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Li X, Lin Z, Zhao F, Huang T, Fan W, Cen L, Ma J. Unveiling the cellular landscape: insights from single-cell RNA sequencing in multiple myeloma. Front Immunol 2024; 15:1458638. [PMID: 39281682 PMCID: PMC11392786 DOI: 10.3389/fimmu.2024.1458638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 08/13/2024] [Indexed: 09/18/2024] Open
Abstract
Objective The aim of this research was to gain a thorough understanding of the processes involved in cell communication and discover potential indicators for treating multiple myeloma (MM) through the use of single-cell RNA sequencing (scRNA-seq). And explored the expression of multiple myeloma-related subgroups on metal ion-related pathways to explore the relationship between MM and metal ions. Methods We performed a fair examination using single-cell RNA sequencing on 32 bone marrow specimens collected from 22 individuals at different points of MM advancement and 9 individuals without any health issues. To analyze the scRNA-seq data, we employed advanced computational algorithms, including Slingshot, Monocle2, and other methodologies. Specifically, Slingshot and Monocle2 enabled us to simulate the biological functionalities of different cell populations and map trajectories of cell developmental pathways. Additionally, we utilized the UMAP algorithm, a powerful dimension reduction technique, to cluster cells and identify genes that were differentially expressed across clusters. Results Our study revealed distinct gene expression patterns and molecular pathways within each patient, which exhibited associations with disease progression. The analysis provided insights into the tumor microenvironment (TME), intra- and inter-patient heterogeneity, and cell-cell interactions mediated by ligand-receptor signaling. And found that multiple myeloma-related subgroups were expressed higher levels in MMP and TIMP pathways, there were some associations. Conclusion Our study presents a fresh perspective for future research endeavors and clinical interventions in the field of MM. The identified gene expression patterns and molecular pathways hold immense potential as therapeutic targets for the treatment of multiple myeloma. The utilization of scRNA-seq technology has significantly contributed to a more precise understanding of the complex cellular processes and interactions within MM. Through these advancements, we are now better equipped to unravel the underlying mechanisms driving the development and progression of this complex disease.
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Affiliation(s)
- Xinhan Li
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Zhiheng Lin
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Fu Zhao
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Tianjiao Huang
- The First School of Clinical Medicine, Heilongjiang University of Traditional Chinese Medicine, Harbin, China
| | - Weisen Fan
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Lijun Cen
- Key Laboratory of Molecular Pathology in Tumors of Guangxi, Department of Transfusion Medicine, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Jun Ma
- Department of Cardiology, Yantai Hospital of Traditional Chinese Medicine, Yantai, China
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Hosoi H, Tabata S, Kosako H, Hori Y, Okamura T, Yamashita Y, Fujimoto K, Kajioka D, Suzuki K, Osato M, Yamada G, Sonoki T. IGLL5 controlled by super-enhancer affects cell survival and MYC expression in mature B-cell lymphoma. Leuk Res Rep 2024; 21:100451. [PMID: 38444524 PMCID: PMC10912717 DOI: 10.1016/j.lrr.2024.100451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 01/03/2024] [Accepted: 02/20/2024] [Indexed: 03/07/2024] Open
Abstract
IGLL5 is shown to be located near super-enhancer (SE) in B-cell tumors, and this gene is frequently mutated and a target of translocation in B-cell tumors. These results suggest roles of the IGLL5 in tumorigenesis; however, its functional properties have been unclear. We found that two mature B-cell lymphoma cell lines expressed IGLL5 mRNA with Cλ1 segment. JQ1 treatment resulted in down-expression of IGLL5, indicating that IGLL5 is controlled by SE. IGLL5 knockdown induced cell death with down-expression of MYC. Our results suggested that IGLL5 might have a role in survival of mature B-cell tumors and involvement in MYC expression. (100 words).
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Affiliation(s)
- Hiroki Hosoi
- Department of Hematology/Oncology, Wakayama Medical University, Wakayama, Japan
| | - Shotaro Tabata
- Department of Hematology/Oncology, Wakayama Medical University, Wakayama, Japan
| | - Hideki Kosako
- Department of Hematology/Oncology, Wakayama Medical University, Wakayama, Japan
| | - Yoshikazu Hori
- Department of Hematology/Oncology, Wakayama Medical University, Wakayama, Japan
| | - Tadashi Okamura
- Department of Hematology/Oncology, Wakayama Medical University, Wakayama, Japan
| | - Yusuke Yamashita
- Department of Hematology/Oncology, Wakayama Medical University, Wakayama, Japan
| | - Kota Fujimoto
- Department of Developmental Genetics, Institute of Advanced Medicine, Wakayama Medical University, Wakayama, Japan
| | - Daiki Kajioka
- Department of Developmental Genetics, Institute of Advanced Medicine, Wakayama Medical University, Wakayama, Japan
| | - Kentaro Suzuki
- Faculty of Life and Environmental Sciences, University of Yamanashi, Takeda 4-4-37, Kofu City, Yamanashi, Japan
| | - Motomi Osato
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Gen Yamada
- Department of Developmental Genetics, Institute of Advanced Medicine, Wakayama Medical University, Wakayama, Japan
| | - Takashi Sonoki
- Department of Hematology/Oncology, Wakayama Medical University, Wakayama, Japan
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3
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Zhang Y, Liu C. Transcriptomic analysis of mRNAs in human whole blood identified age-specific changes in healthy individuals. Medicine (Baltimore) 2023; 102:e36486. [PMID: 38065846 PMCID: PMC10713173 DOI: 10.1097/md.0000000000036486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/14/2023] [Indexed: 12/18/2023] Open
Abstract
Older age is one of the most important shared risk factors for multiple chronic diseases, increasing the medical burden to contemporary societies. Current research focuses on identifying aging biomarkers to predict aging trajectories and developing interventions aimed at preventing and delaying the progression of multimorbidity with aging. Here, a transcriptomic changes analysis of whole blood genes with age was conducted. The age-related whole blood gene-expression profiling datasets were downloaded from the Gene Expression Omnibus (GEO) database. We screened the differentially expressed genes (DEGs) between healthy young and old individuals and performed functional enrichment analysis. Cytoscape with Cytohubba and MCODE was used to perform an interaction network of DEGs and identify hub genes. In addition, ROC curves and correlation analysis were used to evaluate the accuracy of hub genes. In total, we identified 29 DEGs between young and old samples that were enriched mainly in immunoglobulin binding and complex, humoral immune response, and immune response-activating signaling pathways. In combination with the PPI network and topological analysis, 4 hub genes (IGLL5, Jchain, POU2AF1, and Bach2) were identified. Pearson analysis showed that the expression changes of these hub genes were highly correlated with age. Among them, 3 hub genes (IGLL5, POU2AF1, and Bach2) were identified with good accuracy (AUC score > 0.7), indicating that these genes were the best indicators of age. Together, our results provided potential biomarkers IGLL5, POU2AF1, and Bach2 to identify individuals at high early risk of age-related disease to be targeted for early interventions and contribute to understanding the molecular mechanisms in the progression of aging.
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Affiliation(s)
- Yan Zhang
- Department of Ophthalmology, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chonghui Liu
- College of Life Science, Northeast Forestry University, Harbin, China
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4
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Zheng B, Yi K, Zhang Y, Pang T, Zhou J, He J, Lan H, Xian H, Li R. Multi-omics analysis of multiple myeloma patients with differential response to first-line treatment. Clin Exp Med 2023; 23:3833-3846. [PMID: 37515690 DOI: 10.1007/s10238-023-01148-4] [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: 05/29/2023] [Accepted: 07/20/2023] [Indexed: 07/31/2023]
Abstract
The genome backgrounds of multiple myeloma (MM) would affect the efficacy of specific treatment. However, the mutational and transcriptional landscapes in MM patients with differential response to first-line treatment remains unclear. We collected paired whole-exome sequencing (WES) and transcriptomic data of over 200 MM cases from MMRF-COMPASS project. R package, maftools was applied to analyze the somatic mutations and mutational signatures across MM samples. Differential expressed genes (DEG) was calculated using R package, DESeq2. The feature selection of the predictive model was determined by LASSO regression. In silico analysis revealed newly discovered recurrent mutated genes such as TTN, MUC16. TP53 mutation was observed more frequent in nonCR (complete remission) group with poor prognosis. DNA repair-associated mutational signatures were enriched in CR patients. Transcriptomic profiling showed that the activity of NF-kappa B and TGF-β pathways was suppressed in CR patients. A transcriptome-based response predictive model was constructed and showed promising predictive accuracy in MM patients receiving first-line treatment. Our study delineated distinctive mutational and transcriptional landscapes in MM patients with differential response to first-line treatment. Furthermore, we constructed a 20-gene predictive model which showed promising accuracy in predicting treatment response in newly diagnosed MM patients.
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Affiliation(s)
- Bo Zheng
- Nuclear Radiation Injury Protection and Treatment Department, Navy Medical Center of PLA, Naval Medical University, Huaihai West Road No. 338, Shanghai, 200050, China.
| | - Ke Yi
- Nuclear Radiation Injury Protection and Treatment Department, Navy Medical Center of PLA, Naval Medical University, Huaihai West Road No. 338, Shanghai, 200050, China
| | - Yajun Zhang
- Nuclear Radiation Injury Protection and Treatment Department, Navy Medical Center of PLA, Naval Medical University, Huaihai West Road No. 338, Shanghai, 200050, China
| | - Tongfang Pang
- Nuclear Radiation Injury Protection and Treatment Department, Navy Medical Center of PLA, Naval Medical University, Huaihai West Road No. 338, Shanghai, 200050, China
| | - Jieyi Zhou
- Nuclear Radiation Injury Protection and Treatment Department, Navy Medical Center of PLA, Naval Medical University, Huaihai West Road No. 338, Shanghai, 200050, China
| | - Jie He
- Nuclear Radiation Injury Protection and Treatment Department, Navy Medical Center of PLA, Naval Medical University, Huaihai West Road No. 338, Shanghai, 200050, China
| | - Hongyan Lan
- Nuclear Radiation Injury Protection and Treatment Department, Navy Medical Center of PLA, Naval Medical University, Huaihai West Road No. 338, Shanghai, 200050, China
| | - Hongming Xian
- Nuclear Radiation Injury Protection and Treatment Department, Navy Medical Center of PLA, Naval Medical University, Huaihai West Road No. 338, Shanghai, 200050, China
| | - Rong Li
- Nuclear Radiation Injury Protection and Treatment Department, Navy Medical Center of PLA, Naval Medical University, Huaihai West Road No. 338, Shanghai, 200050, China.
