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Machado I, Damaskou V, Ioannidis E, Jour G, Linos K. Superficial acral calcified chondroid mesenchymal neoplasm harboring an FN1::FGFR2 fusion and review of the literature. J Cutan Pathol 2024; 51:338-344. [PMID: 38328983 PMCID: PMC11001517 DOI: 10.1111/cup.14593] [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: 09/03/2023] [Revised: 12/16/2023] [Accepted: 12/21/2023] [Indexed: 02/09/2024]
Abstract
Calcified chondroid mesenchymal neoplasm is a recently recognized bone and soft tissue entity primarily found in the extremities and the temporomandibular joint. This neoplasm is typically driven by the fusion of the FN1 gene with a kinase. In this case report, we provide a detailed account of a rare superficial calcified chondroid mesenchymal neoplasm located on the left big toe, characterized by an FN1::FGFR2 fusion. The tumor exhibited a peripheral collarette and consisted of large intradermal histiocytoid to epithelioid cells with no mitotic activity. These cells displayed fine chromatin and abundant pale eosinophilic cytoplasm, forming a swirling syncytium. They were interspersed with localized areas of glassy chondromyxoid matrix containing randomly mineralized calcific material and isolated osteoclast-like giant cells. RNA sequencing confirmed the presence of an FN1 (exon 29)::FGFR2 (exon 7) gene fusion. Our report emphasizes the importance for dermatopathologists to consider this entity when evaluating superficial lesions displaying mesenchymal, chondroid, and calcified attributes.
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Affiliation(s)
- Isidro Machado
- Department of Pathology, Instituto Valenciano de Oncología, Patologika Laboratory Hospital Quirón-Salud. Pathology Department, University of Valencia. Cancer CIBER (CIBERONC), Madrid, Spain
| | - Vasileia Damaskou
- 2nd Department of Pathology, National and Kapodistrian University of Athens, School of Medicine, “Attikon” University Hospital, Athens, Greece
| | | | - George Jour
- Department of Pathology and Dermatology, New York School of Medicine, New York, USA
| | - Konstantinos Linos
- Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
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2
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Galbraith K, Serrano J, Shen G, Tran I, Slocum CC, Ketchum C, Abdullaev Z, Turakulov R, Bale T, Ladanyi M, Sukhadia P, Zaidinski M, Mullaney K, DiNapoli S, Liechty BL, Barbaro M, Allen JC, Gardner SL, Wisoff J, Harter D, Hidalgo ET, Golfinos JG, Orringer DA, Aldape K, Benhamida J, Wrzeszczynski KO, Jour G, Snuderl M. Impact of Rare and Multiple Concurrent Gene Fusions on Diagnostic DNA Methylation Classifier in Brain Tumors. Mol Cancer Res 2024; 22:21-28. [PMID: 37870438 PMCID: PMC10942665 DOI: 10.1158/1541-7786.mcr-23-0627] [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: 08/06/2023] [Revised: 10/01/2023] [Accepted: 10/18/2023] [Indexed: 10/24/2023]
Abstract
DNA methylation is an essential molecular assay for central nervous system (CNS) tumor diagnostics. While some fusions define specific brain tumors, others occur across many different diagnoses. We performed a retrospective analysis of 219 primary CNS tumors with whole genome DNA methylation and RNA next-generation sequencing. DNA methylation profiling results were compared with RNAseq detected gene fusions. We detected 105 rare fusions involving 31 driver genes, including 23 fusions previously not implicated in brain tumors. In addition, we identified 6 multi-fusion tumors. Rare fusions and multi-fusion events can impact the diagnostic accuracy of DNA methylation by decreasing confidence in the result, such as BRAF, RAF, or FGFR1 fusions, or result in a complete mismatch, such as NTRK, EWSR1, FGFR, and ALK fusions. IMPLICATIONS DNA methylation signatures need to be interpreted in the context of pathology and discordant results warrant testing for novel and rare gene fusions.
