathryn A. Wikenheiser-Brokamp
- From the Department of Pathology, Division of Pulmonary and Critical
Care Medicine, Massachusetts General Hospital, Harvard Medical School, 55 Fruit
St, Boston, MA 02114 (L.P.H.); Department of Pathology, the Icahn School of
Medicine at Mount Sinai, New York, NY (M.B.B.); Department of Pathology, Brigham
and Women’s Hospital, Harvard Medical School, Boston, Mass (L.M.S.);
Division of Pathology and Laboratory Medicine, Division of Pulmonary Medicine,
and Perinatal Institute Division of Pulmonary Biology, Cincinnati
Children’s Hospital Medical Center, Cincinnati, Ohio (K.A.W.B.); and
Department of Pathology and Laboratory Medicine, University of Cincinnati,
Cincinnati, Ohio (K.A.W.B.)
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Bou Farhat E, Adib E, Daou M, Naqash AR, Matulonis U, Ng K, Kwiatkowski DJ, Sholl LM, Nassar AH. Benchmarking mismatch repair testing for patients with cancer receiving immunotherapy. Cancer Cell 2024; 42:323. [PMID: 38350424 DOI: 10.1016/j.ccell.2024.01.009] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
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8
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Sholl LM, Adem P. Federal Oversight of Laboratory-Developed Tests. N Engl J Med 2024; 390:482. [PMID: 38294991 DOI: 10.1056/nejmc2314290] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Affiliation(s)
| | - Patricia Adem
- Memorial Sloan Kettering Cancer Center, New York, NY
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9
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Moon I, LoPiccolo J, Baca SC, Sholl LM, Kehl KL, Hassett MJ, Liu D, Schrag D, Gusev A. Publisher Correction: Machine learning for genetics-based classification and treatment response prediction in cancer of unknown primary. Nat Med 2024; 30:607. [PMID: 37968374 DOI: 10.1038/s41591-023-02693-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Affiliation(s)
- Intae Moon
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Jaclyn LoPiccolo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sylvan C Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kenneth L Kehl
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Michael J Hassett
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - David Liu
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Deborah Schrag
- Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Alexander Gusev
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
- The Broad Institute of MIT & Harvard, Cambridge, MA, USA.
- Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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Bou Farhat E, Adib E, Daou M, Naqash AR, Matulonis U, Ng K, Kwiatkowski DJ, Sholl LM, Nassar AH. Benchmarking mismatch repair testing for patients with cancer receiving immunotherapy. Cancer Cell 2024; 42:6-7. [PMID: 38157866 DOI: 10.1016/j.ccell.2023.12.001] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024]
Abstract
Immunohistochemistry (IHC) is currently the first-line test for mismatch repair deficiency (MMR-D). Bou Farhat et al. show that mismatch repair (MMR) mutation signature by next-generation sequencing is a highly sensitive assay capable of detecting MMR-D cases that are missed in 1% and 5% of patients with MMR-D colorectal cancer (CRC) and endometrial cancer (EC), respectively. Patients with MMR-D tumors missed by IHC have similar clinical outcomes to patients with MMR-D by both IHC and mutation signature.
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Affiliation(s)
| | - Elio Adib
- Brigham and Women's Hospital, Boston, MA, USA
| | | | - Abdul Rafeh Naqash
- University of Oklahoma, Stephenson Cancer Center, Oklahoma City, OK, USA
| | | | - Kimmie Ng
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Amin H Nassar
- Brigham and Women's Hospital, Boston, MA, USA; Yale Cancer Center, New Haven, CT, USA.
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11
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Acosta AM, Sholl LM, Maclean F, Kao CS, Ulbright TM. Testicular Neoplasms With Sex Cord and Stromal Components Harbor a Recurrent Pattern of Chromosomal Gains. Mod Pathol 2024; 37:100368. [PMID: 37871653 DOI: 10.1016/j.modpat.2023.100368] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 05/22/2023] [Revised: 09/05/2023] [Accepted: 10/15/2023] [Indexed: 10/25/2023]
Abstract
A small subset of testicular sex cord-stromal tumors, designated as Sertoli-stromal cell tumors (SSCTs), comprises a mixture of Sertoli, spindle, and/or Leydig cells. The clinicopathologic features of these tumors have not been studied in any detail, and their molecular features are unknown. We, therefore, assessed the morphologic and genomic features of 14 SSCTs, including 1 tumor with features similar to the ovarian Sertoli-Leydig cell tumor (SLCT) with retiform tubules. The median age of the patients was 24 years (range, 10-55 years), and the median tumor size was 2.3 cm (range, 0.7-4.7 cm). All tumors showed Sertoli-like sex cord cells arranged in variably developed tubular structures, typically also forming nests and cords. These imperceptibly blended with a neoplastic spindle cell stroma or, in the SLCT, vacuolated to eosinophilic Leydig cells. Genomic analysis demonstrated the presence of a hotspot loss-of-function DICER1 mutation in the SLCT (patient 1) and hotspot gain-of-function CTNNB1 mutations in the tumors of patients 2 and 3, with both CTNNB1 variants being interpreted as possible subclonal events. The mutations were the only relevant findings in the tumors of patients 1 and 2, whereas the tumor of patient 3 harbored concurrent chromosomal arm-level and chromosome-level copy number gains. Among the remaining 11 tumors, all of those that had interpretable copy number data (9 tumors) harbored multiple recurrent chromosomal arm-level and chromosome-level copy number gains suggestive of a shift in ploidy without concurrent pathogenic mutations. The results of the present study suggest that CTNNB1 mutations (likely subclonal) are only rarely present in SSCTs; instead, most of them harbor genomic alterations similar to those seen in testicular sex cord-stromal tumors with pure or predominant spindle cell components. A notable exception was a testicular SLCT with morphologic features identical to the ovarian counterpart, which harbored a DICER1 mutation.
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Affiliation(s)
- Andres M Acosta
- Department of Pathology, Brigham and Women's Hospital, Harvard, Medical School, Boston, Massachusetts; Department of Pathology, Indiana University, Indianapolis, Indiana.
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Harvard, Medical School, Boston, Massachusetts
| | - Fiona Maclean
- Department of Pathology, Douglass Hanly Moir Pathology, Sonic Healthcare, Sydney, Australia
| | - Chia-Sui Kao
- Department of Pathology, Stanford University, Stanford, California
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12
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Gupta S, Sholl LM, Yang Y, Osunkoya AO, Gordetsky JB, Cornejo KM, Michalova K, Maclean F, Dvindenko E, Snuderl M, Hirsch MS, Anderson WJ, Rowsey RA, Jimenez RE, Cheville JC, Sadow PM, Colecchia M, Ricci C, Ulbright TM, Berney DM, Acosta AM. Genomic analysis of spermatocytic tumors demonstrates recurrent molecular alterations in cases with malignant clinical behavior. J Pathol 2024; 262:50-60. [PMID: 37792634 DOI: 10.1002/path.6210] [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: 06/12/2023] [Revised: 08/03/2023] [Accepted: 08/24/2023] [Indexed: 10/06/2023]
Abstract
Spermatocytic tumor (ST) is a rare type of germ cell tumor that occurs exclusively in the postpubertal testis and typically affects elderly men. Most STs are benign, but rare cases exhibit aggressive clinical behavior, often in association with transition to sarcomatoid histology. Limited molecular analyses have been performed on STs; therefore, their genomic and epigenomic features remain incompletely described. Twenty-seven samples from 25 individual patients were analyzed with a combination of DNA sequencing panels, genomic methylation profiling, SNP array, isochromosome (12p) [i(12p)] FISH, and immunohistochemistry. The series included five metastasizing tumors (three with sarcomatoid transformation, one anaplastic, and one conventional) and 20 non-metastasizing tumors (14 anaplastic and six conventional). Anaplastic tumors comprised a monomorphic population of intermediate-sized neoplastic cells, as previously described. Multiomic analyses demonstrated that there were two genomic subgroups of STs: one with diploid genomes and hotspot RAS/RAF variants and the other with global ploidy shift and absence of recurrent mutations. Relative gain of chromosome 9 was a consistent finding in both subgroups. A comparison of metastasizing and non-metastasizing cases demonstrated that aggressive behavior was associated with the acquisition of pathogenic TP53 mutations and/or relative gains of 12p/i(12p). In cases with sarcomatoid transformation, TP53 mutations seem to underlie the transition to sarcomatoid histology. Genomic methylation analysis demonstrated that aggressive cases with gains of 12p cluster closer to pure seminomas than to STs without gains of 12p. In conclusion, STs include two genomic subgroups, characterized by global ploidy shifts without recurrent mutations and diploid genomes with RAS/RAF hotspot mutations, respectively. Biologic progression was associated with relative gains of 12p and TP53 mutations. The findings in STs with relative gains of 12p suggest that they may exhibit biologic characteristics akin to those seen in germ cell neoplasia in situ-related germ cell tumors rather than non-germ cell neoplasia in situ-derived STs. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Sounak Gupta
- Department of Pathology, Mayo Clinic, Rochester, MN, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yiying Yang
- Department of Pathology, New York University, New York, NY, USA
| | - Adeboye O Osunkoya
- Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Kristine M Cornejo
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Fiona Maclean
- Department of Pathology, Douglass Hanly Moir Pathology, Macquarie University, Sydney, NSW, Australia
| | - Eugénia Dvindenko
- Department of Pathology, Instituto Português de Oncologia, Lisbon, Portugal
| | - Matija Snuderl
- Department of Pathology, New York University, New York, NY, USA
| | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - William J Anderson
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ross A Rowsey
- Department of Pathology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Peter M Sadow
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Maurizio Colecchia
- Department of Pathology, Universita Vita Salute San Raffaele, Milan, Italy
| | - Costantino Ricci
- Pathology Unit, Maggiore Hospital-AUSL Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | | | - Daniel M Berney
- Centre for Cancer Biomarkers & Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Andres Martin Acosta
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Indiana University, Indianapolis, IN, USA
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13
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Luo J, Sanchez M, Lee E, Hertzler H, Luong N, Mazzola E, Finstein B, Tamen R, Brisbane G, Nguyen T, Paik PK, Chaft JE, Cheng ML, Khalil H, Piha-Paul SA, Sholl LM, Nishino M, Jänne PA, DuBois SG, Hanna GJ, Shapiro GI, French CA. Initial Chemotherapy for Locally Advanced and Metastatic NUT Carcinoma. J Thorac Oncol 2023:S1556-0864(23)02431-0. [PMID: 38154515 DOI: 10.1016/j.jtho.2023.12.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/11/2023] [Accepted: 12/16/2023] [Indexed: 12/30/2023]
Abstract
INTRODUCTION NUT carcinoma (NC) is an underdiagnosed and aggressive poorly differentiated or squamous cell cancer. A subset of NC is sensitive to chemotherapy, but the optimal regimen is unknown. Experts have recommended platinum- and ifosfamide-based therapy based on case reports. METHODS Patients with pathologically confirmed NC with known survival outcomes after chemotherapy and consented to participate in a worldwide registry were studied. Results were summarized using descriptive methods. RESULTS The study included 118 patients with NC. Median age was 34 (range: 1-82) years, 39% were women, and 61% harbored a BRD4::NUTM1 fusion. Patients received platinum (74%) or ifosfamide (26%, including regimens with both, 13%). Of 62 patients with nonmetastatic disease, 40% had a thoracic primary. Compared with platinum-based chemotherapy, patients who received ifosfamide-based chemotherapy had nominally higher progression-free survival (12 mo: 59% [95% CI: 32-87] versus 37% [95% CI: 22-52], hazard ratio = 0.68 [0.32, 1.42], p = 0.3) but not overall survival (OS). Among the 56 patients with metastatic disease, 80% had a thoracic primary. Ifosfamide had an objective response rate (ORR) of 75% (six of eight) and platinum had an ORR of 31% (11 of 36). Nevertheless, there was no difference in progression-free survival or OS. The 3-year OS of the entire cohort was 19% (95% CI: 10%-28%). Of the 11 patients alive greater than 3 years, all presented with nonmetastatic and operable or resectable disease. CONCLUSION There is a numerically higher ORR for ifosfamide-based therapy compared with platinum-based therapy, with limited durability. OS at 3 years is only 19%, and development of effective therapies is an urgent unmet need for this patient population.
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Affiliation(s)
- Jia Luo
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Michelle Sanchez
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Elinton Lee
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Hans Hertzler
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Nhi Luong
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Emanuele Mazzola
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Bryanna Finstein
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Rubii Tamen
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gifty Brisbane
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Tom Nguyen
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Paul K Paik
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jamie E Chaft
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael L Cheng
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Hassan Khalil
- Department of Thoracic Surgery, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Sarina A Piha-Paul
- Department of Investigational Cancer Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Mizuki Nishino
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts; Department of Imaging, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Pasi A Jänne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Steven G DuBois
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts; Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Glenn J Hanna
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; Center for Head and Neck Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Geoffrey I Shapiro
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; Center for Cancer Therapeutic Innovation, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Christopher A French
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.
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14
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Odintsov I, Makarem M, Nishino M, Bachert SE, Zhang T, LoPiccolo J, Paweletz CP, Gokhale PC, Ivanova E, Saldanha A, Rudin CM, Lockwood WW, Ladanyi M, Somwar R, Jänne PA, Sholl LM. Prevalence and Therapeutic Targeting of High-Level ERBB2 Amplification in NSCLC. J Thorac Oncol 2023:S1556-0864(23)02428-0. [PMID: 38154514 DOI: 10.1016/j.jtho.2023.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/12/2023] [Accepted: 12/16/2023] [Indexed: 12/30/2023]
Abstract
INTRODUCTION ERBB2 amplification in lung cancer remains poorly characterized. HER2 (encoded by ERBB2) is a transmembrane tyrosine kinase capable of ligand-independent dimerization and signaling when overexpressed, and a common cause of HER2 overexpression is ERBB2 amplification. Here, we evaluated the clinicopathologic and genomic characteristics of ERBB2-amplified NSCLC and explored a HER2 antibody-drug conjugate (ADC) therapeutic strategy. METHODS Our institutional next-generation DNA sequencing data (OncoPanel) from 5769 NSCLC samples (5075 patients) were queried for cases having high-level ERBB2 amplification (≥6 copies). Clinical and demographic characteristics were extracted from the electronic medical records. Efficacy of the pan-ERBB inhibitor afatinib or HER2 ADCs (trastuzumab deruxtecan and trastuzumab emtansine) was evaluated in NSCLC preclinical models and patients with ERBB2 amplification. RESULTS High-level ERBB2 amplification was identified in 0.9% of lung adenocarcinomas and reliably predicted overexpression of HER2. ERBB2 amplification events are detected in two distinct clinicopathologic and genomic subsets of NSCLC: as the sole mitogenic driver in tumors arising in patients with a smoking history or as a concomitant alteration with other mitogenic drivers in patients with a light or never smoking history. We further reveal that trastuzumab deruxtecan is effective therapy in in vitro and in vivo preclinical models of NSCLC harboring ERBB2 amplification and report two cases of clinical activity of an anti-HER2 ADC in patients who acquired ERBB2 amplification after previous targeted therapy. CONCLUSIONS High-level ERBB2 amplification reliably predicts HER2 overexpression in patients with NSCLC, and HER2 ADC is effective therapy in this population.