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5
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Lauinger M, Christen D, Klar RFU, Roubaty C, Heilig CE, Stumpe M, Knox JJ, Radulovich N, Tamblyn L, Xie IY, Horak P, Forschner A, Bitzer M, Wittel UA, Boerries M, Ball CR, Heining C, Glimm H, Fröhlich M, Hübschmann D, Gallinger S, Fritsch R, Fröhling S, O'Kane GM, Dengjel J, Brummer T. BRAF Δβ3-αC in-frame deletion mutants differ in their dimerization propensity, HSP90 dependence, and druggability. SCIENCE ADVANCES 2023; 9:eade7486. [PMID: 37656784 DOI: 10.1126/sciadv.ade7486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 08/02/2023] [Indexed: 09/03/2023]
Abstract
In-frame BRAF exon 12 deletions are increasingly identified in various tumor types. The resultant BRAFΔβ3-αC oncoproteins usually lack five amino acids in the β3-αC helix linker and sometimes contain de novo insertions. The dimerization status of BRAFΔβ3-αC oncoproteins, their precise pathomechanism, and their direct druggability by RAF inhibitors (RAFi) has been under debate. Here, we functionally characterize BRAFΔLNVTAP>F and two novel mutants, BRAFdelinsFS and BRAFΔLNVT>F, and compare them with other BRAFΔβ3-αC oncoproteins. We show that BRAFΔβ3-αC oncoproteins not only form stable homodimers and large multiprotein complexes but also require dimerization. Nevertheless, details matter as aromatic amino acids at the deletion junction of some BRAFΔβ3-αC oncoproteins, e.g., BRAFΔLNVTAP>F, increase their stability and dimerization propensity while conferring resistance to monomer-favoring RAFi such as dabrafenib or HSP 90/CDC37 inhibition. In contrast, dimer-favoring inhibitors such as naporafenib inhibit all BRAFΔβ3-αC mutants in cell lines and patient-derived organoids, suggesting that tumors driven by such oncoproteins are vulnerable to these compounds.
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Affiliation(s)
- Manuel Lauinger
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Daniel Christen
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Rhena F U Klar
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Freeze-O Organoid Bank, University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Internal Medicine I (Hematology, Oncology, and Stem Cell Transplantation), University Hospital of Freiburg, Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Carole Roubaty
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Christoph E Heilig
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Michael Stumpe
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Jennifer J Knox
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nikolina Radulovich
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Laura Tamblyn
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Irene Y Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Peter Horak
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Andrea Forschner
- Department of Dermatology, University Hospital of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University, Tübingen, Germany
| | - Michael Bitzer
- German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University, Tübingen, Germany
- Center for Personalized Medicine Tübingen, Eberhard Karls University, Tübingen, Germany
- Department of Internal Medicine I, Eberhard-Karls University, Tübingen, Germany
| | - Uwe A Wittel
- Department of General and Visceral Surgery, University of Freiburg Medical Center, Faculty of Medicine, 79106 Freiburg, Germany
| | - Melanie Boerries
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Claudia R Ball
- Department for Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Technische Universität Dresden, Faculty of Biology, Technische Universität Dresden, Dresden, Germany
| | - Christoph Heining
- Department for Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
| | - Hanno Glimm
- Department for Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), Dresden, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Fröhlich
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Hübschmann
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Pattern Recognition and Digital Medicine Group, Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Steven Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ralph Fritsch
- Department of Internal Medicine I (Hematology, Oncology, and Stem Cell Transplantation), University Hospital of Freiburg, Freiburg, Germany
- Department of Medical Oncology and Haematology, University Hospital of Zurich, Zurich, Switzerland
| | - Stefan Fröhling
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Grainne M O'Kane
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Tilman Brummer
- Institute of Molecular Medicine, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Freeze-O Organoid Bank, University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Center for Biological Signalling Studies BIOSS, University of Freiburg, 79104 Freiburg, Germany
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Deng X, Zhang M, Wang J, Zhou X, Xiao M. Characterization of clonal immunoglobulin heavy V-D-J gene rearrangements in Chinese patients with chronic lymphocytic leukemia: Clinical features and molecular profiles. Front Oncol 2023; 13:1120867. [PMID: 36874132 PMCID: PMC9978106 DOI: 10.3389/fonc.2023.1120867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 01/26/2023] [Indexed: 02/18/2023] Open
Abstract
Introduction Several prognostic factors of chronic lymphocytic leukemia (CLL) have been identified, such as cytogenetic aberrations and recurrent gene mutations. B-cell receptor (BCR) signaling plays an important role in the tumorigenesis of CLL, and its clinical significance in predicting prognosis is also under study. Methods Therefore, we assessed the already-known prognostic markers, immunoglobulin heavy chain (IGH) gene usage and the associations among these factors in 71 patients diagnosed with CLL in our center from October 2017 to March 2022. Sequencing of IGH gene rearrangements was performed using Sanger sequencing or IGH-based next-generation sequencing, and the results were further analyzed for distinct IGH/IGHD/IGHJ genes and the mutational status of the clonotypic IGHV (IGH variable) gene. Results In summary, by analyzing the distribution of potential prognostic factors in CLL patients, we displayed a landscape of molecular profiles, confirmed the predictive value of recurrent genetic mutations and chromosome aberrations, and found that IGHJ3 was associated with favorable markers (mutated IGHV, trisomy 12), while IGHJ6 tended to correlate with unfavorable factors (unmutated IGHV, del17p). Discussion These results provided an indication for IGH gene sequencing in predicting the prognosis of CLL.
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Affiliation(s)
- Xinyue Deng
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, China
| | - Meilan Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, China
| | - Jiachen Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, China
| | - Xiaoxi Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, China
| | - Min Xiao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, China
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7
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Yao PA, Sun HJ, Li XY. Identification of key genes in late-onset major depressive disorder through a co-expression network module. Front Genet 2022; 13:1048761. [PMID: 36561317 PMCID: PMC9763307 DOI: 10.3389/fgene.2022.1048761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
Late-onset major depressive disorder (LOD) increases the risk of disability and suicide in elderly patients. However, the complex pathological mechanism of LOD still remains unclear. We selected 10 LOD patients and 12 healthy control samples from the GSE76826 dataset for statistical analysis. Under the screening criteria, 811 differentially expressed genes (DEGs) were screened. We obtained a total of two most clinically significant modules through the weighted gene co-expression network analysis (WGCNA). Functional analysis of the genes in the most clinically significant modules was performed to explore the potential mechanism of LOD, followed by protein-protein interaction (PPI) analysis and hub gene identification in the core area of the PPI network. Furthermore, we identified immune infiltrating cells using the cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) algorithm between healthy subjects and LOD patients with the GSE98793 dataset. Next, six hub genes (CD27, IL7R, CXCL1, CCR7, IGLL5, and CD79A) were obtained by intersecting hub genes with DEGs, followed by verifying the diagnostic accuracy with the receiver operating characteristic curve (ROC). In addition, we constructed the least absolute shrinkage and selection operator (LASSO) regression model for hub gene cross-validation. Finally, we found that CD27 and IGLL5 were good diagnostic indicators of LOD, and CD27 may be the key gene of immune function change in LOD. In conclusion, our research shows that the changes in the immune function may be an important mechanism in the development of LOD, which can provide some guidance for the related research of LOD in the future.
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Affiliation(s)
- Ping-An Yao
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China,Department of Neurobiology and Acupuncture Research, The Third Clinical Medical College, Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Hangzhou, China
| | - Hai-Ju Sun
- Department of Neurobiology and Acupuncture Research, The Third Clinical Medical College, Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Hangzhou, China
| | - Xiao-Yu Li
- Department of Neurobiology and Acupuncture Research, The Third Clinical Medical College, Zhejiang Chinese Medical University, Key Laboratory of Acupuncture and Neurology of Zhejiang Province, Hangzhou, China,The Third Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China,*Correspondence: Xiao-Yu Li,
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8
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Al‐Kuraishy HM, Al‐Gareeb AI, Mohammed AA, Alexiou A, Papadakis M, Batiha GE. The potential link between Covid-19 and multiple myeloma: A new saga. Immun Inflamm Dis 2022; 10:e701. [PMID: 36444620 PMCID: PMC9673426 DOI: 10.1002/iid3.701] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Covid-19 is considered a primary respiratory disease-causing viral pneumonia and, in severe cases, leads to acute lung injury and acute respiratory distress syndrome (ARDS). In addition, though, extra-pulmonary manifestations of Covid-19 have been shown. Furthermore, severe acute respiratory distress syndrome coronavirus type 2 (SARS-CoV-2) infection may coexist with several malignancies, including multiple myeloma (MM). METHODS This critical literature review aimed to find the potential association between SARS-CoV-2 infection and MM in Covid-19 patients with underlying MM. Narrative literature and databases search revealed that ARDS is developed in both MM and Covid-19 due to hypercalcemia and proteasome dysfunction. RESULTS Notably, the expression of angiogenic factors and glutamine deficiency could link Covid-19 severity and MM in the pathogenesis of cardiovascular complications. MM and Covid-19 share thrombosis as a typical complication; unlike thrombosis in Covid-19, which reflects disease severity, thrombosis does not reflect disease severity in MM. In both conditions, thromboprophylaxis is essential to prevent pulmonary thrombosis and other thromboembolic disorders. Moreover, Covid-19 may exacerbate the development of acute kidney injury and neurological complications in MM patients. CONCLUSION These findings highlighted that MM patients might be a risk group for Covid-19 severity due to underlying immunosuppression and most of those patients need specific management in the Covid-19 era.
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Affiliation(s)
- Hayder M. Al‐Kuraishy
- Department of Clinical Pharmacology and Medicine, College of MedicineALmustansiriyia UniversityBaghdadIraq
| | - Ali I. Al‐Gareeb
- Department of Clinical Pharmacology and Medicine, College of MedicineALmustansiriyia UniversityBaghdadIraq
| | - Ali A Mohammed
- The Chest Clinic, Barts Health NHS TrustWhipps Cross University HospitalLondonUK
| | - Athanasios Alexiou
- Department of Science and EngineeringNovel Global Community Educational FoundationHebershamAustralia
- AFNP MedWienAustria
| | - Marios Papadakis
- Department of Surgery II, University Hospital Witten‐HerdeckeUniversity of Witten‐HerdeckeWuppertalGermany
| | - Gaber El‐Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary MedicineDamanhour UniversityDamanhourEgypt
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Sudha P, Ahsan A, Ashby C, Kausar T, Khera A, Kazeroun MH, Hsu CC, Wang L, Fitzsimons E, Salminen O, Blaney P, Czader M, Williams J, Abu Zaid MI, Ansari-Pour N, Yong KL, van Rhee F, Pierceall WE, Morgan GJ, Flynt E, Gooding S, Abonour R, Ramasamy K, Thakurta A, Walker BA. Myeloma Genome Project Panel is a Comprehensive Targeted Genomics Panel for Molecular Profiling of Patients with Multiple Myeloma. Clin Cancer Res 2022; 28:2854-2864. [PMID: 35522533 PMCID: PMC9250632 DOI: 10.1158/1078-0432.ccr-21-3695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/11/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE We designed a comprehensive multiple myeloma targeted sequencing panel to identify common genomic abnormalities in a single assay and validated it against known standards. EXPERIMENTAL DESIGN The panel comprised 228 genes/exons for mutations, 6 regions for translocations, and 56 regions for copy number abnormalities (CNA). Toward panel validation, targeted sequencing was conducted on 233 patient samples and further validated using clinical FISH (translocations), multiplex ligation probe analysis (MLPA; CNAs), whole-genome sequencing (WGS; CNAs, mutations, translocations), or droplet digital PCR (ddPCR) of known standards (mutations). RESULTS Canonical immunoglobulin heavy chain translocations were detected in 43.2% of patients by sequencing, and aligned with FISH except for 1 patient. CNAs determined by sequencing and MLPA for 22 regions were comparable in 103 samples and concordance between platforms was R2 = 0.969. Variant allele frequency (VAF) for 74 mutations were compared between sequencing and ddPCR with concordance of R2 = 0.9849. CONCLUSIONS In summary, we have developed a targeted sequencing panel that is as robust or superior to FISH and WGS. This molecular panel is cost-effective, comprehensive, clinically actionable, and can be routinely deployed to assist risk stratification at diagnosis or posttreatment to guide sequencing of therapies.