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Affiliation(s)
- Kristyn Galbraith
- Department of Pathology, NYU Langone Health and NYU Grossman School of Medicine, New York, NY, USA
| | - Jonathan Serrano
- Department of Pathology, NYU Langone Health and NYU Grossman School of Medicine, New York, NY, USA
| | - Guomiao Shen
- Department of Pathology, NYU Langone Health and NYU Grossman School of Medicine, New York, NY, USA
| | - Ivy Tran
- Department of Pathology, NYU Langone Health and NYU Grossman School of Medicine, New York, NY, USA
| | - Cheyanne C. Slocum
- Department of Pathology & Laboratory Medicine, Weill Cornell Medical College - New York Presbyterian Hospital, New York, NY, USA
| | - Courtney Ketchum
- Department of Pathology & Laboratory Medicine, National Institute of Health-Bethesda, Maryland, USA
| | - Zied Abdullaev
- Department of Pathology & Laboratory Medicine, National Institute of Health-Bethesda, Maryland, USA
| | - Rust Turakulov
- Department of Pathology & Laboratory Medicine, National Institute of Health-Bethesda, Maryland, USA
| | - Tejus Bale
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Purvil Sukhadia
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Zaidinski
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kerry Mullaney
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sara DiNapoli
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin L. Liechty
- Department of Pathology & Laboratory Medicine, Weill Cornell Medical College - New York Presbyterian Hospital, New York, NY, USA
| | - Marissa Barbaro
- Department of Neuro-oncology, NYU Langone Health and NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jeffrey C. Allen
- Department of Pediatrics, NYU Langone Health and NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Sharon L. Gardner
- Department of Pediatrics, NYU Langone Health and NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jeffrey Wisoff
- Department of Neurosurgery, NYU Langone Health and NYU Grossman School of Medicine, New York, NY 10016, USA
| | - David Harter
- Department of Neurosurgery, NYU Langone Health and NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Eveline Teresa Hidalgo
- Department of Neurosurgery, NYU Langone Health and NYU Grossman School of Medicine, New York, NY 10016, USA
| | - John G. Golfinos
- Department of Neurosurgery, NYU Langone Health and NYU Grossman School of Medicine, New York, NY 10016, USA
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, New York, NY, USA
| | - Daniel A. Orringer
- Department of Neurosurgery, NYU Langone Health and NYU Grossman School of Medicine, New York, NY 10016, USA
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, New York, NY, USA
| | - Kenneth Aldape
- Department of Pathology & Laboratory Medicine, National Institute of Health-Bethesda, Maryland, USA
| | - Jamal Benhamida
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - George Jour
- Department of Pathology, NYU Langone Health and NYU Grossman School of Medicine, New York, NY, USA
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, New York, NY, USA
| | - Matija Snuderl
- Department of Pathology, NYU Langone Health and NYU Grossman School of Medicine, New York, NY, USA
- Brain and Spine Tumor Center, Laura and Isaac Perlmutter Cancer Center, New York, NY, USA
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3
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Schieffer KM, Moccia A, Bucknor BA, Stonerock E, Jayaraman V, Jenkins H, McKinney A, Koo SC, Mathew MT, Mardis ER, Lee K, Reshmi SC, Cottrell CE. Expanding the Clinical Utility of Targeted RNA Sequencing Panels beyond Gene Fusions to Complex, Intragenic Structural Rearrangements. Cancers (Basel) 2023; 15:4394. [PMID: 37686670 PMCID: PMC10486946 DOI: 10.3390/cancers15174394] [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: 07/31/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Gene fusions are a form of structural rearrangement well established as driver events in pediatric and adult cancers. The identification of such events holds clinical significance in the refinement, prognostication, and provision of treatment in cancer. Structural rearrangements also extend beyond fusions to include intragenic rearrangements, such as internal tandem duplications (ITDs) or exon-level deletions. These intragenic events have been increasingly implicated as cancer-promoting events. However, the detection of intragenic rearrangements may be challenging to resolve bioinformatically with short-read sequencing technologies and therefore may not be routinely assessed in panel-based testing. Within an academic clinical laboratory, over three years, a total of 608 disease-involved samples (522 hematologic malignancy, 86 solid tumors) underwent clinical testing using Anchored Multiplex PCR (AMP)-based RNA sequencing. Hematologic malignancies were evaluated using a custom Pan-Heme 154 gene panel, while solid tumors were assessed using a custom Pan-Solid 115 gene panel. Gene fusions, ITDs, and intragenic deletions were assessed for diagnostic, prognostic, or therapeutic significance. When considering gene fusions alone, we report an overall diagnostic yield of 36% (37% hematologic malignancy, 41% solid tumors). When including intragenic structural rearrangements, the overall diagnostic yield increased to 48% (48% hematologic malignancy, 45% solid tumor). We demonstrate the clinical utility of reporting structural rearrangements, including gene fusions and intragenic structural rearrangements, using an AMP-based RNA sequencing panel.
