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Turk A, Čeh E, Calin GA, Kunej T. Multiple omics levels of chronic lymphocytic leukemia. Cell Death Discov 2024; 10:293. [PMID: 38906881 PMCID: PMC11192936 DOI: 10.1038/s41420-024-02068-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 06/23/2024] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a lymphoproliferative malignancy characterized by the proliferation of functionally mature but incompetent B cells. It is the most prevalent type of leukemia in Western populations, accounting for approximately 25% of new leukemia cases. While recent advances, such as ibrutinib and venetoclax treatment have improved patient outlook, aggressive forms of CLL such as Richter transformation still pose a significant challenge. This discrepancy may be due to the heterogeneity of factors contributing to CLL development at multiple -omics levels. However, information on the omics of CLL is fragmented, hindering multi-omics-based research into potential treatment options. To address this, we aggregated and presented a selection of important aspects of various omics levels of the disease in this review. The purpose of the present literature analysis is to portray examples of CLL studies from different omics levels, including genomics, epigenomics, transcriptomics, epitranscriptomics, proteomics, epiproteomics, metabolomics, glycomics and lipidomics, as well as those identified by multi-omics approaches. The review includes the list of 102 CLL-associated genes with relevant genomics information. While single-omics studies yield substantial and useful data, they omit a significant level of complex biological interplay present in the disease. As multi-omics studies integrate several different layers of data, they may be better suited for complex diseases such as CLL and have thus far yielded promising results. Future multi-omics studies may assist clinicians in improved treatment choices based on CLL subtypes as well as allow the identification of novel biomarkers and targets for treatments.
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Grants
- P4-0220 Javna Agencija za Raziskovalno Dejavnost RS (Slovenian Research Agency)
- Dr. Calin is the Felix L. Haas Endowed Professor in Basic Science. Work in G.A.C.’s laboratory is supported by NCI grants 1R01 CA182905-01 and 1R01CA222007-01A1, NIGMS grant 1R01GM122775-01, DoD Idea Award W81XWH-21-1-0030, a Team DOD grant in Gastric Cancer W81XWH-21-1-0715, a Chronic Lymphocytic Leukemia Moonshot Flagship project, a CLL Global Research Foundation 2019 grant, a CLL Global Research Foundation 2020 grant, a CLL Global Research Foundation 2022 grant, The G. Harold & Leila Y. Mathers Foundation, two grants from Torrey Coast Foundation, an Institutional Research Grant and Development Grant associated with the Brain SPORE 2P50CA127001.
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Affiliation(s)
- Aleksander Turk
- Clinical Institute of Genomic Medicine, University Clinical Centre Ljubljana, Ljubljana, Slovenia
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Eva Čeh
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - George A Calin
- Department of Translational Molecular Pathology, Division of Pathology, MD Anderson Cancer Center, University of Texas, Houston, TX, 77030, USA.
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
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Leeman-Neill RJ, Bhagat G, Basu U. AID in non-Hodgkin B-cell lymphomas: The consequences of on- and off-target activity. Adv Immunol 2024; 161:127-164. [PMID: 38763700 DOI: 10.1016/bs.ai.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
Activation induced cytidine deaminase (AID) is a key element of the adaptive immune system, required for immunoglobulin isotype switching and affinity maturation of B-cells as they undergo the germinal center (GC) reaction in peripheral lymphoid tissue. The inherent DNA damaging activity of this enzyme can also have off-target effects in B-cells, producing lymphomagenic chromosomal translocations that are characteristic features of various classes of non-Hodgkin B-cell lymphoma (B-NHL), and generating oncogenic mutations, so-called aberrant somatic hypermutation (aSHM). Additionally, AID has been found to affect gene expression through demethylation as well as altered interactions between gene regulatory elements. These changes have been most thoroughly studied in B-NHL arising from GC B-cells. Here, we describe the most common classes of GC-derived B-NHL and explore the consequences of on- and off-target AID activity in B and plasma cell neoplasms. The relationships between AID expression, including effects of infection and other exposures/agents, mutagenic activity and lymphoma biology are also discussed.
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Affiliation(s)
- Rebecca J Leeman-Neill
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States; Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.
| | - Govind Bhagat
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
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3
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Aslam S, Zhang Z, Latif Z. Identification of novel homozygous missense and deletion mutations manifesting oligospermia infertility in Kashmiri population. J Gene Med 2024; 26:e3589. [PMID: 37649129 DOI: 10.1002/jgm.3589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 07/03/2023] [Accepted: 08/13/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Human male infertility has a lot of known molecular components that have an accurate diagnosis, such as Y chromosome deletion and monogenic causes. Only 4% of all infertile males are diagnosed with genetic causes, while 60-70% of infertile men remain without an accurate diagnosis and are classified as unexplained. Oligospermia is a major cause of human male infertility. Its etiology and pathogenesis are linked to genetic abnormalities. The majority of genetic causes related to human male infertility remain unclear. RESULTS Generally, we found a significant association between the specific type of disease and gender (p = 0.003), and the regression value (R2 ) for this association was 0.75. Association of the type of disease with body mass index was not significant (p = 0.34). There was no statistically significant difference (p = 0.40) among disease types with patients occupations. All explored mutations are listed for primary and secondary infertility in relation to the oligospermia condition. p.Arg286X is the outcome of a mismatch mutation in which the nucleotide change resulted in the substitution of Arg (arginine) amino acid with X (any amino acid) at position 286 in the Hyal3 gene of primary infertile patients having oligospermia. In primary infertile patients with the p.Arg286X mutation, a frameshift deletion mutation was also found just after the 25 nucleotide sequences of the Hyal3 genes of the second mutated exon. This deletion mutation was only detected in patients with primary infertility and was not found in people with secondary infertility or healthy controls. The other mutations in secondary infertile patients with oligospermia were: p.Lys168Ser, replacement of lysine (Lys) with serine (Ser) at position 168; p.Lys168The, replacement of lysine (Lys) with threonine (The) at position 168; p.His113X, substitution of histidine (His) with an unknown amino acid (X) at position 113; p.Pro162X, substitution of proline (Pro) with an unknown amino acid (X) at position 162; and p.Phe157X, phenylalanine (Phe) substitution with an unknown amino acid (X) at position 157. CONCLUSION This study clarifies the site of novel mismatch and frameshift deletion mutations in the Hyal3 gene in primary infertile oligospermia patients.
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Affiliation(s)
- Sanwal Aslam
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Zhen Zhang
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- State key Laboratory of Environmental Chemistry and Ecotoxicology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou, China
| | - Zahid Latif
- Department of Zoology, The University of Azad Jammu and Kashmir Muzaffarabad, Muzaffarabad, Pakistan
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4
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Robbe P, Schuh A. Genomic Stratification of Hematological Malignancies. Hemasphere 2023; 7:e902. [PMID: 37251914 PMCID: PMC10219718 DOI: 10.1097/hs9.0000000000000902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 04/25/2023] [Indexed: 05/31/2023] Open
Affiliation(s)
- Pauline Robbe
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Anna Schuh
- Department of Oncology, University of Oxford, United Kingdom
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5
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Kulis M, Martin-Subero JI. Integrative epigenomics in chronic lymphocytic leukaemia: Biological insights and clinical applications. Br J Haematol 2023; 200:280-290. [PMID: 36121003 DOI: 10.1111/bjh.18465] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/10/2022] [Accepted: 09/05/2022] [Indexed: 01/21/2023]
Abstract
Chronic lymphocytic leukaemia (CLL) is not only characterised by driver genetic alterations but by extensive epigenetic changes. Over the last decade, epigenomic studies have described the DNA methylome, chromatin accessibility, histone modifications and the three-dimensional (3D) genome architecture of CLL. Beyond its regulatory role, the DNA methylome contains imprints of the cellular origin and proliferative history of CLL cells. These two aspects are strong independent prognostic factors. Integrative analyses of chromatin marks have uncovered novel regulatory elements and altered transcription factor networks as non-genetic means mediating gene deregulation in CLL. Additionally, CLL cells display a disease-specific pattern of 3D genome interactions. From the technological perspective, we are currently witnessing a transition from bulk omics to single-cell analyses. This review aims at summarising the major findings from the epigenomics field as well as providing a prospect of the present and future of single-cell analyses in CLL.
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Affiliation(s)
- Marta Kulis
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Jose Ignacio Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
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6
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Knisbacher BA, Lin Z, Hahn CK, Nadeu F, Duran-Ferrer M, Stevenson KE, Tausch E, Delgado J, Barbera-Mourelle A, Taylor-Weiner A, Bousquets-Muñoz P, Diaz-Navarro A, Dunford A, Anand S, Kretzmer H, Gutierrez-Abril J, López-Tamargo S, Fernandes SM, Sun C, Sivina M, Rassenti LZ, Schneider C, Li S, Parida L, Meissner A, Aguet F, Burger JA, Wiestner A, Kipps TJ, Brown JR, Hallek M, Stewart C, Neuberg DS, Martín-Subero JI, Puente XS, Stilgenbauer S, Wu CJ, Campo E, Getz G. Molecular map of chronic lymphocytic leukemia and its impact on outcome. Nat Genet 2022; 54:1664-1674. [PMID: 35927489 PMCID: PMC10084830 DOI: 10.1038/s41588-022-01140-w] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/21/2022] [Indexed: 01/02/2023]
Abstract
Recent advances in cancer characterization have consistently revealed marked heterogeneity, impeding the completion of integrated molecular and clinical maps for each malignancy. Here, we focus on chronic lymphocytic leukemia (CLL), a B cell neoplasm with variable natural history that is conventionally categorized into two subtypes distinguished by extent of somatic mutations in the heavy-chain variable region of immunoglobulin genes (IGHV). To build the 'CLL map,' we integrated genomic, transcriptomic and epigenomic data from 1,148 patients. We identified 202 candidate genetic drivers of CLL (109 new) and refined the characterization of IGHV subtypes, which revealed distinct genomic landscapes and leukemogenic trajectories. Discovery of new gene expression subtypes further subcategorized this neoplasm and proved to be independent prognostic factors. Clinical outcomes were associated with a combination of genetic, epigenetic and gene expression features, further advancing our prognostic paradigm. Overall, this work reveals fresh insights into CLL oncogenesis and prognostication.