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Affiliation(s)
- Parvathi Sudha
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
| | - Aarif Ahsan
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
| | - Cody Ashby
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Tasneem Kausar
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
| | - Akhil Khera
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Mohammad H. Kazeroun
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Chih-Chao Hsu
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
| | - Lin Wang
- Department of Pathology and Laboratory Research, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
| | | | - Outi Salminen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Patrick Blaney
- Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Magdalena Czader
- Department of Pathology and Laboratory Research, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
| | - Jonathan Williams
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Mohammad I. Abu Zaid
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
| | - Naser Ansari-Pour
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Kwee L. Yong
- Cancer Institute, University College London, London, United Kingdom
| | - Frits van Rhee
- Myeloma Center, Winthrop P. Rockefeller Cancer institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | | | - Gareth J. Morgan
- Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Erin Flynt
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
| | - Sarah Gooding
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Oxford Center for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
| | - Rafat Abonour
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
| | - Karthik Ramasamy
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- Oxford Center for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Anjan Thakurta
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
- Oxford Center for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Brian A. Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
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10
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Zhao A, Wu F, Wang Y, Li J, Xu W, Liu H. Analysis of Genetic Alterations in Ocular Adnexal Mucosa-Associated Lymphoid Tissue Lymphoma With Whole-Exome Sequencing. Front Oncol 2022; 12:817635. [PMID: 35359413 PMCID: PMC8962736 DOI: 10.3389/fonc.2022.817635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Next-generation sequencing studies on ocular adnexal marginal zone lymphoma of mucosa-associated lymphoid tissue (OAML) have to date revealed several targets of genetic aberrations. However, most of our current understanding of the pathogenesis and prognosis of OAML is primarily based on studies conducted in populations from Europe and the US. Furthermore, the majority were based on formalin-fixed paraffin-embedded (FFPE) tissue, which generally has poor integrity and creates many sequencing artifacts. To better investigate the coding genome landscapes of OAML, especially in the Chinese population, we performed whole-exome sequencing of 21 OAML cases with fresh frozen tumor tissue and matched peripheral blood samples. IGLL5, as a novel recurrently mutated gene, was found in 24% (5/21) of patients, with a higher relapse rate (P=0.032). In addition, mutations of MSH6, DIS3, FAT1, and TMEM127 were found in 10% of cases. These novel somatic mutations indicate the existence of additional/alternative lymphomagenesis pathways in OAML. Moreover, the difference between our and previous studies suggests genetic heterogeneity of OAML between Asian and Western individuals.
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Affiliation(s)
- Andi Zhao
- Department of Ophthalmology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- The First Clinical Medical College, Nanjing Medical University, Nanjing, China
| | - Fangtian Wu
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University Jiangsu Province Hospital, Nanjing, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Yue Wang
- Department of Ophthalmology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- The First Clinical Medical College, Nanjing Medical University, Nanjing, China
| | - Jianyong Li
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University Jiangsu Province Hospital, Nanjing, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- *Correspondence: Hu Liu, ; Wei Xu, ; Jianyong Li,
| | - Wei Xu
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University Jiangsu Province Hospital, Nanjing, China
- Key Laboratory of Hematology, Nanjing Medical University, Nanjing, China
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- *Correspondence: Hu Liu, ; Wei Xu, ; Jianyong Li,
| | - Hu Liu
- Department of Ophthalmology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- The First Clinical Medical College, Nanjing Medical University, Nanjing, China
- *Correspondence: Hu Liu, ; Wei Xu, ; Jianyong Li,
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11
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Oben B, Cosemans C, Geerdens E, Linsen L, Vanhees K, Maes B, Theunissen K, Cruys B, Lionetti M, Arijs I, Bolli N, Froyen G, Rummens JL. The Dynamics of Nucleotide Variants in the Progression from Low-Intermediate Myeloma Precursor Conditions to Multiple Myeloma: Studying Serial Samples with a Targeted Sequencing Approach. Cancers (Basel) 2022; 14:cancers14041035. [PMID: 35205782 PMCID: PMC8870380 DOI: 10.3390/cancers14041035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/28/2022] [Accepted: 02/16/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Multiple myeloma (MM), characterized by the expansion of plasma cells in the bone marrow, is the second most common hematological malignancy. This incurable cancer is consistently preceded by non-malignant asymptomatic precursor conditions known as monoclonal gammopathy of undetermined significance (MGUS) and/or smoldering multiple myeloma (SMM). These pre-stages are relatively frequent, but only a select percentage of them will progress to MM. However, it is still not possible to individually predict when and which patients will develop MM. Therefore, this study aimed to investigate the mutational profile in the progression in serial bone marrow samples with a custom targeted sequencing panel, designed to detect variants in myeloma-related genes. Remarkably, almost all variants identified in the MM samples were also already present in the pre-stages, sometimes even many years before the progression. These results provide new important insights into the molecular mechanisms of the precursor conditions and progression to MM. Abstract Multiple myeloma (MM), or Kahler’s disease, is an incurable plasma cell (PC) cancer in the bone marrow (BM). This malignancy is preceded by one or more asymptomatic precursor conditions, monoclonal gammopathy of undetermined significance (MGUS) and/or smoldering multiple myeloma (SMM). The molecular mechanisms and exact cause of this progression are still not completely understood. In this study, the mutational profile underlying the progression from low–intermediate risk myeloma precursor conditions to MM was studied in serial BM smears. A custom capture-based sequencing platform was developed, including 81 myeloma-related genes. The clonal evolution of single nucleotide variants and short insertions and deletions was studied in serial BM smears from 21 progressed precursor patients with a median time of progression of six years. From the 21 patients, four patients had no variation in one of the 81 studied genes. Interestingly, in 16 of the 17 other patients, at least one variant present in MM was also detected in its precursor BM, even years before progression. Here, the variants were present in the pre-stage at a median of 62 months before progression to MM. Studying these paired BM samples contributes to the knowledge of the evolutionary genetic landscape and provides additional insight into the mutational behavior of mutant clones over time throughout progression.
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Affiliation(s)
- Bénedith Oben
- Laboratory Experimental Hematology, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (C.C.); (L.L.); (J.-L.R.)
- Faculty of Medicine and Life Sciences, Hasselt University, 3500 Hasselt, Belgium; (K.V.); (I.A.); (G.F.)
- Correspondence:
| | - Charlotte Cosemans
- Laboratory Experimental Hematology, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (C.C.); (L.L.); (J.-L.R.)
- Faculty of Medicine and Life Sciences, Hasselt University, 3500 Hasselt, Belgium; (K.V.); (I.A.); (G.F.)
- Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Ellen Geerdens
- Laboratory Molecular Diagnostics, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (E.G.); (B.M.); (B.C.)
| | - Loes Linsen
- Laboratory Experimental Hematology, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (C.C.); (L.L.); (J.-L.R.)
- Activity Center Biobanking, University Hospitals Leuven, 3000 Leuven, Belgium
- University Biobank Limburg (UBiLim), Clinical Biobank, Jessa Hospital, 3500 Hasselt, Belgium
| | - Kimberly Vanhees
- Faculty of Medicine and Life Sciences, Hasselt University, 3500 Hasselt, Belgium; (K.V.); (I.A.); (G.F.)
- University Biobank Limburg (UBiLim), Clinical Biobank, Jessa Hospital, 3500 Hasselt, Belgium
| | - Brigitte Maes
- Laboratory Molecular Diagnostics, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (E.G.); (B.M.); (B.C.)
| | - Koen Theunissen
- Department Hematology, Jessa Hospital, 3500 Hasselt, Belgium;
| | - Bert Cruys
- Laboratory Molecular Diagnostics, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (E.G.); (B.M.); (B.C.)
| | - Marta Lionetti
- Department Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (M.L.); (N.B.)
| | - Ingrid Arijs
- Faculty of Medicine and Life Sciences, Hasselt University, 3500 Hasselt, Belgium; (K.V.); (I.A.); (G.F.)
- Laboratory for Translational Genetics, Department Human Genetics, University of Leuven, 3000 Leuven, Belgium
- Belgian Inflammatory Bowel Disease Research and Development (BIRD), 1930 Zaventem, Belgium
| | - Niccolò Bolli
- Department Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (M.L.); (N.B.)
- Unità Operativa Complessa di Ematologia, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Guy Froyen
- Faculty of Medicine and Life Sciences, Hasselt University, 3500 Hasselt, Belgium; (K.V.); (I.A.); (G.F.)
- Laboratory Molecular Diagnostics, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (E.G.); (B.M.); (B.C.)
| | - Jean-Luc Rummens
- Laboratory Experimental Hematology, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (C.C.); (L.L.); (J.-L.R.)
- Faculty of Medicine and Life Sciences, Hasselt University, 3500 Hasselt, Belgium; (K.V.); (I.A.); (G.F.)
- University Biobank Limburg (UBiLim), Clinical Biobank, Jessa Hospital, 3500 Hasselt, Belgium
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12
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Zheng B, Xie F, Cheng F, Wang J, Yao Z, He W, Niu Z. Integrative Analysis of Immune-Related Genes in the Tumor Microenvironment of Renal Clear Cell Carcinoma and Renal Papillary Cell Carcinoma. Front Mol Biosci 2021; 8:760031. [PMID: 34888353 PMCID: PMC8650138 DOI: 10.3389/fmolb.2021.760031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/15/2021] [Indexed: 12/12/2022] Open
Abstract
Kidney cancer encompasses a range of primary cancers, such as clear cell renal cell carcinoma (ccRCC) and papillary renal cell carcinoma (pRCC). Our knowledge about the tumor microenvironment (TME) of kidney cancer is still limited. Therefore, we comprehensively assessed the TME of kidney cancers (including ccRCC and pRCC) using the ESTIAMTE, and CIBERSORT algorithms, and conducted distinct functional and correlation analyses with data from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), Gene Expression Omnibus (GEO), Connectivity map and CellMiner database. Next, we identified two immune-related hub genes, IGLL5 and IL2RA, which play essential roles in the TME as well as on survival in ccRCC and pRCC. Furthermore, ccRCC and pRCC samples from our medical center were collected to verify the clinical application value of these two immune-related genes. A specific enrichment analysis of immune cells related to IGLL5 and IL2RA was also conducted in two types of renal cell cancer. Based on selected genes, we predicted the drug response and uncovered novel drug candidate for RCC treatment. Considering the unfavorable outcomes of kidney cancer and emerging interest in TME-targeted treatments, our results may offer insights into immune-related molecular mechanisms and possible targets to control the kidney cancer.
