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Fischer GM, Mahadevan NR, Hornick JL, Fletcher CD, Russell-Goldman E. A Comparative Genomic Study of Conventional and Undifferentiated Melanoma. Mod Pathol 2024:100626. [PMID: 39332711 DOI: 10.1016/j.modpat.2024.100626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 08/05/2024] [Accepted: 09/13/2024] [Indexed: 09/29/2024]
Abstract
Undifferentiated melanoma, defined as melanoma which has lost all usual phenotypic and immunohistochemical characteristics of conventional melanoma, can pose significant diagnostic challenges. Molecular studies have advanced our understanding of undifferentiated melanoma by demonstrating that a subset of these tumors harbor known melanoma driver alterations in genes such as BRAF, NRAS, and NF1. However, there is a paucity of data describing genetic alterations which may distinguish undifferentiated melanoma from conventional melanoma. In this study, we directly compared the genomic profiles of undifferentiated melanoma to a cohort of conventional melanomas, including 14 undifferentiated melanoma cases (comprised of two primary cases, two cutaneous recurrences and 10 metastases) and a cohort of 127 conventional melanomas including primary, recurrent, and metastatic cases. Targeted sequencing of 447 cancer-associated genes was performed, including identification of mutations and copy number alterations (CNAs). NRAS was the most frequent melanoma driver in undifferentiated melanoma (8/14 cases, 57%), although notably only one undifferentiated melanoma harbored an NRAS Q61R mutation. Compared to the conventional melanoma cohort, undifferentiated melanoma demonstrated statistically significant enrichment of pathogenic activating RAC1 mutations (6/14 total cases, 43%), including P29S (4/6 cases), P29L (1/6 cases) and D11E (1/6 cases). In addition to providing insight into the molecular pathogenesis of undifferentiated melanoma, these findings also suggest that RAS Q61R immunohistochemistry may have limited utility for its diagnosis. The presence of recurrent RAC1 mutations in undifferentiated melanoma is also notable as these alterations may contribute to mitogen-activated protein (MAP) kinase pathway targeted therapy resistance. Furthermore, the RAC1 alterations identified in this cohort have been shown to drive a melanocytic to mesenchymal switch in melanocytes, offering a possible explanation for the undifferentiated phenotype of these melanomas.
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Affiliation(s)
- Grant M Fischer
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Navin R Mahadevan
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Christopher Dm Fletcher
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Eleanor Russell-Goldman
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts..
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2
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Martínez-Quintanilla J, Cabot D, Sabia D, Arqués O, Vergés J, Chicote I, Bijelic L, Cabellos L, Alcántara AM, Ramos I, Barrios P, Crusellas O, Palacio LM, Cámara JA, Barriuso J, Jiménez JJ, Muñoz-Torres P, Nonell L, Flores R, Médico E, Guaglio M, Ros J, Élez E, Tabernero J, Aziz O, Deraco M, Palmer HG. Precision Oncology and Systemic Targeted Therapy in Pseudomyxoma Peritonei. Clin Cancer Res 2024; 30:4082-4099. [PMID: 39018564 PMCID: PMC11393541 DOI: 10.1158/1078-0432.ccr-23-4072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/18/2024] [Accepted: 07/10/2024] [Indexed: 07/19/2024]
Abstract
PURPOSE Pseudomyxoma peritonei (PMP) is a rare and poorly understood malignant condition characterized by the accumulation of intra-abdominal mucin produced from peritoneal metastases. Currently, cytoreductive surgery remains the mainstay of treatment but disease recurrence and death after relapse frequently occur in patients with PMP. New therapeutic strategies are therefore urgently needed for these patients. EXPERIMENTAL DESIGN A total of 120 PMP samples from 50 patients were processed to generate a collection of 50 patient-derived organoid (PDO) and xenograft (PDX) models. Whole exome sequencing, immunohistochemistry analyses, and in vitro and in vivo drug efficacy studies were performed. RESULTS In this study, we have generated a collection of PMP preclinical models and identified druggable targets, including BRAFV600E, KRASG12C, and KRASG12D, that could also be detected in intra-abdominal mucin biopsies of patients with PMP using droplet digital PCR. Preclinical models preserved the histopathological markers from the original patient sample. The BRAFV600E inhibitor encorafenib reduced cell viability of BRAFV600E PMP-PDO models. Proof-of-concept in vivo experiments showed that a systemic treatment with encorafenib significantly reduced tumor growth and prolonged survival in subcutaneous and orthotopic BRAFV600E-PMP-PDX mouse models. CONCLUSIONS Our study demonstrates for the first time that systemic targeted therapies can effectively control PMP tumors. BRAF signaling pathway inhibition represents a new therapeutic opportunity for patients with BRAFV600E PMP who have a poor prognosis. Importantly, our present data and collection of preclinical models pave the way for evaluating the efficacy of other systemic targeted therapies toward extending the promise of precision oncology to patients with PMP.