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Affiliation(s)
| | - Ziao Lin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard University, Cambridge, MA, USA
| | - Cynthia K Hahn
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ferran Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Martí Duran-Ferrer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Eugen Tausch
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Julio Delgado
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Servicio de Hematología, Hospital Clínic, IDIBAPS, Barcelona, Spain
| | - Alex Barbera-Mourelle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | | | - Pablo Bousquets-Muñoz
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Ander Diaz-Navarro
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | | | | | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jesus Gutierrez-Abril
- Computational Oncology Service, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sara López-Tamargo
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Stacey M Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Clare Sun
- Laboratory of Lymphoid Malignancies, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mariela Sivina
- Department of Leukemia, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Laura Z Rassenti
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | | | - Shuqiang Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Alexander Meissner
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | | | - Jan A Burger
- Department of Leukemia, The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Adrian Wiestner
- Laboratory of Lymphoid Malignancies, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thomas J Kipps
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Jennifer R Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Michael Hallek
- Center for Molecular Medicine, Cologne, Germany
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf and German CLL Study Group, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Chip Stewart
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - José I Martín-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Xose S Puente
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | | | - Catherine J Wu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
- Hematopathology Section, Laboratory of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
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7
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Robbe P, Ridout KE, Vavoulis DV, Dréau H, Kinnersley B, Denny N, Chubb D, Appleby N, Cutts A, Cornish AJ, Lopez-Pascua L, Clifford R, Burns A, Stamatopoulos B, Cabes M, Alsolami R, Antoniou P, Oates M, Cavalieri D, Gibson J, Prabhu AV, Schwessinger R, Jennings D, James T, Maheswari U, Duran-Ferrer M, Carninci P, Knight SJL, Månsson R, Hughes J, Davies J, Ross M, Bentley D, Strefford JC, Devereux S, Pettitt AR, Hillmen P, Caulfield MJ, Houlston RS, Martín-Subero JI, Schuh A. Whole-genome sequencing of chronic lymphocytic leukemia identifies subgroups with distinct biological and clinical features. Nat Genet 2022; 54:1675-1689. [PMID: 36333502 PMCID: PMC9649442 DOI: 10.1038/s41588-022-01211-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/16/2022] [Indexed: 11/06/2022]
Abstract
The value of genome-wide over targeted driver analyses for predicting clinical outcomes of cancer patients is debated. Here, we report the whole-genome sequencing of 485 chronic lymphocytic leukemia patients enrolled in clinical trials as part of the United Kingdom's 100,000 Genomes Project. We identify an extended catalog of recurrent coding and noncoding genetic mutations that represents a source for future studies and provide the most complete high-resolution map of structural variants, copy number changes and global genome features including telomere length, mutational signatures and genomic complexity. We demonstrate the relationship of these features with clinical outcome and show that integration of 186 distinct recurrent genomic alterations defines five genomic subgroups that associate with response to therapy, refining conventional outcome prediction. While requiring independent validation, our findings highlight the potential of whole-genome sequencing to inform future risk stratification in chronic lymphocytic leukemia.
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Affiliation(s)
- Pauline Robbe
- Department of Oncology, University of Oxford, Oxford, UK
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kate E Ridout
- Department of Oncology, University of Oxford, Oxford, UK
| | | | - Helene Dréau
- Department of Oncology, University of Oxford, Oxford, UK
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - Nicholas Denny
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Daniel Chubb
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - Niamh Appleby
- Department of Oncology, University of Oxford, Oxford, UK
| | - Anthony Cutts
- Department of Oncology, University of Oxford, Oxford, UK
| | - Alex J Cornish
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | | | - Ruth Clifford
- Department of Haematology, University Hospital Limerick, Limerick, Ireland
- Limerick Digital Cancer Research Centre, School of Medicine,University of Limerick, Limerick, Ireland
| | - Adam Burns
- Department of Oncology, University of Oxford, Oxford, UK
| | - Basile Stamatopoulos
- Laboratory of Clinical Cell Therapy, Jules Bordet Institute, ULB Cancer Research Center (U-CRC)- Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Maite Cabes
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Reem Alsolami
- Department of Medical Laboratory Technology, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | | | - Doriane Cavalieri
- Department of Haematology, CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | - Jane Gibson
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Anika V Prabhu
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ron Schwessinger
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Daisy Jennings
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | | | - Martí Duran-Ferrer
- Biomedical Epigenomics Group, Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Samantha J L Knight
- Oxford University Clinical Academic Graduate School, University of Oxford Medical Sciences Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Robert Månsson
- Center for Hematology and Regenerative Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Jim Hughes
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - James Davies
- Department of Medicine, Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Mark Ross
- Illumina Cambridge Ltd., Cambridge, UK
| | | | - Jonathan C Strefford
- Cancer Genomics, Cancer Sciences, Faculty of Medicine, Group University of Southampton, Southampton, UK
| | - Stephen Devereux
- King's College Hospital, NHS Foundation Trust, London, UK
- Kings College London, London, UK
| | - Andrew R Pettitt
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
- Clatterbridge Cancer Centre NHS Foundation Trust, Liverpool, UK
| | | | - Mark J Caulfield
- Genomics England, London, UK
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - José I Martín-Subero
- Human Technopole, Milan, Italy
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Anna Schuh
- Department of Oncology, University of Oxford, Oxford, UK.
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8
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Lee AC, Pingali SR, Pinilla-Ibarz JA, Atchison ML, Koumenis C, Argon Y, Thomas-Tikhonenko A, De Trez C, Hu CCA, Tang CHA. Loss of AID exacerbates the malignant progression of CLL. Leukemia 2022; 36:2430-2442. [PMID: 36042317 PMCID: PMC9522595 DOI: 10.1038/s41375-022-01663-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/17/2022] [Accepted: 07/20/2022] [Indexed: 01/16/2023]
Abstract
Activation-induced cytidine deaminase (AID) has been implicated as both a positive and a negative factor in the progression of B cell chronic lymphocytic leukemia (CLL), but the role that it plays in the development and progression of this disease is still unclear. We generated an AID knockout CLL mouse model, AID-/-/Eμ-TCL1, and found that these mice die significantly earlier than their AID-proficient counterparts. AID-deficient CLL cells exhibit a higher ER stress response compared to Eμ-TCL1 controls, particularly through activation of the IRE1/XBP1s pathway. The increased production of secretory IgM in AID-deficient CLL cells contributes to their elevated expression levels of XBP1s, while secretory IgM-deficient CLL cells express less XBP1s. This increase in XBP1s in turn leads AID-deficient CLL cells to exhibit higher levels of B cell receptor signaling, supporting leukemic growth and survival. Further, AID-/-/Eμ-TCL1 CLL cells downregulate the tumor suppressive SMAD1/S1PR2 pathway and have altered homing to non-lymphoid organs. Notably, CLL cells from patients with IgHV-unmutated disease express higher levels of XBP1s mRNA compared to those from patients with IgHV-mutated CLL. Our studies thus reveal novel mechanisms by which the loss of AID leads to worsened CLL and may explain why unmutated CLL is more aggressive than mutated CLL.
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Affiliation(s)
- Avery C Lee
- Center for Translational Research in Hematologic Malignancies, Houston Methodist Cancer Center, Houston Methodist Research Institute, Houston, TX, USA
- Cell & Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sai Ravi Pingali
- Center for Translational Research in Hematologic Malignancies, Houston Methodist Cancer Center, Houston Methodist Research Institute, Houston, TX, USA
| | - Javier A Pinilla-Ibarz
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Michael L Atchison
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Constantinos Koumenis
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yair Argon
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Cell Pathology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Andrei Thomas-Tikhonenko
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Carl De Trez
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Chih-Chi Andrew Hu
- Center for Translational Research in Hematologic Malignancies, Houston Methodist Cancer Center, Houston Methodist Research Institute, Houston, TX, USA.
| | - Chih-Hang Anthony Tang
- Center for Translational Research in Hematologic Malignancies, Houston Methodist Cancer Center, Houston Methodist Research Institute, Houston, TX, USA.
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9
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Bühler MM, Martin-Subero JI, Pan-Hammarström Q, Campo E, Rosenquist R. Towards precision medicine in lymphoid malignancies. J Intern Med 2022; 292:221-242. [PMID: 34875132 DOI: 10.1111/joim.13423] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Careful histopathologic examination remains the cornerstone in the diagnosis of the clinically and biologically heterogeneous group of lymphoid malignancies. However, recent advances in genomic and epigenomic characterization using high-throughput technologies have significantly improved our understanding of these tumors. Although no single genomic alteration is completely specific for a lymphoma entity, some alterations are highly recurrent in certain entities and thus can provide complementary diagnostic information when integrated in the hematopathological diagnostic workup. Moreover, other alterations may provide important information regarding the clinical course, that is, prognostic or risk-stratifying markers, or response to treatment, that is, predictive markers, which may allow tailoring of the patient's treatment based on (epi)genetic characteristics. In this review, we will focus on clinically relevant diagnostic, prognostic, and predictive biomarkers identified in more common types of B-cell malignancies, and discuss how diagnostic assays designed for comprehensive molecular profiling may pave the way for the implementation of precision diagnostics/medicine approaches. We will also discuss future directions in this rapidly evolving field, including the application of single-cell sequencing and other omics technologies, to decipher clonal dynamics and evolution in lymphoid malignancies.
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Affiliation(s)
- Marco M Bühler
- Department of Pathology and Molecular Pathology, University Hospital of Zurich, Zurich, Switzerland.,Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hematopathology Section, Laboratory of Pathology, Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain
| | - José I Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hematopathology Section, Laboratory of Pathology, Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomedica en Red de Cancer (CIBERONC), Madrid, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hematopathology Section, Laboratory of Pathology, Hospital Clínic de Barcelona, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomedica en Red de Cancer (CIBERONC), Madrid, Spain
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Solna, Sweden
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10
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Ramos-Campoy S, Puiggros A, Kamaso J, Beà S, Bougeon S, Larráyoz MJ, Costa D, Parker H, Rigolin GM, Blanco ML, Collado R, Ancín I, Salgado R, Moro-García MA, Baumann T, Gimeno E, Moreno C, Salido M, Calvo X, Calasanz MJ, Cuneo A, Nguyen-Khac F, Oscier D, Haferlach C, Strefford JC, Schoumans J, Espinet B. TP53 Abnormalities Are Underlying the Poor Outcome Associated with Chromothripsis in Chronic Lymphocytic Leukemia Patients with Complex Karyotype. Cancers (Basel) 2022; 14:3715. [PMID: 35954380 PMCID: PMC9367500 DOI: 10.3390/cancers14153715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 11/17/2022] Open
Abstract
Chromothripsis (cth) has been associated with a dismal outcome and poor prognosis factors in patients with chronic lymphocytic leukemia (CLL). Despite being correlated with high genome instability, previous studies have not assessed the role of cth in the context of genomic complexity. Herein, we analyzed a cohort of 33 CLL patients with cth and compared them against a cohort of 129 non-cth cases with complex karyotypes. Nine cth cases were analyzed using optical genome mapping (OGM). Patterns detected by genomic microarrays were compared and the prognostic value of cth was analyzed. Cth was distributed throughout the genome, with chromosomes 3, 6 and 13 being those most frequently affected. OGM detected 88.1% of the previously known copy number alterations and several additional cth-related rearrangements (median: 9, range: 3-26). Two patterns were identified: one with rearrangements clustered in the region with cth (3/9) and the other involving both chromothriptic and non-chromothriptic chromosomes (6/9). Cases with cth showed a shorter time to first treatment (TTFT) than non-cth patients (median TTFT: 2 m vs. 15 m; p = 0.013). However, when stratifying patients based on TP53 status, cth did not affect TTFT. Only TP53 maintained its significance in the multivariate analysis for TTFT, including cth and genome complexity defined by genomic microarrays (HR: 1.60; p = 0.029). Our findings suggest that TP53 abnormalities, rather than cth itself, underlie the poor prognosis observed in this subset.
