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Nilforoushan N, Liu L, Cheang G, Sui AC, Andersen J, Finkelman BS, Liu Y, Nasseri-Nik N, Vang R, Ronnett BM, Song W, Xing D. Mucinous Tumor Coexisting With Mesonephric-like Proliferation/Tumor in the Ovary: A Novel Association. Am J Surg Pathol 2022; 46:1095-1105. [PMID: 35405716 PMCID: PMC9296548 DOI: 10.1097/pas.0000000000001903] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The literature indicates that mesonephric carcinoma (MC) and mesonephric-like adenocarcinoma (MLA) typically lack mucinous and squamous features/differentiation. We report 4 cases of ovarian mucinous tumors (1 mucinous cystadenofibroma and 3 mucinous borderline tumors/atypical proliferative mucinous tumors [MBT/APMT]) co-existing with mesonephric-like lesions which were highlighted by Gata3 and Pax8 expression. All cases contained benign mesonephric-like proliferations (MLP) which focally displayed gastrointestinal-type mucinous metaplasia/differentiation and some were intimately admixed with mucinous glands associated with the mucinous tumor. Metaplastic mucinous epithelium retained expression of Gata3 and Pax8 in some areas while 1 mucinous cystadenofibroma and 1 MBT/APMT were focally positive for Pax8. Along with these mesonephric components, case 1 exhibited features of mesonephric hyperplasia and in 2 cases, 3 and 4, MLA was identified. In case 4, a KRAS c.35G>T (p.Gly12Val) somatic mutation was detected in both the MBT/APMT and the MLA, indicating a clonal origin. This same mutation was also detected in the benign MLP, indicating that it was likely an early genetic event. A CTNNB1 c.98C>T (p.Ser33Phe) somatic mutation, FGFR2 amplification, and CDKN2A/p16 deletion were only detected in the MLA but not in the MBT/APMT. Our result provides evidence to demonstrate the clonal relationship between these morphologically distinct components. Although speculative, we postulate that benign MLPs may give rise to lineage-specific mucinous and mesonephric-like lesions and propose that the MLPs are a new possible origin of some ovarian mucinous tumors. Whether these MLPs arise through transdifferentiation of Müllerian tissue or represent true mesonephric remnants, however, remains largely unknown.
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Affiliation(s)
- Neshat Nilforoushan
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD
| | - Lian Liu
- Department of Pathology, Sky Ridge Medical Center/Forward Pathology Solutions, Denver Division, Lone Tree, CO
| | - Gloria Cheang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Amy C. Sui
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - John Andersen
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD
| | - Brian S. Finkelman
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD
| | - Ying Liu
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD
| | | | - Russell Vang
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD
- Department of Gynecology and Obstetrics, The Johns Hopkins Medical Institutions, Baltimore, MD
| | - Brigitte M. Ronnett
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD
- Department of Gynecology and Obstetrics, The Johns Hopkins Medical Institutions, Baltimore, MD
| | - Wei Song
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Deyin Xing
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD
- Department of Gynecology and Obstetrics, The Johns Hopkins Medical Institutions, Baltimore, MD
- Department of Oncology, The Johns Hopkins Medical Institutions, Baltimore, MD
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Park HJ, Baek I, Cheang G, Solomon JP, Song W. Comparison of RNA-Based Next-Generation Sequencing Assays for the Detection of NTRK Gene Fusions. J Mol Diagn 2021; 23:1443-1451. [PMID: 34756276 DOI: 10.1016/j.jmoldx.2021.07.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/28/2021] [Accepted: 07/16/2021] [Indexed: 12/29/2022] Open
Abstract
Recently, the US Food and Drug Administration approved several targeted therapies directed against oncogenic fusions. One of the most effective such targeted therapies is Vitrakvi (larotrectinib), highly specific oral tropomyosin receptor kinase inhibitor indicated for the treatment of patients with any solid tumor harboring a fusion involving one of the neurotrophic receptor tyrosine kinase (NTRK) genes. Although several diagnostic approaches can be used to detect these NTRK fusions, RNA-based next-generation sequencing remains one of the most sensitive methods, as it can directly detect the transcribed end product of gene fusion at the mRNA level. In this study, performance characteristics of three RNA-based next-generation sequencing assays with distinct mechanisms and chemistries were investigated: anchored multiplex PCR, amplicon-based multiplex PCR, and hybrid capture-based enrichment method. Analytical sensitivity analysis shows that the amplicon-based multiplex PCR method has the lowest limit of detection. However, both hybrid-capture and anchored multiplex PCR methods can detect NTRK fusions with uncommon or novel fusion partners, which is challenging for the amplicon-based multiplex method. As for clinical sensitivity, all three methods were highly concordant in detecting NTRK fusions in patient samples. Additionally, they all presented equivalent high-level performance in specificity, suggesting that all three platforms can detect NTRK fusions in clinical samples with similar performance characteristics.