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Affiliation(s)
- Jordi Martínez-Quintanilla
- Translational Program, Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Débora Cabot
- Translational Program, Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Doménico Sabia
- Peritoneal Surface Malignancies Surgery Unit, Hospital Sant Joan Despí, Moises Broggi, Sant Joan Despí, Spain
| | - Oriol Arqués
- Translational Program, Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Jordi Vergés
- Translational Program, Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Irene Chicote
- Translational Program, Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Lana Bijelic
- Peritoneal Surface Malignancies Surgery Unit, Hospital Sant Joan Despí, Moises Broggi, Sant Joan Despí, Spain
| | - Laia Cabellos
- Translational Program, Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Anna M Alcántara
- Translational Program, Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Isabel Ramos
- Department of General Surgery, Hospital Sant Joan Despí, Consorci Sanitari Integral, Sant Joan Despí, Spain
| | - Pedro Barrios
- Former Peritoneal Surface Malignancies Surgery Unit, Hospital Sant Joan Despí, Moises Broggi, Sant Joan Despí, Spain
| | - Oriol Crusellas
- Department of General Surgery, Hospital Sant Joan Despí, Consorci Sanitari Integral, Sant Joan Despí, Spain
- Department of General Surgery, Hospital de Barcelona, Assistència Sanitària Col·legial, Barcelona, Spain
| | - Lina M Palacio
- Peritoneal Surface Malignancies Surgery Unit, Hospital Sant Joan Despí, Moises Broggi, Sant Joan Despí, Spain
| | - Juan A Cámara
- Preclinical Therapeutics Core, University of California, San Francisco, California
| | - Jorge Barriuso
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Colorectal and Peritoneal Oncology Centre, The Christie NHSFT, Manchester, United Kingdom
| | - Juan J Jiménez
- Preclinical Imaging Platform, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Pau Muñoz-Torres
- Bioinformatics Unit, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Lara Nonell
- Bioinformatics Unit, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Raquel Flores
- Translational Program, Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Enzo Médico
- Department of Oncology, University of Turin, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Marcello Guaglio
- Consultant Surgeon, Peritoneal Surface Malignancies Unit, Division of Colorectal Surgery, National Cancer Institute, Milan, Italy
| | - Javier Ros
- Medical Oncology Service, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Elena Élez
- Medical Oncology Service, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Josep Tabernero
- Medical Oncology Service, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- CIBERONC, Madrid, Spain
| | - Omer Aziz
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Colorectal and Peritoneal Oncology Centre, The Christie NHSFT, Manchester, United Kingdom
| | - Marcello Deraco
- Peritoneal Surfaces Malignance Unit, Fondazione IRCCS Instituto Nazionale dei Tumori, Milan, Italy
| | - Héctor G Palmer
- Translational Program, Stem Cells and Cancer Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- CIBERONC, Madrid, Spain
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Sangoi AR, Tsai H, Harik L, Mahlow J, Tretiakova M, Williamson SR, Hirsch MS. Vascular, adipose tissue, and/or calyceal invasion in clear cell tubulopapillary renal cell tumour: potentially problematic diagnostic scenarios. Histopathology 2024; 84:1167-1177. [PMID: 38422612 DOI: 10.1111/his.15166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 03/02/2024]
Abstract
AIMS The 2022 WHO classification for kidney tumours recently downgraded clear cell tubulopapillary (also known as clear cell papillary) renal cell carcinoma (RCC) to a benign neoplasm (i.e. clear cell tubulopapillary renal cell tumour) based on the overwhelmingly banal nature of this neoplasm. However, it has been recognized that some clear cell tubulopapillary renal cell tumours demonstrate vascular, adipose or pelvicalyceal invasion, raising the possibility of more aggressive behaviour. The goal of this study was to determine if these 'high stage' features have an effect on tumour prognosis, warranting a carcinoma designation. METHODS AND RESULTS After excluding cases with tissue artefact (i.e. prior core biopsy track changes) and other RCC subtypes with next-generation sequencing, nine clear cell tubulopapillary renal cell tumours with these so-called 'high stage' features, and otherwise classic morphologic and immunophenotypic findings, including low-grade cytology and 'cup-like' CA9 expression, were evaluated. Median tumour size was 2.2 cm with a range of 0.8 to 6.7 cm. Eight cases (89%) demonstrated perinephric or hilar adipose tissue invasion, although most of these cases showed a bulging (in contrast to an infiltrative) growth pattern. One case demonstrated renal vascular invasion in addition to hilar adipose tissue invasion, and one case demonstrated extension into the pelvicalyceal system. There were no recurrences or evidence of metastatic disease. CONCLUSION These overall findings continue to support the benign designation for clear cell tubulopapillary renal cell tumours, despite morphologic features that might raise the possibility of a 'higher stage' neoplasm.
