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Jelinek T, Zihala D, Sevcikova T, Anilkumar Sithara A, Kapustova V, Sahinbegovic H, Venglar O, Muronova L, Broskevicova L, Nenarokov S, Bilek D, Popkova T, Plonkova H, Vrana J, Zidlik V, Hurnik P, Havel M, Hrdinka M, Chyra Z, Stracquadanio G, Simicek M, Hajek R. Beyond the marrow: insights from comprehensive next-generation sequencing of extramedullary multiple myeloma tumors. Leukemia 2024; 38:1323-1333. [PMID: 38493239 PMCID: PMC11147761 DOI: 10.1038/s41375-024-02206-w] [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: 12/12/2023] [Revised: 02/16/2024] [Accepted: 02/23/2024] [Indexed: 03/18/2024]
Abstract
Extramedullary multiple myeloma (EMM) is an aggressive form of multiple myeloma (MM). This study represents the most comprehensive next-generation sequencing analysis of EMM tumors (N = 14) to date, uncovering key molecular features and describing the tumor microenvironment. We observed the co-occurrence of 1q21 gain/amplification and MAPK pathway mutations in 79% of EMM samples, suggesting that these are crucial mutational events in EMM development. We also demonstrated that patients with mutated KRAS and 1q21 gain/amplification at the time of diagnosis have a significantly higher risk of EMM development (HR = 2.4, p = 0.011) using data from a large CoMMpass dataset. We identified downregulation of CXCR4 and enhanced cell proliferation, along with reduced expression of therapeutic targets (CD38, SLAMF7, GPRC5D, FCRH5), potentially explaining diminished efficacy of immunotherapy. Conversely, we identified significantly upregulated EZH2 and CD70 as potential future therapeutic options. For the first time, we report on the tumor microenvironment of EMM, revealing CD8+ T cells and NK cells as predominant immune effector cells using single-cell sequencing. Finally, this is the first longitudinal study in EMM revealing the molecular changes from the time of diagnosis to EMM relapse.
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Affiliation(s)
- T Jelinek
- Department of Hematooncology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czech Republic
| | - D Zihala
- Department of Hematooncology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czech Republic
| | - T Sevcikova
- Department of Hematooncology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - A Anilkumar Sithara
- Department of Hematooncology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - V Kapustova
- Department of Hematooncology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czech Republic
| | - H Sahinbegovic
- Department of Hematooncology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - O Venglar
- Department of Hematooncology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - L Muronova
- Department of Hematooncology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czech Republic
| | - L Broskevicova
- Department of Hematooncology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czech Republic
| | - S Nenarokov
- Department of Hematooncology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czech Republic
| | - D Bilek
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - T Popkova
- Department of Hematooncology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czech Republic
| | - H Plonkova
- Department of Hematooncology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - J Vrana
- Department of Hematooncology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czech Republic
| | - V Zidlik
- Department of Pathology, University Hospital Ostrava, Ostrava, Czech Republic
| | - P Hurnik
- Department of Pathology, University Hospital Ostrava, Ostrava, Czech Republic
| | - M Havel
- Department of Nuclear Medicine, University Hospital Ostrava, Ostrava, Czech Republic
- Department of Imaging Methods, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - M Hrdinka
- Department of Hematooncology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czech Republic
| | - Z Chyra
- Department of Hematooncology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czech Republic
| | - G Stracquadanio
- School of Biological Sciences, The University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - M Simicek
- Department of Hematooncology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czech Republic
| | - R Hajek
- Department of Hematooncology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic.
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czech Republic.
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Johnson TS, Sudha P, Liu E, Becker N, Robertson S, Blaney P, Morgan G, Chopra VS, Dos Santos C, Nixon M, Huang K, Suvannasankha A, Zaid MA, Abonour R, Walker BA. 1q amplification and PHF19 expressing high-risk cells are associated with relapsed/refractory multiple myeloma. Nat Commun 2024; 15:4144. [PMID: 38755140 PMCID: PMC11099140 DOI: 10.1038/s41467-024-48327-9] [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: 08/09/2023] [Accepted: 04/29/2024] [Indexed: 05/18/2024] Open
Abstract
Multiple Myeloma is an incurable plasma cell malignancy with a poor survival rate that is usually treated with immunomodulatory drugs (iMiDs) and proteosome inhibitors (PIs). The malignant plasma cells quickly become resistant to these agents causing relapse and uncontrolled growth of resistant clones. From whole genome sequencing (WGS) and RNA sequencing (RNA-seq) studies, different high-risk translocation, copy number, mutational, and transcriptional markers can be identified. One of these markers, PHF19, epigenetically regulates cell cycle and other processes and is already studied using RNA-seq. In this study, we generate a large (325,025 cells and 49 patients) single cell multi-omic dataset and jointly quantify ATAC- and RNA-seq for each cell and matched genomic profiles for each patient. We identify an association between one plasma cell subtype with myeloma progression that we call relapsed/refractory plasma cells (RRPCs). These cells are associated with chromosome 1q alterations, TP53 mutations, and higher expression of PHF19. We also identify downstream regulation of cell cycle inhibitors in these cells, possible regulation by the transcription factor (TF) PBX1 on chromosome 1q, and determine that PHF19 may be acting primarily through this subset of cells.