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Affiliation(s)
- Hyeon J Park
- Department of Laboratory Medicine and Pathology, Weill Cornell Medicine, New York, New York
| | - Inji Baek
- Department of Laboratory Medicine and Pathology, Weill Cornell Medicine, New York, New York
| | - Gloria Cheang
- Department of Laboratory Medicine and Pathology, Weill Cornell Medicine, New York, New York
| | - James P Solomon
- Department of Laboratory Medicine and Pathology, Weill Cornell Medicine, New York, New York
| | - Wei Song
- Department of Laboratory Medicine and Pathology, Weill Cornell Medicine, New York, New York.
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Sboner A, Sternberg C, Mosquera JM, Song W, Kluk M, Tam W, Rennert H, Pisapia D, Catalano J, Cheang G, Wilkes D, Bulaon D, Martin ML, Sigaras A, Eng K, Bareja R, Kim R, Loda M, Elemento O. Abstract IA33: Precision medicine at Weill Cornell Medicine/New York Presbyterian: Breaking silos, integrating resources, being inclusive. Cancer Epidemiol Biomarkers Prev 2020. [DOI: 10.1158/1538-7755.disp19-ia33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Genomic testing with next-generation sequencing (NGS) has become a pillar of precision medicine, whose aim is to identify the genomic alterations of a patient’s tumor and provide guidelines to clinicians for optimal treatment. Clinical testing is typically performed with targeted panels interrogating a limited set of genes, selected based on our best scientific knowledge on their diagnostic or prognostic role. Despite more recent efforts to be more inclusive, most genomic databases have a limited representation of non-European populations, resulting in a biased selection of those genes, and the potential exclusion of under-represented groups from the benefit of precision medicine. At the Englander Institute for Precision Medicine (EIPM), we developed a whole-exome sequencing (WES) clinical test, EXaCT-1, which interrogates about 21,000 protein coding genes for single-nucleotide variants, indels, and copy number. EXaCT-1 enables an unbiased view of the genomic landscape of a patient’s tumor and allows for the collection of data to investigate genomic diversity. We also tackled one of the major barriers of precision medicine: the infrastructure to execute clinical sequencing. From ordering a test, collecting and processing samples, to the analysis and review of the data and generation of reports, several systems, procedures, and expertise are involved, and their effective coordination is a key component for the timely delivery of results. We have built a framework supporting the entire process of clinical genomic testing: a Laboratory Information Management System (LIMS) helps the clinical lab to receive orders, acquire and process specimens, and seamlessly communicate with the sequencers and the computational pipelines. Molecular pathologists use NGSReporter, a secure web application, to review the data and sign-out reports. NGSReporter integrates the results of a test with our Precision Medicine Knowledge Base (PMKB – https://pmkb.weill.cornell.edu), which classifies variants based on their relevance to clinical management and provides standardized interpretations. Reports are sent to the electronic health record (EHR) as PDFs as well as discrete entities, enabling queries such as: “Which Hispanic patients with KRAS mutations are diabetic?” Sharing de-identified data is also a key aspect of precision medicine. To this end, we provide our investigators and collaborators with a protected cBioPortal instance that, in addition to publicly available datasets, includes internal data, thus enabling the exploration of hypotheses about the role of alterations across different cohorts and clinical features. Being in the center of New York City has the added benefit of an ethnically diverse patient population. Finding the “right treatment for the right person and at the right time” requires a concerted effort of multiple partners. The EIPM infrastructure facilitates these efforts, with the goal of making precision medicine accessible to everyone.
Citation Format: Andrea Sboner, Cora Sternberg, Juan Miguel Mosquera, Wei Song, Michael Kluk, Wayne Tam, Hanna Rennert, David Pisapia, Jeffrey Catalano, Gloria Cheang, David Wilkes, Danielle Bulaon, M. Laura Martin, Alexandros Sigaras, Kenneth Eng, Rohan Bareja, Rob Kim, Massimo Loda, Olivier Elemento. Precision medicine at Weill Cornell Medicine/New York Presbyterian: Breaking silos, integrating resources, being inclusive [abstract]. In: Proceedings of the Twelfth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2019 Sep 20-23; San Francisco, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl_2):Abstract nr IA33.