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Affiliation(s)
- Silvia Ramos-Campoy
- Molecular Cytogenetics and Hematological Cytology Laboratories, Pathology Department, Hospital del Mar, 08003 Barcelona, Spain; (S.R.-C.); (J.K.); (E.G.); (M.S.); (X.C.)
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain
| | - Anna Puiggros
- Molecular Cytogenetics and Hematological Cytology Laboratories, Pathology Department, Hospital del Mar, 08003 Barcelona, Spain; (S.R.-C.); (J.K.); (E.G.); (M.S.); (X.C.)
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain
| | - Joanna Kamaso
- Molecular Cytogenetics and Hematological Cytology Laboratories, Pathology Department, Hospital del Mar, 08003 Barcelona, Spain; (S.R.-C.); (J.K.); (E.G.); (M.S.); (X.C.)
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain
| | - Sílvia Beà
- Hematopathology Section, Department of Pathology, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain; (S.B.); (D.C.); (T.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Sandrine Bougeon
- Oncogenomic Laboratory, Hematology Service, Lausanne University Hospital, 1011 Lausanne, Switzerland; (S.B.); (J.S.)
| | - María José Larráyoz
- Cytogenetics and Hematological Genetics Services, Department of Genetics, University of Navarra, 31008 Pamplona, Spain; (M.J.L.); (M.J.C.)
| | - Dolors Costa
- Hematopathology Section, Department of Pathology, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain; (S.B.); (D.C.); (T.B.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Helen Parker
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (H.P.); (J.C.S.)
| | - Gian Matteo Rigolin
- Hematology Section, St. Anna University Hospital, 44121 Ferrara, Italy; (G.M.R.); (A.C.)
| | - María Laura Blanco
- Department of Hematology, Hospital de la Santa Creu I Sant Pau, 08041 Barcelona, Spain; (M.L.B.); (C.M.)
| | - Rosa Collado
- Department of Hematology, Consorcio Hospital General Universitario, 46014 Valencia, Spain;
| | - Idoya Ancín
- Department of Hematology and Hemotherapy, Hospital Universitario Cruces, 48903 Bilbao, Spain;
| | - Rocío Salgado
- Cytogenetics Laboratory, Hematology Department, Fundación Jiménez Díaz, 28040 Madrid, Spain;
| | - Marco A. Moro-García
- Laboratory Medicine Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain;
| | - Tycho Baumann
- Hematopathology Section, Department of Pathology, Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain; (S.B.); (D.C.); (T.B.)
| | - Eva Gimeno
- Molecular Cytogenetics and Hematological Cytology Laboratories, Pathology Department, Hospital del Mar, 08003 Barcelona, Spain; (S.R.-C.); (J.K.); (E.G.); (M.S.); (X.C.)
- Applied Clinical Research in Hematological Malignances, Cancer Research Program, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain
| | - Carol Moreno
- Department of Hematology, Hospital de la Santa Creu I Sant Pau, 08041 Barcelona, Spain; (M.L.B.); (C.M.)
| | - Marta Salido
- Molecular Cytogenetics and Hematological Cytology Laboratories, Pathology Department, Hospital del Mar, 08003 Barcelona, Spain; (S.R.-C.); (J.K.); (E.G.); (M.S.); (X.C.)
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain
| | - Xavier Calvo
- Molecular Cytogenetics and Hematological Cytology Laboratories, Pathology Department, Hospital del Mar, 08003 Barcelona, Spain; (S.R.-C.); (J.K.); (E.G.); (M.S.); (X.C.)
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain
| | - María José Calasanz
- Cytogenetics and Hematological Genetics Services, Department of Genetics, University of Navarra, 31008 Pamplona, Spain; (M.J.L.); (M.J.C.)
| | - Antonio Cuneo
- Hematology Section, St. Anna University Hospital, 44121 Ferrara, Italy; (G.M.R.); (A.C.)
| | - Florence Nguyen-Khac
- Sorbonne University, Hematology Department, Hôpital Pitié-Salpêtrière, APHP, INSERM U1138, 75013 Paris, France;
| | - David Oscier
- Department of Molecular Pathology, Royal Bournemouth Hospital, Bournemouth BH7 7DW, UK;
| | | | - Jonathan C. Strefford
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (H.P.); (J.C.S.)
| | - Jacqueline Schoumans
- Oncogenomic Laboratory, Hematology Service, Lausanne University Hospital, 1011 Lausanne, Switzerland; (S.B.); (J.S.)
| | - Blanca Espinet
- Molecular Cytogenetics and Hematological Cytology Laboratories, Pathology Department, Hospital del Mar, 08003 Barcelona, Spain; (S.R.-C.); (J.K.); (E.G.); (M.S.); (X.C.)
- Translational Research on Hematological Neoplasms Group, Cancer Research Program, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain
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11
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Targeting SAMHD1: to overcome multiple anti-cancer drugs resistance in hematological malignancies. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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12
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Kwok M, Wu CJ. Clonal Evolution of High-Risk Chronic Lymphocytic Leukemia: A Contemporary Perspective. Front Oncol 2021; 11:790004. [PMID: 34976831 PMCID: PMC8716560 DOI: 10.3389/fonc.2021.790004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/24/2021] [Indexed: 12/13/2022] Open
Abstract
Clonal evolution represents the natural process through which cancer cells continuously search for phenotypic advantages that enable them to develop and expand within microenvironmental constraints. In chronic lymphocytic leukemia (CLL), clonal evolution underpins leukemic progression and therapeutic resistance, with differences in clonal evolutionary dynamics accounting for its characteristically diverse clinical course. The past few years have witnessed profound changes in our understanding of CLL clonal evolution, facilitated by a maturing definition of high-risk CLL and an increasing sophistication of next-generation sequencing technology. In this review, we offer a modern perspective on clonal evolution of high-risk CLL, highlighting recent discoveries, paradigm shifts and unresolved questions. We appraise recent advances in our understanding of the molecular basis of CLL clonal evolution, focusing on the genetic and non-genetic sources of intratumoral heterogeneity, as well as tumor-immune dynamics. We review the technological innovations, particularly in single-cell technology, which have fostered these advances and represent essential tools for future discoveries. In addition, we discuss clonal evolution within several contexts of particular relevance to contemporary clinical practice, including the settings of therapeutic resistance to CLL targeted therapy and immunotherapy, as well as Richter transformation of CLL to high-grade lymphoma.
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Affiliation(s)
- Marwan Kwok
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
- Centre for Clinical Haematology, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
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13
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Zavacka K, Plevova K. Chromothripsis in Chronic Lymphocytic Leukemia: A Driving Force of Genome Instability. Front Oncol 2021; 11:771664. [PMID: 34900721 PMCID: PMC8661134 DOI: 10.3389/fonc.2021.771664] [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: 09/06/2021] [Accepted: 11/01/2021] [Indexed: 11/22/2022] Open
Abstract
Chromothripsis represents a mechanism of massive chromosome shattering and reassembly leading to the formation of derivative chromosomes with abnormal functions and expression. It has been observed in many cancer types, importantly, including chronic lymphocytic leukemia (CLL). Due to the associated chromosomal rearrangements, it has a significant impact on the pathophysiology of the disease. Recent studies have suggested that chromothripsis may be more common than initially inferred, especially in CLL cases with adverse clinical outcome. Here, we review the main features of chromothripsis, the challenges of its assessment, and the potential benefit of its detection. We summarize recent findings of chromothripsis occurrence across hematological malignancies and address its causes and consequences in the context of CLL clinical features, as well as chromothripsis-related molecular abnormalities described in published CLL studies. Furthermore, we discuss the use of the current knowledge about genome functions associated with chromothripsis in the optimization of treatment strategies in CLL.
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Affiliation(s)
- Kristyna Zavacka
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno & Faculty of Medicine, Masaryk University, Brno, Czechia.,Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Karla Plevova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno & Faculty of Medicine, Masaryk University, Brno, Czechia.,Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czechia.,Institute of Medical Genetics and Genomics, University Hospital Brno & Masaryk University, Brno, Czechia
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14
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Lévy V, Delmer A, Cymbalista F. Frontline treatment in CLL: the case for time-limited treatment. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2021; 2021:59-67. [PMID: 34889444 PMCID: PMC8791103 DOI: 10.1182/hematology.2021000233] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Over the last decade, the advent of Bruton tyrosine kinase inhibitors (BTKi) has profoundly modified the therapeutic strategy in chronic lymphocytic leukemia (CLL), introducing the concept of treatment until progression. Initially, the bcl-2 inhibitor venetoclax (VEN) was used as a single agent and then was rapidly combined in VEN-based regimens associated with either anti-CD20 or with BTKi. These regimens yielded a high rate of complete remission, leading to their use as a fixed duration treatment. The decision between continuous treatment with BTKi and VEN-based combinations relies mostly on comorbidities, comedications, and patient/physician preferences. Notably, with BTKi, cardiovascular comorbidities, hypertension, and potential pharmacological interactions should be carefully evaluated. On the other hand, the risk of tumor lysis syndrome with VEN should be monitored at treatment initiation. TP53 alteration and IGHV mutational status should also be assessed, as they remain important for therapeutic decisions. Fit patients with a TP53 wild type and IGHV-mutated CLL may still benefit from fludarabine-cyclophosphamide-rituximab chemoimmunotherapy (CIT), as it may result in a very long remission duration. VEN-based treatments are well tolerated, and no additional toxicity has been observed when combined with anti-CD20 or BTKi. The 1-year fixed-duration association of VEN plus obinutuzumab was evaluated in frontline for older adult patients. Nonetheless, considering the favorable outcome, an extension of indication for fit younger patients is expected. The association of VEN and BTKi is promising, even if the follow-up is still short. It is currently being tested against CIT, BTKi continuous treatment, and VEN plus anti-CD20.