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Affiliation(s)
- Bin Zheng
- Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Fang Xie
- Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Urology, Weihai Municipal Hospital, Weihai, China
| | - Fajuan Cheng
- Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China.,Department of Nephrology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jianwei Wang
- Department of Urology, Shandong Provincial ENT Hospital Affiliated to Shandong University, Jinan, China
| | - Zhongshun Yao
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Wei He
- Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Zhihong Niu
- Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.,Department of Urology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
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13
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Molecular interactions of IRF4 in B cell development and malignancies. Biophys Rev 2021; 13:1219-1227. [DOI: 10.1007/s12551-021-00825-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 07/29/2021] [Indexed: 10/20/2022] Open
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14
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Aksenova AY, Zhuk AS, Lada AG, Zotova IV, Stepchenkova EI, Kostroma II, Gritsaev SV, Pavlov YI. Genome Instability in Multiple Myeloma: Facts and Factors. Cancers (Basel) 2021; 13:5949. [PMID: 34885058 PMCID: PMC8656811 DOI: 10.3390/cancers13235949] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/20/2021] [Accepted: 11/22/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple myeloma (MM) is a malignant neoplasm of terminally differentiated immunoglobulin-producing B lymphocytes called plasma cells. MM is the second most common hematologic malignancy, and it poses a heavy economic and social burden because it remains incurable and confers a profound disability to patients. Despite current progress in MM treatment, the disease invariably recurs, even after the transplantation of autologous hematopoietic stem cells (ASCT). Biological processes leading to a pathological myeloma clone and the mechanisms of further evolution of the disease are far from complete understanding. Genetically, MM is a complex disease that demonstrates a high level of heterogeneity. Myeloma genomes carry numerous genetic changes, including structural genome variations and chromosomal gains and losses, and these changes occur in combinations with point mutations affecting various cellular pathways, including genome maintenance. MM genome instability in its extreme is manifested in mutation kataegis and complex genomic rearrangements: chromothripsis, templated insertions, and chromoplexy. Chemotherapeutic agents used to treat MM add another level of complexity because many of them exacerbate genome instability. Genome abnormalities are driver events and deciphering their mechanisms will help understand the causes of MM and play a pivotal role in developing new therapies.
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Affiliation(s)
- Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anna S. Zhuk
- International Laboratory “Computer Technologies”, ITMO University, 197101 St. Petersburg, Russia;
| | - Artem G. Lada
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA;
| | - Irina V. Zotova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Elena I. Stepchenkova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Ivan I. Kostroma
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Sergey V. Gritsaev
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Departments of Biochemistry and Molecular Biology, Microbiology and Pathology, Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
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15
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Park H, Kim I, Kim HJ, Shin DY, Lee SY, Kwon OH, Kim DY, Lee KH, Ahn JS, Park J, Sohn SK, Lee JO, Cheong JW, Kim KH, Kim HG, Kim H, Lee YJ, Nam SH, Do YR, Park SG, Park SK, Bae SH, Song HH, Oh D, Jung CW, Park S. Ultra-deep sequencing mutation analysis of the BCR/ABL1 kinase domain in newly diagnosed chronic myeloid leukemia patients. Leuk Res 2021; 111:106728. [PMID: 34673444 DOI: 10.1016/j.leukres.2021.106728] [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: 02/28/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 11/28/2022]
Abstract
Ultra-deep sequencing detects low-frequency genetic mutations with high sensitivity. We used this approach to prospectively examine mutations in the BCR/ABL1 tyrosine kinase from patients with newly diagnosed, chronic-phase chronic myeloid leukemia (CML) treated with the tyrosine kinase inhibitor nilotinib. Between May 2013 and November 2014, 50 patients from 18 institutions were enrolled in the study. We screened 103 somatic mutations and found that mutations in the P-loop domain were the most frequent (173/454 mutations in the P-loop) and noted the presence of the V299 L mutation (dasatinib-resistant/nilotinib-sensitive) in 98 % of patients (49/50). No patients had Y253H, E255 V, or F359 V/C/I mutations, which would recommend dasatinib rather than nilotinib treatment. The S417Y mutation was associated with lower achievement of a major molecular response (MMR) at 6 months, and the V371A mutation was associated with reduced MMR and MR4.5 durations (MMR for 2 years: 100 % for no mutation vs. 75 % for mutation, P=0.039; MR4.5 for 15 months: 94.1 % vs. 25 %, P=0.002). Patients with known nilotinib-resistant mutations had lower rates of MR4.5 achievement. In conclusion, ultra-deep sequencing is a sensitive method for genetic-based treatment decisions. Based on the results of these mutational analyses, nilotinib treatment is a promising option for Korean patients with CML.
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Affiliation(s)
- Hyunkyung Park
- Department of Internal Medicine, Seoul National University Hospital, Biomedical Research Institute, Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea; Department of Internal Medicine, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul, South Korea
| | - Inho Kim
- Department of Internal Medicine, Seoul National University Hospital, Biomedical Research Institute, Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea.
| | - Hyeong-Joon Kim
- Department of Internal Medicine, Chonnam National University, Hwasun Hospital, Hwasun, South Korea.
| | - Dong-Yeop Shin
- Department of Internal Medicine, Seoul National University Hospital, Biomedical Research Institute, Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | | | | | - Dae-Young Kim
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Kyoo-Hyung Lee
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Jae-Sook Ahn
- Department of Internal Medicine, Chonnam National University, Hwasun Hospital, Hwasun, South Korea
| | - Jinny Park
- Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, South Korea
| | - Sang-Kyun Sohn
- Department of Internal Medicine, Kyungpook National University Hospital, Daegu, South Korea
| | - Jeong-Ok Lee
- Department of Internal Medicine, Seoul National University, Bundang Hospital, Seongnam, South Korea
| | - June-Won Cheong
- Department of Internal Medicine, Yonsei University, Severance Hospital, Seoul, South Korea
| | - Kyoung Ha Kim
- Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul, South Korea
| | - Hoon-Gu Kim
- Department of Internal Medicine, Gyeongsang Institute of Health Sciences, Gyeongsang National University College of Medicine and Gyeongsang National University Changwon Hospital, Changwon, South Korea
| | - Hawk Kim
- Department of Internal Medicine, Ulsan University Hospital, Ulsan, South Korea
| | - Yoo Jin Lee
- Department of Internal Medicine, Ulsan University Hospital, Ulsan, South Korea
| | - Seung-Hyun Nam
- Department of Internal Medicine, VHS Medical Center, Seoul, South Korea
| | - Young Rok Do
- Department of Internal Medicine, Keimyung University Dongsan Medical Center, Daegu, South Korea
| | - Sang-Gon Park
- Department of Internal Medicine, Chosun University Hospital, Gwangju, South Korea
| | - Seong Kyu Park
- Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, South Korea
| | - Sung Hwa Bae
- Department of Internal Medicine, Daegu Catholic University Medical Center, Daegu, South Korea
| | - Hun Ho Song
- Department of Internal Medicine, Kangdong Sacred Heart Hospital, Seoul, South Korea
| | - Doyeun Oh
- Department of Internal Medicine, CHA Bundang Medical Center, Seongnam, South Korea
| | - Chul Won Jung
- Department of Internal Medicine, Samsung Medical Center, Seoul, South Korea
| | - Seonyang Park
- Department of Internal Medicine, Inje University, Haeundae Paik Hospital, Busan, South Korea
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16
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Shafie A, Khan S, Batra S, Anjum F, Mohammad T, Alam S, Yadav DK, Islam A, Hassan MI. Investigating single amino acid substitutions in PIM1 kinase: A structural genomics approach. PLoS One 2021; 16:e0258929. [PMID: 34679086 PMCID: PMC8535467 DOI: 10.1371/journal.pone.0258929] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/09/2021] [Indexed: 12/30/2022] Open
Abstract
PIM1, is a serine/threonine proto-oncogene kinase, involved in many biological functions, including cell survival, proliferation, and differentiation, thus play a key role in oncogenesis. It plays a crucial role in the onset and progression of various hematopoietic and non-hematopoietic malignancies, including acute myeloid leukemia and prostate cancer. Mutations in PIM1, especially in its kinase domain, can induce abnormal structural changes and thus alter functionalities that can lead to disease progression and other complexities. Herein, we have performed an extensive analysis of the PIM1 mutations at sequence and structure level while utilizing state-of-the-art computational approaches. Based on the impact on PIM1, numerous pathogenic and destabilizing mutations were identified and subsequently analyzed in detail. Finally, two amino acid substitutions (W109C and F147C) in the kinase domain of PIM1 were selected to explore their impact on the PIM1 structure in a time evolution manner using all-atom molecular dynamics (MD) simulations for 200 ns. MD results indicate significant conformational altercations in the structure of PIM1, especially upon F147C mutation. This study provides a significant insight into the PIM1 dysfunction upon single amino acid substitutions, which can be utilized to get insights into the molecular basis of PIM1-associated disease progression.
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Affiliation(s)
- Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Shama Khan
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch, Cape Town, South Africa
| | - Sagar Batra
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, Rajasthan, India
| | - Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Shoaib Alam
- Department of Biotechnology, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Dharmendra Kumar Yadav
- College of Pharmacy, Gachon University of Medicine and Science, Yeonsu-gu, Incheon City, South Korea
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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Validation of the EuroClonality-NGS DNA capture panel as an integrated genomic tool for lymphoproliferative disorders. Blood Adv 2021; 5:3188-3198. [PMID: 34424321 DOI: 10.1182/bloodadvances.2020004056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/16/2021] [Indexed: 11/20/2022] Open
Abstract
Current diagnostic standards for lymphoproliferative disorders include multiple tests for detection of clonal immunoglobulin (IG) and/or T-cell receptor (TCR) rearrangements, translocations, copy-number alterations (CNAs), and somatic mutations. The EuroClonality-NGS DNA Capture (EuroClonality-NDC) assay was designed as an integrated tool to characterize these alterations by capturing IGH switch regions along with variable, diversity, and joining genes of all IG and TCR loci in addition to clinically relevant genes for CNA and mutation analysis. Diagnostic performance against standard-of-care clinical testing was assessed in a cohort of 280 B- and T-cell malignancies from 10 European laboratories, including 88 formalin-fixed paraffin-embedded samples and 21 reactive lesions. DNA samples were subjected to the EuroClonality-NDC protocol in 7 EuroClonality-NGS laboratories and analyzed using a bespoke bioinformatic pipeline. The EuroClonality-NDC assay detected B-cell clonality in 191 (97%) of 197 B-cell malignancies and T-cell clonality in 71 (97%) of 73 T-cell malignancies. Limit of detection (LOD) for IG/TCR rearrangements was established at 5% using cell line blends. Chromosomal translocations were detected in 145 (95%) of 152 cases known to be positive. CNAs were validated for immunogenetic and oncogenetic regions, highlighting their novel role in confirming clonality in somatically hypermutated cases. Single-nucleotide variant LOD was determined as 4% allele frequency, and an orthogonal validation using 32 samples resulted in 98% concordance. The EuroClonality-NDC assay is a robust tool providing a single end-to-end workflow for simultaneous detection of B- and T-cell clonality, translocations, CNAs, and sequence variants.