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Affiliation(s)
- Ankur R Sangoi
- Department of Pathology, Stanford Medical Center, Stanford, CA, USA
| | - Harrison Tsai
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Advanced Molecular Diagnostics, Brigham and Womens Hospital, Boston, MA, USA
| | - Lara Harik
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Jonathan Mahlow
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Maria Tretiakova
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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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 2024; 19:732-748. [PMID: 38154514 DOI: 10.1016/j.jtho.2023.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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5
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Siegmund SE, Al-Obaidy KI, Tsai HK, Idrees MT, Akgul M, Acosta AM, Hirsch MS. Concordance of MTOR Pathway Mutations and the Diagnosis of Renal Low-Grade Oncocytic Tumor (LOT). Int J Surg Pathol 2024; 32:316-330. [PMID: 37357748 DOI: 10.1177/10668969231178032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
The differential diagnosis for oncocytic renal tumors spans the spectrum from benign entities to more aggressive renal cell carcinomas (RCC). Recent work has characterized a provisional renal oncocytic neoplasm, namely the low-grade oncocytic tumor (LOT), which demonstrates overlapping morphologic features with oncocytoma and chromophobe RCC, but also has a unique immunoprofile (ie, diffusely positive for KRT7, negative for KIT) and a high rate (80% to 100%) of mTOR pathway gene alterations. Given the diagnostic overlap among oncocytic tumors, we looked for concordance between mTOR pathway mutations and LOT. Thirty low-grade renal oncocytic neoplasms underwent histologic review and immunohistochemistry for KRT7 and KIT. Tumors were classified as "determinate" (eg, LOT) for tumors with solid, nested or vaguely tubular growth and diffuse KRT7 staining and negative KIT, or "indeterminate" if the morphology and/or immunostains did not fully support a definitive LOT diagnosis. Next-generation sequencing was performed without any knowledge of the diagnoses, and identified mTOR pathway mutations in 80% (12/15) of the determinate tumors, compared with 7% (1/15) in the indeterminate group. One determinate tumor was reclassified as papillary RCC (MTOR mutation negative) and 6 indeterminate tumors were confirmed to be oncocytoma (N = 4), clear cell RCC or papillary RCC with reverse polarity, respectively. Overall, integration of morphology, immunohistochemistry, and molecular data enabled a final definitive diagnosis for 70% of tumors (21 of the total 30), with a high concordance (93%) for LOT specifically in the determinate group; the remaining 9 tumors (30%) were classified as renal oncocytic neoplasm, not otherwise specified.
