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Benard C, Le Loarer F, Gomez-Mascard A, Azmani R, Garcia J, Perret R, de Pinieux G, Miquelestorena-Standley E, Weingertner N, Karanian M, Meurgey A, Michot A, Tirode F, Truffaux N, Macagno N, Bouvier C. Comprehensive Molecular Characterization of a Large Series of Calcified Chondroid Mesenchymal Neoplasms Widening Their Morphologic Spectrum. Am J Surg Pathol 2024; 48:991-1004. [PMID: 39016330 DOI: 10.1097/pas.0000000000002260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Recently, FN1 fusions to receptor tyrosine kinase genes have been identified in soft tissue tumors with calcified chondroid matrix named calcifying chondroid mesenchymal neoplasms (CCMNs). We collected 33 cases of CCMN from the French network for soft tissue and bone tumors. We performed whole-exome RNA sequencing, expression analysis, and genome-wide DNA methylation profiling in 33, 30, and 20 cases of CCMN compared with a control group of tumors, including noncalcified tenosynovial giant cell tumor (TGCT). Among them, 15 cases showed morphologic overlap with soft tissue chondroma, 8 cases with tophaceous pseudogout, and 10 cases with chondroid TGCT. RNA-sequencing revealed a fusion of FN1 in 76% of cases (25/33) with different 5' partners, including most frequently FGFR2 (14 cases), TEK or FGFR1. Among CCMN associated with FGFR1 fusions, 2 cases had overexpression of FGF23 without tumor-induced osteomalacia. Four CCMN had PDGFRA::USP8 fusions; 3 of which had histologic features of TGCT and were located in the hip, foot, and temporomandibular joint (TMJ). All cases with FN1::TEK fusion were located at TMJ and had histologic features of TGCT with or without chondroid matrix. They formed a distinct cluster on unsupervised clustering analyses based on whole transcriptome and genome-wide methylome data. Our study confirms the high prevalence of FN1 fusions in CCMN. In addition, through transcriptome and methylome analyses, we have identified a novel subgroup of tumors located at the TMJ, exhibiting TGCT-like features and FN1::TEK fusions.
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Affiliation(s)
- Clément Benard
- Department of Pathology, Timone University Hospital, Marseille
| | - François Le Loarer
- Department of Biopathology, Bergonié Institute, Regional Comprehensive Cancer Center
- UMR1312, University of Bordeaux, Inserm, BRIC, BoRdeaux Institute of Oncology
| | | | | | - Jeremy Garcia
- Department of Pathology, Timone University Hospital, Marseille
| | - Raul Perret
- Department of Biopathology, Bergonié Institute, Regional Comprehensive Cancer Center
- UMR1312, University of Bordeaux, Inserm, BRIC, BoRdeaux Institute of Oncology
| | | | | | | | | | | | - Audrey Michot
- UMR1312, University of Bordeaux, Inserm, BRIC, BoRdeaux Institute of Oncology
- Department of Surgery, Bergonié Institute, Bordeaux
| | | | - Nathalene Truffaux
- UMR1312, University of Bordeaux, Inserm, BRIC, BoRdeaux Institute of Oncology
| | - Nicolas Macagno
- UMR1251, Aix Marseille Univ, MMG, Marmara Institute, Timone University Hospital
| | - Corinne Bouvier
- Department of Pathology, Timone University Hospital, Marseille
- UMR7051, INP, Equipe 8 GlioME - Gliomagenèse et MicroEnvironnement, Aix Marseille Univ, Marseille, France
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Tjota MY, Segal JP, Wang P. Clinical Utility and Benefits of Comprehensive Genomic Profiling in Cancer. J Appl Lab Med 2024; 9:76-91. [PMID: 38167763 DOI: 10.1093/jalm/jfad091] [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: 07/05/2023] [Accepted: 09/28/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Comprehensive genomic profiling (CGP) with next-generation sequencing detects genetic alterations of hundreds of genes simultaneously and multiple molecular biomarkers with one test. In the personalized medicine era, CGP is increasingly used for cancer diagnosis, treatment selection, and prognosis prediction. CONTENT In this review, we summarize the benefits of CGP, clinical utility of CGP, and challenges of setting up CGP in the clinical laboratories. Besides the genetic alterations identified in the cancer-related genes, other biomarkers such as tumor mutational burden, microsatellite instability, and homologous recombination deficiency are critical for initiating targeted therapy. Compared with conventional tests, CGP uses less specimen and shortens the turnaround time if multiple biomarkers need to be tested. RNA fusion assay and liquid biopsy are helpful additions to DNA-based CGP by detecting fusions/splicing variants and complementing tissue-based CGP findings, respectively. SUMMARY Many previous hurdles for implementing CGP in the clinical laboratories have been gradually alleviated such as the decrease in sequencing cost, availability of both open-source and commercial bioinformatics tools, and improved reimbursement. These changes have helped to make CGP available to a greater population of cancer patients for improving characterization of their tumors and expanding their eligibility for clinical trials. Additionally, sequencing results of the hundreds of genes on CGP panels could be further analyzed to better understand the biology of various cancers and identify new biomarkers.