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Affiliation(s)
- Travis S Johnson
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, USA
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
- Melvin and Bren Simon Comprehensive Cancer Center, Experimental and Developmental Therapeutics, School of Medicine, Indiana University, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Parvathi Sudha
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Enze Liu
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Nathan Becker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | | | - Patrick Blaney
- Perlmutter Cancer Center, Langone Health, New York University, New York, NY, USA
| | - Gareth Morgan
- Perlmutter Cancer Center, Langone Health, New York University, New York, NY, USA
| | | | | | | | - Kun Huang
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, USA
- Melvin and Bren Simon Comprehensive Cancer Center, Experimental and Developmental Therapeutics, School of Medicine, Indiana University, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Attaya Suvannasankha
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
- Roudebush VAMC, Indianapolis, IN, USA
| | - Mohammad Abu Zaid
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Rafat Abonour
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Brian A Walker
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA.
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA.
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3
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Xie C, Zhong L, Luo J, Luo J, Wu Y, Zheng S, Jiang L, Zhang J, Shi Y. Identification of mutation gene prognostic biomarker in multiple myeloma through gene panel exome sequencing and transcriptome analysis in Chinese population. Comput Biol Med 2023; 163:107224. [PMID: 37406588 DOI: 10.1016/j.compbiomed.2023.107224] [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] [Received: 04/17/2023] [Revised: 06/06/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND The 5-year survival rate of multiple myeloma (MM) in China is less than 40%, with considerable individual heterogeneity. Gene mutations are important predictive biomarkers that influence MM treatment decision. The aim of our study was to uncover the clinical significance of mutated genes in MM in the Chinese population. METHODS Targeted exon panel sequencing was performed of 400 genes to detect the gene mutation status in plasma cells from 50 patients with MM. DAVID was used to explore the functions and pathways of mutated genes. Detection of mutant gene expression, prognosis and immune cell infiltration with GSE6477. GEO2R was utilized to identify differentially expressed genes (DEGs). Kaplan-Meier and CIBERSORT were applied to compare survival distributions and evaluate the gene expression associated with immune cell infiltration, respectively. RESULTS Mutations of 337 genes were identified in MM. The mutation types included SNP, INS, and DEL, but the dominant mutation type was SNP. Function and pathway analysis of mutant genes were performed to elucidate DNA modifications. We identified a total number of 660 downregulated and 587 upregulated genes from the GSE6477 dataset. Thirty-three common genes were present in both the mutant genes and DEGs. The functions and pathways of the mutated genes were enriched in myeloid cell differentiation, regulation of hemopoiesis, etc. Moreover, we found that the low expression of BCL6, BIRC3, HLA-DQA1, and VCAN was correlated with poor prognosis in MM. CONCLUSIONS The mutations and low expression of BCL6, BIRC3, HLA-DQA1, and VCAN were correlated with poor prognosis and immune cell infiltration in MM. This study is the first to reveal the spectrum of mutations in the Chinese population by the use of an NGS panel.
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Affiliation(s)
- Chunbao Xie
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Ling Zhong
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Jiangrong Luo
- Department of Anesthesiology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Ji Luo
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Yingmiao Wu
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Shuai Zheng
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Lingxi Jiang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China; Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China; Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China.
| | - Jianbo Zhang
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
| | - Yi Shi
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China; Health Management Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China; Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China.