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Affiliation(s)
- Stephanie E Siegmund
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Khaleel I Al-Obaidy
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Harrison K Tsai
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Boston, MA, USA
| | - Muhammad T Idrees
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Mahmut Akgul
- Department of Pathology, Albany Medical Center, Albany, NY, USA
| | - Andres M Acosta
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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6
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Collins K, Acosta AM, Siegmund SE, Cheng L, Hirsch MS, Idrees MT. Genetic Profiling Uncovers Genome-Wide Loss of Heterozygosity and Provides Insight into Mechanisms of Sarcomatoid Transformation in Chromophobe Renal Cell Carcinoma. Mod Pathol 2024; 37:100396. [PMID: 38043790 DOI: 10.1016/j.modpat.2023.100396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 11/07/2023] [Accepted: 11/26/2023] [Indexed: 12/05/2023]
Abstract
Sarcomatoid transformation occurs in ∼8% of chromophobe renal cell carcinoma (chRCC) and is associated with aggressive clinical behavior. In recent years, several studies have identified genomic, transcriptomic, and epigenomic correlates of aggressive behavior in chRCC; however, the molecular mechanisms associated with sarcomatoid transformation remain incompletely understood. In this study, we analyzed paired conventional and sarcomatoid histologic components of individual chRCC to elucidate the genomic alterations that underlie sarcomatoid transformation in this tumor type. Massively parallel sequencing was performed on paired (conventional and sarcomatoid) components from 8 chRCCs. All cases harbored TP53 variants (87.5% showing TP53 variants in both components and 12.5% only in the sarcomatoid component). Intratumor comparisons revealed that TP53 variants were concordant in 71% and discordant in 29% of cases. Additional recurrent single-nucleotide variants were found in RB1 (37.5% of cases) and PTEN (25% of cases), with the remaining single-nucleotide variants detected in these tumors (PBRM1, NF1, and ASXL1) being nonrecurrent. Copy number variant analysis showed the characteristic pattern of chromosomal losses associated with chRCC (1, 2, 6, 10, 13, 17, and 21) in the conventional histologic components only. Interestingly, the sarcomatoid components of these tumors demonstrated widespread loss of heterozygosity but lacked the above chromosomal losses, likely as a consequence of whole-genome duplication/imbalanced chromosomal duplication events. Overall, the findings suggest that TP53 variants followed by whole-genome duplication/imbalanced chromosomal duplication events underlie sarcomatoid transformation in chRCC.
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Affiliation(s)
- Katrina Collins
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana.
| | - Andres M Acosta
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Stephanie E Siegmund
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Liang Cheng
- Department of Pathology, Warren Alpert Medical School of Brown University, Lifespan Academic Medical Center, Providence, Rhode Island
| | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Muhammad T Idrees
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
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7
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Frei AL, Oberson R, Baumann E, Perren A, Grobholz R, Lugli A, Dawson H, Abbet C, Lertxundi I, Reinhard S, Mookhoek A, Feichtinger J, Sarro R, Gadient G, Dommann-Scherrer C, Barizzi J, Berezowska S, Glatz K, Dertinger S, Banz Y, Schoenegg R, Rubbia-Brandt L, Fleischmann A, Saile G, Mainil-Varlet P, Biral R, Giudici L, Soltermann A, Chaubert AB, Stadlmann S, Diebold J, Egervari K, Bénière C, Saro F, Janowczyk A, Zlobec I. Pathologist Computer-Aided Diagnostic Scoring of Tumor Cell Fraction: A Swiss National Study. Mod Pathol 2023; 36:100335. [PMID: 37742926 DOI: 10.1016/j.modpat.2023.100335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/25/2023] [Accepted: 09/15/2023] [Indexed: 09/26/2023]
Abstract
Tumor cell fraction (TCF) estimation is a common clinical task with well-established large interobserver variability. It thus provides an ideal test bed to evaluate potential impacts of employing a tumor cell fraction computer-aided diagnostic (TCFCAD) tool to support pathologists' evaluation. During a National Slide Seminar event, pathologists (n = 69) were asked to visually estimate TCF in 10 regions of interest (ROIs) from hematoxylin and eosin colorectal cancer images intentionally curated for diverse tissue compositions, cellularity, and stain intensities. Next, they re-evaluated the same ROIs while being provided a TCFCAD-created overlay highlighting predicted tumor vs nontumor cells, together with the corresponding TCF percentage. Participants also reported confidence levels in their assessments using a 5-tier scale, indicating no confidence to high confidence, respectively. The TCF ground truth (GT) was defined by manual cell-counting by experts. When assisted, interobserver variability significantly decreased, showing estimates converging to the GT. This improvement remained even when TCFCAD predictions deviated slightly from the GT. The standard deviation (SD) of the estimated TCF to the GT across ROIs was 9.9% vs 5.8% with TCFCAD (P < .0001). The intraclass correlation coefficient increased from 0.8 to 0.93 (95% CI, 0.65-0.93 vs 0.86-0.98), and pathologists stated feeling more confident when aided (3.67 ± 0.81 vs 4.17 ± 0.82 with the computer-aided diagnostic [CAD] tool). TCFCAD estimation support demonstrated improved scoring accuracy, interpathologist agreement, and scoring confidence. Interestingly, pathologists also expressed more willingness to use such a CAD tool at the end of the survey, highlighting the importance of training/education to increase adoption of CAD systems.