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Affiliation(s)
- Kathleen M. Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Amanda Moccia
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Brianna A. Bucknor
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Eileen Stonerock
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Vijayakumar Jayaraman
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Heather Jenkins
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Aimee McKinney
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
| | - Selene C. Koo
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pathology and Laboratory Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Mariam T. Mathew
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Elaine R. Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Kristy Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Shalini C. Reshmi
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Catherine E. Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
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4
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Georgantzoglou N, Shen G, Jour G, Linos K. A case of FN1-fused calcified chondroid mesenchymal neoplasm of the hand with novel FGFR3 partner gene. Genes Chromosomes Cancer 2023; 62:237-241. [PMID: 36504176 DOI: 10.1002/gcc.23115] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 12/14/2022] Open
Abstract
Calcified chondroid neoplasms with FN1::FGFR1 or FGFR2 fusions constitute a recently described category of mesenchymal neoplasms mostly encountered in the extremities and temporomandibular joint. Herein, we report a case of FNI1-fused calcified chondroid neoplasm of the hand with a novel FGFR3 fusion partner. The tumor exhibited a multilobulated growth pattern composed of epithelioid cells embedded in abundant stroma with myxoid, chondroid, and fibrous areas and scattered osteoclast-like giant cells. RNA sequencing revealed an in-frame fusion between Exon 31 of FN1 and Exon 3 of FGFR3, which was subsequently confirmed by reverse transcription-polymerase chain reaction. Our findings expand on the spectrum of potential fusion partners in FN1-fused calcified chondroid neoplasms.
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Affiliation(s)
- Natalia Georgantzoglou
- Department of Pathology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Guomiao Shen
- Department of Pathology, New York University, New York, New York, USA
| | - George Jour
- Department of Pathology, New York University, New York, New York, USA
| | - Konstantinos Linos
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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5
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Pei XM, Yeung MHY, Wong ANN, Tsang HF, Yu ACS, Yim AKY, Wong SCC. Targeted Sequencing Approach and Its Clinical Applications for the Molecular Diagnosis of Human Diseases. Cells 2023; 12:493. [PMID: 36766834 PMCID: PMC9913990 DOI: 10.3390/cells12030493] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/19/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The outbreak of COVID-19 has positively impacted the NGS market recently. Targeted sequencing (TS) has become an important routine technique in both clinical and research settings, with advantages including high confidence and accuracy, a reasonable turnaround time, relatively low cost, and fewer data burdens with the level of bioinformatics or computational demand. Since there are no clear consensus guidelines on the wide range of next-generation sequencing (NGS) platforms and techniques, there is a vital need for researchers and clinicians to develop efficient approaches, especially for the molecular diagnosis of diseases in the emergency of the disease and the global pandemic outbreak of COVID-19. In this review, we aim to summarize different methods of TS, demonstrate parameters for TS assay designs, illustrate different TS panels, discuss their limitations, and present the challenges of TS concerning their clinical application for the molecular diagnosis of human diseases.