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4
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Johnson TS, Sudha P, Liu E, Blaney P, Morgan G, Chopra VS, Santos CD, Nixon M, Huang K, Suvannasankha A, Zaid MA, Abonour R, Walker BA. Identifying 1q amplification and PHF19 expressing high-risk cells associated with relapsed/refractory multiple myeloma. RESEARCH SQUARE 2023:rs.3.rs-3221549. [PMID: 37645789 PMCID: PMC10462227 DOI: 10.21203/rs.3.rs-3221549/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Multiple Myeloma is an incurable plasma cell malignancy with a poor survival rate that is usually treated with immunomodulatory drugs (iMiDs) and proteosome inhibitors (PIs). The malignant plasma cells quickly become resistant to these agents causing relapse and uncontrolled growth of resistant clones. From whole genome sequencing (WGS) and RNA sequencing (RNA-seq) studies, different high-risk translocation, copy number, mutational, and transcriptional markers have been identified. One of these markers, PHF19, epigenetically regulates cell cycle and other processes and has already been studied using RNA-seq. In this study a massive (325,025 cells and 49 patients) single cell multiomic dataset was generated with jointly quantified ATAC- and RNA-seq for each cell and matched genomic profiles for each patient. We identified an association between one plasma cell subtype with myeloma progression that we have called relapsed/refractory plasma cells (RRPCs). These cells are associated with 1q alterations, TP53 mutations, and higher expression of PHF19. We also identified downstream regulation of cell cycle inhibitors in these cells, possible regulation of the transcription factor (TF) PBX1 on 1q, and determined that PHF19 may be acting primarily through this subset of cells.
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Affiliation(s)
- Travis S. Johnson
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, USA
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
- Melvin and Bren Simon Comprehensive Cancer Center, Experimental and Developmental Therapeutics, School of Medicine, Indiana University, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Parvathi Sudha
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Enze Liu
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Patrick Blaney
- Perlmutter Cancer Center, Langone Health, New York University, New York, NY, USA
| | - Gareth Morgan
- Perlmutter Cancer Center, Langone Health, New York University, New York, NY, USA
| | | | | | | | - Kun Huang
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, USA
- Melvin and Bren Simon Comprehensive Cancer Center, Experimental and Developmental Therapeutics, School of Medicine, Indiana University, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Attaya Suvannasankha
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
- Roudebush VAMC, Indianapolis, IN, USA
| | - Mohammad Abu Zaid
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Rafat Abonour
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Brian A. Walker
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
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Rosa-Rosa JM, Cuenca I, Medina A, Vázquez I, Sánchez-delaCruz A, Buenache N, Sánchez R, Jiménez C, Rosiñol L, Gutiérrez NC, Ruiz-Heredia Y, Barrio S, Oriol A, Martin-Ramos ML, Blanchard MJ, Ayala R, Ríos-Tamayo R, Sureda A, Hernández MT, de la Rubia J, Alkorta-Aranburu G, Agirre X, Bladé J, Mateos MV, Lahuerta JJ, San-Miguel JF, Calasanz MJ, Garcia-Sanz R, Martínez-Lopez J. NGS-Based Molecular Karyotyping of Multiple Myeloma: Results from the GEM12 Clinical Trial. Cancers (Basel) 2022; 14:cancers14205169. [PMID: 36291952 PMCID: PMC9601262 DOI: 10.3390/cancers14205169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/07/2022] [Accepted: 10/12/2022] [Indexed: 12/01/2022] Open
Abstract
Simple Summary Multiple Myeloma (MM) is considered an incurable chronic disease, which prognosis depends on the presence of different genomic alterations. To accomplish a complete molecular diagnosis in a single essay, we have designed and validated a capture-based NGS approach to reliably identify pathogenic mutations (SNVs and indels), genomic alterations (CNVs and chromosomic translocations), and IGH rearrangements. We have observed a good correlation of the results obtained using our capture panel with data obtained by both FISH and WES techniques. In this study, the molecular classification performed using our approach was significantly associated with the stratification and outcome of MM patients. Additionally, this panel has been proven to detect specific IGH rearrangements that could be used as biomarkers in patient follow-ups through minimal residual disease (MRD) assays. In conclusion, we think that MM patients could benefit from the use of this capture-based NGS approach with a more accurate, single-essay molecular diagnosis. Abstract Next-generation sequencing (NGS) has greatly improved our ability to detect the genomic aberrations occurring in multiple myeloma (MM); however, its transfer to routine clinical labs and its validation in clinical trials remains to be established. We designed a capture-based NGS targeted panel to identify, in a single assay, known genetic alterations for the prognostic stratification of MM. The NGS panel was designed for the simultaneous study of single nucleotide and copy number variations, insertions and deletions, chromosomal translocations and V(D)J rearrangements. The panel was validated using a cohort of 149 MM patients enrolled in the GEM2012MENOS65 clinical trial. The results showed great global accuracy, with positive and negative predictive values close to 90% when compared with available data from fluorescence in situ hybridization and whole-exome sequencing. While the treatments used in the clinical trial showed high efficacy, patients defined as high-risk by the panel had shorter progression-free survival (p = 0.0015). As expected, the mutational status of TP53 was significant in predicting patient outcomes (p = 0.021). The NGS panel also efficiently detected clonal IGH rearrangements in 81% of patients. In conclusion, molecular karyotyping using a targeted NGS panel can identify relevant prognostic chromosomal abnormalities and translocations for the clinical management of MM patients.