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Affiliation(s)
- Melissa Yuwono Tjota
- Department of Pathology, The University of Chicago, Chicago, IL 60637, United States
| | - Jeremy P Segal
- Department of Pathology, The University of Chicago, Chicago, IL 60637, United States
| | - Peng Wang
- Department of Pathology, The University of Chicago, Chicago, IL 60637, United States
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Drula R, Iluta S, Gulei D, Iuga C, Dima D, Ghiaur G, Buzoianu AD, Ciechanover A, Tomuleasa C. Exploiting the ubiquitin system in myeloid malignancies. From basic research to drug discovery in MDS and AML. Blood Rev 2022; 56:100971. [PMID: 35595613 DOI: 10.1016/j.blre.2022.100971] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 12/19/2022]
Abstract
The ubiquitin-proteasome system is the crucial homeostatic mechanism responsible for the degradation and turnover of proteins. As such, alterations at this level are often associated with oncogenic processes, either through accumulation of undegraded pathway effectors or, conversely, excessive degradation of tumor-suppressing factors. Therefore, investigation of the ubiquitin- proteasome system has gained much attraction in recent years, especially in the context of hematological malignancies, giving rise to efficient therapeutics such as bortezomib for multiple myeloma. Current investigations are now focused on manipulating protein degradation via fine-tuning of the ubiquitination process through inhibition of deubiquitinating enzymes or development of PROTAC systems for stimulation of ubiquitination and protein degradation. On the other hand, the efficiency of Thalidomide derivates in myelodysplastic syndromes (MDS), such as Lenalidomide, acted as the starting point for the development of targeted leukemia-associated protein degradation molecules. These novel molecules display high efficiency in overcoming the limitations of current therapeutic regimens, such as refractory diseases. Therefore, in this manuscript we will address the therapeutic opportunities and strategies based on the ubiquitin-proteasome system, ranging from the modulation of deubiquitinating enzymes and, conversely, describing the potential of modern targeted protein degrading molecules and their progress into clinical implementation.
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Affiliation(s)
- Rares Drula
- Research Center for Advanced Medicine - MedFUTURE, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Sabina Iluta
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania; Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj Napoca, Romania
| | - Diana Gulei
- Research Center for Advanced Medicine - MedFUTURE, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Cristina Iuga
- Research Center for Advanced Medicine - MedFUTURE, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania; Department of Pharmaceutical Analysis, Faculty of Pharmacy, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Delia Dima
- Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj Napoca, Romania
| | - Gabriel Ghiaur
- Department of Oncology, The Johns Hopkins Hospital, Johns Hopkins Medicine, Baltimore, MD, United States
| | - Anca Dana Buzoianu
- Department of Pharmacology, Toxicology and Clinical Pharmacology, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Aaron Ciechanover
- Research Center for Advanced Medicine - MedFUTURE, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania; Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania; Rappaport Technion Integrated Cancer Center, Technion-Israel Institute of Technology, Haifa 3109601, Israel; Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3109601, Israel
| | - Ciprian Tomuleasa
- Research Center for Advanced Medicine - MedFUTURE, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania; Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania; Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj Napoca, Romania.