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Affiliation(s)
- Xiao Meng Pei
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Martin Ho Yin Yeung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Alex Ngai Nick Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Hin Fung Tsang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
- Department of Clinical Laboratory and Pathology, Hong Kong Adventist Hospital, Hong Kong, China
| | - Allen Chi Shing Yu
- Codex Genetics Limited, Unit 212, 2/F., Building 16W, No. 16 Science Park West Avenue, The Hong Kong Science Park, Hong Kong 852, China
| | - Aldrin Kay Yuen Yim
- Codex Genetics Limited, Unit 212, 2/F., Building 16W, No. 16 Science Park West Avenue, The Hong Kong Science Park, Hong Kong 852, China
| | - Sze Chuen Cesar Wong
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, China
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6
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Galbraith K, Vasudevaraja V, Serrano J, Shen G, Tran I, Abdallat N, Wen M, Patel S, Movahed-Ezazi M, Faustin A, Spino-Keeton M, Roberts LG, Maloku E, Drexler SA, Liechty BL, Pisapia D, Krasnozhen-Ratush O, Rosenblum M, Shroff S, Boué DR, Davidson C, Mao Q, Suchi M, North P, Hopp A, Segura A, Jarzembowski JA, Parsons L, Johnson MD, Mobley B, Samore W, McGuone D, Gopal PP, Canoll PD, Horbinski C, Fullmer JM, Farooqi MS, Gokden M, Wadhwani NR, Richardson TE, Umphlett M, Tsankova NM, DeWitt JC, Sen C, Placantonakis DG, Pacione D, Wisoff JH, Teresa Hidalgo E, Harter D, William CM, Cordova C, Kurz SC, Barbaro M, Orringer DA, Karajannis MA, Sulman EP, Gardner SL, Zagzag D, Tsirigos A, Allen JC, Golfinos JG, Snuderl M. Clinical utility of whole-genome DNA methylation profiling as a primary molecular diagnostic assay for central nervous system tumors-A prospective study and guidelines for clinical testing. Neurooncol Adv 2023; 5:vdad076. [PMID: 37476329 PMCID: PMC10355794 DOI: 10.1093/noajnl/vdad076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023] Open
Abstract
Background Central nervous system (CNS) cancer is the 10th leading cause of cancer-associated deaths for adults, but the leading cause in pediatric patients and young adults. The variety and complexity of histologic subtypes can lead to diagnostic errors. DNA methylation is an epigenetic modification that provides a tumor type-specific signature that can be used for diagnosis. Methods We performed a prospective study using DNA methylation analysis as a primary diagnostic method for 1921 brain tumors. All tumors received a pathology diagnosis and profiling by whole genome DNA methylation, followed by next-generation DNA and RNA sequencing. Results were stratified by concordance between DNA methylation and histopathology, establishing diagnostic utility. Results Of the 1602 cases with a World Health Organization histologic diagnosis, DNA methylation identified a diagnostic mismatch in 225 cases (14%), 78 cases (5%) did not classify with any class, and in an additional 110 (7%) cases DNA methylation confirmed the diagnosis and provided prognostic information. Of 319 cases carrying 195 different descriptive histologic diagnoses, DNA methylation provided a definitive diagnosis in 273 (86%) cases, separated them into 55 methylation classes, and changed the grading in 58 (18%) cases. Conclusions DNA methylation analysis is a robust method to diagnose primary CNS tumors, improving diagnostic accuracy, decreasing diagnostic errors and inconclusive diagnoses, and providing prognostic subclassification. This study provides a framework for inclusion of DNA methylation profiling as a primary molecular diagnostic test into professional guidelines for CNS tumors. The benefits include increased diagnostic accuracy, improved patient management, and refinements in clinical trial design.