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Affiliation(s)
- Juan Manuel Rosa-Rosa
- Hematology Department, Hospital 12 de Octubre, 28041 Madrid, Spain
- H12O–CNIO Hematological Malignancies Clinical Research Unit, Spanish National Cancer Research (CNIO), 29029 Madrid, Spain
- Correspondence: (J.M.R.-R.); (J.M.-L.)
| | - Isabel Cuenca
- Hematology Department, Hospital 12 de Octubre, 28041 Madrid, Spain
- H12O–CNIO Hematological Malignancies Clinical Research Unit, Spanish National Cancer Research (CNIO), 29029 Madrid, Spain
| | - Alejandro Medina
- Unidad de Biología Molecular-HLA, Laboratorio de Hematología, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | - Iria Vázquez
- Center for Applied Medical Research (CIMA) LAB Diagnostics, Universidad de Navarra, 31008 Pamplona, Spain
| | - Andrea Sánchez-delaCruz
- H12O–CNIO Hematological Malignancies Clinical Research Unit, Spanish National Cancer Research (CNIO), 29029 Madrid, Spain
| | - Natalia Buenache
- Hematology Department, Hospital 12 de Octubre, 28041 Madrid, Spain
- H12O–CNIO Hematological Malignancies Clinical Research Unit, Spanish National Cancer Research (CNIO), 29029 Madrid, Spain
| | - Ricardo Sánchez
- Hematology Department, Hospital 12 de Octubre, 28041 Madrid, Spain
- H12O–CNIO Hematological Malignancies Clinical Research Unit, Spanish National Cancer Research (CNIO), 29029 Madrid, Spain
| | - Cristina Jiménez
- Unidad de Biología Molecular-HLA, Laboratorio de Hematología, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
- Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Laura Rosiñol
- Hospital Clinic de Barcelona, 08036 Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Norma C. Gutiérrez
- Unidad de Biología Molecular-HLA, Laboratorio de Hematología, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
- Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Yanira Ruiz-Heredia
- Hematology Department, Hospital 12 de Octubre, 28041 Madrid, Spain
- H12O–CNIO Hematological Malignancies Clinical Research Unit, Spanish National Cancer Research (CNIO), 29029 Madrid, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Santiago Barrio
- Hematology Department, Hospital 12 de Octubre, 28041 Madrid, Spain
- H12O–CNIO Hematological Malignancies Clinical Research Unit, Spanish National Cancer Research (CNIO), 29029 Madrid, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Albert Oriol
- Clinical Research Support Unit, Institut Català d’Oncologia, 08036 Barcelona, Spain
| | | | | | - Rosa Ayala
- Hematology Department, Hospital 12 de Octubre, 28041 Madrid, Spain
| | | | - Anna Sureda
- Institut Catalá d’Oncologia-l’Hospitalet, Institut de Investigació Biomèdica de Bellvitge (IDIBELL), Universitat de Barcelona, 08908 Barcelona, Spain
| | | | | | - Gorka Alkorta-Aranburu
- Center for Applied Medical Research (CIMA) LAB Diagnostics, Universidad de Navarra, 31008 Pamplona, Spain
| | - Xabier Agirre
- Center for Applied Medical Research (CIMA) LAB Diagnostics, Universidad de Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
- Instituto de Investigaciones Sanitarias de Navarra (IdiSNA), Universidad de Navarra, 31008 Pamplona, Spain
| | - Joan Bladé
- Hospital Clinic de Barcelona, 08036 Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - María-Victoria Mateos
- Unidad de Biología Molecular-HLA, Laboratorio de Hematología, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
- Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Juan-José Lahuerta
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Jesús F. San-Miguel
- Center for Applied Medical Research (CIMA) LAB Diagnostics, Universidad de Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
- Instituto de Investigaciones Sanitarias de Navarra (IdiSNA), Universidad de Navarra, 31008 Pamplona, Spain
| | - María-José Calasanz
- Center for Applied Medical Research (CIMA) LAB Diagnostics, Universidad de Navarra, 31008 Pamplona, Spain
| | - Ramón Garcia-Sanz
- Unidad de Biología Molecular-HLA, Laboratorio de Hematología, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
- Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Joaquín Martínez-Lopez
- Hematology Department, Hospital 12 de Octubre, 28041 Madrid, Spain
- H12O–CNIO Hematological Malignancies Clinical Research Unit, Spanish National Cancer Research (CNIO), 29029 Madrid, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
- Correspondence: (J.M.R.-R.); (J.M.-L.)