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18
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Zhang H, Zhang SH, Hu JL, Wu YT, Ma XY, Chen Y, Yu B, Liao S, Huang H, Gao S. Structural and functional characterization of multiple myeloma associated cytoplasmic poly(A) polymerase FAM46C. Cancer Commun (Lond) 2021; 41:615-630. [PMID: 34048638 PMCID: PMC8286142 DOI: 10.1002/cac2.12163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 03/28/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022] Open
Abstract
Background Multiple myeloma (MM) is a hematologic malignancy characterized by the accumulation of aberrant plasma cells within the bone marrow. The high frequent mutation of family with sequence similarity 46, member C (FAM46C) is closely related with the occurrence and progression of MM. Recently, FAM46C has been identified as a non‐canonical poly(A) polymerase (PAP) that functions as a tumor suppressor in MM. This study aimed to elucidate the structural features of this novel non‐canonical PAP and how MM‐related mutations affect the structural and biochemical properties of FAM46C, eventually advancing our understandings towards FAM46C mutation‐related MM occurrence. Methods We purified and crystallized a mammalian FAM46C construct, and solved its structure. Next, we characterized the property of FAM46C as a PAP through a combination of structural analysis, site‐directed mutagenesis and biochemical assays, and by comparison with its homolog FAM46B. Finally, we structurally analyzed MM‐related FAM46C mutations and tested the enzymatic activity of corresponding mutants. Results We determined the crystal structure of a mammalian FAM46C protein at 2.35 Å, and confirmed that FAM46C preferentially consumed adenosine triphosphate (ATP) and extended A‐rich RNA substrates. FAM46C showed a weaker PAP activity than its homolog FAM46B, and this difference was largely dependent on the residue variance at particular sites. Of them, residues at positions 77, 290, and 298 of mouse FAM46C were most important for the divergence in enzymatic activity. Among the MM‐associated FAM46C mutants, those residing at the catalytic site (D90G and D90H) or putative RNA‐binding site (I155L, S156F, D182Y, F184L, Y247V, and M270V) showed abolished or compromised PAP activity of FAM46C, while N72A and S248A did not severely affect the PAP activity. FAM46C mutants D90G, D90H, I155L, S156F, F184L, Y247V, and M270V had significantly lower inhibitory effect on apoptosis of RPMI‐8226 cells as compared to wild‐type FAM46C. Conclusions FAM46C is a prokaryotic‐like PAP with preference for A‐rich RNA substrates, and showed distinct enzymatic efficiency with its homolog FAM46B. The MM‐related missense mutations of FAM46C lead to various structural and biochemical outcomes to the protein.
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Affiliation(s)
- Hong Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Shi-Hui Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Jia-Li Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China.,Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, P. R. China
| | - Yu-Tong Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Xiao-Yan Ma
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Yang Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Bing Yu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Shuang Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Huilin Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Song Gao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, Guangdong, 510530, P. R. China
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19
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Lee N, Kim SM, Lee Y, Jeong D, Yun J, Ryu S, Yoon SS, Ahn YO, Hwang SM, Lee DS. Prognostic value of integrated cytogenetic, somatic variation, and copy number variation analyses in Korean patients with newly diagnosed multiple myeloma. PLoS One 2021; 16:e0246322. [PMID: 33544757 PMCID: PMC7864461 DOI: 10.1371/journal.pone.0246322] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/15/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND To investigate the prognostic value of gene variants and copy number variations (CNVs) in patients with newly diagnosed multiple myeloma (NDMM), an integrative genomic analysis was performed. METHODS Sixty-seven patients with NDMM exhibiting more than 60% plasma cells in the bone marrow aspirate were enrolled in the study. Whole-exome sequencing was conducted on bone marrow nucleated cells. Mutation and CNV analyses were performed using the CNVkit and Nexus Copy Number software. In addition, karyotype and fluorescent in situ hybridization were utilized for the integrated analysis. RESULTS Eighty-three driver gene mutations were detected in 63 patients with NDMM. The median number of mutations per patient was 2.0 (95% confidence interval [CI] = 2.0-3.0, range = 0-8). MAML2 and BHLHE41 mutations were associated with decreased survival. CNVs were detected in 56 patients (72.7%; 56/67). The median number of CNVs per patient was 6.0 (95% CI = 5.7-7.0; range = 0-16). Among the CNVs, 1q gain, 6p gain, 6q loss, 8p loss, and 13q loss were associated with decreased survival. Additionally, 1q gain and 6p gain were independent adverse prognostic factors. Increased numbers of CNVs and driver gene mutations were associated with poor clinical outcomes. Cluster analysis revealed that patients with the highest number of driver mutations along with 1q gain, 6p gain, and 13q loss exhibited the poorest prognosis. CONCLUSIONS In addition to the known prognostic factors, the integrated analysis of genetic variations and CNVs could contribute to prognostic stratification of patients with NDMM.
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Affiliation(s)
- Nuri Lee
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Korea
| | - Sung-Min Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Youngeun Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Dajeong Jeong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Jiwon Yun
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sohee Ryu
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sung-Soo Yoon
- Department of Internal Medicine, Clinical Research Institute, Seoul National University Hospital, Cancer Research Institute, Seoul National University, College of Medicine, Seoul, Korea
| | - Yong-Oon Ahn
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Sang Mee Hwang
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Dong Soon Lee
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
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20
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Xia ZN, Wang XY, Cai LC, Jian WG, Zhang C. IGLL5 is correlated with tumor-infiltrating immune cells in clear cell renal cell carcinoma. FEBS Open Bio 2021; 11:898-910. [PMID: 33449444 PMCID: PMC7931224 DOI: 10.1002/2211-5463.13085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/23/2020] [Accepted: 01/12/2021] [Indexed: 02/06/2023] Open
Abstract
Renal cell carcinomas (RCCs) account for about 90% of renal tumors, and their major histological subtype is ccRCC (clear cell RCC). Increasing evidence has indicated that the tumor microenvironment plays a significant role in the occurrence and development of ccRCC. In this study, we used ESTIMATE and CIBERSORT computational methods to calculate the proportion of immune and stromal components and the rate of TICs (tumor‐infiltrating immune cells) in 539 ccRCC samples from The Cancer Genome Atlas database. By examining the intersection of the differentially expressed genes obtained by the protein–protein interaction network and Cox regression analysis, we identified only one overlapping gene: IGLL5 (immunoglobulin lambda‐like polypeptide 5). We report that IGLL5 expression is correlated with TICs. Furthermore, our immunoinfiltration analyses revealed that three types of TIC are positively correlated with IGLL5 expression. IGLL5 may have potential as a prognostic biomarker of ccRCC.
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Affiliation(s)
- Zhi-Nan Xia
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, China
| | - Xing-Yuan Wang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, China
| | - Li-Cheng Cai
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, China
| | - Wen-Gang Jian
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, China
| | - Cheng Zhang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, China
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21
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Williams LS, Caro J, Razzo B, Boyle EM, Morgan GJ. Deep sequencing as an approach to understanding the complexity and improving the treatment of multiple myeloma. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2020. [DOI: 10.1080/23808993.2020.1792285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Louis S. Williams
- Department of Hematology & Medical Oncology, NYU Langone Medical Center, New York, NY, USA
| | - Jessica Caro
- Department of Hematology & Medical Oncology, NYU Langone Medical Center, New York, NY, USA
| | - Beatrice Razzo
- Department of Internal Medicine, NYU Langone Medical Center, New York, NY, USA
| | - Eileen M. Boyle
- Department of Hematology & Medical Oncology, Multiple Myeloma Research Program, NYU Langone Medical Center, New York, NY, USA
| | - Gareth J. Morgan
- Department of Hematology & Medical Oncology, Multiple Myeloma Research Program, NYU Langone Medical Center, New York, NY, USA
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Yasuda T, Sanada M, Nishijima D, Kanamori T, Iijima Y, Hattori H, Saito A, Miyoshi H, Ishikawa Y, Asou N, Usuki K, Hirabayashi S, Kato M, Ri M, Handa H, Ishida T, Shibayama H, Abe M, Iriyama C, Karube K, Nishikori M, Ohshima K, Kataoka K, Yoshida K, Shiraishi Y, Goto H, Adachi S, Kobayashi R, Kiyoi H, Miyazaki Y, Ogawa S, Kurahashi H, Yokoyama H, Manabe A, Iida S, Tomita A, Horibe K. Clinical utility of target capture-based panel sequencing in hematological malignancies: A multicenter feasibility study. Cancer Sci 2020; 111:3367-3378. [PMID: 32619037 PMCID: PMC7469806 DOI: 10.1111/cas.14552] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 01/22/2023] Open
Abstract
Although next-generation sequencing-based panel testing is well practiced in the field of cancer medicine for the identification of target molecules in solid tumors, the clinical utility and clinical issues surrounding panel testing in hematological malignancies have yet to be fully evaluated. We conducted a multicenter prospective clinical sequencing study to verify the feasibility of a panel test for hematological tumors, including acute myeloid leukemia, acute lymphoblastic leukemia, multiple myeloma, and diffuse large B-cell lymphoma. Out of 96 eligible patients, 79 patients (82%) showed potentially actionable findings, based on the clinical sequencing assays. We identified that genetic alterations with a strong clinical significance were found at a higher frequency in terms of diagnosis (n = 60; 63%) and prognosis (n = 61; 64%) than in terms of therapy (n = 8; 8%). Three patients who harbored a germline mutation in either DDX41 (n = 2) or BRCA2 (n = 1) were provided with genetic counseling. At 6 mo after sequencing, clinical actions based on the diagnostic (n = 5) or prognostic (n = 3) findings were reported, but no patients were enrolled in a clinical trial or received targeted therapies based on the sequencing results. These results suggest that panel testing for hematological malignancies would be feasible given the availability of useful diagnostic and prognostic information. This study is registered with the UMIN Clinical Trial Registry (UMIN000029879, multiple myeloma; UMIN000031343, adult acute myeloid leukemia; UMIN000033144, diffuse large B-cell lymphoma; and UMIN000034243, childhood leukemia).