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Affiliation(s)
- Vincent Lévy
- Département de Recherche Clinique, Hôpital Avicenne AP-HP, Université Sorbonne Paris Nord, Bobigny, France, and INSERM CRESS-UMR 1153, Hôpital Saint Louis, Paris, France
| | - Alain Delmer
- Hematology Department, Reims University Hospital and Reims Champagne Ardenne University, Reims, France
| | - Florence Cymbalista
- Hematology Biology, Hôpital Avicenne, AP-HP, Université Sorbonne Paris Nord, Bobigny, France, and INSERM UMR 978, Bobigny, France
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15
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Sepulveda-Yanez JH, Alvarez-Saravia D, Fernandez-Goycoolea J, Aldridge J, van Bergen CAM, Posthuma W, Uribe-Paredes R, Veelken H, Navarrete MA. Integration of Mutational Signature Analysis with 3D Chromatin Data Unveils Differential AID-Related Mutagenesis in Indolent Lymphomas. Int J Mol Sci 2021; 22:ijms222313015. [PMID: 34884820 PMCID: PMC8657711 DOI: 10.3390/ijms222313015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/20/2021] [Accepted: 11/29/2021] [Indexed: 01/19/2023] Open
Abstract
Activation-induced deaminase (AID) is required for somatic hypermutation in immunoglobulin genes, but also induces off-target mutations. Follicular lymphoma (FL) and chronic lymphocytic leukemia (CLL), the most frequent types of indolent B-cell tumors, are exposed to AID activity during lymphomagenesis. We designed a workflow integrating de novo mutational signatures extraction and fitting of COSMIC (Catalogue Of Somatic Mutations In Cancer) signatures, with tridimensional chromatin conformation data (Hi-C). We applied the workflow to exome sequencing data from lymphoma samples. In 33 FL and 30 CLL samples, 42% and 34% of the contextual mutations could be traced to a known AID motif. We demonstrate that both CLL and FL share mutational processes dominated by spontaneous deamination, failures in DNA repair, and AID activity. The processes had equiproportional distribution across active and nonactive chromatin compartments in CLL. In contrast, canonical AID activity and failures in DNA repair pathways in FL were significantly higher within the active chromatin compartment. Analysis of DNA repair genes revealed a higher prevalence of base excision repair gene mutations (p = 0.02) in FL than CLL. These data indicate that AID activity drives the genetic landscapes of FL and CLL. However, the final result of AID-induced mutagenesis differs between these lymphomas depending on chromatin compartmentalization and mutations in DNA repair pathways.
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MESH Headings
- Alleles
- Chromatin/metabolism
- Cytidine Deaminase/genetics
- DNA Mutational Analysis
- DNA Repair/genetics
- Databases, Genetic
- Gene Frequency
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lymphoma, Follicular/genetics
- Lymphoma, Follicular/pathology
- Polymorphism, Single Nucleotide
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Affiliation(s)
- Julieta H. Sepulveda-Yanez
- Department of Hematology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (J.H.S.-Y.); (C.A.M.v.B.); (H.V.)
- School of Medicine, University of Magallanes, Punta Arenas 6210427, Chile;
- Centro Asistencial Docente y de Investigación, University of Magallanes, Punta Arenas 6210005, Chile
| | - Diego Alvarez-Saravia
- School of Medicine, University of Magallanes, Punta Arenas 6210427, Chile;
- Centro Asistencial Docente y de Investigación, University of Magallanes, Punta Arenas 6210005, Chile
| | | | - Jacqueline Aldridge
- Department of Computer Engineering, University of Magallanes, Punta Arenas 6210427, Chile; (J.A.); (R.U.-P.)
| | - Cornelis A. M. van Bergen
- Department of Hematology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (J.H.S.-Y.); (C.A.M.v.B.); (H.V.)
| | - Ward Posthuma
- Department of Oncology, Reinier de Graaf Hospital, 2625 AD Delft, The Netherlands;
| | - Roberto Uribe-Paredes
- Department of Computer Engineering, University of Magallanes, Punta Arenas 6210427, Chile; (J.A.); (R.U.-P.)
| | - Hendrik Veelken
- Department of Hematology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (J.H.S.-Y.); (C.A.M.v.B.); (H.V.)
| | - Marcelo A. Navarrete
- School of Medicine, University of Magallanes, Punta Arenas 6210427, Chile;
- Centro Asistencial Docente y de Investigación, University of Magallanes, Punta Arenas 6210005, Chile
- Correspondence: ; Tel.: +56-61-229-9630
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16
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Rare t(X;14)(q28;q32) translocation reveals link between MTCP1 and chronic lymphocytic leukemia. Nat Commun 2021; 12:6338. [PMID: 34732719 PMCID: PMC8566464 DOI: 10.1038/s41467-021-26400-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 09/21/2021] [Indexed: 11/27/2022] Open
Abstract
Rare, recurrent balanced translocations occur in a variety of cancers but are often not functionally interrogated. Balanced translocations with the immunoglobulin heavy chain locus (IGH; 14q32) in chronic lymphocytic leukemia (CLL) are infrequent but have led to the discovery of pathogenic genes including CCND1, BCL2, and BCL3. Following identification of a t(X;14)(q28;q32) translocation that placed the mature T cell proliferation 1 gene (MTCP1) adjacent to the immunoglobulin locus in a CLL patient, we hypothesized that this gene may have previously unrecognized importance. Indeed, here we report overexpression of human MTCP1 restricted to the B cell compartment in mice produces a clonal CD5+/CD19+ leukemia recapitulating the major characteristics of human CLL and demonstrates favorable response to therapeutic intervention with ibrutinib. We reinforce the importance of genetic interrogation of rare, recurrent balanced translocations to identify cancer driving genes via the story of MTCP1 as a contributor to CLL pathogenesis.
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17
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Schott K, Majer C, Bulashevska A, Childs L, Schmidt MHH, Rajalingam K, Munder M, König R. SAMHD1 in cancer: curse or cure? J Mol Med (Berl) 2021; 100:351-372. [PMID: 34480199 PMCID: PMC8843919 DOI: 10.1007/s00109-021-02131-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 07/15/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022]
Abstract
Human sterile α motif and HD domain-containing protein 1 (SAMHD1), originally described as the major cellular deoxyribonucleoside triphosphate triphosphohydrolase (dNTPase) balancing the intracellular deoxynucleotide (dNTP) pool, has come recently into focus of cancer research. As outlined in this review, SAMHD1 has been reported to be mutated in a variety of cancer types and the expression of SAMHD1 is dysregulated in many cancers. Therefore, SAMHD1 is regarded as a tumor suppressor in certain tumors. Moreover, it has been proposed that SAMHD1 might fulfill the requirements of a driver gene in tumor development or might promote a so-called mutator phenotype. Besides its role as a dNTPase, several novel cellular functions of SAMHD1 have come to light only recently, including a role as negative regulator of innate immune responses and as facilitator of DNA end resection during DNA replication and repair. Therefore, SAMHD1 can be placed at the crossroads of various cellular processes. The present review summarizes the negative role of SAMHD1 in chemotherapy sensitivity, highlights reported SAMHD1 mutations found in various cancer types, and aims to discuss functional consequences as well as underlying mechanisms of SAMHD1 dysregulation potentially involved in cancer development.
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Affiliation(s)
- Kerstin Schott
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Catharina Majer
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Alla Bulashevska
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Liam Childs
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Mirko H H Schmidt
- Institute of Anatomy, Medical Faculty Carl Gustav Carus, Technische Universität Dresden School of Medicine, Dresden, Germany
| | - Krishnaraj Rajalingam
- Cell Biology Unit, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- University Cancer Center Mainz, University Medical Center Mainz, Mainz, Germany
| | - Markus Munder
- Third Department of Medicine, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Renate König
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany.
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18
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Chauzeix J, Pastoret C, Donaty L, Gachard N, Fest T, Feuillard J, Rizzo D. A reduced panel of eight genes (ATM, SF3B1, NOTCH1, BIRC3, XPO1, MYD88, TNFAIP3, and TP53) as an estimator of the tumor mutational burden in chronic lymphocytic leukemia. Int J Lab Hematol 2021; 43:683-692. [PMID: 33325634 PMCID: PMC8451785 DOI: 10.1111/ijlh.13435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/10/2020] [Accepted: 11/24/2020] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Mutational complexity or tumor mutational burden (TMB) influences the course of chronic lymphocytic leukemia (CLL). However, this information is not routinely used because TMB is usually obtained from whole genome or exome, or from large gene panel high-throughput sequencing. METHODS Here, we used the C-Harrel concordance index to determine the minimum panel of genes for which mutations predict treatment-free survival (TFS) as well as large resequencing panels. RESULTS An eight gene estimator was defined encompassing ATM, SF3B1, NOTCH1, BIRC3, XPO1, MYD88, TNFAIP3, and TP53. TMB estimated from either a large panel of genes or the eight gene estimator was increased in treated patients or in those with a short TFS (<2 years), unmutated IGHV gene or with an unfavorable karyotype. Being an independent prognostic parameter, any mutation in the eight gene estimator predicted a shorter TFS better than Binet stage and IGHV mutational status among patients with an apparently non-progressive disease (TFS >6 months). Strikingly, the eight gene estimator was also highly informative for patients with Binet stage A CLL or with a good prognosis karyotype. CONCLUSION These results suggest that the eight gene estimator, that is easily achievable by high-throughput resequencing, brings robust and valuable information that predicts evolution of untreated patients at diagnosis better than any other parameter.
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Affiliation(s)
- Jasmine Chauzeix
- Laboratoire d'Hématologie etUMR CNRS 7276/INSERM 1262CRIBLCentre de Biologie et de Recherche en SantéCHU et Université de LimogesLimogesFrance
| | - Cédric Pastoret
- InsermMICMAC ‐ UMR_S 1236CHU RennesUniversité Rennes 1RennesFrance
| | - Lucie Donaty
- Laboratoire d'Hématologie etUMR CNRS 7276/INSERM 1262CRIBLCentre de Biologie et de Recherche en SantéCHU et Université de LimogesLimogesFrance
| | - Nathalie Gachard
- Laboratoire d'Hématologie etUMR CNRS 7276/INSERM 1262CRIBLCentre de Biologie et de Recherche en SantéCHU et Université de LimogesLimogesFrance
| | - Thierry Fest
- InsermMICMAC ‐ UMR_S 1236CHU RennesUniversité Rennes 1RennesFrance
| | - Jean Feuillard
- Laboratoire d'Hématologie etUMR CNRS 7276/INSERM 1262CRIBLCentre de Biologie et de Recherche en SantéCHU et Université de LimogesLimogesFrance
| | - David Rizzo
- Laboratoire d'Hématologie etUMR CNRS 7276/INSERM 1262CRIBLCentre de Biologie et de Recherche en SantéCHU et Université de LimogesLimogesFrance
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19
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Schubert M, Gassner FJ, Huemer M, Höpner JP, Akimova E, Steiner M, Egle A, Greil R, Zaborsky N, Geisberger R. AID Contributes to Accelerated Disease Progression in the TCL1 Mouse Transplant Model for CLL. Cancers (Basel) 2021; 13:cancers13112619. [PMID: 34073525 PMCID: PMC8198502 DOI: 10.3390/cancers13112619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/11/2021] [Accepted: 05/21/2021] [Indexed: 12/01/2022] Open
Abstract
Simple Summary Cancers, such as chronic lymphocytic leukemia, frequently acquire consecutive somatic mutations in the genome, which contribute to disease progression and treatment resistance. Activation-induced deaminase is an enzyme responsible for generating the highly diverse B cell repertoire but it can also induce substantial collateral damage within the genome of cells. Hence, it is important to assess whether AID contributes to cancer mutations and to the course of disease. This research shows that AID contributes to the acquisition of somatic cancer-specific mutations in a mouse model for chronic lymphocytic leukemia reflected in prolonged overall survival of leukemic mice lacking AID expression. These data should initiate future studies to assess the effect of AID inhibition on the occurrence of drug resistance. Abstract Adaptive somatic mutations conferring treatment resistance and accelerated disease progression is still a major problem in cancer therapy. Additionally in CLL, patients receiving novel, efficient drugs frequently become treatment refractory and eventually relapse. Activation-induced deaminase (AID) is a cytosine deaminase that catalyzes somatic hypermutation of genomic DNA at the immunoglobulin locus in activated B cells. As considerable off-target mutations by AID have been discerned in chronic lymphocytic leukemia, it is essential to investigate to which extent these mutations contribute to disease progression to estimate whether AID inhibition could counteract drug resistance mechanisms. In this study, we examined the TCL1 mouse model for CLL on an AID pro- and deficient background by comparing disease development and mutational landscapes. We provide evidence that AID contributes to the acquisition of somatic cancer-specific mutations also in the TCL1 model and accelerates CLL development particularly in the transplant setting. We conclude that AID is directly determining the fitness of the CLL clone, which prompts further studies to assess the effect of AID inhibition on the occurrence of drug resistance.