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Affiliation(s)
- Igor Odintsov
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Maisam Makarem
- Lowe Center for Thoracic Oncology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mizuki Nishino
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Sara Emily Bachert
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, Kentucky
| | - Tom Zhang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; School of Medicine, New York Medical College, Valhalla, New York
| | - Jaclyn LoPiccolo
- Lowe Center for Thoracic Oncology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Cloud P Paweletz
- Lowe Center for Thoracic Oncology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Prafulla C Gokhale
- Lowe Center for Thoracic Oncology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Elena Ivanova
- Lowe Center for Thoracic Oncology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Aisha Saldanha
- Lowe Center for Thoracic Oncology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Charles M Rudin
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William W Lockwood
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Romel Somwar
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pasi A Jänne
- Lowe Center for Thoracic Oncology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
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15
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Parrack PH, Hornick JL, Sholl LM. PAX1 expression in thymic epithelial neoplasms and morphologic mimics. Hum Pathol 2023; 142:7-14. [PMID: 37776957 DOI: 10.1016/j.humpath.2023.09.007] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/18/2023] [Accepted: 09/23/2023] [Indexed: 10/02/2023]
Abstract
Thymic epithelial neoplasms are morphologically diverse and can pose a diagnostic challenge that is complicated by a lack of immunohistochemistry (IHC) markers that are entirely sensitive and specific for thymic epithelium. Polyclonal PAX8 is often used in this context, but it is not a specific marker. The PAX1 transcription factor shares significant homology with PAX8 and plays an integral role in thymic development in humans and murine models. This study evaluated the role of PAX1 IHC in differentiating thymic epithelial neoplasms from morphologic mimics on whole slide tissue sections. The PAX1 antibody stained all 74 thymoma cases; however, there was wide variability in staining intensity within each subtype. The antibody was less sensitive in thymic carcinomas and thymic neuroendocrine tumors compared to thymomas and demonstrated weak staining in a subset of morphologic mimics (21 squamous cell carcinomas, 6 pulmonary neuroendocrine tumors, 1 mesothelioma, 1 lymphoblastic lymphoma, and 1 granulosa cell tumor). With a H-score positive threshold of 75, the antibody had 100% specificity, and sensitivities of 92%, 56%, and 47% in thymomas, thymic neuroendocrine tumors, and thymic carcinomas respectively. The PAX1 antibody showed frequent geographic reduction in staining consistent with compromised antigenicity from variable formalin fixation. PAX1 IHC has a moderate-to-high sensitivity for thymic epithelial neoplasms; however, the wide staining variability and fixation effects may lead to difficulty with consistent interpretation. This marker is unlikely to supplant the role of PAX8 in diagnostic practice, but it may be a useful addition to immunohistochemistry panels when evaluating for thymic primary tumors.
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Affiliation(s)
- Paige H Parrack
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA, 02115.
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA, 02115
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA, 02115
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16
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Villaseñor-Altamirano AB, Jain D, Jeong Y, Menon JA, Kamiya M, Haider H, Manandhar R, Sheikh MDA, Athar H, Merriam LT, Ryu MH, Sasaki T, Castaldi PJ, Rao DA, Sholl LM, Vivero M, Hersh CP, Zhou X, Veerkamp J, Yun JH, Kim EY. Activation of CD8 + T Cells in Chronic Obstructive Pulmonary Disease Lung. Am J Respir Crit Care Med 2023; 208:1177-1195. [PMID: 37756440 PMCID: PMC10868372 DOI: 10.1164/rccm.202305-0924oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 09/27/2023] [Indexed: 09/29/2023] Open
Abstract
Rationale: Despite the importance of inflammation in chronic obstructive pulmonary disease (COPD), the immune cell landscape in the lung tissue of patients with mild-moderate disease has not been well characterized at the single-cell and molecular level. Objectives: To define the immune cell landscape in lung tissue from patients with mild-moderate COPD at single-cell resolution. Methods: We performed single-cell transcriptomic, proteomic, and T-cell receptor repertoire analyses on lung tissue from patients with mild-moderate COPD (n = 5, Global Initiative for Chronic Obstructive Lung Disease I or II), emphysema without airflow obstruction (n = 5), end-stage COPD (n = 2), control (n = 6), or donors (n = 4). We validated in an independent patient cohort (N = 929) and integrated with the Hhip+/- murine model of COPD. Measurements and Main Results: Mild-moderate COPD lungs have increased abundance of two CD8+ T cell subpopulations: cytotoxic KLRG1+TIGIT+CX3CR1+ TEMRA (T effector memory CD45RA+) cells, and DNAM-1+CCR5+ T resident memory (TRM) cells. These CD8+ T cells interact with myeloid and alveolar type II cells via IFNG and have hyperexpanded T-cell receptor clonotypes. In an independent cohort, the CD8+KLRG1+ TEMRA cells are increased in mild-moderate COPD lung compared with control or end-stage COPD lung. Human CD8+KLRG1+ TEMRA cells are similar to CD8+ T cells driving inflammation in an aging-related murine model of COPD. Conclusions: CD8+ TEMRA cells are increased in mild-moderate COPD lung and may contribute to inflammation that precedes severe disease. Further study of these CD8+ T cells may have therapeutic implications for preventing severe COPD.
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Affiliation(s)
| | - Dhawal Jain
- Pulmonary Drug Discovery Laboratory, Pharmaceuticals Research and Development, Bayer US LLC, Boston, Massachusetts; and
| | - Yunju Jeong
- Division of Pulmonary and Critical Care Medicine
- Harvard Medical School, Boston, Massachusetts
| | | | - Mari Kamiya
- Division of Pulmonary and Critical Care Medicine
- Harvard Medical School, Boston, Massachusetts
| | - Hibah Haider
- Division of Pulmonary and Critical Care Medicine
| | | | | | - Humra Athar
- Division of Pulmonary and Critical Care Medicine
- Pulmonary Drug Discovery Laboratory, Pharmaceuticals Research and Development, Bayer US LLC, Boston, Massachusetts; and
| | | | - Min Hyung Ryu
- Channing Division of Network Medicine, and
- Harvard Medical School, Boston, Massachusetts
| | - Takanori Sasaki
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, and
- Harvard Medical School, Boston, Massachusetts
| | - Peter J. Castaldi
- Channing Division of Network Medicine, and
- Harvard Medical School, Boston, Massachusetts
| | - Deepak A. Rao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, and
- Harvard Medical School, Boston, Massachusetts
| | - Lynette M. Sholl
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Marina Vivero
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Craig P. Hersh
- Channing Division of Network Medicine, and
- Harvard Medical School, Boston, Massachusetts
| | - Xiaobo Zhou
- Channing Division of Network Medicine, and
- Harvard Medical School, Boston, Massachusetts
| | - Justus Veerkamp
- Pharmaceuticals, Research & Early Development Precision Medicine RED (preMED), Pharmaceuticals Research and Development, Bayer AG, Wuppertal, Germany
| | - Jeong H. Yun
- Channing Division of Network Medicine, and
- Harvard Medical School, Boston, Massachusetts
| | - Edy Y. Kim
- Division of Pulmonary and Critical Care Medicine
- Harvard Medical School, Boston, Massachusetts
| | - the MGB-Bayer Pulmonary Drug Discovery Lab
- Division of Pulmonary and Critical Care Medicine
- Channing Division of Network Medicine, and
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, and
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Pulmonary Drug Discovery Laboratory, Pharmaceuticals Research and Development, Bayer US LLC, Boston, Massachusetts; and
- Pharmaceuticals, Research & Early Development Precision Medicine RED (preMED), Pharmaceuticals Research and Development, Bayer AG, Wuppertal, Germany
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17
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Oxnard GR, Chen R, Pharr JC, Koeller DR, Bertram AA, Dahlberg SE, Rainville I, Shane-Carson K, Taylor KA, Sable-Hunt A, Sholl LM, Teerlink CC, Thomas A, Cannon-Albright LA, Fay AP, Ashton-Prolla P, Yang H, Salvatore MM, Addario BJ, Jänne PA, Carbone DP, Wiesner GL, Garber JE. Germline EGFR Mutations and Familial Lung Cancer. J Clin Oncol 2023; 41:5274-5284. [PMID: 37579253 DOI: 10.1200/jco.23.01372] [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: 06/27/2023] [Accepted: 08/05/2023] [Indexed: 08/16/2023] Open
Abstract
PURPOSE The genomic underpinnings of inherited lung cancer risk are poorly understood. This prospective study characterized the clinical phenotype of patients and families with germline EGFR pathogenic variants (PVs). METHODS The Investigating Hereditary Risk from T790M study (ClinicalTrials.gov identifier: NCT01754025) enrolled patients with lung cancer whose tumor profiling harbored possible germline EGFR PVs and their relatives, either in person or remotely, providing germline testing and follow-up. RESULTS A total of 141 participants were enrolled over a 5-year period, 100 (71%) remotely. Based upon previous genotyping, 116 participants from 59 kindreds were tested for EGFR T790M, demonstrating a pattern of Mendelian inheritance with variable lung cancer penetrance. In confirmed or obligate carriers of a germline EGFR PV from 39 different kindreds, 50/91 (55%) were affected with lung cancer with 34/65 (52%) diagnosed by age 60 years. Somatic testing of lung cancers in carriers revealed that 35 of 37 (95%) had an EGFR driver comutation. Among 36 germline carriers without a cancer diagnosis, 15 had computed tomography (CT) imaging and nine had lung nodules, including a 28-year-old with >10 lung nodules. Given geographic enrichment of germline EGFR T790M in the southeast United States, genome-wide haplotyping of 46 germline carriers was performed and identified a 4.1-Mb haplotype shared by 41 (89%), estimated to originate 223-279 years ago. CONCLUSION To our knowledge, this is the first prospective description of familial EGFR-mutant lung cancer, identifying a recent founder germline EGFR T790M variant enriched in the Southeast United States. The high prevalence of EGFR-driver lung adenocarcinomas and lung nodules in germline carriers supports effort to identify affected patients and family members for investigation of CT-based screening for these high-risk individuals.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Alun Thomas
- Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT
| | | | - André P Fay
- PUCRS School of Medicine, Porto Alegre, Brazil
| | | | - Hao Yang
- Columbia University Medical Center, New York, NY
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Alessi JV, Wang X, Elkrief A, Ricciuti B, Li YY, Gupta H, Spurr LF, Rizvi H, Luo J, Pecci F, Lamberti G, Recondo G, Venkatraman D, Di Federico A, Gandhi MM, Vaz VR, Nishino M, Sholl LM, Cherniack AD, Ladanyi M, Price A, Richards AL, Donoghue M, Lindsay J, Sharma B, Turner MM, Pfaff KL, Felt KD, Rodig SJ, Lin X, Meyerson ML, Johnson BE, Christiani DC, Schoenfeld AJ, Awad MM. Impact of Aneuploidy and Chromosome 9p Loss on Tumor Immune Microenvironment and Immune Checkpoint Inhibitor Efficacy in NSCLC. J Thorac Oncol 2023; 18:1524-1537. [PMID: 37247843 PMCID: PMC10913104 DOI: 10.1016/j.jtho.2023.05.019] [Citation(s) in RCA: 3] [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] [Received: 12/08/2022] [Revised: 04/28/2023] [Accepted: 05/13/2023] [Indexed: 05/31/2023]
Abstract
INTRODUCTION Although gene-level copy number alterations have been studied as a potential biomarker of immunotherapy efficacy in NSCLC, the impact of aneuploidy burden and chromosomal arm-level events on immune checkpoint inhibitor (ICI) efficacy in NSCLC is uncertain. METHODS Patients who received programmed cell death protein 1 or programmed death-ligand 1 (PD-L1) inhibitor at two academic centers were included. Across all 22 chromosomes analyzed, an arm was considered altered if at least 70% of its territory was either gained or deleted. Among nonsquamous NSCLCs which underwent targeted next-generation sequencing, we retrospectively quantified aneuploidy using the adjusted fraction of chromosomal arm alterations (FAA), defined as the number of altered chromosome arms divided by the number of chromosome arms assessed, adjusted for tumor purity. RESULTS Among 2293 nonsquamous NSCLCs identified, the median FAA increased with more advanced cancer stage and decreased with higher PD-L1 tumor proportion score (TPS) levels (median FAA in TPS < 1%: 0.09, TPS 1%-49%: 0.08, TPS ≥ 50%: 0.05, p < 0.0001). There was a very weak correlation between FAA and tumor mutational burden when taken as continuous variables (R: 0.07, p = 0.0005). A total of 765 advanced nonsquamous NSCLCs with available FAA values were treated with ICIs. With decreasing FAA tertiles, there was a progressive improvement in objective response rate (ORR 15.1% in upper tertile versus 23.2% in middle tertile versus 28.4% in lowest tertile, p = 0.001), median progression-free survival (mPFS 2.5 versus 3.3 versus 4.1 mo, p < 0.0001), and median overall survival (mOS 12.5 versus 13.9 versus 16.4 mo, p = 0.006), respectively. In the arm-level enrichment analysis, chromosome 9p loss (OR = 0.22, Q = 0.0002) and chromosome 1q gain (OR = 0.43, Q = 0.002) were significantly enriched in ICI nonresponders after false discovery rate adjustment. Compared with NSCLCs without chromosome 9p loss (n = 452), those with 9p loss (n = 154) had a lower ORR (28.1% versus 7.8%, p < 0.0001), a shorter mPFS (4.1 versus 2.3 mo, p < 0.0001), and a shorter mOS (18.0 versus 9.6 mo, p < 0.0001) to immunotherapy. In addition, among NSCLCs with high PD-L1 expression (TPS ≥ 50%), chromosome 9p loss was associated with lower ORR (43% versus 6%, p < 0.0001), shorter mPFS (6.4 versus 2.6 mo, p = 0.0006), and shorter mOS (30.2 versus 14.3 mo, p = 0.0008) to immunotherapy compared with NSCLCs without 9p loss. In multivariable analysis, adjusting for key variables including FAA, chromosome 9p loss, but not 1q gain, retained a significant impact on ORR (hazard ratio [HR] = 0.25, p < 0.001), mPFS (HR = 1.49, p = 0.001), and mOS (HR = 1.47, p = 0.003). Multiplexed immunofluorescence and computational deconvolution of RNA sequencing data revealed that tumors with either high FAA levels or chromosome 9p loss had significantly fewer tumor-associated cytotoxic immune cells. CONCLUSIONS Nonsquamous NSCLCs with high aneuploidy and chromosome 9p loss have a distinct tumor immune microenvironment and less favorable outcomes to ICIs.