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Affiliation(s)
- Kristyn Galbraith
- Department of Pathology, NYU Langone Health, New York, Department of Pathology, NYU Langone, New York, USA
| | - Varshini Vasudevaraja
- Department of Pathology, NYU Langone Health, New York, Department of Pathology, NYU Langone, New York, USA
| | - Jonathan Serrano
- Department of Pathology, NYU Langone Health, New York, Department of Pathology, NYU Langone, New York, USA
| | - Guomiao Shen
- Department of Pathology, NYU Langone Health, New York, Department of Pathology, NYU Langone, New York, USA
| | - Ivy Tran
- Department of Pathology, NYU Langone Health, New York, Department of Pathology, NYU Langone, New York, USA
| | - Nancy Abdallat
- Department of Pathology, NYU Langone Health, New York, Department of Pathology, NYU Langone, New York, USA
| | - Mandisa Wen
- Department of Pathology, NYU Langone Health, New York, Department of Pathology, NYU Langone, New York, USA
| | - Seema Patel
- Department of Pathology, NYU Langone Health, New York, Department of Pathology, NYU Langone, New York, USA
| | - Misha Movahed-Ezazi
- Department of Pathology, NYU Langone Health, New York, Department of Pathology, NYU Langone, New York, USA
| | - Arline Faustin
- Department of Pathology, NYU Langone Health, New York, Department of Pathology, NYU Langone, New York, USA
| | - Marissa Spino-Keeton
- Department of Pathology, NYU Langone Health, New York, Department of Pathology, NYU Langone, New York, USA
| | - Leah Geiser Roberts
- Department of Pathology, NYU Langone Health, New York, Department of Pathology, NYU Langone, New York, USA
| | - Ekrem Maloku
- Department of Pathology, NYU Langone Health, New York, Department of Pathology, NYU Langone, New York, USA
| | - Steven A Drexler
- Department of Pathology and Laboratory Medicine, NYU, Mineola, New York, USA
- Current affiliations: Department of Pathology, Mount Sinai South Nassau Hospital, Oceanside, New York, USA
| | - Benjamin L Liechty
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College - New York Presbyterian Hospital, New York, New York, USA
| | - David Pisapia
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College - New York Presbyterian Hospital, New York, New York, USA
| | - Olga Krasnozhen-Ratush
- Department of Pathology and Laboratory Medicine, Baystate Health, Springfield, Massachusetts, USA
| | - Marc Rosenblum
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Seema Shroff
- Department of Pathology and Laboratory Medicine, AdventHealth Orlando, Orlando, Florida, USA
| | - Daniel R Boué
- Department of Pathology and Laboratory Medicine, Nationwide Children’s Hospital, and the Ohio State University, Columbus, Ohio, USA
| | | | - Qinwen Mao
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Mariko Suchi
- Department of Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Paula North
- Department of Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | | | - Annette Segura
- Department of Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jason A Jarzembowski
- Department of Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Lauren Parsons
- Department of Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Mahlon D Johnson
- Department of Pathology, University of Rochester School of Medicine, New York, USA
| | - Bret Mobley
- Department of Pathology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Wesley Samore
- Department of Pathology, Advocate Aurora Health, Chicago, Illinois, USA
| | - Declan McGuone
- Department of Pathology, Yale University School of Medicine, Connecticut, USA
| | - Pallavi P Gopal
- Department of Pathology, Yale University School of Medicine, Connecticut, USA
| | - Peter D Canoll
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, USA
| | - Craig Horbinski
- Departments of Pathology and Neurosurgery, Feinberg School of Medicine, Northwestern University, Illinois, USA
| | - Joseph M Fullmer
- Department of Pathology, Beaumont Hospital, Royal Oak, Michigan, USA
| | - Midhat S Farooqi
- Department of Pathology and Laboratory Medicine, Children’s Mercy Kansas City, Kansas City, Missouri, USA
| | - Murat Gokden
- Department of Pathology, University of Arkansas and Arkansas Children’s Hospital, Little Rock, Arkansas, USA
| | - Nitin R Wadhwani
- Department of Pathology and Laboratory Medicine, Ann and Robert H. Lurie Children’s Hospital of Chicago, Illinois, USA
| | - Timothy E Richardson