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Affiliation(s)
- Maria Schubert
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute-Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, 5020 Salzburg, Austria; (M.S.); (F.J.G.); (M.H.); (J.P.H.); (E.A.); (M.S.); (A.E.); (R.G.); (N.Z.)
| | - Franz Josef Gassner
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute-Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, 5020 Salzburg, Austria; (M.S.); (F.J.G.); (M.H.); (J.P.H.); (E.A.); (M.S.); (A.E.); (R.G.); (N.Z.)
| | - Michael Huemer
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute-Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, 5020 Salzburg, Austria; (M.S.); (F.J.G.); (M.H.); (J.P.H.); (E.A.); (M.S.); (A.E.); (R.G.); (N.Z.)
- Department of Biosciences, Paris Lodron University of Salzburg, 5020 Salzburg, Austria
| | - Jan Philip Höpner
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute-Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, 5020 Salzburg, Austria; (M.S.); (F.J.G.); (M.H.); (J.P.H.); (E.A.); (M.S.); (A.E.); (R.G.); (N.Z.)
- Department of Biosciences, Paris Lodron University of Salzburg, 5020 Salzburg, Austria
| | - Ekaterina Akimova
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute-Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, 5020 Salzburg, Austria; (M.S.); (F.J.G.); (M.H.); (J.P.H.); (E.A.); (M.S.); (A.E.); (R.G.); (N.Z.)
- Department of Biosciences, Paris Lodron University of Salzburg, 5020 Salzburg, Austria
| | - Markus Steiner
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute-Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, 5020 Salzburg, Austria; (M.S.); (F.J.G.); (M.H.); (J.P.H.); (E.A.); (M.S.); (A.E.); (R.G.); (N.Z.)
| | - Alexander Egle
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute-Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, 5020 Salzburg, Austria; (M.S.); (F.J.G.); (M.H.); (J.P.H.); (E.A.); (M.S.); (A.E.); (R.G.); (N.Z.)
| | - Richard Greil
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute-Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, 5020 Salzburg, Austria; (M.S.); (F.J.G.); (M.H.); (J.P.H.); (E.A.); (M.S.); (A.E.); (R.G.); (N.Z.)
| | - Nadja Zaborsky
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute-Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, 5020 Salzburg, Austria; (M.S.); (F.J.G.); (M.H.); (J.P.H.); (E.A.); (M.S.); (A.E.); (R.G.); (N.Z.)
| | - Roland Geisberger
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology Infectiology and Rheumatology, Oncologic Center, Salzburg Cancer Research Institute-Laboratory for Immunological and Molecular Cancer Research (SCRI-LIMCR), Paracelsus Medical University, 5020 Salzburg, Austria; (M.S.); (F.J.G.); (M.H.); (J.P.H.); (E.A.); (M.S.); (A.E.); (R.G.); (N.Z.)
- Correspondence:
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20
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Klintman J, Appleby N, Stamatopoulos B, Ridout K, Eyre TA, Robbe P, Pascua LL, Knight SJL, Dreau H, Cabes M, Popitsch N, Ehinger M, Martín-Subero JI, Campo E, Månsson R, Rossi D, Taylor JC, Vavoulis DV, Schuh A. Genomic and transcriptomic correlates of Richter transformation in chronic lymphocytic leukemia. Blood 2021; 137:2800-2816. [PMID: 33206936 PMCID: PMC8163497 DOI: 10.1182/blood.2020005650] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023] Open
Abstract
The transformation of chronic lymphocytic leukemia (CLL) to high-grade B-cell lymphoma is known as Richter syndrome (RS), a rare event with dismal prognosis. In this study, we conducted whole-genome sequencing (WGS) of paired circulating CLL (PB-CLL) and RS biopsies (tissue-RS) from 17 patients recruited into a clinical trial (CHOP-O). We found that tissue-RS was enriched for mutations in poor-risk CLL drivers and genes in the DNA damage response (DDR) pathway. In addition, we identified genomic aberrations not previously implicated in RS, including the protein tyrosine phosphatase receptor (PTPRD) and tumor necrosis factor receptor-associated factor 3 (TRAF3). In the noncoding genome, we discovered activation-induced cytidine deaminase-related and unrelated kataegis in tissue-RS affecting regulatory regions of key immune-regulatory genes. These include BTG2, CXCR4, NFATC1, PAX5, NOTCH-1, SLC44A5, FCRL3, SELL, TNIP2, and TRIM13. Furthermore, differences between the global mutation signatures of pairs of PB-CLL and tissue-RS samples implicate DDR as the dominant mechanism driving transformation. Pathway-based clonal deconvolution analysis showed that genes in the MAPK and DDR pathways demonstrate high clonal-expansion probability. Direct comparison of nodal-CLL and tissue-RS pairs from an independent cohort confirmed differential expression of the same pathways by RNA expression profiling. Our integrated analysis of WGS and RNA expression data significantly extends previous targeted approaches, which were limited by the lack of germline samples, and it facilitates the identification of novel genomic correlates implicated in RS transformation, which could be targeted therapeutically. Our results inform the future selection of investigative agents for a UK clinical platform study. This trial was registered at www.clinicaltrials.gov as #NCT03899337.
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MESH Headings
- Aged
- Aged, 80 and over
- Antibodies, Monoclonal, Humanized/therapeutic use
- Antineoplastic Combined Chemotherapy Protocols/administration & dosage
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Base Sequence
- Clonal Evolution/genetics
- Clone Cells/pathology
- Combined Modality Therapy
- Cyclophosphamide/administration & dosage
- DNA Repair
- Disease Progression
- Doxorubicin/administration & dosage
- Female
- Gene Expression Regulation, Neoplastic/genetics
- Gene Regulatory Networks
- Genes, Neoplasm
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lymphoma, Large B-Cell, Diffuse/drug therapy
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/pathology
- Male
- Middle Aged
- Mutation
- Neoplasm Proteins/genetics
- Prednisone/administration & dosage
- Prospective Studies
- RNA, Neoplasm/biosynthesis
- RNA, Neoplasm/genetics
- Syndrome
- Transcriptome
- Vincristine/administration & dosage
- Whole Genome Sequencing
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Affiliation(s)
- Jenny Klintman
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Translational Medicine, Skåne University Hospital, Lund University, Lund, Sweden
| | - Niamh Appleby
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Hematology, Oxford University Hospitals National Health Service (NHS) Trust, Oxford, United Kingdom
| | - Basile Stamatopoulos
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Laboratory of Clinical Cell Therapy, Jules Bordet Institute, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Katie Ridout
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Toby A Eyre
- Department of Hematology, Oxford University Hospitals National Health Service (NHS) Trust, Oxford, United Kingdom
| | - Pauline Robbe
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Laura Lopez Pascua
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Samantha J L Knight
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Helene Dreau
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Maite Cabes
- Department of Hematology, Oxford University Hospitals National Health Service (NHS) Trust, Oxford, United Kingdom
| | - Niko Popitsch
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- The Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Mats Ehinger
- Pathology, Department of Clinical Sciences, Skåne University Hospital, Lund University, Lund, Sweden
| | - Jose I Martín-Subero
- Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Elías Campo
- Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Barcelona, Spain
| | - Robert Månsson
- Center for Hematology and Regenerative Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Hematology Center, Karolinska University Hospital, Stockholm, Sweden; and
| | - Davide Rossi
- Institute of Oncology Research (IOR), Bellinzona, Switzerland
| | - Jenny C Taylor
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Dimitrios V Vavoulis
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Anna Schuh
- Molecular Diagnostic Centre, Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Oncology, University of Oxford, Oxford, United Kingdom
- Department of Hematology, Oxford University Hospitals National Health Service (NHS) Trust, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
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21
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Roberts HE, Lopopolo M, Pagnamenta AT, Sharma E, Parkes D, Lonie L, Freeman C, Knight SJL, Lunter G, Dreau H, Lockstone H, Taylor JC, Schuh A, Bowden R, Buck D. Short and long-read genome sequencing methodologies for somatic variant detection; genomic analysis of a patient with diffuse large B-cell lymphoma. Sci Rep 2021; 11:6408. [PMID: 33742045 PMCID: PMC7979876 DOI: 10.1038/s41598-021-85354-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 02/24/2021] [Indexed: 12/14/2022] Open
Abstract
Recent advances in throughput and accuracy mean that the Oxford Nanopore Technologies PromethION platform is a now a viable solution for genome sequencing. Much of the validation of bioinformatic tools for this long-read data has focussed on calling germline variants (including structural variants). Somatic variants are outnumbered many-fold by germline variants and their detection is further complicated by the effects of tumour purity/subclonality. Here, we evaluate the extent to which Nanopore sequencing enables detection and analysis of somatic variation. We do this through sequencing tumour and germline genomes for a patient with diffuse B-cell lymphoma and comparing results with 150 bp short-read sequencing of the same samples. Calling germline single nucleotide variants (SNVs) from specific chromosomes of the long-read data achieved good specificity and sensitivity. However, results of somatic SNV calling highlight the need for the development of specialised joint calling algorithms. We find the comparative genome-wide performance of different tools varies significantly between structural variant types, and suggest long reads are especially advantageous for calling large somatic deletions and duplications. Finally, we highlight the utility of long reads for phasing clinically relevant variants, confirming that a somatic 1.6 Mb deletion and a p.(Arg249Met) mutation involving TP53 are oriented in trans.