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Affiliation(s)
| | | | | | - Wei Song
- Weill Cornell Medicine, New York, NY
| | | | - Wayne Tam
- Weill Cornell Medicine, New York, NY
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- Weill Cornell Medicine, New York, NY
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Xing D, Liu Y, Park HJ, Baek I, Tran H, Cheang G, Novo J, Dillon J, Matoso A, Farmer E, Cheng MA, Tsai YC, Lombardo K, Conner MG, Vang R, Hung CF, Wu TC, Song W. Recurrent genetic alterations and biomarker expression in primary and metastatic squamous cell carcinomas of the vulva. Hum Pathol 2019; 92:67-80. [PMID: 31437519 DOI: 10.1016/j.humpath.2019.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/30/2019] [Accepted: 08/07/2019] [Indexed: 12/26/2022]
Abstract
Using a comprehensive next-generation sequencing pipeline (143 genes), Oncomine Comprehensive v.2, we analyzed genetic alterations on a set of vulvar squamous cell carcinomas (SCCs) with emphasis on the primary and metastatic samples from the same patient, to identify amenable therapeutic targets. Clinicopathologic features were reported and genomic DNA was extracted from 42 paraffin-embedded tumor tissues of 32 cases. PD-L1 expression was evaluated in 20 tumor tissues (10 cases with paired primary and metastatic tumors). Fifteen (88%) of 17 successfully analyzed HPV-unrelated SCCs harbored TP53 mutations. 2 different TP53 mutations had been detected in the same tumor in 4 of 15 cases. Other recurrent genetic alterations in this group of tumors included CDKN2a mutations (41%), HRAS mutations (12%), NOTCH1 mutations (12%) and BIRC3 (11q22.1-22.2) amplification (12%). Six HPV-related tumors harbored PIK3CA, BAP1, PTEN, KDR, CTNNB1, and BRCA2 mutations, of which, one case also contained TP53 mutation. Six cases showed identical mutations in paired primary site and distant metastatic location and four cases displayed different mutational profiles. PD-L1 expression was seen in 6 of 10 primary tumors and all 6 paired cases showed discordant PD-L1 expression in the primary and metastatic sites. Our results further confirmed the genetic alterations that are amenable to targeted therapy, offering the potential for individualized management strategies for the treatment of these aggressive tumors with different etiology. Discordant PD-L1 expression in the primary and metastatic vulvar SCCs highlights the importance of evaluation of PD-L1 expression in different locations to avoid false negative information provided for immunotherapy.
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Affiliation(s)
- Deyin Xing
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore 21231, MD; Department of Oncology, The Johns Hopkins Medical Institutions, Baltimore 21231, MD.
| | - Yuehua Liu
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore 21231, MD
| | - Hyeon Jin Park
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York 10065, NY
| | - Inji Baek
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York 10065, NY
| | - Hung Tran
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York 10065, NY
| | - Gloria Cheang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York 10065, NY
| | - Jorge Novo
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore 21231, MD
| | - Jessica Dillon
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore 21231, MD
| | - Andres Matoso
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore 21231, MD
| | - Emily Farmer
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore 21231, MD
| | - Max A Cheng
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore 21231, MD
| | - Ya-Chea Tsai
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore 21231, MD
| | - Kara Lombardo
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore 21231, MD
| | - Michael G Conner
- Department of Pathology, The University of Alabama at Birmingham, Birmingham 35233, AL
| | - Russell Vang
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore 21231, MD; Department of Gynecology and Obstetrics, The Johns Hopkins Medical Institutions, Baltimore 21231, MD
| | - Chien-Fu Hung
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore 21231, MD; Department of Oncology, The Johns Hopkins Medical Institutions, Baltimore 21231, MD
| | - Tzyy-Choou Wu
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore 21231, MD; Department of Oncology, The Johns Hopkins Medical Institutions, Baltimore 21231, MD; Department of Gynecology and Obstetrics, The Johns Hopkins Medical Institutions, Baltimore 21231, MD
| | - Wei Song
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York 10065, NY.
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Catalano J, Pancirer D, Tran H, Cheang G, Li Y, Merzier E. 346 Clinical Operations in the Molecular Laboratory: A Cross-Functional Team Approach. Am J Clin Pathol 2018. [DOI: 10.1093/ajcp/aqx128.345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Tran H, Pancirer D, Cheang G, Li Y, Merzier E, Catalano J. 345 Evaluation and Validation of an Automated Platform for Ribonucleic Acid Extraction From Formalin-Fixed Paraffin-Embedded Tissue. Am J Clin Pathol 2018. [DOI: 10.1093/ajcp/aqx127.344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Catalano J, Cheang G, Pancirer D, Merzier E, Li Y, Tran H, Sigaras A. 331 The Development of a Custom LIMS: An Introduction and Guide to Successful Implementation. Am J Clin Pathol 2018. [DOI: 10.1093/ajcp/aqx127.330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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