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23
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D'Agostino M, Zaccaria GM, Ziccheddu B, Rustad EH, Genuardi E, Capra A, Oliva S, Auclair D, Yesil J, Colucci P, Keats JJ, Gambella M, Bringhen S, Larocca A, Boccadoro M, Bolli N, Maura F, Gay F. Early Relapse Risk in Patients with Newly Diagnosed Multiple Myeloma Characterized by Next-generation Sequencing. Clin Cancer Res 2020; 26:4832-4841. [DOI: 10.1158/1078-0432.ccr-20-0951] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/29/2020] [Accepted: 06/30/2020] [Indexed: 11/16/2022]
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24
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Thakral D, Das N, Basnal A, Gupta R. Cell-free DNA for genomic profiling and minimal residual disease monitoring in Myeloma- are we there yet? AMERICAN JOURNAL OF BLOOD RESEARCH 2020; 10:26-45. [PMID: 32685257 PMCID: PMC7364270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 06/11/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVE Multiple myeloma (MM), a plasma cell neoplasm, afflicts elder individuals accounting for 10% of hematologic malignancies. The MM plasma cells largely reside within the bone marrow niche and are accessible through an invasive bone marrow biopsy, which is challenging during serial monitoring of patients. In this setting, cell free DNA (cfDNA) may have a role to ascertain the molecular aberrations at diagnosis and in assessment of residual disease during therapy. The aim of this review was to explore the utility and current status of cfDNA in MM. METHOD PubMed was searched with terms including cell-free DNA, circulating-tumor DNA, Multiple Myeloma, diagnosis, genomic profiling, Minimal Residual Disease individually or in combination to shortlist the relevant studies. RESULT cfDNA serves as a non-invasive source of tumor-specific molecular biomarker, ctDNA that has immense potential in facilitating management of cancer patients. The mutation detection platforms for ctDNA include hybrid capture and ultra-deep sequencing. Hybrid capture allows full length gene sequencing for mutation and CNV detection. The disease progression can be monitored by profiling prognostic somatic copy number alterations by ultra-low pass whole genome sequencing of ctDNA cost-effectively. Evolution of both the laboratory protocols and bioinformatics tools may further improve the sensitivity of ctDNA detection for better disease management. Only a limited number of studies were available in MM exploring the potential utility of cfDNA. CONCLUSION In this review, we discuss the nuances and challenges associated with molecular evaluation of cfDNA and its potential role in diagnosis and monitoring of treatment response in MM.
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Affiliation(s)
- Deepshi Thakral
- Laboratory Oncology Unit, Dr BR Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences New Delhi, India
| | - Nupur Das
- Laboratory Oncology Unit, Dr BR Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences New Delhi, India
| | - Atul Basnal
- Laboratory Oncology Unit, Dr BR Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences New Delhi, India
| | - Ritu Gupta
- Laboratory Oncology Unit, Dr BR Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences New Delhi, India
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25
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Manzoni M, Marchica V, Storti P, Ziccheddu B, Sammarelli G, Todaro G, Pelizzoni F, Salerio S, Notarfranchi L, Pompa A, Baldini L, Bolli N, Neri A, Giuliani N, Lionetti M. Application of Next-Generation Sequencing for the Genomic Characterization of Patients with Smoldering Myeloma. Cancers (Basel) 2020; 12:cancers12051332. [PMID: 32456143 PMCID: PMC7281620 DOI: 10.3390/cancers12051332] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/12/2020] [Accepted: 05/20/2020] [Indexed: 12/12/2022] Open
Abstract
Genomic analysis could contribute to a better understanding of the biological determinants of the evolution of multiple myeloma (MM) precursor disease and an improved definition of high-risk patients. To assess the feasibility and value of next-generation sequencing approaches in an asymptomatic setting, we performed a targeted gene mutation analysis and a genome-wide assessment of copy number alterations (CNAs) by ultra-low-pass whole genome sequencing (ULP-WGS) in six patients with monoclonal gammopathy of undetermined significance and 25 patients with smoldering MM (SMM). Our comprehensive genomic characterization highlighted heterogeneous but substantial values of the tumor fraction, especially in SMM; a rather high degree of genomic complexity, in terms of both mutations and CNAs, and inter-patient variability; a higher incidence of gene mutations and CNAs in SMM, confirming ongoing evolution; intraclonal heterogeneity; and instances of convergent evolution. ULP-WGS of these patients proved effective in revealing the marked genome-wide level of their CNAs, most of which are not routinely investigated. Finally, the analysis of our small SMM cohort suggested that chr(8p) deletions, the DNA tumor fraction, and the number of alterations may have clinical relevance in the progression to overt MM. Although validation in larger series is mandatory, these findings highlight the promising impact of genomic approaches in the clinical management of SMM.
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Affiliation(s)
- Martina Manzoni
- Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy; (M.M.); (L.B.); (N.B.); (M.L.)
| | - Valentina Marchica
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (V.M.); (P.S.); (L.N.); (N.G.)
| | - Paola Storti
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (V.M.); (P.S.); (L.N.); (N.G.)
| | - Bachisio Ziccheddu
- Department of Clinical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy;
| | - Gabriella Sammarelli
- Hematology, “Azienda Ospedaliero-Universitaria di Parma”, 43126 Parma, Italy; (G.S.); (G.T.)
| | - Giannalisa Todaro
- Hematology, “Azienda Ospedaliero-Universitaria di Parma”, 43126 Parma, Italy; (G.S.); (G.T.)
| | - Francesca Pelizzoni
- Hematology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (F.P.); (S.S.); (A.P.)
| | - Simone Salerio
- Hematology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (F.P.); (S.S.); (A.P.)
| | - Laura Notarfranchi
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (V.M.); (P.S.); (L.N.); (N.G.)
| | - Alessandra Pompa
- Hematology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (F.P.); (S.S.); (A.P.)
| | - Luca Baldini
- Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy; (M.M.); (L.B.); (N.B.); (M.L.)
- Hematology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (F.P.); (S.S.); (A.P.)
| | - Niccolò Bolli
- Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy; (M.M.); (L.B.); (N.B.); (M.L.)
- Department of Clinical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy;
| | - Antonino Neri
- Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy; (M.M.); (L.B.); (N.B.); (M.L.)
- Hematology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (F.P.); (S.S.); (A.P.)
- Correspondence:
| | - Nicola Giuliani
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (V.M.); (P.S.); (L.N.); (N.G.)
- Hematology, “Azienda Ospedaliero-Universitaria di Parma”, 43126 Parma, Italy; (G.S.); (G.T.)
| | - Marta Lionetti
- Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy; (M.M.); (L.B.); (N.B.); (M.L.)
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26
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Hecht-Höger AM, Braun BC, Krause E, Meschede A, Krahe R, Voigt CC, Greenwood AD, Czirják GÁ. Plasma proteomic profiles differ between European and North American myotid bats colonized by Pseudogymnoascus destructans. Mol Ecol 2020; 29:1745-1755. [PMID: 32279365 DOI: 10.1111/mec.15437] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 03/27/2020] [Accepted: 04/01/2020] [Indexed: 12/18/2022]
Abstract
Emerging fungal diseases have become challenges for wildlife health and conservation. North American hibernating bat species are threatened by the psychrophilic fungus Pseudogymnoascus destructans (Pd) causing the disease called white-nose syndrome (WNS) with unprecedented mortality rates. The fungus is widespread in North America and Europe, however, disease is not manifested in European bats. Differences in epidemiology and pathology indicate an evolution of resistance or tolerance mechanisms towards Pd in European bats. We compared the proteomic profile of blood plasma in healthy and Pd-colonized European Myotis myotis and North American Myotis lucifugus in order to identify pathophysiological changes associated with Pd colonization, which might also explain the differences in bat survival. Expression analyses of plasma proteins revealed differences in healthy and Pd-colonized M. lucifugus, but not in M. myotis. We identified differentially expressed proteins for acute phase response, constitutive and adaptive immunity, oxidative stress defence, metabolism and structural proteins of exosomes and desmosomes, suggesting a systemic response against Pd in North American M. lucifugus but not European M. myotis. The differences in plasma proteomic profiles between European and North American bat species colonized by Pd suggest European bats have evolved tolerance mechanisms towards Pd infection.
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Affiliation(s)
| | - Beate C Braun
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Eberhard Krause
- Leibniz Institute for Molecular Pharmacology, Berlin, Germany
| | - Angelika Meschede
- Institute of Zoology II, University of Erlangen-Nuremberg, Erlangen, Germany
| | | | - Christian C Voigt
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Alex D Greenwood
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Gábor Á Czirják
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
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27
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Kanamori T, Sanada M, Ri M, Ueno H, Nishijima D, Yasuda T, Tachita T, Narita T, Kusumoto S, Inagaki A, Ishihara R, Murakami Y, Kobayashi N, Shiozawa Y, Yoshida K, Nakagawa MM, Nannya Y, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Horibe K, Handa H, Ogawa S, Iida S. Genomic analysis of multiple myeloma using targeted capture sequencing in the Japanese cohort. Br J Haematol 2020; 191:755-763. [PMID: 32386081 DOI: 10.1111/bjh.16720] [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: 02/16/2020] [Revised: 04/10/2020] [Accepted: 04/13/2020] [Indexed: 11/29/2022]
Abstract
Previous genomic studies have revealed the genomic landscape of myeloma cells. Although some of the genomic abnormalities shown are believed to be correlated to the molecular pathogenesis of multiple myeloma and/or clinical outcome, these correlations are not fully understood. The aim of this study is to elucidate the correlation between genomic abnormalities and clinical characteristics by targeted capture sequencing in the Japanese multiple myeloma cohort. We analysed 154 patients with newly diagnosed multiple myeloma. The analysis revealed that the study cohort consisted of a less frequent hyperdiploid subtype (37·0%) with relatively high frequencies of KRAS mutation (36·4%) and IGH-CCND1 translocation (26·6%) compared with previous reports. Moreover, our targeted capture sequencing strategy was able to detect rare IGH-associated chromosomal translocations, such as IGH-CCND2 and IGH-MAFA. Interestingly, all 10 patients harboured MAX mutations accompanied by 14q23 deletion. The patients with del(17p) exhibited an unfavourable clinical outcome, and the presence of KRAS mutation was associated with shorter survival in patients with multiple myeloma, harbouring IGH-CCND1. Thus, our study provides a detailed landscape of genomic abnormalities, which may have potential clinical application for patients with multiple myeloma.