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Affiliation(s)
- Hannah E Roberts
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Maria Lopopolo
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alistair T Pagnamenta
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK
| | - Eshita Sharma
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Duncan Parkes
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lorne Lonie
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Colin Freeman
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Samantha J L Knight
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK
| | - Gerton Lunter
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Epidemiology, University Medical Centre Groningen, Groningen, The Netherlands
| | - Helene Dreau
- Oxford University Hospitals NHS Trust, Oxford, UK
- Department of Haematology, University of Oxford, Oxford, UK
| | - Helen Lockstone
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jenny C Taylor
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK.
| | - Anna Schuh
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK.
- Oxford University Hospitals NHS Trust, Oxford, UK.
- Department of Oncology, University of Oxford, Oxford, UK.
| | - Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David Buck
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
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22
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Cornish AJ, Chubb D, Frangou A, Hoang PH, Kaiser M, Wedge DC, Houlston RS. Reference bias in the Illumina Isaac aligner. Bioinformatics 2021; 36:4671-4672. [PMID: 32437525 PMCID: PMC7653636 DOI: 10.1093/bioinformatics/btaa514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/23/2020] [Accepted: 05/17/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Alex J Cornish
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SM2 5NG 2, UK
| | - Daniel Chubb
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SM2 5NG 2, UK
| | - Anna Frangou
- Nuffield Department of Medicine, Big Data Institute University of Oxford, OX3 7LF 3, UK.,Molecular Diagnostics Theme, Oxford NIHR Biomedical Research Centre, Oxford, OX3 7LF 3, UK
| | - Phuc H Hoang
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SM2 5NG 2, UK
| | - Martin Kaiser
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG 5, UK
| | - David C Wedge
- Nuffield Department of Medicine, Big Data Institute University of Oxford, OX3 7LF 3, UK.,Molecular Diagnostics Theme, Oxford NIHR Biomedical Research Centre, Oxford, OX3 7LF 3, UK.,Manchester Cancer Research Centre, University of Manchester, M20 4GJ, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SM2 5NG 2, UK
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23
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Abstract
Patients with chronic lymphocytic leukemia can be divided into three categories: those who are minimally affected by the problem, often never requiring therapy; those that initially follow an indolent course but subsequently progress and require therapy; and those that from the point of diagnosis exhibit an aggressive disease necessitating treatment. Likewise, such patients pass through three phases: development of the disease, diagnosis, and need for therapy. Finally, the leukemic clones of all patients appear to require continuous input from the exterior, most often through membrane receptors, to allow them to survive and grow. This review is presented according to the temporal course that the disease follows, focusing on those external influences from the tissue microenvironment (TME) that support the time lines as well as those internal influences that are inherited or develop as genetic and epigenetic changes occurring over the time line. Regarding the former, special emphasis is placed on the input provided via the B-cell receptor for antigen and the C-X-C-motif chemokine receptor-4 and the therapeutic agents that block these inputs. Regarding the latter, prominence is laid upon inherited susceptibility genes and the genetic and epigenetic abnormalities that lead to the developmental and progression of the disease.
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Affiliation(s)
- Nicholas Chiorazzi
- The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, New York 11030, USA
| | - Shih-Shih Chen
- The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, New York 11030, USA
| | - Kanti R. Rai
- The Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York 11549, USA
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24
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Smith PAD, Waugh EM, Crichton C, Jarrett RF, Morris JS. The prevalence and characterisation of TRAF3 and POT1 mutations in canine B-cell lymphoma. Vet J 2020; 266:105575. [PMID: 33323169 DOI: 10.1016/j.tvjl.2020.105575] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/28/2022]
Abstract
The genetic and mutational basis of canine lymphoma remains poorly understood. Several genes, including TRAF3 and POT1, are mutated in canine B-cell lymphoma (cBCL), and are likely involved in the pathogenesis of this disease. The purpose of this study was to assess the prevalence of TRAF3 and POT1 mutations in a cohort of dogs with cBCL, compared to dogs with non-cBCL diseases (including four dogs with T-cell lymphoma [cTCL]). Forty-nine dogs were included (n = 24 cBCL; n = 25 non-cBCL). Eleven dogs had matched non-tumour DNA assessed to determine if mutations were germline or somatic. All dogs had TRAF3 and POT1 assessed by Sanger sequencing. The prevalence of deleterious TRAF3 and POT1 mutations in cBCL was 36% and 17%, respectively. A deleterious TRAF3 mutation was suspected to be germline in 1/5 cases with matched non-tumour DNA available for comparison. Deleterious mutations were not found in specimens from the non-cBCL group. Several synonymous variants were identified in both genes in cBCL and non-cBCL samples, which likely represent polymorphisms. These results indicate TRAF3 and POT1 mutations are common in cBCL. Deleterious TRAF3 and POT1 mutations were only identified in dogs with cBCL, and not in dogs with non-cBCL diseases, suggesting they are important in the pathogenesis of cBCL. Future studies to investigate the prognostic and therapeutic implications of these mutations are required.
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Affiliation(s)
- P A D Smith
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, Glasgow, UK.
| | - E M Waugh
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, Glasgow, UK
| | - C Crichton
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, Glasgow, UK
| | - R F Jarrett
- MRC-University of Glasgow Centre for Virus Research, G61 1QH, Glasgow, UK
| | - J S Morris
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, Glasgow, UK
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25
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Hobeika C, Rached G, Chebly A, Chouery E, Kourie HR. Whole-exome and whole-genome sequencing in chronic lymphocytic leukemia: new biomarkers to target. Pharmacogenomics 2020; 21:957-962. [PMID: 32799640 DOI: 10.2217/pgs-2020-0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Many biomarkers indicate prognosis in chronic lymphocytic leukemia; such as fluorescence in situ hybridization testing: 17p or 11q deletions have a worse prognosis than trisomy 12, 13q deletion or normal result, or the mutational status of the immunoglobulin heavy chain (IGHV): unmutated IGHV have a worse prognosis than mutated IGHV. Recently, many gene mutations (TP53, NOTCH1 etc.,) have been linked to a worse prognosis. With the new era of high-throughput sequencing, it has become easier to study gene mutations and their implication in predicting prognosis. In this review, we aim to review all the studies that performed whole-exome sequencing or whole-genome sequencing on chronic lymphocytic leukemia cells and explore the implication of various genes in disease prognosis.
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Affiliation(s)
- Charbel Hobeika
- Laboratory of Medical Genetics, Faculty of Medicine, Saint Joseph University of Beirut, BP-17 5208, Lebanon
| | - Gaelle Rached
- Laboratory of Medical Genetics, Faculty of Medicine, Saint Joseph University of Beirut, BP-17 5208, Lebanon
| | - Alain Chebly
- Laboratory of Medical Genetics, Faculty of Medicine, Saint Joseph University of Beirut, BP-17 5208, Lebanon
| | - Eliane Chouery
- Laboratory of Medical Genetics, Faculty of Medicine, Saint Joseph University of Beirut, BP-17 5208, Lebanon
| | - Hampig Raphael Kourie
- Laboratory of Medical Genetics, Faculty of Medicine, Saint Joseph University of Beirut, BP-17 5208, Lebanon.,Department of Hematology-Oncology, Hotel Dieu de France University Hospital, Faculty of Medicine, Saint Joseph University, Beirut, BP-17 5208, Lebanon
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26
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Kleinstern G, O'Brien DR, Li X, Tian S, Kabat BF, Rabe KG, Norman AD, Yan H, Vachon CM, Boddicker NJ, Call TG, Parikh SA, Bruins L, Bonolo de Campos C, Leis JF, Shanafelt TD, Ding W, Cerhan JR, Kay NE, Slager SL, Braggio E. Tumor mutational load predicts time to first treatment in chronic lymphocytic leukemia (CLL) and monoclonal B-cell lymphocytosis beyond the CLL international prognostic index. Am J Hematol 2020; 95:906-917. [PMID: 32279347 DOI: 10.1002/ajh.25831] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/21/2020] [Accepted: 04/08/2020] [Indexed: 01/01/2023]
Abstract
Next-generation sequencing identified about 60 genes recurrently mutated in chronic lymphocytic leukemia (CLL). We examined the additive prognostic value of the total number of recurrently mutated CLL genes (i.e., tumor mutational load [TML]) or the individually mutated genes beyond the CLL international prognostic index (CLL-IPI) in newly diagnosed CLL and high-count monoclonal B-cell lymphocytosis (HC MBL). We sequenced 59 genes among 557 individuals (112 HC MBL/445 CLL) in a multi-stage design, to estimate hazard ratios (HR) and 95% confidence intervals (CI) for time-to-first treatment (TTT), adjusted for CLL-IPI and sex. TML was associated with shorter TTT in the discovery and validation cohorts, with a combined estimate of continuous HR = 1.27 (CI:1.17-1.39, P = 2.6 × 10-8 ; c-statistic = 0.76). When stratified by CLL-IPI, the association of TML with TTT was stronger and validated within low/intermediate risk (combined HR = 1.54, CI:1.37-1.72, P = 7.0 × 10-14 ). Overall, 80% of low/intermediate CLL-IPI cases with two or more mutated genes progressed to require therapy within 5 years, compared to 24% among those without mutations. TML was also associated with shorter TTT in the HC MBL cohort (HR = 1.53, CI:1.12-2.07, P = .007; c-statistic = 0.71). TML is a strong prognostic factor for TTT independent of CLL-IPI, especially among low/intermediate CLL-IPI risk, and a better predictor than any single gene. Mutational screening at early stages may improve risk stratification and better predict TTT.