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Affiliation(s)
- Joao V Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Xinan Wang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Arielle Elkrief
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Yvonne Y Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Hersh Gupta
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Liam F Spurr
- Pritzker School of Medicine, The University of Chicago, Chicago, Illinois
| | - Hira Rizvi
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jia Luo
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Federica Pecci
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Giuseppe Lamberti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gonzalo Recondo
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Deepti Venkatraman
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Malini M Gandhi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Victor R Vaz
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mizuki Nishino
- Department of Radiology, Brigham and Women's Hospital and Department of Imaging, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Andrew D Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Adam Price
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Allison L Richards
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James Lindsay
- Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Bijaya Sharma
- ImmunoProfile, Brigham & Women's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Madison M Turner
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kathleen L Pfaff
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kristen D Felt
- ImmunoProfile, Brigham & Women's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Matthew L Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Bruce E Johnson
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - David C Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Adam J Schoenfeld
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark M Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
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Khalil HA, Shi W, Mazzola E, Lee DN, Norton-Hughes E, Dolan D, Corman S, White A, Sholl LM, Swanson SJ. Analysis of recurrence in lung adenocarcinoma with spread through air spaces. J Thorac Cardiovasc Surg 2023; 166:1317-1328.e4. [PMID: 36935300 DOI: 10.1016/j.jtcvs.2023.01.030] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/22/2022] [Accepted: 01/20/2023] [Indexed: 02/17/2023]
Abstract
OBJECTIVES Spread through air spaces is defined as tumor cells in air spaces away from the edge of tumor in lung carcinoma. It is associated with higher locoregional recurrence and lower survival in lung adenocarcinoma. The features of spread through air spaces portending worse outcomes are still under investigation. We reviewed our lung cancer experience to define potential factors related to spread through air spaces that influence recurrence and survival. METHODS Between January 2010 and December 2017, we identified 968 patients who underwent resection for T1-3N0M0 lung adenocarcinoma. Of these, histologic examination was possible in 787 patients. We examined the presence of spread through air spaces, spread through air spaces characteristics (micropapillary, solid nest, or single cell), average density (number per slide), and farthest distance from tumor at which spread through air spaces was detected, or maximal spread distance. Overall survival and recurrence-free survival were estimated using Kaplan-Meier curves, and differences between spread through air spaces positive versus spread through air spaces negative groups were assessed using the log-rank test. RESULTS Spread through air spaces was present in 389 of 787 of the reviewed cases (49.4%). Overall survival and recurrence-free survival were significantly lower in the spread through air spaces positive group over 10 years (P < .0001). The incidences of locoregional and distant recurrence were nearly doubled over 10 years in the spread through air spaces positive group compared with the spread through air spaces negative group (P = .002 and <.0001, respectively). In a multivariable Cox regression model adjusted for spread through air spaces characteristics, distance, and tumor size, lobar resection did not confer survival advantage in patients with spread through air spaces (hazard ratio of sublobar resection with respect to lobar resection, 1.44; 95% confidence interval, 0.98-2.11; P = .067). In the spread through air spaces positive group, spread through air spaces density was 2.7 ± 1.4 clusters per slide and the maximal spread distance was 2.2 ± 1.7 mm from the tumor edge. There was no observed correlation between spread through air spaces density or maximal spread distance and overall survival or recurrence. CONCLUSIONS We show increased distant recurrence in spread through air spaces positive lung adenocarcinoma. Quantifiable measures of spread through air spaces do not appear to correlate with recurrence or survival metrics.
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Affiliation(s)
- Hassan A Khalil
- Division of Thoracic and Cardiac Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Mass.
| | - Weiwei Shi
- Thoracic Pathology, Department of Pathology, Brigham and Women's Hospital, Boston, Mass
| | - Emanuele Mazzola
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Mass
| | - Daniel Nahum Lee
- Division of Thoracic and Cardiac Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Mass
| | - Emily Norton-Hughes
- Division of Thoracic and Cardiac Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Mass
| | - Daniel Dolan
- Division of Thoracic and Cardiac Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Mass
| | - Samantha Corman
- Division of Thoracic and Cardiac Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Mass
| | - Abby White
- Division of Thoracic and Cardiac Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Mass
| | - Lynette M Sholl
- Thoracic Pathology, Department of Pathology, Brigham and Women's Hospital, Boston, Mass
| | - Scott J Swanson
- Division of Thoracic and Cardiac Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Mass
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20
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Schaefer IM, Mariño-Enríquez A, Hammer MM, Padera RF, Sholl LM. Recurrent Tumor Suppressor Alterations in Primary Pericardial Mesothelioma. Mod Pathol 2023; 36:100237. [PMID: 37295554 PMCID: PMC10529127 DOI: 10.1016/j.modpat.2023.100237] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/25/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
Primary pericardial mesotheliomas are extremely rare, accounting for <1% of all mesotheliomas, and their molecular genetic features and predisposing factors remain to be determined. Here, we report the clinicopathologic, immunohistochemical, and molecular genetic findings of 3 pericardial mesotheliomas without pleural involvement. Three cases diagnosed between 2004 and 2022 were included in the study and analyzed by immunohistochemistry and targeted next-generation sequencing (NGS); corresponding nonneoplastic tissue was sequenced in all cases. Two patients were female and 1 was male, aged between 66 and 75 years. Two patients each had prior asbestos exposure and were smokers. Histologic subtypes were epithelioid in 2 cases and biphasic in 1 case. Immunohistochemical staining identified expression of cytokeratin AE1/AE3 and calretinin in all cases, D2-40 in 2 cases, and WT1 in 1 case. Staining for tumor suppressors revealed loss of p16, MTAP, and Merlin (NF2) expression in 2 cases and loss of BAP1 and p53 in 1 case. Abnormal cytoplasmic BAP1 expression was observed in an additional case. Protein expression abnormalities correlated with NGS results, which showed concurrent complete genomic inactivation of CDKN2A/p16, CDKN2B, MTAP, and NF2 in 2 mesotheliomas and of BAP1 and TP53 in 1 mesothelioma each, respectively. In addition, 1 patient harbored a pathogenic BRCA1 germline mutation, which resulted in biallelic inactivation in the mesothelioma. All mesotheliomas were mismatch repair proficient and showed several chromosomal gains and losses. All patients died from disease. Our study demonstrates that pericardial mesotheliomas share common morphologic, immunohistochemical, and molecular genetic features with pleural mesothelioma, including recurrent genomic inactivation of canonical tumor suppressors. Our study adds new insights into the genetic landscape of primary pericardial mesothelioma and highlights BRCA1 loss as a potential contributing factor in a subset of cases, thereby contributing to refined precision diagnostics for this rare cancer.
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Affiliation(s)
- Inga-Marie Schaefer
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
| | - Adrian Mariño-Enríquez
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mark M Hammer
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Robert F Padera
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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21
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Lechner A, Rai A, Rojas-Rudilla V, Kuang Y, Paweletz CP, Sholl LM, Dong F. Atypical Droplet Digital Polymerase Chain Reaction Patterns That Indicate Uncommon but Clinically Actionable EGFR Mutations in Lung Cancer. Arch Pathol Lab Med 2023:495431. [PMID: 37639432 DOI: 10.5858/arpa.2023-0088-oa] [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] [Accepted: 06/16/2023] [Indexed: 08/31/2023]
Abstract
CONTEXT.— Droplet digital polymerase chain reaction (ddPCR) is a sensitive method to detect common pathogenic EGFR mutations in non-small cell lung cancer. Although targeted assays have not been specifically designed to detect them, uncommon EGFR mutations have been linked to response to targeted therapy. OBJECTIVE.— To describe atypical ddPCR patterns that correspond to uncommon but clinically actionable EGFR mutations. DESIGN.— A cohort of 1134 consecutive non-small cell lung cancers that underwent targeted next-generation sequencing was reviewed. Uncommon EGFR mutations involving probe binding sites were evaluated by ddPCR. RESULTS.— Two hundred fifty-five of 1134 cancers (22.5%) harbored pathogenic EGFR mutations. One hundred eighty-six of 255 (72.9%) had canonical EGFR exon 19 deletion or exon 21 p.L858R variants designed for detection by ddPCR. An additional 25 of 255 cases (9.8%) had uncommon EGFR mutations within the probe-binding site, including one case with concurrent uncommon mutations in both exon 19 and exon 21. These mutations included uncommon EGFR exon 19 deletions (n = 6), EGFR exon 19 substitutions p.L747P (n = 3) and p.L747A (n = 1), dinucleotide substitutions leading to EGFR p.L858R (n = 5), EGFR exon 21 substitutions p.K860I (n = 1) and p.L861Q (n = 9), and EGFR p.[L858R;K860I] (n = 1). Droplet digital polymerase chain reaction generated atypical but reproducible signal for each of these uncommon variants. CONCLUSIONS.— Droplet digital polymerase chain reaction analysis of uncommon pathogenic EGFR variants can yield unique and reproducible results. Recognition of atypical patterns in EGFR ddPCR testing can prompt confirmatory molecular testing and aid appropriate targeted therapy selection for patients with non-small cell lung cancer.
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Affiliation(s)
- Adam Lechner
- From the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Lechner, Rai, Rojas-Rudilla, Sholl, Dong)
- the University of Missouri School of Medicine, Columbia (Lechner)
| | - Anooja Rai
- From the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Lechner, Rai, Rojas-Rudilla, Sholl, Dong)
| | - Vanesa Rojas-Rudilla
- From the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Lechner, Rai, Rojas-Rudilla, Sholl, Dong)
| | - Yanan Kuang
- and the Belfer Center for Applied Cancer Science (Kuang)
- and the Department of Medical Oncology (Kuang, Paweletz), Dana Farber Cancer Institute, Boston, Massachusetts. Dong is currently located in the Department of Pathology at Stanford University School of Medicine, Stanford, California
| | - Cloud P Paweletz
- and the Department of Medical Oncology (Kuang, Paweletz), Dana Farber Cancer Institute, Boston, Massachusetts. Dong is currently located in the Department of Pathology at Stanford University School of Medicine, Stanford, California
| | - Lynette M Sholl
- From the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Lechner, Rai, Rojas-Rudilla, Sholl, Dong)
| | - Fei Dong
- From the Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Lechner, Rai, Rojas-Rudilla, Sholl, Dong)
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22
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Moon I, LoPiccolo J, Baca SC, Sholl LM, Kehl KL, Hassett MJ, Liu D, Schrag D, Gusev A. Machine learning for genetics-based classification and treatment response prediction in cancer of unknown primary. Nat Med 2023; 29:2057-2067. [PMID: 37550415 DOI: 10.1038/s41591-023-02482-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 06/30/2023] [Indexed: 08/09/2023]
Abstract
Cancer of unknown primary (CUP) is a type of cancer that cannot be traced back to its primary site and accounts for 3-5% of all cancers. Established targeted therapies are lacking for CUP, leading to generally poor outcomes. We developed OncoNPC, a machine-learning classifier trained on targeted next-generation sequencing (NGS) data from 36,445 tumors across 22 cancer types from three institutions. Oncology NGS-based primary cancer-type classifier (OncoNPC) achieved a weighted F1 score of 0.942 for high confidence predictions ([Formula: see text]) on held-out tumor samples, which made up 65.2% of all the held-out samples. When applied to 971 CUP tumors collected at the Dana-Farber Cancer Institute, OncoNPC predicted primary cancer types with high confidence in 41.2% of the tumors. OncoNPC also identified CUP subgroups with significantly higher polygenic germline risk for the predicted cancer types and with significantly different survival outcomes. Notably, patients with CUP who received first palliative intent treatments concordant with their OncoNPC-predicted cancers had significantly better outcomes (hazard ratio (HR) = 0.348; 95% confidence interval (CI) = 0.210-0.570; P = [Formula: see text]). Furthermore, OncoNPC enabled a 2.2-fold increase in patients with CUP who could have received genomically guided therapies. OncoNPC thus provides evidence of distinct CUP subgroups and offers the potential for clinical decision support for managing patients with CUP.
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Affiliation(s)
- Intae Moon
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Jaclyn LoPiccolo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sylvan C Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kenneth L Kehl
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Michael J Hassett
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - David Liu
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Deborah Schrag
- Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Alexander Gusev
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
- The Broad Institute of MIT & Harvard, Cambridge, MA, USA.
- Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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23
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Ricciuti B, Elkrief A, Alessi J, Wang X, Li Y, Gupta H, Muldoon DM, Bertram AA, Pecci F, Lamberti G, Federico AD, Barrichello A, Vaz VR, Gandhi M, Lee E, Shapiro GI, Park H, Nishino M, Lindsay J, Felt KD, Sharma B, Cherniack AD, Rodig S, Gomez DR, Shaverdian N, Rakaee M, Bandlamudi C, Ladanyi M, Janne PA, Schoenfeld AJ, Sholl LM, Awad MM, Cheng ML. Clinicopathologic, Genomic, and Immunophenotypic Landscape of ATM Mutations in Non-Small Cell Lung Cancer. Clin Cancer Res 2023; 29:2540-2550. [PMID: 37097610 PMCID: PMC11031845 DOI: 10.1158/1078-0432.ccr-22-3413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/09/2023] [Accepted: 04/20/2023] [Indexed: 04/26/2023]
Abstract
PURPOSE ATM is the most commonly mutated DNA damage and repair gene in non-small cell lung cancer (NSCLC); however, limited characterization has been pursued. EXPERIMENTAL DESIGN Clinicopathologic, genomic, and treatment data were collected for 5,172 patients with NSCLC tumors which underwent genomic profiling. ATM IHC was performed on 182 NSCLCs with ATM mutations. Multiplexed immunofluorescence was performed on a subset of 535 samples to examine tumor-infiltrating immune cell subsets. RESULTS A total of 562 deleterious ATM mutations were identified in 9.7% of NSCLC samples. ATM-mutant (ATMMUT) NSCLC was significantly associated with female sex (P = 0.02), ever smoking status (P < 0.001), non-squamous histology (P = 0.004), and higher tumor mutational burden (DFCI, P < 0.0001; MSK, P < 0.0001) compared with ATM-wild-type (ATMWT) cases. Among 3,687 NSCLCs with comprehensive genomic profiling, co-occurring KRAS, STK11, and ARID2 oncogenic mutations were significantly enriched among ATMMUT NSCLCs (Q < 0.05), while TP53 and EGFR mutations were enriched in ATMWT NSCLCs. Among 182 ATMMUT samples with ATM IHC, tumors with nonsense, insertions/deletions, or splice site mutations were significantly more likely to display ATM loss by IHC (71.4% vs. 28.6%; P < 0.0001) compared with tumors with only predicted pathogenic missense mutations. Clinical outcomes to PD-(L)1 monotherapy (N = 1,522) and chemo-immunotherapy (N = 951) were similar between ATMMUT and ATMWT NSCLCs. Patients with concurrent ATM/TP53 mutations had significantly improved response rate and progression-free survival with PD-(L)1 monotherapy. CONCLUSIONS Deleterious ATM mutations defined a subset of NSCLC with unique clinicopathologic, genomic, and immunophenotypic features. Our data may serve as resource to guide interpretation of specific ATM mutations in NSCLC.
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Affiliation(s)
- Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Arielle Elkrief
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joao Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Xinan Wang
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Yvonne Li
- Department of Analytics and Informatics, Dana-Farber Cancer Institute, Boston, Massachusetts; Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts
| | - Hersh Gupta
- Department of Analytics and Informatics, Dana-Farber Cancer Institute, Boston, Massachusetts; Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts
| | - Daniel M. Muldoon
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Arrien A. Bertram
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Federica Pecci
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Giuseppe Lamberti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alessandro Di Federico
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Adriana Barrichello
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Victor R. Vaz
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Malini Gandhi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Elinton Lee
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Geoffrey I. Shapiro
- Center for DNA Damage and Repair (CDDR), Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Hyesun Park
- Department of Radiology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Mizuki Nishino
- Department of Radiology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - James Lindsay
- ImmunoProfile, Brigham & Women’s Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kristen D. Felt
- ImmunoProfile, Brigham & Women’s Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Bijaya Sharma
- ImmunoProfile, Brigham & Women’s Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Andrew D. Cherniack
- Department of Analytics and Informatics, Dana-Farber Cancer Institute, Boston, Massachusetts; Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts
| | - Scott Rodig
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Daniel R. Gomez
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Narek Shaverdian
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mehrdad Rakaee
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Chaitanya Bandlamudi
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pasi A. Janne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Adam J. Schoenfeld
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lynette M. Sholl
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Mark M. Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Michael L. Cheng
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
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Boiarsky D, Lydon CA, Chambers ES, Sholl LM, Nishino M, Skoulidis F, Heymach JV, Luo J, Awad MA, Janne PA, Van Allen EM, Barbie DA, Vokes NI. Molecular markers of metastatic disease in KRAS-mutant lung adenocarcinoma. Ann Oncol 2023; 34:589-604. [PMID: 37121400 PMCID: PMC10425882 DOI: 10.1016/j.annonc.2023.04.514] [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: 02/03/2023] [Revised: 04/11/2023] [Accepted: 04/19/2023] [Indexed: 05/02/2023] Open
Abstract
BACKGROUND Prior studies characterized the association of molecular alterations with treatment-specific outcomes in KRAS-mutant (KRASMUT) lung adenocarcinoma (LUAD). Less is known about the prognostic role of molecular alterations and their associations with metastatic disease. PATIENTS AND METHODS We analyzed clinicogenomic data from 1817 patients with KRASMUT LUAD sequenced at the Dana-Farber Cancer Institute (DFCI) and Memorial Sloan Kettering Cancer Center (MSKCC). Patients with metastatic (M1) and nonmetastatic (M0) disease were compared. Transcriptomic data from The Cancer Genome Atlas (TCGA) were investigated to characterize the biology of differential associations with clinical outcomes. Organ-specific metastasis was associated with overall survival (OS). RESULTS KEAP1 (DFCI: OR = 2.3, q = 0.04; MSKCC: OR = 2.2, q = 0.00027) and SMARCA4 mutations (DFCI: OR = 2.5, q = 0.06; MSKCC: OR = 2.6, q = 0.0021) were enriched in M1 versus M0 tumors. On integrative modeling, NRF2 activation was the genomic feature most associated with OS. KEAP1 mutations were enriched in M1 versus M0 tumors independent of STK11 status (KEAP1MUT/STK11WT: DFCI OR = 3.0, P = 0.0064; MSKCC OR = 2.0, P = 0.041; KEAP1MUT/STK11MUT: DFCI OR = 2.3, P = 0.0063; MSKCC OR = 2.5, P = 3.6 × 10-05); STK11 mutations without KEAP1 loss were not associated with stage (KEAP1WT/STK11MUT: DFCI OR = 0.97, P = 1.0; MSKCC OR = 1.2, P = 0.33) or outcome. KEAP1/KRAS-mutated tumors with and without STK11 mutations exhibited high functional STK11 loss. The negative effects of KEAP1 were compounded in the presence of bone (HR = 2.3, P = 4.4 × 10-14) and negated in the presence of lymph node metastasis (HR = 1.0, P = 0.91). CONCLUSIONS Mutations in KEAP1 and SMARCA4, but not STK11, were associated with metastatic disease and poor OS. Functional STK11 loss, however, may contribute to poor outcomes in KEAP1MUT tumors. Integrating molecular data with clinical and metastatic-site annotations can more accurately risk stratify patients.
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Affiliation(s)
- D Boiarsky
- Department of Medicine, Tufts Medical Center, Boston
| | - C A Lydon
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston
| | - E S Chambers
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston
| | - L M Sholl
- Center for Advanced Molecular Diagnostics, Brigham & Women's Hospital & Harvard Medical School, Boston
| | - M Nishino
- Department of Radiology, Brigham and Women's Hospital, Boston
| | - F Skoulidis
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas M.D. Anderson Cancer Center, Houston
| | - J V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas M.D. Anderson Cancer Center, Houston
| | - J Luo
- Department of Medicine, Dana-Farber Cancer Institute, Boston
| | - M A Awad
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston
| | - P A Janne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston
| | - E M Van Allen
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston; Broad Institute of Harvard & MIT, Cambridge; Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston
| | - D A Barbie
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston
| | - N I Vokes
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas M.D. Anderson Cancer Center, Houston; Department of Genomic Medicine, University of Texas M.D. Anderson Cancer Center, Houston, USA.
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25
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Collins K, Sholl LM, Vargas SO, Cornejo KM, Kravtsov O, Dickson BC, Idrees MT, Ulbright TM, Acosta AM. Testicular Juvenile Granulosa Cell Tumors Demonstrate Recurrent Loss of Chromosome 10 and Absence of Molecular Alterations Described in Ovarian Counterparts. Mod Pathol 2023; 36:100142. [PMID: 36813116 DOI: 10.1016/j.modpat.2023.100142] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/10/2023] [Accepted: 02/10/2023] [Indexed: 02/22/2023]
Abstract
Testicular juvenile granulosa cell tumors (JGCTs) are a rare type of sex cord-stromal tumor, accounting for <5% of all neoplasms of the prepubertal testis. Previous reports have demonstrated sex chromosome anomalies in a small subset of cases, but the molecular alterations associated with JGCTs remain largely undescribed. We evaluated 18 JGCTs using massive parallel DNA and RNA sequencing panels. The median patient age was <1 month (range, newborn to 5 months). The patients presented with scrotal or intra-abdominal masses/enlargement, and all underwent radical orchiectomy (17 unilateral and 1 bilateral). The median tumor size was 1.8 cm (range, 1.3-10.5 cm). Histologically, the tumors were purely cystic/follicular or mixed (ie, solid and cystic/follicular). All cases were predominantly epithelioid, with 2 exhibiting prominent spindle cell components. Nuclear atypia was mild or absent, and the median number of mitoses was 0.4/mm2 (range, 0-10/mm2). Tumors frequently expressed SF-1 (11/12 cases, 92%), inhibin (6/7 cases, 86%), calretinin (3/4 cases, 75%), and keratins (2/4 cases, 50%). Single-nucleotide variant analysis demonstrated the absence of recurrent mutations. RNA sequencing did not detect gene fusions in 3 cases that were sequenced successfully. Recurrent monosomy 10 was identified in 8 of 14 cases (57%) with interpretable copy number variant data, and multiple whole-chromosome gains were present in the 2 cases with significant spindle cell components. This study demonstrated that testicular JGCTs harbor recurrent loss of chromosome 10 and lack the GNAS and AKT1 variants described in their ovarian counterparts.
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Affiliation(s)
- Katrina Collins
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Sara O Vargas
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts
| | - Kristine M Cornejo
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | | | - Brendan C Dickson
- Department of Pathology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Muhammad T Idrees
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Thomas M Ulbright
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Andrés M Acosta
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
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26
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Cheng ML, Huang Y, Luong N, LoPiccolo J, Nishino M, Sholl LM, Chirieac LR, Santucci AD, Rabin MS, Jänne PA, Coker S, Diamond JR, Hilton J, Shapiro GI, French CA. Exceptional Response to Bromodomain and Extraterminal Domain Inhibitor Therapy With BMS-986158 in BRD4-NUTM1 NUT Carcinoma Harboring a BRD4 Splice Site Mutation. JCO Precis Oncol 2023; 7:e2200633. [PMID: 37384867 PMCID: PMC10581614 DOI: 10.1200/po.22.00633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 04/24/2023] [Accepted: 05/25/2023] [Indexed: 07/01/2023] Open
Affiliation(s)
- Michael L. Cheng
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Yeying Huang
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Nhi Luong
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Jaclyn LoPiccolo
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Mizuki Nishino
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Department of Imaging, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Lynette M. Sholl
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Lucian R. Chirieac
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Alison D. Santucci
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
- Boston Medical Center, Boston, MA
| | - Michael S. Rabin
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Pasi A. Jänne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | | | - John Hilton
- Division of Medical Oncology, Ottawa Hospital, Ottawa, ON
| | - Geoffrey I. Shapiro
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Christopher A. French
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
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27
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Goldman JW, Sholl LM, Dacic S, Fishbein MC, Murciano-Goroff YR, Rajaram R, Szymczak S, Szpurka AM, Chao BH, Drilon A. Case Report: Complete pathologic response to neoadjuvant selpercatinib in a patient with resectable early-stage RET fusion-positive non-small cell lung cancer. Front Oncol 2023; 13:1178313. [PMID: 37274265 PMCID: PMC10232990 DOI: 10.3389/fonc.2023.1178313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/03/2023] [Indexed: 06/06/2023] Open
Abstract
The LIBRETTO-001 trial demonstrated the activity of the selective rearrangement during transfection (RET) inhibitor selpercatinib in advanced RET fusion-positive non-small cell lung cancer (NSCLC) and resulted in the drug's approval for this indication. A cohort that included neoadjuvant and adjuvant selpercatinib was opened on LIBRETTO-001 for early-stage RET fusion-positive NSCLC with the primary endpoint of major pathologic response. A patient with a stage IB (cT2aN0M0) KIF5B-RET fusion-positive NSCLC received 8 weeks of neoadjuvant selpercatinib at 160 mg twice daily followed by surgery. While moderate regression in the primary tumor (stable disease, Response Evaluation Criteria in Solid Tumors (RECIST) guidelines version 1.1) was observed radiologically, assessment via an Independent Pathologic Review Committee revealed a pathologic complete response (0% viable tumor). This consensus assessment by three independent pathologists was aided by RET fluorescence in situ hybridization testing of a reactive pneumocyte proliferation showing no rearrangement. Neoadjuvant selpercatinib was well-tolerated with only low-grade treatment-emergent adverse events. The activity of prospective preoperative selpercatinib in this case establishes proof of concept of the potential utility of RET inhibitor therapy in early-stage RET fusion-positive NSCLC.
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Affiliation(s)
- Jonathan W. Goldman
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Lynette M. Sholl
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Sanja Dacic
- Department of Pathology, Yale School of Medicine, New Haven, CT, United States
| | - Michael C. Fishbein
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | | | - Ravi Rajaram
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | - Anna M. Szpurka
- Loxo@Lilly, Eli Lilly and Company, Indianapolis, IN, United States
| | - Bo H. Chao
- Loxo@Lilly, Eli Lilly and Company, New York, NY, United States
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan-Kettering Cancer CenterNew York, NY, United States
- Department of Medicine, Weill Cornell Medical College, New York, NY, United States
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28
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Lindsay J, Sharma B, Felt KD, Giobbie-Hurder A, Dryg I, Weirather JL, Altreuter J, Mazor T, Kumari P, Alessi JV, Nirmal AJ, Manos MP, Kumar AR, Lotter W, Cerami E, Johnson BE, Lindeman NI, Sholl LM, Nowak JA, Rodig SJ. Abstract 5706: ImmunoPROFILE: A prospective implementation of clinically validated, quantitative immune cell profiling test identifies tumor-infiltrating CD8+ and PD-1+ cell densities as prognostic biomarkers across a 2,023 patient pan-cancer cohort treated with different therapies. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-5706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Tumor-infiltrating lymphocyte (TIL) density has been identified as a prognostic and predictive biomarker in select tumors treated with defined therapies. These observations suggest that TILs may be general markers of patient outcomes, but evidence in support of this hypothesis has been limited by small cohorts.