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Melissa Umphlett
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nadejda M Tsankova
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - John C DeWitt
- Department of Pathology, University of Vermont Medical Center
| | - Chandra Sen
- Department of Neurosurgery, NYU Langone, New York, New York, USA
| | | | - Donato Pacione
- Department of Neurosurgery, NYU Langone, New York, New York, USA
| | - Jeffrey H Wisoff
- Department of Neurosurgery, NYU Langone, New York, New York, USA
| | | | - David Harter
- Department of Neurosurgery, NYU Langone, New York, New York, USA
| | - Christopher M William
- Department of Pathology, NYU Langone Health, New York, Department of Pathology, NYU Langone, New York, USA
| | - Christine Cordova
- Department of Neuro-oncology, NYU Langone, New York, New York, USA
- Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, OH
| | - Sylvia C Kurz
- Department of Neuro-oncology, NYU Langone, New York, New York, USA
- Department of Interdisciplinary Neuro-Oncology, Comprehensive Cancer Center, University of Tuebingen, Tübingen, Germany
| | - Marissa Barbaro
- Department of Neuro-oncology, NYU Langone, New York, New York, USA
| | | | - Matthias A Karajannis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Erik P Sulman
- Department of Radiation Oncology, NYU Langone, New York, New York, USA
| | | | - David Zagzag
- Department of Pathology, NYU Langone Health, New York, Department of Pathology, NYU Langone, New York, USA
- Department of Neurosurgery, NYU Langone, New York, New York, USA
| | | | - Jeffrey C Allen
- Department of Pediatrics, NYU Langone, New York, New York, USA
| | - John G Golfinos
- Department of Neurosurgery, NYU Langone, New York, New York, USA
| | - Matija Snuderl
- Department of Pathology, NYU Langone Health, New York, Department of Pathology, NYU Langone, New York, USA
- Laura and Isaac Perlmutter Cancer Center, New York, New York, USA
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7
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Vougiouklakis T, Zhu K, Vasudevaraja V, Serrano J, Shen G, Linn RL, Feng X, Chiang S, Barroeta JE, Thomas KM, Schwartz LE, Shukla PS, Malpica A, Oliva E, Cotzia P, DeLair DF, Snuderl M, Jour G. Integrated analysis of ovarian juvenile granulosa cell tumors reveals distinct epigenetic signatures and recurrent TERT rearrangements. Clin Cancer Res 2022; 28:1724-1733. [PMID: 35031544 DOI: 10.1158/1078-0432.ccr-21-3394] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/01/2021] [Accepted: 01/12/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Adult granulosa cell tumor (AGCT) is characterized by the somatic FOXL2 p.C134W mutation, and recurrences have been associated with TERT promoter and KMT2D-truncating mutations. Conversely, the molecular underpinnings of the rare juvenile granulosa cell tumor (JGCT) have not been well elucidated. To this end, we applied a tumor-only integrated approach to investigate the genomic, transcriptomic, and epigenomic landscape of 31 JGCTs to identify putative oncogenic drivers. EXPERIMENTAL DESIGN Multipronged analyses of 31 JGCTs were performed utilizing a clinically validated next-generation sequencing (NGS)-panel targeting 580 cancer-related genes for genomic interrogation, in addition to targeted RNA NGS for transcriptomic exploration. Genome-wide DNA methylation profiling was conducted using an Infinium Methylation EPIC array targeting 866,562 CpG methylation sites. RESULTS We identified frequent KMT2C-truncating mutations along with other mutated genes implicated in the switch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex, in addition to previously reported hotspot AKT1 and DICER1 mutations. Targeted transcriptome sequencing revealed recurrent TERT rearrangements (13%) involving partners CLPTM1L or DROSHA, and differential gene expression analysis showed FGFR1 upregulation in the TERT non-rearranged JGCTs under direct promoter control. Genome-wide DNA methylation rendered a clear delineation between AGCTs and JGCTs at the epigenomic level further supporting its diagnostic utility in distinguishing among these tumors. CONCLUSIONS This is the largest comprehensive molecular study of JGCTs, where we further expand our current understanding of JGCT pathogenesis and demonstrate putative oncogenic drivers and TERT rearrangements in a subset of tumors. Our findings further offer insights into possible targeted therapies in a rare entity.