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Affiliation(s)
- Geffen Kleinstern
- Department of Health Sciences ResearchMayo Clinic Rochester Minnesota USA
| | - Daniel R. O'Brien
- Department of Health Sciences ResearchMayo Clinic Rochester Minnesota USA
| | - Xing Li
- Department of Health Sciences ResearchMayo Clinic Rochester Minnesota USA
| | - Shulan Tian
- Department of Health Sciences ResearchMayo Clinic Rochester Minnesota USA
| | - Brian F. Kabat
- Department of Health Sciences ResearchMayo Clinic Rochester Minnesota USA
| | - Kari G. Rabe
- Department of Health Sciences ResearchMayo Clinic Rochester Minnesota USA
| | - Aaron D. Norman
- Department of Health Sciences ResearchMayo Clinic Rochester Minnesota USA
| | - Huihuang Yan
- Department of Health Sciences ResearchMayo Clinic Rochester Minnesota USA
| | - Celine M. Vachon
- Department of Health Sciences ResearchMayo Clinic Rochester Minnesota USA
| | | | | | | | - Laura Bruins
- Division of Hematology /OncologyMayo Clinic Scottsdale Arizona USA
| | | | - Jose F. Leis
- Division of Hematology /OncologyMayo Clinic Scottsdale Arizona USA
| | - Tait D. Shanafelt
- Department of Medicine, Division of HematologyStanford University Stanford California USA
| | - Wei Ding
- Division of HematologyMayo Clinic Rochester Minnesota USA
| | - James R. Cerhan
- Department of Health Sciences ResearchMayo Clinic Rochester Minnesota USA
| | - Neil E. Kay
- Division of HematologyMayo Clinic Rochester Minnesota USA
| | - Susan L. Slager
- Department of Health Sciences ResearchMayo Clinic Rochester Minnesota USA
| | - Esteban Braggio
- Division of Hematology /OncologyMayo Clinic Scottsdale Arizona USA
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High CXCR3 on Leukemic Cells Distinguishes IgHV mut from IgHV unmut in Chronic Lymphocytic Leukemia: Evidence from CD5 high and CD5 low Clones. J Immunol Res 2020; 2020:7084268. [PMID: 32802894 PMCID: PMC7322588 DOI: 10.1155/2020/7084268] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/21/2020] [Indexed: 01/04/2023] Open
Abstract
Despite the shared pattern of surface antigens, neoplastic cells in chronic lymphocytic leukemia (CLL) are highly heterogeneous in CD5 expression, a marker linked to a proliferative pool of neoplastic cells. To further characterize CD5high and CD5low neoplastic cells, we assessed the chemokine receptors (CCR5, CCR7, CCR10, CXCR3, CXCR4, CXCR5) and adhesion molecules (CD54, CD62L, CD49d) on the CD5high and CD5low subpopulations, defined by CD5/CD19 coexpression, in peripheral blood of CLL patients (n = 60) subgrouped according to the IgHV mutational status (IgHVmut, n = 24; IgHVunmut, n = 36). CD5high subpopulation showed a high percentage of CXCR3 (P < 0.001), CCR10 (P = 0.001), and CD62L (P = 0.031) and high levels of CXCR5 (P = 0.005), CCR7 (P = 0.013) compared to CD5low cells expressing high CXCR4 (P < 0.001). Comparing IgHVmut and IgHVunmut patients, high levels of CXCR3 on CD5high and CD5low subpopulations were detected in the IgHVmut patients, with better discrimination in CD5low subpopulation. Levels of CXCR3 on CD5low subpopulation were associated with time to the next treatment, thus further confirming its prognostic value. Taken together, our analysis revealed higher CXCR3 expression on both CD5high and CD5low neoplastic cells in IgHVmut with a better prognosis compared to IgHVunmut patients. Contribution of CXCR3 to CLL pathophysiology and its suitability for prognostication and therapeutic exploitation deserves future investigations.
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Nadeu F, Diaz-Navarro A, Delgado J, Puente XS, Campo E. Genomic and Epigenomic Alterations in Chronic Lymphocytic Leukemia. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2020; 15:149-177. [PMID: 31977296 DOI: 10.1146/annurev-pathmechdis-012419-032810] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chronic lymphocytic leukemia is a common disease in Western countries and has heterogeneous clinical behavior. The relevance of the genetic basis of the disease has come to the forefront recently, with genome-wide studies that have provided a comprehensive view of structural variants, somatic mutations, and different layers of epigenetic changes. The mutational landscape is characterized by relatively common copy number alterations, a few mutated genes occurring in 10-15% of cases, and a large number of genes mutated in a small number of cases. The epigenomic profile has revealed a marked reprogramming of regulatory regions in tumor cells compared with normal B cells. All of these alterations are differentially distributed in clinical and biological subsets of the disease, indicating that they may underlie the heterogeneous evolution of the disease. These global studies are revealing the molecular complexity of chronic lymphocytic leukemia and provide new perspectives that have helped to understand its pathogenic mechanisms and improve the clinical management of patients.
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Affiliation(s)
- Ferran Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; , , .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; ,
| | - Ander Diaz-Navarro
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; , .,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Julio Delgado
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; , , .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; , .,Hematology Department, Hospital Clinic of Barcelona, University of Barcelona, 08036 Barcelona, Spain
| | - Xose S Puente
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; , .,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Elías Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; , , .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain; , .,Hematopathology Section, Laboratory of Pathology, Hospital Clinic of Barcelona, University of Barcelona, 08036 Barcelona, Spain
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Development of a Precision Medicine Workflow in Hematological Cancers, Aalborg University Hospital, Denmark. Cancers (Basel) 2020; 12:cancers12020312. [PMID: 32013121 PMCID: PMC7073219 DOI: 10.3390/cancers12020312] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/10/2020] [Accepted: 01/27/2020] [Indexed: 12/17/2022] Open
Abstract
Within recent years, many precision cancer medicine initiatives have been developed. Most of these have focused on solid cancers, while the potential of precision medicine for patients with hematological malignancies, especially in the relapse situation, are less elucidated. Here, we present a demographic unbiased and observational prospective study at Aalborg University Hospital Denmark, referral site for 10% of the Danish population. We developed a hematological precision medicine workflow based on sequencing analysis of whole exome tumor DNA and RNA. All steps involved are outlined in detail, illustrating how the developed workflow can provide relevant molecular information to multidisciplinary teams. A group of 174 hematological patients with progressive disease or relapse was included in a non-interventional and population-based study, of which 92 patient samples were sequenced. Based on analysis of small nucleotide variants, copy number variants, and fusion transcripts, we found variants with potential and strong clinical relevance in 62% and 9.5% of the patients, respectively. The most frequently mutated genes in individual disease entities were in concordance with previous studies. We did not find tumor mutational burden or micro satellite instability to be informative in our hematologic patient cohort.
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30
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Celebrating 20 Years of IGHV Mutation Analysis in CLL. Hemasphere 2020; 4:e334. [PMID: 32382709 PMCID: PMC7000474 DOI: 10.1097/hs9.0000000000000334] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/28/2019] [Accepted: 12/13/2019] [Indexed: 12/22/2022] Open
Abstract
The division of CLL into 2 broad subsets with highly significant differences in clinical behavior was reported in 2 landmark papers in Blood in 1999.1,2 The simple analysis of the mutational status of the IGV regions provided both a prognostic indicator and an insight into the cellular origins. Derivation from B cells with very low or no IGV mutations generally leads to a more aggressive disease course than derivation from B cells with higher levels. This finding focused attention on surface Ig (sIg), the major B-cell receptor, and revealed dynamic antigen engagement in vivo as a tumor driver. It has also led to new drugs aimed at components of the intracellular activation cascades. After 20 years, the 2 senior authors of those papers have looked at the history of the observations and at the increasing understanding of the role of sIg in CLL that have emanated from them. As in the past, studies of CLL have provided a link between biology and the clinic, enabling more precise targeting which attacks critical pathways but minimizes side effects.
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Zhang L, Dong X, Lee M, Maslov AY, Wang T, Vijg J. Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan. Proc Natl Acad Sci U S A 2019; 116:9014-9019. [PMID: 30992375 PMCID: PMC6500118 DOI: 10.1073/pnas.1902510116] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Accumulation of mutations in somatic cells has been implicated as a cause of aging since the 1950s. However, attempts to establish a causal relationship between somatic mutations and aging have been constrained by the lack of methods to directly identify mutational events in primary human tissues. Here we provide genome-wide mutation frequencies and spectra of human B lymphocytes from healthy individuals across the entire human lifespan using a highly accurate single-cell whole-genome sequencing method. We found that the number of somatic mutations increases from <500 per cell in newborns to >3,000 per cell in centenarians. We discovered mutational hotspot regions, some of which, as expected, were located at Ig genes associated with somatic hypermutation (SHM). B cell-specific mutation signatures associated with development, aging, or SHM were found. The SHM signature strongly correlated with the signature found in human B cell tumors, indicating that potential cancer-causing events are already present even in B cells of healthy individuals. We also identified multiple mutations in sequence features relevant to cellular function (i.e., transcribed genes and gene regulatory regions). Such mutations increased significantly during aging, but only at approximately one-half the rate of the genome average, indicating selection against mutations that impact B cell function. This full characterization of the landscape of somatic mutations in human B lymphocytes indicates that spontaneous somatic mutations accumulating with age can be deleterious and may contribute to both the increased risk for leukemia and the functional decline of B lymphocytes in the elderly.
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Affiliation(s)
- Lei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Xiao Dong
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Moonsook Lee
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Alexander Y Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Tao Wang
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461;
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China
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32
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Gohil SH, Wu CJ. Dissecting CLL through high-dimensional single-cell technologies. Blood 2019; 133:1446-1456. [PMID: 30728142 PMCID: PMC6440295 DOI: 10.1182/blood-2018-09-835389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/07/2018] [Indexed: 12/11/2022] Open
Abstract
We now have the potential to undertake detailed analysis of the inner workings of thousands of cancer cells, one cell at a time, through the emergence of a range of techniques that probe the genome, transcriptome, and proteome combined with the development of bioinformatics pipelines that enable their interpretation. This provides an unprecedented opportunity to better understand the heterogeneity of chronic lymphocytic leukemia and how mutations, activation states, and protein expression at the single-cell level have an impact on disease course, response to treatment, and outcomes. Herein, we review the emerging application of these new techniques to chronic lymphocytic leukemia and examine the insights already attained through this transformative technology.
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Affiliation(s)
- Satyen H Gohil
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
- Harvard Medical School, Boston, MA; and
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
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The frequency of NOTCH1 variants in T-acute lymphoblastic leukemia/lymphoma and chronic lymphocytic leukemia/small lymphocytic lymphoma among Jordanian patients. Ann Diagn Pathol 2019; 39:53-58. [PMID: 30718223 DOI: 10.1016/j.anndiagpath.2019.01.004] [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: 12/16/2018] [Revised: 01/13/2019] [Accepted: 01/21/2019] [Indexed: 11/23/2022]
Abstract
The transmembrane receptor NOTCH1 is thought to be associated with the development and progression of T-acute lymphoblastic leukemia (T-ALL)/T-lymphoblastic lymphoma (T-LBL) and chronic lymphocytic leukemia (CLL)/small lymphocytic lymphoma (SLL). The current study aimed to characterize NOTCH1 expression and elucidate the variants in the functional PEST domain of the receptor in T-ALL/LBL and CLL/SLL. The nuclear expression of NOTCH1 protein was detected in 25% and 5% of cases of T-ALL/LBL and CLL/SLL, respectively, whereas cytoplasmic expression was detected in 33.3% and 15% cases, respectively. The frequency of variants in T-ALL/LBL was 33%, whereas 40% of CLL/SLL cases possessed variants. Four novel variants were identified; three of which were non-synonymous and one common variant c.7280_7280delG between T-ALL/LBL and CLL/SLL cases. The previously described variant, c.7541_7542delCT, was detected in 3 cases of CLL/SLL. These results provide support for the contribution of NOTCH1 in the etiology of these types of cancers.