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Hou YCC, Neidich JA, Duncavage EJ, Spencer DH, Schroeder MC. Clinical whole-genome sequencing in cancer diagnosis. Hum Mutat 2022; 43:1519-1530. [PMID: 35471774 DOI: 10.1002/humu.24381] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/24/2022] [Accepted: 04/04/2022] [Indexed: 11/10/2022]
Abstract
Characterizing the genomic landscape of cancers is a routine part of clinical care that began with the discovery of the Philadelphia chromosome and has since coevolved with genomic technologies. Genomic analysis of tumors at the nucleotide level using DNA sequencing has revolutionized the understanding of cancer biology and identified new molecular drivers of disease that have led to therapeutic advances and improved patient outcomes. However, the application of next-generation sequencing in the clinical laboratory has generally been limited until very recently to targeted analysis of selected genes. Recent technological innovations and reductions in sequencing costs are now able to deliver the long-promised goal of tumor whole-genome sequencing as a practical clinical assay.
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Affiliation(s)
- Ying-Chen C Hou
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Julie A Neidich
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Eric J Duncavage
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - David H Spencer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.,Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Molly C Schroeder
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
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Hehir-Kwa JY, Koudijs MJ, Verwiel ETP, Kester LA, van Tuil M, Strengman E, Buijs A, Kranendonk MEG, Hiemcke-Jiwa LS, de Haas V, van de Geer E, de Leng W, van der Lugt J, Lijnzaad P, Holstege FCP, Kemmeren P, Tops BBJ. Improved Gene Fusion Detection in Childhood Cancer Diagnostics Using RNA Sequencing. JCO Precis Oncol 2022; 6:e2000504. [PMID: 35085008 PMCID: PMC8830514 DOI: 10.1200/po.20.00504] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 08/27/2021] [Accepted: 12/03/2021] [Indexed: 12/16/2022] Open
Abstract
PURPOSE Gene fusions play a significant role in cancer etiology, making their detection crucial for accurate diagnosis, prognosis, and determining therapeutic targets. Current diagnostic methods largely focus on either targeted or low-resolution genome-wide techniques, which may be unable to capture rare events or both fusion partners. We investigate if RNA sequencing can overcome current limitations with traditional diagnostic techniques to identify gene fusion events. METHODS We first performed RNA sequencing on a validation cohort of 24 samples with a known gene fusion event, after which a prospective pan-pediatric cancer cohort (n = 244) was tested by RNA sequencing in parallel to existing diagnostic procedures. This cohort included hematologic malignancies, tumors of the CNS, solid tumors, and suspected neoplastic samples. All samples were processed in the routine diagnostic workflow and analyzed for gene fusions using standard-of-care methods and RNA sequencing. RESULTS We identified a clinically relevant gene fusion in 83 of 244 cases in the prospective cohort. Sixty fusions were detected by both routine diagnostic techniques and RNA sequencing, and one fusion was detected only in routine diagnostics, but an additional 24 fusions were detected solely by RNA sequencing. RNA sequencing, therefore, increased the diagnostic yield by 38%-39%. In addition, RNA sequencing identified both gene partners involved in the gene fusion, in contrast to most routine techniques. For two patients, the newly identified fusion by RNA sequencing resulted in treatment with targeted agents. CONCLUSION We show that RNA sequencing is sufficiently robust for gene fusion detection in routine diagnostics of childhood cancers and can make a difference in treatment decisions.