We validated ImmunoPROFILE, a multiplexed immunofluorescence (MIF)-based assay coupled with machine-learning-based image analysis, to identify and quantify tumor cells (cytokeratin, PAX5, PAX8, SOX10), T cells (CD8), T-regulatory cells (FOXP3), exhausted cells (PD-1) and immunosuppressive tumor and immune cells (PD-L1). We applied the MIF panel to specimens from patients collected prospectively over three years and analyzed 2,023 cases across 27 tumor types. The association between biomarkers and overall survival (OS) was investigated using Cox models controlling for patient risk factors such as cancer type, metastatic vs. primary disease, age, and gender. Multivariable biomarker selection was based on likelihood ratios.
The assay was highly robust (success rate 97%), reproducible (inter-scanning and intra-staining density controls within 1 SD, inter-staining PD-L1 scores ≤11% CV), and operator-independent (R2 >0.7 to >0.9 for each biomarker and 95% concordance in PD-L1 score-based interpretation between technicians). From whole slide images, a total of 11,932 individual regions of interest were analyzed across the cohort, resulting in >50 million spatially-resolved single cells which were summarized into cell population densities and PD-L1 scores.
High densities of CD8+ (>64/mm2, p<0.0001), PD-1+ (>50/mm2, p<0.0001), and FOXP3+ (>30/mm2, p<0.0001) T cells were associated with longer overall survival (OS) irrespective of therapy and across all cancer types. PD-L1 metrics were not associated with OS (p=0.43). Compared to patients with low densities of CD8+ and PD-1+ cells, high densities of at least one of these cell types had better OS (Both high, HR: 0.49, 95% CI: 0.41 - 0.59; CD8+ high, HR: 0.63, (0.48 - 0.82); PD-1+ high, HR: 0.71, (0.54 - 0.93)). The results were consistent in the subset of patients (N=1572) who did not receive immunotherapy (IO). In patients who received IO therapy (N=451), only PD-1+ T-cell density associated with OS (HR: 0.48, (0.36 - 0.65)).
To our knowledge, this is the first enterprise-level immune biomarker assay using multiplexed staining, digital imaging, and machine learning to be applied in a prospective manner to clinical specimens at scale. We found that select immune cell densities are prognostic across cancer types and therapies and demonstrated that quantification of multiple cell populations yields better prognostic power than single marker analyses.
Citation Format: James Lindsay, Bijaya Sharma, Kristen D. Felt, Anita Giobbie-Hurder, Ian Dryg, Jason L. Weirather, Jennifer Altreuter, Tali Mazor, Priti Kumari, Joao V. Alessi, Ajit J. Nirmal, Michael P. Manos, Ananth R. Kumar, William Lotter, Ethan Cerami, Burce E. Johnson, Neil I. Lindeman, Lynette M. Sholl, Jonathan A. Nowak, Scott J. Rodig. ImmunoPROFILE: A prospective implementation of clinically validated, quantitative immune cell profiling test identifies tumor-infiltrating CD8+ and PD-1+ cell densities as prognostic biomarkers across a 2,023 patient pan-cancer cohort treated with different therapies. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5706.
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Affiliation(s)
| | - Bijaya Sharma
- 2ImmunoProfile, Brigham and Women’s Hospital, Boston, MA
| | | | | | - Ian Dryg
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Tali Mazor
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | - Joao V. Alessi
- 3Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Ajit J. Nirmal
- 4Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | | | | | | | - Burce E. Johnson
- 4Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Neil I. Lindeman
- 5Harvard Medical School, Brigham and Women’s Hospital, Boston, MA
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29
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Acosta AM, Bridge JA, Dal Cin PS, Sholl LM, Cornejo KM, Fletcher CDM, Ulbright TM. Inflammatory and Nested Testicular Sex Cord Tumor: A Novel Neoplasm With Aggressive Clinical Behavior and Frequent EWSR1::ATF1 Gene Fusions. Am J Surg Pathol 2023; 47:504-517. [PMID: 36791251 DOI: 10.1097/pas.0000000000002022] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
A subset of malignant testicular sex cord tumors (TSCTs), heretofore interpreted as Sertoli cell tumors, not otherwise specified, exhibits distinctive morphologic features that partially overlap with those of seminoma. In this study, we evaluated the clinicopathologic and molecular characteristics of 13 such tumors. The patients were 20 to 73 years old (median, 36 y), and all with available data presented with testicular masses (median size, 3 cm), with 2 having synchronous retroperitoneal metastases. All 11 patients with available follow-up developed metastases to retroperitoneal lymph nodes, nonretroperitoneal lymph nodes, bone, contralateral testis, and/or lung. Microscopically, the tumors showed solid nests and sheets of epithelioid cells with granular, eosinophilic to clear/vacuolated cytoplasm, admixed in most (12/13) cases with variable proportions of lymphocytes, plasma cells, eosinophils, and neutrophils. Additional features included intracytoplasmic hyaline inclusions and a prominent collagenous, sometimes hyalinized stroma. Mitotic activity was relatively low (median, 1 mitosis/10 HPF), but tumor necrosis was frequent (11/13). Local invasion of adjacent structures and lymphovascular invasion were noted in some tumors (4/9 cases with available data for each feature). All were α-inhibin-positive and lacked nuclear reactivity for β-catenin. In addition, all tested cases were positive for epithelial membrane antigen (9/9) and steroidogenic factor-1 (8/8), and 8/10 expressed CD30. Two "index" cases were initially analyzed using a DNA sequencing panel, which identified EWSR1::ATF1 fusions in both. Subsequently, EWSR1::ATF1 fusions were demonstrated in 8 of the remaining 11 cases using fluorescence in situ hybridization or DNA sequencing. One of the 3 cases that were negative for EWSR1::ATF1 harbored ATF1 amplification. This study, therefore, shows that a group of malignant TSCTs resembling seminoma is characterized by α-inhibin and steroidogenic factor-1 positivity, no expression of nuclear β-catenin, frequent CD30 positivity and recurrent EWSR1::ATF1 fusions. We have descriptively termed these neoplasms "inflammatory and nested TSCT." Importantly, inflammatory and nested TSCTs show significant differences in morphology, immunoprofile, molecular biology, and, likely, clinical behavior from Sertoli cell tumors, not otherwise specified and should be classified separately.
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Affiliation(s)
- Andres M Acosta
- Department of Pathology of Brigham and Women's Hospital, Harvard Medical School
| | - Julia A Bridge
- University of Nebraska Medical Center, University of Nebraska, Omaha, NE
- ProPath, Dallas, TX
| | - Paola S Dal Cin
- Department of Pathology of Brigham and Women's Hospital, Harvard Medical School
| | - Lynette M Sholl
- Department of Pathology of Brigham and Women's Hospital, Harvard Medical School
| | | | | | - Thomas M Ulbright
- Indiana University School of Medicine, Indiana University Health Partners, Indianapolis, IN
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30
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Yu S, Sholl LM, Siegmund S, Ulbright TM, Collins K, Colecchia M, Del Pilar Gonzalez-Peramato M, Michalová K, Gordetsky JB, Cornejo KM, Kao CS, Wobker SE, Vargas SO, Maclean F, Idrees MT, Anderson WJ, Fletcher CDM, Acosta AM. Large cell calcifying Sertoli cell tumour: molecular and immunohistochemical assessment of a series comprising non-metastasising and metastasising neoplasms. Histopathology 2023; 82:1079-1088. [PMID: 36929593 DOI: 10.1111/his.14895] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/28/2023] [Accepted: 02/15/2023] [Indexed: 03/18/2023]
Abstract
Large cell calcifying Sertoli cell tumour (LCCSCT) is a type of testicular sex cord-stromal tumour that may occur sporadically or in the context of Carney complex and other genetic syndromes. A subset is clinically malignant, and the molecular mechanisms that drive such aggressive behaviour remain unknown. METHODS AND RESULTS: We analysed 21 samples from 20 patients with LCCSCT (12 non-metastasising and eight metastasising) using PRKAR1A immunohistochemistry (IHC) and next-generation sequencing. All tumours except two (cases 17 and 20, both metastasising) demonstrated loss of PRKAR1A expression. Among 11 cases with interpretable sequencing results, all harboured pathogenic single nucleotide variants of PRKAR1A. Evidence of loss of heterozygosity (LOH) of PRKAR1A was present in all tumours with interpretable zygosity data, but the mechanisms of LOH were different for non-metastasising and metastasising tumours. Non-metastasising tumours demonstrated only copy-neutral LOH, while metastasising tumours demonstrated a spectrum of mechanisms of LOH, including copy-loss LOH, two concurrent mutations or copy-neutral LOH. Relevant molecular findings in non-metastasising LCCSCT were limited to PRKAR1A variants. In contrast, all metastasising LCCSCTs with interpretable data harboured additional pathogenic variants, including (but not restricted to) BRCA2 mutations with evidence of LOH and bi-allelic CDKN2A/B deletions. Three patients harboured PRKAR1A variants of inferred germline origin, including one with Carney complex and two without known syndromic features. CONCLUSIONS: This study further confirms that PRKAR1A IHC is a useful diagnostic tool for both non-metastasising and metastasising tumours and suggests that molecular analyses can be helpful to identify non-metastasising tumours with malignant potential in selected patients. Importantly, these results highlight that germline assessment could be beneficial for all patients presenting with LCCSCT.
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Affiliation(s)
- Sanhong Yu
- 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
| | - Stephanie Siegmund
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Thomas M Ulbright
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Katrina Collins
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Maurizio Colecchia
- Department of Pathology, Vita- Salute San Raffaele University, Milan, Italy
| | | | - Květoslava Michalová
- Department of Pathology, Charles University, Medical Faculty and Charles University Hospital Plzen, Czech Republic
| | - Jennifer B Gordetsky
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kristine M Cornejo
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Chia-Sui Kao
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sara E Wobker
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Sara O Vargas
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Fiona Maclean
- Douglass Hanly Moir Pathology, Macquarie University, Sydney, Australia
| | - Muhammad T Idrees
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - William J Anderson
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Christopher D M Fletcher
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Andres M Acosta
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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31
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Rizzo NM, Sholl LM, Kao CS, Cornejo KM, Sangoi AR, Hirsch MS, Collins K, Gordetsky JB, Reyes Curcio FA, Fletcher CDM, Ulbright TM, Acosta AM. Molecular Correlates of Aggressive Behavior and Biologic Progression in Testicular Sertoli Cell Tumor. Mod Pathol 2023; 36:100152. [PMID: 36906070 DOI: 10.1016/j.modpat.2023.100152] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/03/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023]
Abstract
Sertoli cell tumor (SCT) is the second most common type of sex cord-stromal tumor in men and ∼10% exhibit malignant behavior. Although CTNNB1 variants have been described in SCTs, only a limited number of metastatic cases have been analyzed, and the molecular alterations associated with aggressive behavior remain largely unexplored. This study evaluated a series of nonmetastasizing and metastasizing SCTs using next-generation DNA sequencing to further characterize their genomic landscape. Twenty-two tumors from 21 patients were analyzed. Cases were divided into metastasizing SCTs and nonmetastasizing SCTs. Nonmetastasizing tumors were considered to have aggressive histopathologic features if they exhibited ≥1 of the following: size > 2.4 cm, necrosis, lymphovascular invasion, ≥ 3 mitoses per 10 high-power fields (HPF), severe nuclear atypia or invasive growth. Six patients had metastasizing SCTs and the remaining 15 had nonmetastasizing SCTs; 5 nonmetastasizing tumors had ≥1 aggressive histopathologic feature(s). Gain-of-function CTNNB1 or inactivating APC variants were highly recurrent in nonmetastasizing SCTs (combined frequency >90%), with arm-/chromosomal-level CNVs, loss of 1p and CTNNB1 LOH occurring exclusively in CTNNB1-mutant tumors with aggressive histopathologic features or size >1.5 cm. Nonmetastasizing SCTs were almost invariably driven by WNT pathway activation. In contrast, only 50% of metastasizing SCTs harbored gain-of-function CTNNB1 variants. The remaining 50% of metastasizing SCTs were CTNNB1-wild-type and harbored alterations in TP53, MDM2, CDKN2A/CDKN2B, and TERT pathways. These findings suggest that aggressive SCTs can arise from progression of CTNNB1-mutant benign SCTs, or from CTNNB1-wild type tumors with alterations of TP53, cell cycle regulation, and telomere maintenance pathways.
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Affiliation(s)
- Natalie M Rizzo
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Lynette M Sholl
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | | | | | | | | | | | | | | | | | | | - Andres M Acosta
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA.
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Fox AH, Nishino M, Osarogiagbon RU, Rivera MP, Rosenthal LS, Smith RA, Farjah F, Sholl LM, Silvestri GA, Johnson BE. Acquiring tissue for advanced lung cancer diagnosis and comprehensive biomarker testing: A National Lung Cancer Roundtable best-practice guide. CA Cancer J Clin 2023. [PMID: 36859638 DOI: 10.3322/caac.21774] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/13/2023] [Accepted: 01/24/2023] [Indexed: 03/03/2023] Open
Abstract
Advances in biomarker-driven therapies for patients with nonsmall cell lung cancer (NSCLC) both provide opportunities to improve the treatment (and thus outcomes) for patients and pose new challenges for equitable care delivery. Over the last decade, the continuing development of new biomarker-driven therapies and evolving indications for their use have intensified the importance of interdisciplinary communication and coordination for patients with or suspected to have lung cancer. Multidisciplinary teams are challenged with completing comprehensive and timely biomarker testing and navigating the constantly evolving evidence base for a complex and time-sensitive disease. This guide provides context for the current state of comprehensive biomarker testing for NSCLC, reviews how biomarker testing integrates within the diagnostic continuum for patients, and illustrates best practices and common pitfalls that influence the success and timeliness of biomarker testing using a series of case scenarios.