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Affiliation(s)
- Ana Leni Frei
- Institute for Tissue Medicine and Pathology, University of Bern, Bern, Switzerland.
| | - Raphaël Oberson
- Institute for Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
| | - Elias Baumann
- Institute for Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
| | - Aurel Perren
- Institute for Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
| | - Rainer Grobholz
- Medical Faculty University of Zurich, Institute of Pathology, Cantonal Hospital Aarau, Aarau, Switzerland
| | - Alessandro Lugli
- Institute for Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
| | - Heather Dawson
- Institute for Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
| | - Christian Abbet
- Signal Processing Laboratory 5, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ibai Lertxundi
- Institute for Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
| | - Stefan Reinhard
- Institute for Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
| | - Aart Mookhoek
- Institute for Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
| | | | - Rossella Sarro
- Istituto Cantonale di Patologia, Ente ospedaliero cantonale (EOC), Locarno, Switzerland
| | | | | | - Jessica Barizzi
- Istituto Cantonale di Patologia, Ente ospedaliero cantonale (EOC), Locarno, Switzerland
| | - Sabina Berezowska
- Institute of Pathology, Lausanne University Hospital, Lausanne, Switzerland
| | - Katharina Glatz
- Institut of Pathology, University Hospital Basel, Basel, Switzerland
| | - Susanne Dertinger
- Institute of Pathology, Landeskrankenhaus Feldkirch, Feldkirch, Austria
| | - Yara Banz
- Institute for Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
| | - Rene Schoenegg
- Institute of Pathology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Laura Rubbia-Brandt
- Department of Pathology and Immunology, Geneva University Hospital, Genève, Switzerland
| | - Achim Fleischmann
- Institute of Pathology, Cantonal Hospital Thurgau, Münsterlingen, Switzerland
| | | | | | | | - Luca Giudici
- Istituto Cantonale di Patologia, Ente ospedaliero cantonale (EOC), Locarno, Switzerland
| | | | - Audrey Baur Chaubert
- FMH Pathology, Pathology Department of SYNLAB Switzerland SA, Lausanne, Switzerland
| | - Sylvia Stadlmann
- Institute of Pathology, Cantonal Hospital Baden, Baden, Switzerland
| | - Joachim Diebold
- Institute of Pathology, Cantonal Hospital Luzern, Luzern, Switzerland
| | - Kristof Egervari
- Department of Pathology and Immunology, Geneva University Hospital, Genève, Switzerland
| | | | - Francesca Saro
- Institute of Pathology and Molecular Pathology, University Hospital Zürich, Zürich, Switzerland
| | - Andrew Janowczyk
- Department of Biomedical Engineering, Emory University, Atlanta, Georgia; Department of Oncology, Division of Precision Oncology, University Hospital of Geneva, Geneva, Switzerland; Department of Clinical Pathology, Division of Clinical Pathology, University Hospital of Geneva, Geneva, Switzerland
| | - Inti Zlobec
- Institute for Tissue Medicine and Pathology, University of Bern, Bern, Switzerland.
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Siegmund S, Ricci C, Kao CS, Sangoi AR, Mohanty S, Fletcher CDM, Colecchia M, Acosta AM. Germline APC Alterations May Predispose to Testicular Sex Cord-Stromal Tumors. Am J Surg Pathol 2023; 47:1432-1437. [PMID: 37811860 DOI: 10.1097/pas.0000000000002132] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Sertoli cell tumor is a type of testicular sex cord-stromal tumor (TSCST) typically driven by gain-of-function CTNNB1 variants. Recently, molecular studies have identified TSCSTs (including Sertoli cell tumors) with loss-of-function APC variants, raising the possibility that germline APC alterations may predispose to TSCSTs. In this study, we evaluated 4 TSCSTs from 4 individual patients, including 3 APC -mutant neoplasms identified in prior studies (1 in a patient with familial adenomatous polyposis [FAP] and 2 in patients with unknown syndromic status) and 1 tumor of unknown mutational status diagnosed in a patient with known FAP. Three neoplasms were typical Sertoli cell tumors, and 1 was a malignant unclassified TSCT. All neoplasms exhibited diffuse nuclear beta-catenin expression. Non-neoplastic tissue could be obtained for DNA sequencing in the 3 Sertoli cell tumors. Comparative assessment of non-neoplastic and lesional tissue in these cases suggested that germline APC variants with subsequent inactivation of the gene (loss of heterozygosity) were the likely oncogenic driver of these Sertoli cell tumors. In the malignant unclassified TSCSTs, APC inactivation was also interpreted as the most likely driver event, and the germline origin of the variant was inferred using a recently published method. The results of this study suggest that pathogenic germline APC alterations (eg, FAP and variants thereof) may predispose to TSCSTs.