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Zheng G, Chattopadhyay S, Sud A, Sundquist K, Sundquist J, Försti A, Houlston R, Hemminki A, Hemminki K. Second primary cancers in patients with acute lymphoblastic, chronic lymphocytic and hairy cell leukaemia. Br J Haematol 2019; 185:232-239. [DOI: 10.1111/bjh.15777] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/12/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Guoqiao Zheng
- Division of Molecular Genetic Epidemiology German Cancer Research Centre (DKFZ) Heidelberg Germany
- Faculty of Medicine University of Heidelberg Heidelberg Germany
| | - Subhayan Chattopadhyay
- Division of Molecular Genetic Epidemiology German Cancer Research Centre (DKFZ) Heidelberg Germany
- Faculty of Medicine University of Heidelberg Heidelberg Germany
| | - Amit Sud
- Division of Molecular Genetic Epidemiology German Cancer Research Centre (DKFZ) Heidelberg Germany
- Division of Genetics and Epidemiology The Institute of Cancer Research London UK
| | - Kristina Sundquist
- Centre for Primary Health Care Research Lund University Malmö Sweden
- Department of Family Medicine and Community Health Department of Population Health Science and Policy Icahn School of Medicine at Mount Sinai New York NY USA
- Centre for Community‐based Healthcare Research and Education (CoHRE) Department of Functional Pathology School of Medicine Shimane University Matsue Japan
| | - Jan Sundquist
- Centre for Primary Health Care Research Lund University Malmö Sweden
- Department of Family Medicine and Community Health Department of Population Health Science and Policy Icahn School of Medicine at Mount Sinai New York NY USA
- Centre for Community‐based Healthcare Research and Education (CoHRE) Department of Functional Pathology School of Medicine Shimane University Matsue Japan
| | - Asta Försti
- Division of Molecular Genetic Epidemiology German Cancer Research Centre (DKFZ) Heidelberg Germany
- Centre for Primary Health Care Research Lund University Malmö Sweden
| | - Richard Houlston
- Division of Genetics and Epidemiology The Institute of Cancer Research London UK
- Division of Molecular Pathology The Institute of Cancer Research London UK
| | - Akseli Hemminki
- Cancer Gene Therapy Group Faculty of Medicine University of Helsinki Helsinki Finland
- Comprehensive Cancer Centre Helsinki University Hospital Helsinki Finland
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology German Cancer Research Centre (DKFZ) Heidelberg Germany
- Centre for Primary Health Care Research Lund University Malmö Sweden
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Cavallari M, Cavazzini F, Bardi A, Volta E, Melandri A, Tammiso E, Saccenti E, Lista E, Quaglia FM, Urso A, Laudisi M, Menotti E, Formigaro L, Dabusti M, Ciccone M, Tomasi P, Negrini M, Cuneo A, Rigolin GM. Biological significance and prognostic/predictive impact of complex karyotype in chronic lymphocytic leukemia. Oncotarget 2018; 9:34398-34412. [PMID: 30344950 PMCID: PMC6188145 DOI: 10.18632/oncotarget.26146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 09/01/2018] [Indexed: 12/21/2022] Open
Abstract
The complex karyotype (CK) is an established negative prognostic marker in a number of haematological malignancies. After the introduction of effective mitogens, a growing body of evidence has suggested that the presence of 3 or more aberrations by conventional banding analysis (CBA) is associated with an unfavorable outcome in chronic lymphocytic leukemia (CLL). Thus, the importance of CBA was recognized by the 2018 guidelines of the International Workshop on CLL, which proposed the introduction of CBA in clinical trials to validate the value of karyotype aberrations. Indeed, a number of observational studies showed that cytogenetic aberrations and, particularly, the CK may have a negative independent impact on objective outcome measures (i.e. time to first treatment, progression free survival, time to chemorefractoriness and overall survival) both in patients treated with chemoimmunotherapy and, possibly, in patients receiving novel mechanism-based treatment. Here, we set out to present the scientific evidence supporting the significance of CK as a prognostic marker in CLL and to discuss the biological basis showing that the CK is a consequence of genomic instability.
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Affiliation(s)
- Maurizio Cavallari
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - Francesco Cavazzini
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - Antonella Bardi
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - Eleonora Volta
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - Aurora Melandri
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - Elisa Tammiso
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - Elena Saccenti
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - Enrico Lista
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - Francesca Maria Quaglia
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - Antonio Urso
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - Michele Laudisi
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - Elisa Menotti
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - Luca Formigaro
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - Melissa Dabusti
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - Maria Ciccone
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - Paolo Tomasi
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - Massimo Negrini
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Antonio Cuneo
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - Gian Matteo Rigolin
- Hematology Section, Department of Medical Sciences, Azienda Ospedaliero-Universitaria, Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
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Clonal diversity predicts adverse outcome in chronic lymphocytic leukemia. Leukemia 2018; 33:390-402. [PMID: 30038380 DOI: 10.1038/s41375-018-0215-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 06/17/2018] [Accepted: 06/26/2018] [Indexed: 11/09/2022]
Abstract
Genomic analyses of chronic lymphocytic leukemia (CLL) identified somatic mutations and associations of clonal diversity with adverse outcomes. Clonal evolution likely has therapeutic implications but its dynamic is less well studied. We studied clonal composition and prognostic value of seven recurrently mutated driver genes using targeted next-generation sequencing in 643 CLL patients and found higher frequencies of mutations in TP53 (35 vs. 12%, p < 0.001) and SF3B1 (20 vs. 11%, p < 0.05) and increased number of (sub)clonal (p < 0.0001) mutations in treated patients. We next performed an in-depth evaluation of clonal evolution on untreated CLL patients (50 "progressors" and 17 matched "non-progressors") using a 404 gene-sequencing panel and identified novel mutated genes such as AXIN1, SDHA, SUZ12, and FOXO3. Progressors carried more mutations at initial presentation (2.5 vs. 1, p < 0.0001). Mutations in specific genes were associated with increased (SF3B1, ATM, and FBXW7) or decreased progression risk (AXIN1 and MYD88). Mutations affecting specific signaling pathways, such as Notch and MAP kinase pathway were enriched in progressive relative to non-progressive patients. These data extend earlier findings that specific genomic alterations and diversity of subclones are associated with disease progression and persistence of disease in CLL and identify novel recurrently mutated genes and associated outcomes.
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37
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Luijten MNH, Lee JXT, Crasta KC. Mutational game changer: Chromothripsis and its emerging relevance to cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 777:29-51. [PMID: 30115429 DOI: 10.1016/j.mrrev.2018.06.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/22/2018] [Accepted: 06/28/2018] [Indexed: 12/14/2022]
Abstract
In recent years, the paradigm that genomic abnormalities in cancer cells arise through progressive accumulation of mutational events has been challenged by the discovery of single catastrophic events. One such phenomenon termed chromothripsis, involving massive chromosomal rearrangements arising all at once, has emerged as a major mutational game changer. The strong interest in this process stems from its widespread association with a range of cancer types and its potential as a mutational driver. In this review, we first describe chromothripsis detection and incidence in cancers. We then explore recently proposed underlying mechanistic origins, which explain the curious observations of the highly localised nature of the rearrangements on chromothriptic chromosomes. Detection of chromothriptic patterns following incorporation of single chromosomes into micronuclei or following telomere attrition have greatly contributed to our understanding of the reasons behind this chromosomal restriction. These underlying cellular events have been found to be participants in the tumourigenic process, strongly suggesting a potential role for chromothripsis in cancer development. Thus, we discuss potential implications of chromothripsis for cancer progression and therapy.
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Affiliation(s)
| | - Jeannie Xue Ting Lee
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore.
| | - Karen Carmelina Crasta
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, 61 Biopolis Drive, 138673, Singapore; Department of Medicine, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
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Agathangelidis A, Ljungström V, Scarfò L, Fazi C, Gounari M, Pandzic T, Sutton LA, Stamatopoulos K, Tonon G, Rosenquist R, Ghia P. Highly similar genomic landscapes in monoclonal B-cell lymphocytosis and ultra-stable chronic lymphocytic leukemia with low frequency of driver mutations. Haematologica 2018; 103:865-873. [PMID: 29449433 PMCID: PMC5927998 DOI: 10.3324/haematol.2017.177212] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 02/07/2018] [Indexed: 01/07/2023] Open
Abstract
Despite the recent discovery of recurrent driver mutations in chronic lymphocytic leukemia, the genetic factors involved in disease onset remain largely unknown. To address this issue, we performed whole-genome sequencing in 11 individuals with monoclonal B- cell lymphocytosis, both of the low-count and high-count subtypes, and 5 patients with ultra-stable chronic lymphocytic leukemia (>10 years without progression from initial diagnosis). All three entities were indistinguishable at the genomic level exhibiting low genomic complexity and similar types of somatic mutations. Exonic mutations were not frequently identified in putative chronic lymphocytic leukemia driver genes in all settings, including low-count monoclonal B-cell lymphocytosis. To corroborate these findings, we also performed deep sequencing in 11 known frequently mutated genes in an extended cohort of 28 monoclonal B-cell lymphocytosis/chronic lymphocytic leukemia cases. Interestingly, shared mutations were detected between clonal B cells and paired polymorphonuclear cells, strengthening the notion that at least a fraction of somatic mutations may occur before disease onset, likely at the hematopoietic stem cell level. Finally, we identified previously unreported non-coding variants targeting pathways relevant to B-cell and chronic lymphocytic leukemia development, likely associated with the acquisition of the characteristic neoplastic phenotype typical of both monoclonal B-cell lymphocytosis and chronic lymphocytic leukemia.
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Affiliation(s)
- Andreas Agathangelidis
- Strategic Research Program on CLL and B-cell Neoplasia Unit, Division of Experimental Oncology, Università Vita-Salute San Raffaele and IRCCS Istituto Scientifico San Raffaele, Milan, Italy
| | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Lydia Scarfò
- Strategic Research Program on CLL and B-cell Neoplasia Unit, Division of Experimental Oncology, Università Vita-Salute San Raffaele and IRCCS Istituto Scientifico San Raffaele, Milan, Italy
| | - Claudia Fazi
- Strategic Research Program on CLL and B-cell Neoplasia Unit, Division of Experimental Oncology, Università Vita-Salute San Raffaele and IRCCS Istituto Scientifico San Raffaele, Milan, Italy
| | - Maria Gounari
- Strategic Research Program on CLL and B-cell Neoplasia Unit, Division of Experimental Oncology, Università Vita-Salute San Raffaele and IRCCS Istituto Scientifico San Raffaele, Milan, Italy.,Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - Tatjana Pandzic
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Lesley-Ann Sutton
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - Giovanni Tonon
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS Istituto Scientifico San Raffaele, Milan, Italy
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Paolo Ghia
- Strategic Research Program on CLL and B-cell Neoplasia Unit, Division of Experimental Oncology, Università Vita-Salute San Raffaele and IRCCS Istituto Scientifico San Raffaele, Milan, Italy
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