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Affiliation(s)
- Adam H Fox
- Division of Pulmonary Critical Care, Allergy and Sleep Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Mizuki Nishino
- Department of Imaging, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Raymond U Osarogiagbon
- Multidisciplinary Thoracic Oncology Program, Baptist Cancer Center, Memphis, Tennessee, USA
| | - M Patricia Rivera
- Division of Pulmonary and Critical Care Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Lauren S Rosenthal
- Prevention and Early Detection Department, American Cancer Society, Atlanta, Georgia, USA
| | - Robert A Smith
- Prevention and Early Detection Department, American Cancer Society, Atlanta, Georgia, USA
| | - Farhood Farjah
- Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Gerard A Silvestri
- Division of Pulmonary Critical Care, Allergy and Sleep Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Bruce E Johnson
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
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Vivero M, Davineni P, Nardi V, Chan JKC, Sholl LM. Response to "Expanding the Clinicopathologic Spectrum of YAP1-MAML2-Rearranged Thymic Neoplasm". Mod Pathol 2023; 36:100090. [PMID: 36788097 DOI: 10.1016/j.modpat.2022.100090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 12/19/2022] [Indexed: 02/16/2023]
Affiliation(s)
- Marina Vivero
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.
| | - Phani Davineni
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Valentina Nardi
- Department of Pathology and Center for Integrative Diagnostics, Massachusetts General Hospital, Boston, Massachusetts
| | - John K C Chan
- Department of Pathology, Queen Elizabeth Hospital, Hong Kong, SAR China
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
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34
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Lo YC, Bauer AH, Odintsov I, Siegmund SE, Sholl LM, Dong F. Integrating Molecular Sequencing Into the Pathological Diagnosis of Clinically Suspected Non-Small Cell Lung Carcinomas. Mod Pathol 2023; 36:100126. [PMID: 36842187 DOI: 10.1016/j.modpat.2023.100126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/23/2023] [Accepted: 01/27/2023] [Indexed: 02/10/2023]
Abstract
Cancer panel sequencing has been rapidly adopted into clinical practice for the detection of actionable genetic variants in advanced non-small cell lung carcinomas. Unexpected molecular results may lead to reexamination of the clinical diagnosis; however, this scenario has not been systematically evaluated. We reviewed cancer panel next-generation sequencing results from 1007 consecutive patients performed for the clinical indication of non-small cell lung carcinoma along with the corresponding clinical history and anatomical pathology findings. The final integrative diagnosis was a cancer of extrapulmonary origin in 12 of 1007 patients (1.2%). Molecular evidence supporting the final diagnoses included the detection of an UV radiation-associated mutational signature (n = 6), gene fusions (n = 2), and mutations (n = 4). The integrative diagnoses included undifferentiated melanoma, cutaneous squamous cell, and basal cell carcinomas, thyroid carcinoma, urothelial carcinoma, hepatocellular carcinoma, pancreatic adenocarcinoma, intrahepatic cholangiocarcinoma, and synovial sarcoma. A small but nonnegligible proportion of clinically suspected non-small cell lung carcinomas had a final diagnosis of cancer of extrapulmonary origin after clinical next-generation sequencing. The integration of clinical, microscopic, and molecular evidence can aid diagnosis and guide personalized oncology care.
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Affiliation(s)
- Ying-Chun Lo
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Anna H Bauer
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; University of Missouri School of Medicine, Columbia, Missouri
| | - Igor Odintsov
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | | | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Fei Dong
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.
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35
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Lamberti G, Aizer A, Ricciuti B, Alessi JV, Pecci F, Tseng SC, Sholl LM, Nishino M, Awad MM. Incidence of Brain Metastases and Preliminary Evidence of Intracranial Activity With Sotorasib in Patients With KRASG12C-Mutant Non-Small-Cell Lung Cancer. JCO Precis Oncol 2023; 7:e2200621. [PMID: 36809054 DOI: 10.1200/po.22.00621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Affiliation(s)
- Giuseppe Lamberti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Ayal Aizer
- Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Joao V Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Federica Pecci
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Shu-Chi Tseng
- Department of Radiology, Brigham and Women's Hospital, Boston, MA.,Department of Medical Imaging and Intervention, Chang Gung Memorial Hospital at Linkou and Chang Gung University, Taoyuan, Taiwan
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Mizuki Nishino
- Department of Radiology, Brigham and Women's Hospital, Boston, MA
| | - Mark M Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA
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36
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Naso J, Lo YC, Sholl LM. Updates in pathology and molecular diagnostics to inform the evolving landscape of thoracic surgery and oncology. J Surg Oncol 2023; 127:244-257. [PMID: 36630101 DOI: 10.1002/jso.27184] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 11/13/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 01/12/2023]
Abstract
The pathologic assessment of lung cancers provides essential guidance to the surgeon and oncologist who are considering the best treatment strategies for patients with both early and advanced-stage disease. The management of patients with lung cancer is predicated first and foremost on access to an accurate diagnosis, even when the sample size is limited, as is often the case with use of modern, minimally invasive sampling techniques. Once the diagnosis and disease stage are established, predictive biomarker testing may be essential, particularly for those patients with nonsmall cell lung carcinoma (NSCLC) being considered for immunotherapy or genomic biomarker-driven targeted therapy. This review will discuss the best practices for the diagnosis of NSCLC using morphology and immunohistochemistry, thus providing the surgeon with needed information to understand and critically evaluate pathology reports. Controversial and evolving topics including tumor spread through airspaces, evaluation of multiple tumors, and staging based on invasive tumor size will be addressed. Clinical genomic profiling in NSCLC is driven by published guidelines and reflects evidence based on clinical trials and regulatory approvals. In this fast-moving space, surgeons should be aware of the critical immunohistochemical and genomic biomarkers that drive systemic therapy decisions and anticipate when such testing will be required, both to ensure adequate sampling and to advise the pathologist when tumor material will be required for biomarker analysis. The basic approaches to and sample requirements for molecular biomarker testing will be addressed. As biomarker testing moves exclusively from advanced-stage patients into earlier stage disease, the surgeon should be aware of the relevant markers and work with the pathologist and oncologist to ensure that this information is available to facilitate timely access to therapies not just in the advanced setting, but in consideration of neoadjuvant and adjuvant care.
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Affiliation(s)
- Julia Naso
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ying-Chun Lo
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
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Collins K, Sholl LM, Siegmund S, Dickson BC, Colecchia M, Michalová K, Hwang M, Ulbright TM, Kao CS, van Leenders GJLH, Mehta V, Trpkov K, Yilmaz A, Cimadamore A, Matoso A, Epstein JI, Maclean F, Comperat E, Anderson WJ, Fletcher CDM, Acosta AM. Myoid gonadal stromal tumours are characterised by recurrent chromosome-level copy number gains: molecular assessment of a multi-institutional series. Histopathology 2023; 82:431-438. [PMID: 36226695 DOI: 10.1111/his.14825] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/06/2022] [Accepted: 10/08/2022] [Indexed: 01/27/2023]
Abstract
Myoid gonadal stromal tumours (MGST) represent a rare type of testicular sex cord-stromal tumour that has recently been recognised as a distinct entity by the World Health Organization (WHO) classification of genitourinary tumours. MGSTs affect adult men and have been reported to behave in an indolent fashion. Histologically, MGSTs are pure spindle cell neoplasms that coexpress SMA and S100 protein. Given that the molecular features of these neoplasms remain largely undescribed, we evaluated a multi-institutional series of MGSTs using DNA and RNA sequencing. This study included 12 tumours from 12 patients aged 28 to 57 years. Tumour sizes ranged from 0.6 to 4.3 cm. Aggressive histologic features, such as vascular invasion, necrosis, invasive growth, and atypical mitoses were invariably absent. Mitotic activity was low, with a median of less than 1 mitosis per 10 high power fields (HPF; maximum: 3 mitoses per 10 HPF). Molecular analyses did not identify recurrent mutations or gene fusions. All cases with interpretable copy number variant data (9/10 cases sequenced successfully) demonstrated a consistent pattern of chromosome arm-level and whole-chromosome-level copy number gains indicative of ploidy shifts, with recurrent gains involving chromosomes 3, 6, 7, 8, 9, 11, 12, 14q, 15q, 17, 18q, 20, and 21q. Similar findings have also been recognised in pure spindle cell and spindle-cell predominant sex cord-stromal tumours without S100 protein expression. MGSTs are characterised by ploidy shifts and may be part of a larger spectrum of spindle cell-predominant sex cord-stromal tumours, including cases without S100 protein expression.
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Affiliation(s)
- Katrina Collins
- Departments of Pathology of Indiana University School of Medicine, Indianapolis, IN, USA
| | - Lynette M Sholl
- Departments of Pathology of Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Stephanie Siegmund
- Departments of Pathology of Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Brendan C Dickson
- Departments of Pathology of Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Maurizio Colecchia
- Departments of Pathology of Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Michael Hwang
- Departments of Pathology of Indiana University School of Medicine, Indianapolis, IN, USA
| | - Thomas M Ulbright
- Departments of Pathology of Indiana University School of Medicine, Indianapolis, IN, USA
| | - Chia-Sui Kao
- Departments of Pathology of Stanford University, Stanford, CA, USA
| | | | - Vikas Mehta
- Departments of Pathology of University of Illinois at Chicago, Chicago, IL, USA
| | - Kiril Trpkov
- Departments of Pathology of Alberta Precision Laboratories and University of Calgary, Calgary, Alberta, Canada
| | - Asli Yilmaz
- Departments of Pathology of Alberta Precision Laboratories and University of Calgary, Calgary, Alberta, Canada
| | - Alessia Cimadamore
- Departments of Pathology of Polytechnic University of The Marche Region, Ancona, Italy
| | - Andres Matoso
- Departments of Pathology of The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Jonathan I Epstein
- Departments of Pathology of The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Fiona Maclean
- Departments of Pathology of Douglass Hanly Moir Pathology and Macquarie University, Sydney, Australia
| | - Eva Comperat
- Departments of Pathology of Tenon Hospital and Sorbonne University, Paris, France
| | - William J Anderson
- Departments of Pathology of Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Christopher D M Fletcher
- Departments of Pathology of Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Andrés M Acosta
- Departments of Pathology of Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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Moon I, LoPiccolo J, Baca SC, Sholl LM, Kehl KL, Hassett MJ, Liu D, Schrag D, Gusev A. Utilizing Electronic Health Records (EHR) and Tumor Panel Sequencing to Demystify Prognosis of Cancer of Unknown Primary (CUP) patients. Res Sq 2023:rs.3.rs-2450090. [PMID: 36711812 PMCID: PMC9882677 DOI: 10.21203/rs.3.rs-2450090/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Cancer of unknown primary (CUP) is a type of cancer that cannot be traced back to its original site and accounts for 3-5% of all cancers. It does not have established targeted therapies, leading to poor outcomes. We developed OncoNPC, a machine learning classifier trained on targeted next-generation sequencing data from 34,567 tumors from three institutions. OncoNPC achieved a weighted F1 score of 0.94 for high confidence predictions on known cancer types (65% of held-out samples). When applied to 971 CUP tumors from patients treated at the Dana-Farber Cancer Institute, OncoNPC identified actionable molecular alterations in 23% of the tumors. Furthermore, OncoNPC identified CUP subtypes with significantly higher polygenic germline risk for the predicted cancer type and significantly different survival outcomes, supporting its validity. Importantly, CUP patients who received first palliative intent treatments concordant with their OncoNPC-predicted cancer sites had significantly better outcomes (H.R. 0.348, 95% C.I. 0.210 - 0.570, p-value 2.32 × 10-5). OncoNPC thus provides evidence of distinct CUP subtypes and offers the potential for clinical decision support for managing patients with CUP.
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Affiliation(s)
- Intae Moon
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Jaclyn LoPiccolo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sylvan C. Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lynette M. Sholl
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Kenneth L. Kehl
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Michael J. Hassett
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Deborah Schrag
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander Gusev
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- The Broad Institute of MIT & Harvard, Cambridge, MA, USA
- Division of Genetics, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
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39
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Rakaee M, Adib E, Ricciuti B, Sholl LM, Shi W, Alessi JV, Cortellini A, Fulgenzi CAM, Viola P, Pinato DJ, Hashemi S, Bahce I, Houda I, Ulas EB, Radonic T, Väyrynen JP, Richardsen E, Jamaly S, Andersen S, Donnem T, Awad MM, Kwiatkowski DJ. Association of Machine Learning-Based Assessment of Tumor-Infiltrating Lymphocytes on Standard Histologic Images With Outcomes of Immunotherapy in Patients With NSCLC. JAMA Oncol 2023; 9:51-60. [PMID: 36394839 PMCID: PMC9673028 DOI: 10.1001/jamaoncol.2022.4933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 08/10/2022] [Indexed: 11/18/2022]
Abstract
Importance Currently, predictive biomarkers for response to immune checkpoint inhibitor (ICI) therapy in lung cancer are limited. Identifying such biomarkers would be useful to refine patient selection and guide precision therapy. Objective To develop a machine-learning (ML)-based tumor-infiltrating lymphocytes (TILs) scoring approach, and to evaluate TIL association with clinical outcomes in patients with advanced non-small cell lung cancer (NSCLC). Design, Setting, and Participants This multicenter retrospective discovery-validation cohort study included 685 ICI-treated patients with NSCLC with median follow-up of 38.1 and 43.3 months for the discovery (n = 446) and validation (n = 239) cohorts, respectively. Patients were treated between February 2014 and September 2021. We developed an ML automated method to count tumor, stroma, and TIL cells in whole-slide hematoxylin-eosin-stained images of NSCLC tumors. Tumor mutational burden (TMB) and programmed death ligand-1 (PD-L1) expression were assessed separately, and clinical response to ICI therapy was determined by medical record review. Data analysis was performed from June 2021 to April 2022. Exposures All patients received anti-PD-(L)1 monotherapy. Main Outcomes and Measures Objective response rate (ORR), progression-free survival (PFS), and overall survival (OS) were determined by blinded medical record review. The area under curve (AUC) of TIL levels, TMB, and PD-L1 in predicting ICI response were calculated using ORR. Results Overall, there were 248 (56%) women in the discovery cohort and 97 (41%) in the validation cohort. In a multivariable analysis, high TIL level (≥250 cells/mm2) was independently associated with ICI response in both the discovery (PFS: HR, 0.71; P = .006; OS: HR, 0.74; P = .03) and validation (PFS: HR = 0.80; P = .01; OS: HR = 0.75; P = .001) cohorts. Survival benefit was seen in both first- and subsequent-line ICI treatments in patients with NSCLC. In the discovery cohort, the combined models of TILs/PD-L1 or TMB/PD-L1 had additional specificity in differentiating ICI responders compared with PD-L1 alone. In the PD-L1 negative (<1%) subgroup, TIL levels had superior classification accuracy for ICI response (AUC = 0.77) compared with TMB (AUC = 0.65). Conclusions and Relevance In these cohorts, TIL levels were robustly and independently associated with response to ICI treatment. Patient TIL assessment is relatively easily incorporated into the workflow of pathology laboratories at minimal additional cost, and may enhance precision therapy.