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Affiliation(s)
| | - Kelsey Zhu
- pathology, New York University Langone Medical Center
| | | | | | | | - Rebecca L Linn
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia
| | | | - Sarah Chiang
- Department of Pathology, Memorial Sloan Kettering Cancer Center
| | | | | | - Lauren E Schwartz
- Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania
| | | | - Anais Malpica
- Department of Pathology, The University of Texas MD Anderson Cancer Center
| | - Esther Oliva
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School
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Desmeules P, Boudreau DK, Bastien N, Boulanger MC, Bossé Y, Joubert P, Couture C. Performance of an RNA-based Next-Generation Sequencing Assay for Combined Detection of Clinically Actionable Fusions and Hotspot Mutations in Non-Small Cell Lung Cancer. JTO Clin Res Rep 2022; 3:100276. [PMID: 35252895 PMCID: PMC8888203 DOI: 10.1016/j.jtocrr.2022.100276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/23/2021] [Accepted: 01/04/2022] [Indexed: 12/02/2022] Open
Abstract
Introduction With its expanding list of approved and emerging therapeutic indications, NSCLC is the exemplar tumor type requiring upfront assessment of several biomarkers to guide clinical management. Next-generation sequencing allows identification of different types of molecular alterations, each with specific analytical challenges. Library preparation using parallel DNA and RNA workflows can overcome most of them, but it increases complexity of laboratory operations, turnaround time, and costs. We describe the performance characteristics of a 15-gene RNA panel on the basis of anchored multiplex polymerase chain reaction for combined detection of clinically relevant oncogenic fusion transcripts and hotspot small variants. Methods Formalin-fixed, paraffin-embedded NSCLC clinical samples (N = 58) were used along cell lines and commercial controls to validate the assay’s analytical performance, followed by an exploratory prospective cohort (N = 87). Results The raw assay sensitivity for hotspot mutations and fusions was 83% and 93%, respectively, reaching 100% after filtering for key assay metrics. Those include quantity and quality of input of nucleic acid and sequencing metric from primers on housekeeping genes included in the assay. In the prospective cohort, driver alterations were identified in most cases (≥58%). Conclusions This ultrafocused RNA–next-generation sequencing assay offers an advantageous option with single unified workflow for simultaneous detection of clinically relevant hotspot mutations and fusions in NSCLC, focusing on actionable gene targets.
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Affiliation(s)
- Patrice Desmeules
- Service of Anatomic Pathology and Cytology, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Québec City, Québec, Canada
- Research Center, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Québec City, Québec, Canada
- Corresponding author. Address for correspondence: Patrice Desmeules, MD, MSc, Service of Anatomic Pathology and Cytology, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Quebec City, QC G1V 4G5, Canada.
| | - Dominique K. Boudreau
- Research Center, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Québec City, Québec, Canada
| | - Nathalie Bastien
- Service of Anatomic Pathology and Cytology, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Québec City, Québec, Canada
- Research Center, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Québec City, Québec, Canada
| | - Marie-Chloé Boulanger
- Research Center, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Québec City, Québec, Canada
| | - Yohan Bossé
- Research Center, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Québec City, Québec, Canada
| | - Philippe Joubert
- Service of Anatomic Pathology and Cytology, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Québec City, Québec, Canada
- Research Center, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Québec City, Québec, Canada
| | - Christian Couture
- Service of Anatomic Pathology and Cytology, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Québec City, Québec, Canada
- Research Center, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Québec City, Québec, Canada
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Bruno R, Fontanini G. Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review. Diagnostics (Basel) 2020; 10:E521. [PMID: 32726941 PMCID: PMC7460167 DOI: 10.3390/diagnostics10080521] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 02/07/2023] Open
Abstract
Gene fusions have a pivotal role in non-small cell lung cancer (NSCLC) precision medicine. Several techniques can be used, from fluorescence in situ hybridization and immunohistochemistry to next generation sequencing (NGS). Although several NGS panels are available, gene fusion testing presents more technical challenges than other variants. This is a PubMed-based narrative review aiming to summarize NGS approaches for gene fusion analysis and their performance on NSCLC clinical samples. The analysis can be performed at DNA or RNA levels, using different target enrichment (hybrid-capture or amplicon-based) and sequencing chemistries, with both custom and commercially available panels. DNA sequencing evaluates different alteration types simultaneously, but large introns and repetitive sequences can impact on the performance and it does not discriminate between expressed and unexpressed gene fusions. RNA-based targeted approach analyses and quantifies directly fusion transcripts and is more accurate than DNA panels on tumor tissue, but it can be limited by RNA quality and quantity. On liquid biopsy, satisfying data have been published on circulating tumor DNA hybrid-capture panels. There is not a perfect method for gene fusion analysis, but NGS approaches, though still needing a complete standardization and optimization, present several advantages for the clinical practice.
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Affiliation(s)
- Rossella Bruno
- Unit of Pathological Anatomy, University Hospital of Pisa, Via Roma 67, 56126 Pisa, Italy;
| | - Gabriella Fontanini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi 10, 56126 Pisa, Italy
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