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6
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Gooding S, Ansari-Pour N, Kazeroun M, Karagoz K, Polonskaia A, Salazar M, Fitzsimons E, Sirinukunwattana K, Chavda S, Ortiz Estevez M, Towfic F, Flynt E, Pierceall W, Royston D, Yong K, Ramasamy K, Vyas P, Thakurta A. Loss of COP9 signalosome genes at 2q37 is associated with IMiD resistance in multiple myeloma. Blood 2022; 140:1816-1821. [PMID: 35853156 PMCID: PMC10653034 DOI: 10.1182/blood.2022015909] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/30/2022] [Indexed: 11/20/2022] Open
Abstract
The acquisition of a multidrug refractory state is a major cause of mortality in myeloma. Myeloma drugs that target the cereblon (CRBN) protein include widely used immunomodulatory drugs (IMiDs), and newer CRBN E3 ligase modulator drugs (CELMoDs), in clinical trials. CRBN genetic disruption causes resistance and poor outcomes with IMiDs. Here, we investigate alternative genomic associations of IMiD resistance, using large whole-genome sequencing patient datasets (n = 522 cases) at newly diagnosed, lenalidomide (LEN)-refractory and lenalidomide-then-pomalidomide (LEN-then-POM)-refractory timepoints. Selecting gene targets reproducibly identified by published CRISPR/shRNA IMiD resistance screens, we found little evidence of genetic disruption by mutation associated with IMiD resistance. However, we identified a chromosome region, 2q37, containing COP9 signalosome members COPS7B and COPS8, copy loss of which significantly enriches between newly diagnosed (incidence 5.5%), LEN-refractory (10.0%), and LEN-then-POM-refractory states (16.4%), and may adversely affect outcomes when clonal fraction is high. In a separate dataset (50 patients) with sequential samples taken throughout treatment, we identified acquisition of 2q37 loss in 16% cases with IMiD exposure, but none in cases without IMiD exposure. The COP9 signalosome is essential for maintenance of the CUL4-DDB1-CRBN E3 ubiquitin ligase. This region may represent a novel marker of IMiD resistance with clinical utility.
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Affiliation(s)
- Sarah Gooding
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Department of Haematology, Oxford University Hospitals NHS Trust, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
| | - Naser Ansari-Pour
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Mohammad Kazeroun
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Kubra Karagoz
- Translational Medicine, Bristol Myers Squibb, Summit, NJ
| | - Ann Polonskaia
- Translational Medicine, Bristol Myers Squibb, Summit, NJ
| | - Mirian Salazar
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
| | - Evie Fitzsimons
- Department of Haematology, Cancer Institute, University College London, United Kingdom
| | | | - Selina Chavda
- Department of Haematology, Cancer Institute, University College London, United Kingdom
| | - Maria Ortiz Estevez
- Bristol Myers Squibb Center for Innovation and Translational Research Europe, Sevilla, Spain
| | | | - Erin Flynt
- Translational Medicine, Bristol Myers Squibb, Summit, NJ
| | | | - Daniel Royston
- Nuffield Department of Cellular and Laboratory Sciences, University of Oxford, Oxford, United Kingdom
| | - Kwee Yong
- Department of Haematology, Cancer Institute, University College London, United Kingdom
| | - Karthik Ramasamy
- Department of Haematology, Oxford University Hospitals NHS Trust, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
| | - Paresh Vyas
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Department of Haematology, Oxford University Hospitals NHS Trust, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Anjan Thakurta
- Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
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