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Affiliation(s)
- Mehrdad Rakaee
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
- Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway
| | - Elio Adib
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Biagio Ricciuti
- Lowe Center for Thoracic 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
| | - Weiwei Shi
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Joao V. Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alessio Cortellini
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Claudia A. M. Fulgenzi
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Department of Medical Oncology, University Campus Bio-Medico, Rome, Italy
| | - Patrizia Viola
- Department of Cellular Pathology, Imperial College London NHS Trust, London, United Kingdom
| | - David J. Pinato
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Sayed Hashemi
- Department of Pulmonology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Idris Bahce
- Department of Pulmonology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Ilias Houda
- Department of Pulmonology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Ezgi B. Ulas
- Department of Pulmonology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Teodora Radonic
- Department of Pathology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Juha P. Väyrynen
- Cancer and Translational Medicine Research Unit, Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Elin Richardsen
- Department of Clinical Pathology, University Hospital of North Norway, Tromso, Norway
| | - Simin Jamaly
- Department of Medical Biology, UiT The Arctic University of Norway, Tromso, Norway
| | - Sigve Andersen
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
- Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - Tom Donnem
- Department of Clinical Medicine, UiT The Arctic University of Norway, Tromso, Norway
- Department of Oncology, University Hospital of North Norway, Tromso, Norway
| | - Mark M. Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - David J. Kwiatkowski
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
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40
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Acosta AM, McKenney JK, Sholl LM, Dickson BC, Matoso A, Lu H, Jo VY, Collins K, Ulbright TM, Fletcher CDM. Molecular assessment of paratesticular rhabdomyomas demonstrates recurrent findings, including a novel H3C2 p.K37I mutation. Mod Pathol 2022; 35:1921-1928. [PMID: 35842480 DOI: 10.1038/s41379-022-01134-3] [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: 02/14/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 12/24/2022]
Abstract
Rhabdomyomas are benign tumors with skeletal muscle differentiation that are broadly divided into cardiac and extracardiac types. The latter demonstrate a predilection for head and neck and genital locations and are further subclassified into adult-type rhabdomyoma (ATRM), fetal-type rhabdomyoma (FTRM) and genital rhabdomyoma (GRM). Most extracardiac rhabdomyomas that arise in paratesticular tissues have a somewhat distinctive morphology and have been termed sclerosing rhabdomyomas (SRM). Therefore, we hypothesized that these tumors may harbor recurrent genetic alterations. In this study, we assessed 15 paratesticular rhabdomyomas (11 initially classified as SRM, 2 cellular FTRM and 2 ATRM) using massively parallel DNA and RNA sequencing. Five of 14 successfully sequenced cases harbored a novel H3C2 p.K37I mutation (4 SRM and 1 ATRM). This mutation replaced a highly conserved lysine residue that is a target for epigenetic modifications and plays a role in regulation of DNA replication. Moreover, 4 tumors (2 cellular FTRM, 1 case initially diagnosed as SRM and 1 ATRM) had complex copy number profiles characterized by numerous chromosome-level and arm-level copy number gains, consistent with a ploidy shift. Rereview of the SRM with copy number gains demonstrated that it was significantly more cellular and had a more prominent fascicular architecture than the rest of the SRMs included in this series. Therefore, it was retrospectively reclassified as a cellular FTRM. In conclusion, this study demonstrated that paratesticular rhabdomyomas harbor recurrent somatic H3C2 p.K37I mutations and ploidy shifts.
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Affiliation(s)
- Andres M Acosta
- Department of Pathology, Brigham and Women's Hospital/Harvard Medical School, Boston, MA, USA.
| | - Jesse K McKenney
- Department of Pathology, Robert J. Tomsich Institute of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital/Harvard Medical School, Boston, MA, USA
| | - Brendan C Dickson
- Department of Pathology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Andres Matoso
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Haiyan Lu
- Department of Pathology, Robert J. Tomsich Institute of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Vickie Y Jo
- Department of Pathology, Brigham and Women's Hospital/Harvard Medical School, Boston, MA, USA
| | - Katrina Collins
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Thomas M Ulbright
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA
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41
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Park H, Tseng SC, Sholl LM, Hatabu H, Awad MM, Nishino M. Molecular Characterization and Therapeutic Approaches to Small Cell Lung Cancer: Imaging Implications. Radiology 2022; 305:512-525. [PMID: 36283111 PMCID: PMC9713457 DOI: 10.1148/radiol.220585] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 03/25/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 01/16/2023]
Abstract
Small cell lung cancer (SCLC) is a highly aggressive malignancy with exceptionally poor prognosis, comprising approximately 15% of lung cancers. Emerging knowledge of the molecular and genomic landscape of SCLC and recent successful clinical applications of new systemic agents have allowed for precision oncology treatment approaches. Imaging is essential for the diagnosis, staging, and treatment monitoring of patients with SCLC. The role of imaging is increasing with the approval of new treatment agents, including immune checkpoint inhibitors, which lead to novel imaging manifestations of response and toxicities. The purpose of this state-of-the-art review is to provide the reader with the latest information about SCLC, focusing on the subtyping of this malignancy (molecular characterization) and the emerging systemic therapeutic approaches and their implications for imaging. The review will also discuss the future directions of SCLC imaging, radiomics and machine learning.
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Affiliation(s)
- Hyesun Park
- From the Departments of Radiology (H.P., S.C.T., H.H., M.N.),
Pathology (L.M.S.), Medical Oncology (M.M.A.), and Medicine (M.M.A.),
Dana-Farber Cancer Institute and Brigham and Women's Hospital, 450
Brookline Ave, Boston, MA 02215
| | | | - Lynette M. Sholl
- From the Departments of Radiology (H.P., S.C.T., H.H., M.N.),
Pathology (L.M.S.), Medical Oncology (M.M.A.), and Medicine (M.M.A.),
Dana-Farber Cancer Institute and Brigham and Women's Hospital, 450
Brookline Ave, Boston, MA 02215
| | - Hiroto Hatabu
- From the Departments of Radiology (H.P., S.C.T., H.H., M.N.),
Pathology (L.M.S.), Medical Oncology (M.M.A.), and Medicine (M.M.A.),
Dana-Farber Cancer Institute and Brigham and Women's Hospital, 450
Brookline Ave, Boston, MA 02215
| | - Mark M. Awad
- From the Departments of Radiology (H.P., S.C.T., H.H., M.N.),
Pathology (L.M.S.), Medical Oncology (M.M.A.), and Medicine (M.M.A.),
Dana-Farber Cancer Institute and Brigham and Women's Hospital, 450
Brookline Ave, Boston, MA 02215
| | - Mizuki Nishino
- From the Departments of Radiology (H.P., S.C.T., H.H., M.N.),
Pathology (L.M.S.), Medical Oncology (M.M.A.), and Medicine (M.M.A.),
Dana-Farber Cancer Institute and Brigham and Women's Hospital, 450
Brookline Ave, Boston, MA 02215
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42
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Mahadevan NR, Sholl LM. To Rb or Not to Rb: Uncovering Unique Subsets of Small Cell Lung Carcinoma. Clin Cancer Res 2022; 28:4603-4605. [PMID: 36044394 DOI: 10.1158/1078-0432.ccr-22-2187] [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: 08/02/2022] [Revised: 08/15/2022] [Accepted: 08/19/2022] [Indexed: 01/24/2023]
Abstract
The use of IHC as a surrogate for specific underlying genomic alterations has allowed for increasingly comprehensive and accurate diagnosis of small cell lung carcinoma (SCLC). This is especially relevant in light of the increasing recognition of the biologic heterogeneity of this aggressive and difficult-to-treat lung tumor. Integrated genomic and IHC profiling of Rb status in SCLC yields new diagnostic insights and has translational implications. See related article by Febres-Aldana et al., p. 4702.
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Affiliation(s)
- Navin R Mahadevan
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
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43
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Cheng ML, Lee JK, Kumar R, Klein H, Raskina K, Schrock AB, Michael KS, Mazor T, Cerami E, Oxnard GR, Liu D, Beltran H, Sholl LM, Nishino M, Jänne PA. Response to MEK Inhibitor Therapy in MAP2K1 ( MEK1) K57N Non-Small-Cell Lung Cancer and Genomic Landscape of MAP2K1 Mutations in Non-Small-Cell Lung Cancer. JCO Precis Oncol 2022; 6:e2200382. [PMID: 36455195 DOI: 10.1200/po.22.00382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Affiliation(s)
- Michael L Cheng
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA.,Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Present address: Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA
| | | | - Rachit Kumar
- Harold Alfond Center for Cancer Care, MaineHealth, Augusta, MA
| | - Harry Klein
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Kesi S Michael
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA.,Present address: Foundation Medicine, Cambridge, MA
| | - Tali Mazor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Ethan Cerami
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | | | - David Liu
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Himisha Beltran
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Mizuki Nishino
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Department of Imaging, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Pasi A Jänne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA.,Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA
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44
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Chapel DB, Hornick JL, Barlow J, Bueno R, Sholl LM. Clinical and molecular validation of BAP1, MTAP, P53, and Merlin immunohistochemistry in diagnosis of pleural mesothelioma. Mod Pathol 2022; 35:1383-1397. [PMID: 35459788 PMCID: PMC9529776 DOI: 10.1038/s41379-022-01081-z] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/16/2022] [Accepted: 03/28/2022] [Indexed: 12/28/2022]
Abstract
BAP1 and MTAP immunostains play an important role in diagnosis of mesothelioma, but additional markers are needed to increase sensitivity. We analyzed 84 pleural mesotheliomas (51 epithelioid, 27 biphasic, 6 sarcomatoid) by a hybrid-capture next-generation sequencing (NGS) panel including complete coverage of coding and splicing regions for BAP1, CDKN2A/MTAP, NF2, and TP53 and correlated molecular findings with diagnostic immunostains for BAP1, MTAP, Merlin, and p53, respectively. Fifty-seven reactive mesothelial proliferations served as benign comparators. Loss of BAP1, MTAP, and Merlin protein expression were, respectively, 54%, 46%, and 52% sensitive and 100% specific for mesothelioma. Two-marker immunopanels of BAP1 + MTAP, BAP1 + Merlin, and MTAP + Merlin were 79%, 85%, and 71% sensitive for mesothelioma, while a three-marker immunopanel of BAP1 + MTAP + Merlin was 90% sensitive. Diffuse (mutant-pattern) p53 immunostaining was seen in only 6 (7%) tumors but represented the only immunohistochemical abnormality in 2 cases. Null-pattern p53 was not specific for malignancy. An immunopanel of BAP1 + MTAP + Merlin + p53 was 93% sensitive for mesothelioma, and panel NGS detected a pathogenic alteration in BAP1, MTAP, NF2, and/or TP53 in 95%. Together, 83 (99%) of 84 tumors showed a diagnostic alteration by either immunohistochemistry or panel NGS. Adding Merlin to the standard BAP1 + MTAP immunopanel increases sensitivity for mesothelioma without sacrificing specificity. p53 immunohistochemistry and panel NGS with complete coverage of BAP1, CDKN2A/MTAP, TP53, and NF2 may be useful in diagnostically challenging cases.
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Affiliation(s)
- David B Chapel
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Department of Pathology, University of Michigan - Michigan Medicine, Ann Arbor, MI, 48109, USA.
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Julianne Barlow
- Department of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Raphael Bueno
- Department of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Boston, MA, 02115, USA
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45
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Costigan DC, Nucci MR, Dickson BC, Chang MC, Song S, Sholl LM, Hornick JL, Fletcher CD, Kolin DL. NTRK -Rearranged Uterine Sarcomas: Clinicopathologic Features of 15 Cases, Literature Review, and Risk Stratification. Am J Surg Pathol 2022; 46:1415-1429. [PMID: 35713627 PMCID: PMC9481736 DOI: 10.1097/pas.0000000000001929] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 02/04/2023]
Abstract
NTRK -rearranged uterine sarcomas are rare spindle cell neoplasms that typically arise in the uterine cervix of young women. Some tumors recur or metastasize, but features which predict behavior have not been identified to date. Distinguishing these tumors from morphologic mimics is significant because patients with advanced stage disease may be treated with TRK inhibitors. Herein, we present 15 cases of NTRK- rearranged uterine sarcomas, the largest series to date. Median patient age was 35 years (range: 16 to 61). The majority arose in the uterine cervix (n=14) and all but 2 were organ-confined at diagnosis. Tumors were composed of an infiltrative, fascicular proliferation of spindle cells and most showed mild-to-moderate cytologic atypia. All were pan-TRK positive by immunohistochemistry (13/13); S100 (11/13) and CD34 (6/10) were usually positive. RNA or DNA sequencing found NTRK1 (10/13) and NTRK3 (3/13) fusions with partners TPR , TPM3 , EML4 , TFG , SPECC1L , C16orf72 , and IRF2BP2 . Unusual morphology was seen in 2 tumors which were originally diagnosed as unclassifiable uterine sarcomas, 1 of which also harbored TP53 mutations. Follow up was available for 9 patients, of whom 3 died of disease. By incorporating outcome data of previously reported tumors, adverse prognostic features were identified, including a mitotic index ≥8 per 10 high-power fields, lymphovascular invasion, necrosis, and NTRK3 fusion. Patients with tumors which lacked any of these 4 features had an excellent prognosis. This study expands the morphologic spectrum of NTRK -rearranged uterine sarcomas and identifies features which can be used for risk stratification.