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Affiliation(s)
- Takashi Kanamori
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Japan.,Clinical Research Center, National Hospital Organization Nagoya Medical Center, Japan
| | - Masashi Sanada
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Japan
| | - Masaki Ri
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Japan
| | - Hiroo Ueno
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Dai Nishijima
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Japan
| | - Takahiko Yasuda
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Japan
| | - Takuto Tachita
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Japan
| | - Tomoko Narita
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Japan
| | - Shigeru Kusumoto
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Japan
| | - Atsushi Inagaki
- Department of Hematology and Oncology, Nagoya City West Medical Center, Japan
| | - Rei Ishihara
- Department of Laboratory Science, Gunma University Graduate School of Health Science, Japan
| | - Yuki Murakami
- Department of Laboratory Science, Gunma University Graduate School of Health Science, Japan
| | - Nobuhiko Kobayashi
- Department of Hematology, Gunma University Graduate School of Medicine, Japan
| | - Yusuke Shiozawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan.,Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | | | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Yuichi Shiraishi
- Division of Cellular Signaling, National Cancer Center Research Institute, Japan
| | - Kenichi Chiba
- Human Genome Center, Institute of Medical Science, The University of Tokyo, Japan
| | - Hiroko Tanaka
- Human Genome Center, Institute of Medical Science, The University of Tokyo, Japan
| | - Satoru Miyano
- Human Genome Center, Institute of Medical Science, The University of Tokyo, Japan
| | - Keizo Horibe
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Japan
| | - Hiroshi Handa
- Department of Laboratory Science, Gunma University Graduate School of Health Science, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan.,Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.,Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Japan
| | - Shinsuke Iida
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Japan
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Buedts L, Smits S, Ameye G, Lehnert S, Ding J, Delforge M, Vermeesch J, Boeckx N, Tousseyn T, Michaux L, Vandenberghe P, Dewaele B. Ultra-low depth sequencing of plasma cell DNA for the detection of copy number aberrations in multiple myeloma. Genes Chromosomes Cancer 2020; 59:465-471. [PMID: 32259320 DOI: 10.1002/gcc.22848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 03/22/2020] [Accepted: 04/01/2020] [Indexed: 12/31/2022] Open
Abstract
Cytogenetic abnormalities are powerful prognostic factors in multiple myeloma (MM) and are routinely analyzed by FISH on bone marrow (BM) plasma cells (PC). Although considered the gold standard, FISH experiments can be laborious and expensive. Therefore, array-CGH (aCGH) has been introduced as an alternative approach for detecting copy number aberrations (CNA), reducing the number of FISH experiments per case and yielding genome-wide information. Currently, next generation sequencing (NGS) technologies offer new perspectives for the diagnostic workup of malignant disorders. In this study, we examined ultra-low depth whole genome sequencing (LDS) as a valid alternative for aCGH for the detection of CNA in BM PC in MM. To this end, BM aspirates obtained in a diagnostic setting from 20 MM cases were analyzed. CD138+ cell-sorted samples were subjected to FISH analysis. DNA was extracted for subsequent aCGH and LDS analysis. CNA were detected by aCGH and LDS in all but one case. Importantly, all CNA identified by parallel first generation aCGH analysis were also detected by LDS, along with six additional CNA in five cases. One of these additional aberrations was in a region of prognostic importance in MM and was confirmed using FISH. However, risk stratification in these particular cases was unaffected. Thus, a perfectly concordant prognostication between array-CGH and LDS was observed. This validates LDS as a novel and cost-efficient tool for the detection of CNA in MM.
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Affiliation(s)
| | - Sanne Smits
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Geneviève Ameye
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | | | - Jia Ding
- Genomics Core, KU Leuven, Leuven, Belgium
| | - Michel Delforge
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Joris Vermeesch
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium.,Genomics Core, KU Leuven, Leuven, Belgium
| | - Nancy Boeckx
- Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium.,Department of Oncology, KU Leuven, Leuven, Belgium
| | - Thomas Tousseyn
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Lucienne Michaux
- Center for Human Genetics, KU Leuven, Leuven, Belgium.,Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Peter Vandenberghe
- Center for Human Genetics, KU Leuven, Leuven, Belgium.,Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Barbara Dewaele
- Center for Human Genetics, KU Leuven, Leuven, Belgium.,Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
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29
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Wan B, Liu B, Huang Y, Lv C. Identification of genes of prognostic value in the ccRCC microenvironment from TCGA database. Mol Genet Genomic Med 2020; 8:e1159. [PMID: 32012488 PMCID: PMC7196483 DOI: 10.1002/mgg3.1159] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/24/2019] [Accepted: 01/13/2020] [Indexed: 12/12/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is the most common pathological subtype of renal cell carcinoma. Bioinformatics analyses were used to screen candidate genes associated with the prognosis and microenvironment of ccRCC and elucidate the underlying molecular mechanisms of action. Methods The gene expression profiles and clinical data of ccRCC patients were downloaded from The Cancer Genome Atlas database. The ESTIMATE algorithm was used to compute the immune and stromal scores of patients. Based on the median immune/stromal scores, all patients were sorted into low‐ and high‐immune/stromal score groups. Differentially expressed genes (DEGs) were extracted from high‐ versus low‐immune/stromal score groups and were described using functional annotations and protein‒protein interaction (PPI) network. Results Patients in the high‐immune/stromal score group had poorer survival outcome. In total, 95 DEGs (48 upregulated and 47 downregulated genes) were screened from the gene expression profiles of patients with high immune and stromal scores. The genes were primarily involved in six signaling pathways. Among the 95 DEGs, 43 were markedly related to overall survival of patients. The PPI network identified the top 10 hub genes—CD19, CD79A, IL10, IGLL5, POU2AF1, CCL19, AMBP, CCL18, CCL21, and IGJ—and four modules. Enrichment analyses revealed that the genes in the most important module were involved in the B‐cell receptor signaling pathway. Conclusion This study mainly revealed the relationship between the ccRCC microenvironment and prognosis of patients. These results also increase the understanding of how gene expression patterns can impact the prognosis and development of ccRCC by modulating the tumor microenvironment. The results could contribute to the search for ccRCC biomarkers and therapeutic targets.
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Affiliation(s)
- Bangbei Wan
- Department of Urology, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, Hainan, China
| | - Bo Liu
- Laboratory of Developmental Cell Biology and Disease, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yuan Huang
- Department of Neurology, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, Hainan, China
| | - Cai Lv
- Department of Urology, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, Hainan, China
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Abstract
The evolutionarily conserved RNA exosome is a multisubunit ribonuclease complex that processes and/or degrades numerous RNAs. Recently, mutations in genes encoding both structural and catalytic subunits of the RNA exosome have been linked to human disease. Mutations in the structural exosome gene EXOSC2 cause a distinct syndrome that includes retinitis pigmentosa, hearing loss, and mild intellectual disability. In contrast, mutations in the structural exosome genes EXOSC3 and EXOSC8 cause pontocerebellar hypoplasia type 1b (PCH1b) and type 1c (PCH1c), respectively, which are related autosomal recessive, neurodegenerative diseases. In addition, mutations in the structural exosome gene EXOSC9 cause a PCH-like disease with cerebellar atrophy and spinal motor neuronopathy. Finally, mutations in the catalytic exosome gene DIS3 have been linked to multiple myeloma, a neoplasm of plasma B cells. How mutations in these RNA exosome genes lead to distinct, tissue-specific diseases is not currently well understood. In this chapter, we examine the role of the RNA exosome complex in human disease and discuss the mechanisms by which mutations in different exosome subunit genes could impair RNA exosome function and give rise to diverse diseases.
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Affiliation(s)
- Milo B Fasken
- Department of Biology, RRC 1021, Emory University, Atlanta, GA, USA.
| | - Derrick J Morton
- Department of Biology, RRC 1021, Emory University, Atlanta, GA, USA
| | - Emily G Kuiper
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Stephanie K Jones
- Department of Biology, RRC 1021, Emory University, Atlanta, GA, USA
- Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA, USA
| | - Sara W Leung
- Department of Biology, RRC 1021, Emory University, Atlanta, GA, USA
| | - Anita H Corbett
- Department of Biology, RRC 1021, Emory University, Atlanta, GA, USA.
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31
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Smadbeck J, Peterson JF, Pearce KE, Pitel BA, Figueroa AL, Timm M, Jevremovic D, Shi M, Stewart AK, Braggio E, Riggs DL, Bergsagel PL, Vasmatzis G, Kearney HM, Hoppman NL, Ketterling RP, Kumar S, Rajkumar SV, Greipp PT, Baughn LB. Mate pair sequencing outperforms fluorescence in situ hybridization in the genomic characterization of multiple myeloma. Blood Cancer J 2019; 9:103. [PMID: 31844041 PMCID: PMC6914798 DOI: 10.1038/s41408-019-0255-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/21/2019] [Accepted: 11/04/2019] [Indexed: 02/07/2023] Open
Abstract
Fluorescence in situ hybridization (FISH) is currently the gold-standard assay to detect recurrent genomic abnormalities of prognostic significance in multiple myeloma (MM). Since most translocations in MM involve a position effect with heterogeneous breakpoints, we hypothesize that FISH has the potential to miss translocations involving these regions. We evaluated 70 bone marrow samples from patients with plasma cell dyscrasia by FISH and whole-genome mate-pair sequencing (MPseq). Thirty cases (42.9%) displayed at least one instance of discordance between FISH and MPseq for each primary and secondary abnormality evaluated. Nine cases had abnormalities detected by FISH that went undetected by MPseq including 6 tetraploid clones and three cases with missed copy number abnormalities. In contrast, 19 cases had abnormalities detected by MPseq that went undetected by FISH. Seventeen were MYC rearrangements and two were 17p deletions. MPseq identified 36 MYC abnormalities and 17 (50.0% of MYC abnormal group with FISH results) displayed a false negative FISH result. MPseq identified 10 cases (14.3%) with IgL rearrangements, a recent marker of poor outcome, and 10% with abnormalities in genes associated with lenalidomide response or resistance. In summary, MPseq was superior in the characterization of rearrangement complexity and identification of secondary abnormalities demonstrating increased clinical value compared to FISH.
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Affiliation(s)
- James Smadbeck
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, USA
| | - Jess F Peterson
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kathryn E Pearce
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Beth A Pitel
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Andrea Lebron Figueroa
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Michael Timm
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Dragan Jevremovic
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Min Shi
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - A Keith Stewart
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Esteban Braggio
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Daniel L Riggs
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - P Leif Bergsagel
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - George Vasmatzis
- Center for Individualized Medicine-Biomarker Discovery, Mayo Clinic, Rochester, MN, USA
| | - Hutton M Kearney
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Nicole L Hoppman
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rhett P Ketterling
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Shaji Kumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - S Vincent Rajkumar
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Patricia T Greipp
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linda B Baughn
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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32
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Bewicke-Copley F, Arjun Kumar E, Palladino G, Korfi K, Wang J. Applications and analysis of targeted genomic sequencing in cancer studies. Comput Struct Biotechnol J 2019; 17:1348-1359. [PMID: 31762958 PMCID: PMC6861594 DOI: 10.1016/j.csbj.2019.10.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 10/18/2019] [Accepted: 10/22/2019] [Indexed: 12/31/2022] Open
Abstract
Next Generation Sequencing (NGS) has dramatically improved the flexibility and outcomes of cancer research and clinical trials, providing highly sensitive and accurate high-throughput platforms for large-scale genomic testing. In contrast to whole-genome (WGS) or whole-exome sequencing (WES), targeted genomic sequencing (TS) focuses on a panel of genes or targets known to have strong associations with pathogenesis of disease and/or clinical relevance, offering greater sequencing depth with reduced costs and data burden. This allows targeted sequencing to identify low frequency variants in targeted regions with high confidence, thus suitable for profiling low-quality and fragmented clinical DNA samples. As a result, TS has been widely used in clinical research and trials for patient stratification and the development of targeted therapeutics. However, its transition to routine clinical use has been slow. Many technical and analytical obstacles still remain and need to be discussed and addressed before large-scale and cross-centre implementation. Gold-standard and state-of-the-art procedures and pipelines are urgently needed to accelerate this transition. In this review we first present how TS is conducted in cancer research, including various target enrichment platforms, the construction of target panels, and selected research and clinical studies utilising TS to profile clinical samples. We then present a generalised analytical workflow for TS data discussing important parameters and filters in detail, aiming to provide the best practices of TS usage and analyses.