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Affiliation(s)
- Stephanie Siegmund
- Department of Pathology of Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Costantino Ricci
- Department of Medical and Surgical Sciences (DIMEC), Maggiore Hospital-AUSL Bologna, University of Bologna, Bologna
| | - Chia-Sui Kao
- Department of Pathology, Stanford University, Stanford, CA
| | - Ankur R Sangoi
- Department of Pathology, Stanford University, Stanford, CA
| | - Sambit Mohanty
- Department of Pathology, CORE Diagnostics and Advanced Medical Research Institute, Gurgaon, Haryana, India
| | | | - Maurizio Colecchia
- Department of Pathology, Vita-Salute San Raffaele University, Milan, Lombardy, Italy
| | - Andres M Acosta
- Department of Pathology of Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Department of Pathology, Indiana University, Indianapolis, IN
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9
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Oh JH, Sung CO, Kim HD, Chun SM, Kim J. BRCA-mutated gastric adenocarcinomas are associated with chromosomal instability and responsiveness to platinum-based chemotherapy. J Pathol Transl Med 2023; 57:323-331. [PMID: 37981726 PMCID: PMC10660362 DOI: 10.4132/jptm.2023.10.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/06/2023] [Accepted: 10/22/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND Homologous recombination defect is an important biomarker of chemotherapy in certain tumor types, and the presence of pathogenic or likely pathogenic mutations involving BRCA1 or BRCA2 (p-BRCA) mutations is the most well-established marker for the homologous recombination defect. Gastric cancer, one of the most prevalent tumor types in Asia, also harbors p-BRCA mutations. METHODS To investigate the clinical significance of p-BRCA mutations, we analyzed 366 gastric cancer cases through next-generation sequencing. We determined the zygosity of p-BRCA mutations based on the calculated tumor purity through variant allelic fraction patterns and investigated whether the presence of p-BRCA mutations is associated with platinum-based chemotherapy and a certain molecular subtype. RESULTS Biallelic p-BRCA mutation was associated with better response to platinum-based chemotherapy than heterozygous p-BRCA mutation or wild type BRCA genes. The biallelic p-BRCA mutations was observed only in the chromosomal instability subtype, while all p-BRCA mutations were heterozygous in microsatellite instability subtype. CONCLUSIONS In conclusion, patients with gastric cancer harboring biallelic p-BRCA mutations were associated with a good initial response to platinum-based chemotherapy and those tumors were exclusively chromosomal instability subtype. Further investigation for potential association with homologous recombination defect is warranted.
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Affiliation(s)
- Ji Hyun Oh
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Chang Ohk Sung
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hyung-Don Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sung-Min Chun
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Asan Center for Cancer Genome Discovery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jihun Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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10
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Dong F, Davies KD. Mutational Signatures in Cancer: Laboratory Considerations and Emerging Applications. J Mol Diagn 2023; 25:790-795. [PMID: 37633594 DOI: 10.1016/j.jmoldx.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/29/2023] [Accepted: 08/14/2023] [Indexed: 08/28/2023] Open
Abstract
Patterns of somatic mutations have emerged from the broad sequencing of human cancer genomes. These mutational signatures reflect mechanisms of mutagenesis and DNA repair defects and represent an emerging class of cancer biomarkers. The appropriate interpretation of mutational signatures from sequencing assays holds implications in the reporting of molecular diagnostic results for patients with cancer. This brief review describes the scientific principles, laboratory considerations, and emerging clinical applications of mutational signature analysis from clinical cancer genomes.