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Affiliation(s)
- Danielle C. Costigan
- Division of Women’s and Perinatal Pathology, Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Marisa R. Nucci
- Division of Women’s and Perinatal Pathology, Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
| | - Brendan C. Dickson
- Department of Pathology, Mount Sinai Hospital and University of Toronto, Toronto, ON M5G 1X5
| | - Martin C. Chang
- Department of Pathology & Laboratory Medicine, University of Vermont Medical Center, Burlington, VT, 05401
| | - Sharon Song
- Division of Women’s and Perinatal Pathology, Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
- Spectrum Healthcare Partners, Portland, Maine 04106
| | - Lynette M. Sholl
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
| | - Jason L. Hornick
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
| | | | - David L. Kolin
- Division of Women’s and Perinatal Pathology, Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115
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46
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Ricciuti B, Alessi JV, Elkrief A, Wang X, Cortellini A, Li YY, Vaz VR, Gupta H, Pecci F, Barrichello A, Lamberti G, Nguyen T, Lindsay J, Sharma B, Felt K, Rodig SJ, Nishino M, Sholl LM, Barbie DA, Negrao MV, Zhang J, Cherniack AD, Heymach JV, Meyerson M, Ambrogio C, Jänne PA, Arbour KC, Pinato DJ, Skoulidis F, Schoenfeld AJ, Awad MM, Luo J. Dissecting the clinicopathologic, genomic, and immunophenotypic correlates of KRAS G12D-mutated non-small-cell lung cancer. Ann Oncol 2022; 33:1029-1040. [PMID: 35872166 PMCID: PMC11006449 DOI: 10.1016/j.annonc.2022.07.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [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: 04/17/2022] [Revised: 07/10/2022] [Accepted: 07/14/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Allele-specific KRAS inhibitors are an emerging class of cancer therapies. KRAS-mutant (KRASMUT) non-small-cell lung cancers (NSCLCs) exhibit heterogeneous outcomes, driven by differences in underlying biology shaped by co-mutations. In contrast to KRASG12C NSCLC, KRASG12D NSCLC is associated with low/never-smoking status and is largely uncharacterized. PATIENTS AND METHODS Clinicopathologic and genomic information were collected from patients with NSCLCs harboring a KRAS mutation at the Dana-Farber Cancer Institute (DFCI), Memorial Sloan Kettering Cancer Center, MD Anderson Cancer Center, and Imperial College of London. Multiplexed immunofluorescence for CK7, programmed cell death protein 1 (PD-1), programmed death-ligand 1 (PD-L1), Foxp3, and CD8 was carried out on a subset of samples with available tissue at the DFCI. Clinical outcomes to PD-(L)1 inhibition ± chemotherapy were analyzed according to KRAS mutation subtype. RESULTS Of 2327 patients with KRAS-mutated (KRASMUT) NSCLC, 15% (n = 354) harbored KRASG12D. Compared to KRASnon-G12D NSCLC, KRASG12D NSCLC had a lower pack-year (py) smoking history (median 22.5 py versus 30.0 py, P < 0.0001) and was enriched in never smokers (22% versus 5%, P < 0.0001). KRASG12D had lower PD-L1 tumor proportion score (TPS) (median 1% versus 5%, P < 0.01) and lower tumor mutation burden (TMB) compared to KRASnon-G12D (median 8.4 versus 9.9 mt/Mb, P < 0.0001). Of the samples which underwent multiplexed immunofluorescence, KRASG12D had lower intratumoral and total CD8+PD1+ T cells (P < 0.05). Among 850 patients with advanced KRASMUT NSCLC who received PD-(L)1-based therapies, KRASG12D was associated with a worse objective response rate (ORR) (15.8% versus 28.4%, P = 0.03), progression-free survival (PFS) [hazard ratio (HR) 1.51, 95% confidence interval (CI) 1.45-2.00, P = 0.003], and overall survival (OS; HR 1.45, 1.05-1.99, P = 0.02) to PD-(L)1 inhibition alone but not to chemo-immunotherapy combinations [ORR 30.6% versus 35.7%, P = 0.51; PFS HR 1.28 (95%CI 0.92-1.77), P = 0.13; OS HR 1.36 (95%CI 0.95-1.96), P = 0.09] compared to KRASnon-G12D. CONCLUSIONS KRASG12D lung cancers harbor distinct clinical, genomic, and immunologic features compared to other KRAS-mutated lung cancers and worse outcomes to PD-(L)1 blockade. Drug development for KRASG12D lung cancers will have to take these differences into account.
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Affiliation(s)
- B Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - J V Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - A Elkrief
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - X Wang
- Harvard School of Public Health, Boston, USA
| | - A Cortellini
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Y Y Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA; Cancer Program, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, USA
| | - V R Vaz
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - H Gupta
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - F Pecci
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - A Barrichello
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - G Lamberti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - T Nguyen
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - J Lindsay
- Knowledge Systems Group, Dana-Farber Cancer Institute, Boston, USA
| | - B Sharma
- ImmunoProfile, Brigham & Women's Hospital and Dana-Farber Cancer Institute, Boston, USA
| | - K Felt
- ImmunoProfile, Brigham & Women's Hospital and Dana-Farber Cancer Institute, Boston, USA
| | - S J Rodig
- ImmunoProfile, Brigham & Women's Hospital and Dana-Farber Cancer Institute, Boston, USA; Department of Pathology, Brigham and Women's Hospital, Boston, USA
| | - M Nishino
- Department of Radiology, Brigham and Women's Hospital and Department of Imaging, Dana-Farber Cancer Institute, Boston, USA
| | - L M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
| | - D A Barbie
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - M V Negrao
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Zhang
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, USA
| | - A D Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - J V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, USA
| | - M Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - C Ambrogio
- Molecular Biotechnology and Health Science, University of Turin, Turin, Italy
| | - P A Jänne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - K C Arbour
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - D J Pinato
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - F Skoulidis
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, USA
| | - A J Schoenfeld
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - M M Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - J Luo
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, USA.
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47
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Sholl LM, Halmos B. Biomarker testing in cancer management- can one size fit all? Br J Cancer 2022; 127:1177-1179. [PMID: 36064588 PMCID: PMC9519751 DOI: 10.1038/s41416-022-01967-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/16/2022] [Accepted: 08/19/2022] [Indexed: 11/09/2022] Open
Abstract
Biomarker-guided treatment selection has transformed cancer management. Pruis et al. provide a powerful example of the challenges and promises of whole genome sequencing to match patients with advanced cancer for precision oncology studies and targeted therapies. Expanding genomic testing platforms are reviewed with a view towards future applications to inform clinical cancer research and practice.
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Affiliation(s)
- Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Balazs Halmos
- Department of Oncology, Montefiore Medical Center and Albert Einstein College of Medicine, New York, NY, USA.
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48
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Mino-Kenudson M, Schalper K, Cooper W, Dacic S, Hirsch FR, Jain D, Lopez-Rios F, Tsao MS, Yatabe Y, Beasley MB, Yu H, Sholl LM, Brambilla E, Chou TY, Connolly C, Wistuba I, Kerr KM, Lantuejoul S. Predictive Biomarkers for Immunotherapy in Lung Cancer: Perspective from the IASLC Pathology Committee. J Thorac Oncol 2022; 17:1335-1354. [PMID: 36184066 DOI: 10.1016/j.jtho.2022.09.109] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 10/14/2022]
Abstract
Immunotherapy including immune checkpoint inhibitors (ICIs) has become the backbone of treatment for the majority of lung cancers with advanced or metastatic disease. In addition, they have increasingly been used for early-stage tumors in neoadjuvant and adjuvant settings. Unfortunately, however, only a subset of patients experiences meaningful response to ICIs. While PD-L1 protein expression by immunohistochemistry (IHC) has played a role as the principle predictive biomarker for immunotherapy, its performance may not be optimal, and it suffers multiple practical issues with different companion diagnostic assays approved. Similarly, tumor mutation burden (TMB) has multiple technical issues as a predictive biomarker for ICIs. Now, ongoing research on tumor and host immune-specific factors has identified immunotherapy biomarkers that may provide better response and prognosis prediction, in particular in a multimodal approach. This review by the IASLC Pathology Committee provides an overview of various immunotherapy biomarkers including updated data on PD-L1 IHC and TMB, and assesssments of neoantigens, genetic and epigenetic signatures, immune microenvironment by IHC and transcriptomics, as well as microbiome and pathological response to neoadjuvant immunotherapies. The aim of this review is to underline the efficacy of new individual or combined predictive biomarkers beyond PD-L1 IHC and TMB.
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Affiliation(s)
- Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | - Kurt Schalper
- Department of Pathology, Yale University School of Medicine, New Haven, CT
| | - Wendy Cooper
- Royal Prince Alfred Hospital, NSW Health Pathology and University of Sydney, Camperdown, Australia
| | - Sanja Dacic
- Department of Pathology, Yale University School of Medicine, New Haven, CT
| | - Fred R Hirsch
- Center for Thoracic Oncology, The Tisch Cancer Institute, New York, New York; Ichan School of Medicine, Mount Sinai Health System, New York, NY, USA
| | - Deepali Jain
- All India Institute of Medical Sciences, New Delhi, India
| | - Fernando Lopez-Rios
- Department of Pathology, "Doce de Octubre" University Hospital, Madrid, Spain
| | - Ming Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Mary Beth Beasley
- Ichan School of Medicine, Mount Sinai Health System, New York, NY, USA
| | - Hui Yu
- Center for Thoracic Oncology, The Tisch Cancer Institute, New York, New York; Ichan School of Medicine, Mount Sinai Health System, New York, NY, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | | | | | - Casey Connolly
- International Association for the Study of Lung Cancer, Denver, CO, USA
| | - Ignacio Wistuba
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Keith M Kerr
- Department of Pathology, Aberdeen Royal Infirmary, Aberdeen, United Kingdom
| | - Sylvie Lantuejoul
- Université Grenoble Alpes, Grenoble, France; Centre Léon Bérard Unicancer, Lyon, France.
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49
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Kobayashi Y, Oxnard GR, Cohen EF, Mahadevan NR, Alessi JV, Hung YP, Bertram AA, Heppner DE, Ribeiro MF, Sacardo KP, Saddi R, Macedo MP, Blasco RB, Li J, Kurppa KJ, Nguyen T, Voligny E, Ananda G, Chiarle R, Katz A, Tolstorukov MY, Sholl LM, Jänne PA. Genomic and biological study of fusion genes as resistance mechanisms to EGFR inhibitors. Nat Commun 2022; 13:5614. [PMID: 36153311 PMCID: PMC9509394 DOI: 10.1038/s41467-022-33210-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 07/30/2021] [Accepted: 09/08/2022] [Indexed: 11/28/2022] Open
Abstract
The clinical significance of gene fusions detected by DNA-based next generation sequencing remains unclear as resistance mechanisms to EGFR tyrosine kinase inhibitors in EGFR mutant non-small cell lung cancer. By studying EGFR inhibitor-resistant patients treated with a combination of an EGFR inhibitor and a drug targeting the putative resistance-causing fusion oncogene, we identify patients who benefit and those who do not from this treatment approach. Through evaluation including RNA-seq of potential drug resistance-imparting fusion oncogenes in 504 patients with EGFR mutant lung cancer, we identify only a minority of them as functional, potentially capable of imparting EGFR inhibitor resistance. We further functionally validate fusion oncogenes in vitro using CRISPR-based editing of EGFR mutant cell lines and use these models to identify known and unknown drug resistance mechanisms to combination therapies. Collectively, our results partially reveal the complex nature of fusion oncogenes as potential drug resistance mechanisms and highlight approaches that can be undertaken to determine their functional significance.
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Affiliation(s)
- Yoshihisa Kobayashi
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215, USA
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, 1040045, Japan
| | - Geoffrey R Oxnard
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Elizabeth F Cohen
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Navin R Mahadevan
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Joao V Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Yin P Hung
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Arrien A Bertram
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - David E Heppner
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, NY, 14260-3000, USA
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Mauricio F Ribeiro
- Department of Medical Oncology, Hospital Sírio-Libanês, São Paulo-SP, 01308-050, Brazil
| | - Karina P Sacardo
- Department of Medical Oncology, Hospital Sírio-Libanês, São Paulo-SP, 01308-050, Brazil
| | - Rodrigo Saddi
- Department of Medical Oncology, Hospital Sírio-Libanês, São Paulo-SP, 01308-050, Brazil
| | - Mariana P Macedo
- Department of Pathology, Hospital Sírio-Libanês, São Paulo-SP, 01308-050, Brazil
| | - Rafael B Blasco
- Department of Pathology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Jiaqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215, USA
| | - Kari J Kurppa
- Institute of Biomedicine, and MediCity Research Laboratories, University of Turku, Turku, 20520, Finland
| | - Tom Nguyen
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Emma Voligny
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Guruprasad Ananda
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy
| | - Artur Katz
- Department of Medical Oncology, Hospital Sírio-Libanês, São Paulo-SP, 01308-050, Brazil
| | - Michael Y Tolstorukov
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Pasi A Jänne
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215, USA.
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
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50
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Schwartz A, Manning DK, Koeller DR, Chittenden A, Isidro RA, Hayes CP, Abraamyan F, Manam MD, Dwan M, Barletta JA, Sholl LM, Yurgelun MB, Rana HQ, Garber JE, Ghazani AA. An integrated somatic and germline approach to aid interpretation of germline variants of uncertain significance in cancer susceptibility genes. Front Oncol 2022; 12:942741. [PMID: 36091175 PMCID: PMC9453486 DOI: 10.3389/fonc.2022.942741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Genomic profiles of tumors are often unique and represent characteristic mutational signatures defined by DNA damage or DNA repair response processes. The tumor-derived somatic information has been widely used in therapeutic applications, but it is grossly underutilized in the assessment of germline genetic variants. Here, we present a comprehensive approach for evaluating the pathogenicity of germline variants in cancer using an integrated interpretation of somatic and germline genomic data. We have previously demonstrated the utility of this integrated approach in the reassessment of pathogenic germline variants in selected cancer patients with unexpected or non-syndromic phenotypes. The application of this approach is presented in the assessment of rare variants of uncertain significance (VUS) in Lynch-related colon cancer, hereditary paraganglioma-pheochromocytoma syndrome, and Li-Fraumeni syndrome. Using this integrated method, germline VUS in PMS2, MSH6, SDHC, SHDA, and TP53 were assessed in 16 cancer patients after genetic evaluation. Comprehensive clinical criteria, somatic signature profiles, and tumor immunohistochemistry were used to re-classify VUS by upgrading or downgrading the variants to likely or unlikely actionable categories, respectively. Going forward, collation of such germline variants and creation of cross-institutional knowledgebase datasets that include integrated somatic and germline data will be crucial for the assessment of these variants in a larger cancer cohort.
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Affiliation(s)
- Alison Schwartz
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Danielle K. Manning
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Diane R. Koeller
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Anu Chittenden
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Raymond A. Isidro
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Connor P. Hayes
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Feruza Abraamyan
- Harvard Medical School, Boston, MA, United States
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Monica Devi Manam
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Meaghan Dwan
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Justine A. Barletta
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Lynette M. Sholl
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Matthew B. Yurgelun
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Huma Q. Rana
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Judy E. Garber
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Arezou A. Ghazani
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- *Correspondence: Arezou A. Ghazani,
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