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Key Words
- BAM, Binary Alignment Map
- BWA, Burrows-Wheeler Aligner
- Background error
- CLL, Chronic Lymphocytic Leukaemia
- COSMIC, Catalogue of Somatic Mutations in Cancer
- Cancer genomics
- Clinical samples
- ESP, Exome Sequencing Project
- FF, Fresh Frozen
- FFPE, Formalin Fixed Paraffin Embedded
- FL, Follicular Lymphoma
- GATK, Genome Analysis Toolkit
- ICGC, International Cancer Genome Consortium
- MBC, Molecular Barcode
- NCCN, the National Comprehensive Cancer Network®
- NGS, Next Generation Sequencing
- NHL, Non-Hodgkin Lymphoma
- NSCLC, Non-Small Cell Lung Carcinoma
- PCR duplicates
- QC, Quality Control
- SAM, Sequence Alignment Map
- TCGA, The Cancer Genome Atlas
- TS, Targeted Sequencing
- Targeted sequencing
- UMI, Unique Molecular Identifiers
- VAF, Variant Allele Frequency
- Variant calling
- WES, Whole Exome Sequencing
- WGS, Whole Genome Sequencing
- tFL, Transformed Follicular Lymphoma
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Affiliation(s)
- Findlay Bewicke-Copley
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Emil Arjun Kumar
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Giuseppe Palladino
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Koorosh Korfi
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Jun Wang
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
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Li M, Su X, Wang Y, Fan L, Chai J, Li P, Zhao D, Liu Y, Ma J, Wang K, Yan Q, Guo S, Jin B, Liang R, Wang Z. Lineage-negative lymphoma with a helper innate lymphoid cell phenotype. Virchows Arch 2019; 476:285-293. [PMID: 31522287 DOI: 10.1007/s00428-019-02658-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/19/2019] [Accepted: 08/23/2019] [Indexed: 01/07/2023]
Abstract
Helper innate lymphoid cells (ILCs) were recently recognized as lineage-negative lymphoid cells that do not express rearranged receptors and have important effector and regulatory functions in innate immunity. However, to our knowledge, no cases of hematological malignancies arising from helper ILCs have ever been reported in the literature. Here, we report a case of a 17-year-old man with multiple lymphadenopathy who was diagnosed with lineage-negative lymphoma that displayed a helper ILC phenotype. Histological examination showed large monomorphic atypical lymphoid cells with prominent nucleoli and abundant eosinophilic cytoplasms with scattered and patchy distributions. Large amounts of histiocytes and infiltrating lymphocytes were observed in the background. Immunostaining revealed positive LCA and CD79a expression but negative expression of all lineage markers. IG and TCR rearrangement analysis showed no clonal rearrangements. Tumor cells strongly expressed helper ILC phenotypic markers, such as CD127, IL-1R, GATA3, ST2, IL-17Rβ, and RANKL, and helper ILC-produced cytokines, such as IL-4 and GM-CSF. PD-L1/PD-L2-positive histiocytes and FOXP3-positive Tregs were observed in the tumor microenvironment. Flow cytometry of bone marrow at recurrence was positive for IL-1R and negative for T, B, NK, and myelogenous lineage markers. TP53 sequencing showed that exon 5 was replaced with an intergenic sequence of chromosome 21. Next-generation sequencing demonstrated a novel IGLV2-14/IGLL5 fusion and mutations or deletions of tumor suppressor genes, such as PTPRB, PPP2CB, and UPK1A. This tumor was very aggressive, resistant to chemotherapy, recurred with bone marrow involvement, and caused the death of the patient within 6 months. To our knowledge, this is the first report of a hematological malignancy potentially arising from helper ILCs. We propose negativity for lineage markers and positivity for CD127/IL-1R in combination with specific transcription factor expression as markers of this tumor. This finding represents a novel addition to the growing spectrum of hematological malignancies.
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Affiliation(s)
- Mingyang Li
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Xiaoli Su
- Department of Hematology, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Yingmei Wang
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Linni Fan
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Jia Chai
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Peifeng Li
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Danhui Zhao
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Yixiong Liu
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Jing Ma
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Kaijing Wang
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Qingguo Yan
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Shuangping Guo
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Boquan Jin
- Department of Immunology, School of Basic Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Rong Liang
- Department of Hematology, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China.
| | - Zhe Wang
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, Xi'an, 710032, China.
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Romano A, Palumbo GA, Parrinello NL, Conticello C, Martello M, Terragna C. Minimal Residual Disease Assessment Within the Bone Marrow of Multiple Myeloma: A Review of Caveats, Clinical Significance and Future Perspectives. Front Oncol 2019; 9:699. [PMID: 31482061 PMCID: PMC6710454 DOI: 10.3389/fonc.2019.00699] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/15/2019] [Indexed: 12/11/2022] Open
Abstract
There is an increasing clinical interest in the measure and achievement of minimal residual disease (MRD) negativity in the bone marrow of Multiple Myeloma (MM) patients, as defined equally either by Multicolor Flow Cytometry (MFC) or by Next Generation Sequencing (NGS) technologies. At present, modern technologies allow to detect up to one on 104 or on 105 or even on 106 cells, depending on their throughput. MFC approaches, which have been progressively improved up to the so-called Next Generation Flow (NGF), and NGS, which proved clear advantages over ASO-PCR, can detect very low levels of residual disease in the BM. These methods are actually almost superimposable, in terms of MRD detection power, supporting the lack of unanimous preference for either technique on basis of local availability. However, some technical issues are still open: the optimal assay to use to detect either phenotype (e.g., next generation multidimensional flow cytometry, imaging) or genotype aberrations (e.g., ASO-RQ PCR, digital droplet PCR, NGS) and their standardization, the sample source (BM or peripheral blood, PB) and its pre-processing (red-cell lysis vs. Ficoll, fresh vs. frozen samples, requirement of CD138+ cells enrichment). Overall, MRD negativity is considered as the most powerful predictor of favorable long-term outcomes in MM and is likely to represent the major driver of treatment strategies in the near future. In this manuscript, we reviewed the main pitfalls and caveats of MRD detection within bone marrow in MM patients after front-line therapy, highlighting the improving of the currently employed technology and describing alternative methods for MRD testing in MM, such as liquid biopsy.
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Affiliation(s)
- Alessandra Romano
- Department of Surgery and Medical Specialties, University of Catania, Catania, Italy
| | - Giuseppe Alberto Palumbo
- Division of Hematology, Azienda Ospedaliero-Universitaria Policlinico Vittorio Emanuele di Catania, Catania, Italy
- Dipartimento di Scienze Mediche, Chirurgiche e Tecnologie avanzate “G.F. Ingrassia,” University of Catania, Catania, Italy
| | - Nunziatina Laura Parrinello
- Division of Hematology, Azienda Ospedaliero-Universitaria Policlinico Vittorio Emanuele di Catania, Catania, Italy
- Dipartimento di Scienze Mediche, Chirurgiche e Tecnologie avanzate “G.F. Ingrassia,” University of Catania, Catania, Italy
| | - Concetta Conticello
- Division of Hematology, Azienda Ospedaliero-Universitaria Policlinico Vittorio Emanuele di Catania, Catania, Italy
| | - Marina Martello
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Università degli Studi di Bologna, Bologna, Italy
| | - Carolina Terragna
- Istituto di Ematologia “L.A.Seràgnoli,” Azienda Ospedaliera Sant'Orsola-Malpighi, Bologna, Italy
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Goldsmith SR, Fiala MA, Dukeman J, Ghobadi A, Stockerl-Goldstein K, Schroeder MA, Tomasson M, Wildes TM, Vij R. Next Generation Sequencing-based Validation of the Revised International Staging System for Multiple Myeloma: An Analysis of the MMRF CoMMpass Study. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2019; 19:285-289. [PMID: 30792096 DOI: 10.1016/j.clml.2019.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/26/2018] [Accepted: 01/10/2019] [Indexed: 01/21/2023]
Abstract
INTRODUCTION The clinical application of the Revised International Staging System (R-ISS) for multiple myeloma may be limited by heterogeneity in clinical interphase fluorescent in situ hybridization (FISH) practices for detecting chromosomal abnormalities (CAs). Next generation sequencing (NGS)-based FISH (Seq-FISH) has demonstrated improved sensitivity and similar specificity relative to clinical FISH, and provides a standardized, single-pass method for identifying high-risk CAs. To date, calculating R-ISS stage using Seq-FISH (R-ISS-NGS) has not been validated. PATIENTS AND METHODS We identified 672 patients with sufficient data to calculate R-ISS-NGS from the Multiple Myeloma Research Foundation (MMRF) CoMMpass Study. R-ISS-NGS was calculated from original ISS stage, lactate dehydrogenase, and CAs detected by Seq-FISH. Endpoints included overall survival and progression-free survival. We conducted multivariate analyses controlling for age and gender in order to compare outcomes across stages I to III of both the original ISS and R-ISS-NGS. RESULTS The median follow-up was 24 months. The R-ISS-NGS resulted in significant redistribution of patients into stage II, relative to the original ISS. With respect to stage I, R-ISS-NGS stages II and III of were associated with worse progression-free survival or overall survival, more so than the staging schema of the ISS, thus validating the use of Seq-FISH in staging. CONCLUSION Using CAs detected by Seq-FISH and data from the CoMMpass study, we validated the R-ISS with a large, generalizable cohort. This study validates the substitution of Seq-FISH for clinical FISH, especially in large registry studies. Additionally, use of the validated R-ISS-NGS will strengthen outcomes research generated from the CoMMpass study.
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Affiliation(s)
- Scott R Goldsmith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO.
| | - Mark A Fiala
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - James Dukeman
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Armin Ghobadi
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Keith Stockerl-Goldstein
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Mark A Schroeder
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Michael Tomasson
- Department of Internal Medicine, Carver College of Medicine, Iowa City, IA
| | - Tanya M Wildes
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Ravi Vij
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO
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