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Affiliation(s)
- Fei Dong
- Department of Pathology, Stanford University School of Medicine, Stanford, California.
| | - Kurtis D Davies
- Emerging and Evolving Biomarker Content Committee, A Working Group of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Colorado-Anschutz Medical Campus, Aurora, Colorado
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11
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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] [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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12
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Bauer AH, Basta DW, Hornick JL, Dong F. Loss of function SMAD4 nonstop mutations in human cancer. Histopathology 2023; 82:1098-1104. [PMID: 36740808 DOI: 10.1111/his.14880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/18/2023] [Accepted: 02/02/2023] [Indexed: 02/07/2023]
Abstract
BACKGROUND SMAD4 is a tumour suppressor gene that is mutated in a variety of cancers. SMAD4 nonstop mutations, which convert stop codons to sense codons that extend transcription, have been identified in genomic databases but have not been characterised in human pathology samples. The frequency of SMAD4 nonstop mutations and the consequences of nonstop mutations on SMAD4 protein expression are unknown. METHODS We retrospectively analysed our cancer sequencing database of 38,002 tumour specimens and evaluated the spectrum of SMAD4 mutations. SMAD4 protein expression was evaluated by immunohistochemistry in tumours with SMAD4 nonstop mutations. RESULTS In total, 1956 SMAD4 mutations were identified in 1822 tumours. SMAD4 mutations were most common in tumours of the gastrointestinal tract and included nonsense variants (n = 344), frameshift indels (n = 258), splice site variants (n = 104), and missense variants at codon R361 (n = 245). In a subset of cases with immunohistochemistry, SMAD4 expression was lost in 23 of 25 tumours (92%) with protein truncating variants and in 7 of 27 tumours (26%) with missense variants. Four cases harboured SMAD4 nonstop mutations. SMAD4 nonstop mutations were identified in two pancreatic adenocarcinomas, one colonic adenocarcinoma, and one non-small cell lung carcinoma. Immunohistochemistry demonstrated loss of SMAD4 protein expression in each of the four tumours with SMAD4 nonstop mutations. CONCLUSION SMAD4 nonstop mutations are associated with loss of SMAD4 protein expression in multiple tumour types. SMAD4 nonstop mutations should be clinically interpreted as pathogenic loss of function alterations when identified in cancer sequencing panels.
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Affiliation(s)
- Anna H Bauer
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,University of Missouri School of Medicine, Columbia, MO, USA
| | - David W Basta
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Fei Dong
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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13
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Clinicopathologic and molecular spectrum of testicular sex cord-stromal tumors not amenable to specific histopathologic subclassification. Mod Pathol 2022; 35:1944-1954. [PMID: 36180576 DOI: 10.1038/s41379-022-01155-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 12/24/2022]
Abstract
A subset of testicular sex cord-stromal tumors (SCST), which includes neoplasms with mixed histology, cannot be classified into a specific histologic subtype. This study evaluated the clinicopathologic, immunophenotypic and molecular features of 26 SCST not amenable to specific classification by expert uropathologists. Median age at diagnosis was 43 years and median tumor size was 2.4 cm. Follow-up information was available for 18 (69%) patients, with evidence of an aggressive clinical course in 6 patients (4 alive with disease, 2 dead of disease 3 months and 6 months after orchiectomy). Microscopically, SCST not amenable to specific classification demonstrated monophasic epithelioid (9/26, 35%), monophasic spindle cell (5/26, 19%), and biphasic or mixed histology (12/26, 46%). One or more aggressive histopathologic features were seen in 11 cases. DNA sequencing was successful in 22 tumors. Pathogenic CTNNB1 and APC alterations were seen in 7 (33%) and 2 (10%) cases, respectively, with additional variants (e.g., CDKN2A, RB1, TP53, BRCA2) being identified in individual cases. Combined evaluation of morphology, sequencing data and beta-catenin immunohistochemistry resulted in reclassification of 6 (23%) tumors as Sertoli cell tumor, not otherwise specified. This was supported by comparing the methylation profiles of a subset of these tumors and those of typical Sertoli cell tumors. Additionally, a subset of 5 neoplasms (19%) with spindle cell or biphasic histology and SMA expression was characterized by hyperdiploid genomes with recurrent chromosomal gains and absence of driver mutations, possibly representing a distinct tumor type. The SCST that remained not amenable to specific histologic classification (15/26, 58%) were enriched for aggressive histologic features and malignant clinical behavior. In conclusion, this study demonstrated that a subset of testicular SCST that were originally not amenable to specific classification could be reclassified by combined evaluation of morphology, immunohistochemistry and molecular data.
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