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Affiliation(s)
| | - Marco J. Koudijs
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Department of Laboratories, Pharmacy and Biomedical Genetics, Section of Genome Diagnostics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Lennart A. Kester
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Marc van Tuil
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Eric Strengman
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Arjan Buijs
- Department of Laboratories, Pharmacy and Biomedical Genetics, Section of Genome Diagnostics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | | | - Valerie de Haas
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Ellen van de Geer
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Wendy de Leng
- Department of Laboratories, Pharmacy and Biomedical Genetics, Section Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Philip Lijnzaad
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
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Kanagal-Shamanna R, Bao H, Kearney H, Smoley S, Tang Z, Luthra R, Yang H, Zhang S, Lin P, Wu D, Medeiros LJ, Lu X. Molecular characterization of Novel ATM fusions in chronic lymphocytic leukemia and T-cell prolymphocytic leukemia. Leuk Lymphoma 2021; 63:865-875. [PMID: 34898335 DOI: 10.1080/10428194.2021.2010061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
ATM deletions and/or mutations are recurrent in lymphoid neoplasms while rearrangements are rare. In this study, we used mate pair sequencing (MPseq) technology to characterize two novel ATM rearrangements in one patient with chronic lymphocytic leukemia (CLL) and one patient with T-prolymphocytic leukemia (T-PLL). Both patients showed chromosome 11q22 aberrations encompassing ATM by conventional karyotype and fluorescence in situ hybridization: isolated t(11;13)(q22;q14) in CLL and a complex karyotype with apparent 11q deletion and unbalanced der(14)t(11;14)(q22;p11.2) in T-PLL. MPseq identified ATM-LINC00371 fusion in CLL and ATM-USP28 in T-PLL, both of which led to ATM inactivation, confirmed by loss of immunohistochemical protein expression. Next-generation sequencing mutation analysis detected concurrent ATM mutation(s) CLL patient, while T-PLL lacked ATM mutation. ATM rearrangements, not apparently detectable using standard laboratory technologies, represent another mechanism of loss-of-function. Recent high-throughput technologies such as MPseq can uncover novel pathogenic gene fusions and resolve complex chromosomal rearrangements in hematologic malignancies.
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Affiliation(s)
- Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Haiyan Bao
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Department of Hematology, SooChow University First Affiliated Hospital, Suzhou, Jiangsu, China
| | - Hutton Kearney
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Stephanie Smoley
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Zhenya Tang
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Hui Yang
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Shanshan Zhang
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Pei Lin
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Depei Wu
- Department of Hematology, SooChow University First Affiliated Hospital, Suzhou, Jiangsu, China
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Xinyan Lu
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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Lei H, Wang J, Hu J, Zhu Q, Wu Y. Deubiquitinases in hematological malignancies. Biomark Res 2021; 9:66. [PMID: 34454635 PMCID: PMC8401176 DOI: 10.1186/s40364-021-00320-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/06/2021] [Indexed: 12/18/2022] Open
Abstract
Deubiquitinases (DUBs) are enzymes that control the stability, interactions or localization of most cellular proteins by removing their ubiquitin modification. In recent years, some DUBs, such as USP7, USP9X and USP10, have been identified as promising therapeutic targets in hematological malignancies. Importantly, some potent inhibitors targeting the oncogenic DUBs have been developed, showing promising inhibitory efficacy in preclinical models, and some have even undergone clinical trials. Different DUBs perform distinct function in diverse hematological malignancies, such as oncogenic, tumor suppressor or context-dependent effects. Therefore, exploring the biological roles of DUBs and their downstream effectors will provide new insights and therapeutic targets for the occurrence and development of hematological malignancies. We summarize the DUBs involved in different categories of hematological malignancies including leukemia, multiple myeloma and lymphoma. We also present the recent development of DUB inhibitors and their applications in hematological malignancies. Together, we demonstrate DUBs as potential therapeutic drug targets in hematological malignancies.
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Affiliation(s)
- Hu Lei
- Department of Pathophysiology, International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jiaqi Wang
- Department of Pathophysiology, International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jiacheng Hu
- Department of Pathophysiology, International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Qian Zhu
- Department of Pathophysiology, International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yingli Wu
- Department of Pathophysiology, International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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