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Shlyakhtina Y, Bloechl B, Moran KL, Portal MM. Protocol to study the inheritance and propagation of non-genetically encoded states using barcode decay lineage tracing. STAR Protoc 2024; 5:102809. [PMID: 38180835 PMCID: PMC10801334 DOI: 10.1016/j.xpro.2023.102809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/21/2023] [Accepted: 12/15/2023] [Indexed: 01/07/2024] Open
Abstract
Here, we present a protocol to perform barcode decay lineage tracing followed by single-cell transcriptome analysis (BdLT-Seq). We describe steps for BdLT-Seq experimental design, building barcoded episome reporters, performing episome transfection, and barcode retrieval. We then describe procedures for sequencing library construction while providing options for sample multiplexing and data analysis. This BdLT-Seq technique enables the assessment of clonal evolution in a directional manner while preserving isogeneity, thus allowing the comparison of non-genetic molecular features between isogenic cell lineages. For complete details on the use and execution of this protocol, please refer to Shlyakhtina et al. (2023).1.
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Affiliation(s)
- Yelyzaveta Shlyakhtina
- Cell Plasticity & Epigenetics Lab, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK; Cell Plasticity & Epigenetics Lab, Cancer Research UK - Cancer Research UK Scotland Institute, The University of Glasgow, Glasgow G61 1BD, UK
| | - Bianca Bloechl
- Cell Plasticity & Epigenetics Lab, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK; Cell Plasticity & Epigenetics Lab, Cancer Research UK - Cancer Research UK Scotland Institute, The University of Glasgow, Glasgow G61 1BD, UK
| | - Katherine L Moran
- Cell Plasticity & Epigenetics Lab, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK
| | - Maximiliano M Portal
- Cell Plasticity & Epigenetics Lab, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK; Cell Plasticity & Epigenetics Lab, Cancer Research UK - Cancer Research UK Scotland Institute, The University of Glasgow, Glasgow G61 1BD, UK.
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2
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Knudsen AD, Eskelund CW, Benfield T, Zhao Y, Gelpi M, Køber L, Trøseid M, Kofoed KF, Ostrowski SR, Reilly C, Borges ÁH, Grønbæk K, Nielsen SD. Clonal hematopoiesis of indeterminate potential in persons with HIV. AIDS 2024; 38:487-495. [PMID: 37976039 DOI: 10.1097/qad.0000000000003788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
BACKGROUND Clonal hematopoiesis of indeterminate potential (CHIP) has been associated with older age, inflammation and with risk of coronary artery disease (CAD). We aimed to characterize the burden of CHIP, and to explore the association between CHIP, inflammatory markers, and CAD in older persons with HIV (PWH). METHODS From the Copenhagen Comorbidity in HIV Infection (COCOMO) study, we included 190 individuals older than 55 years of age. We defined CHIP as variant allele fraction at least 2%. CAD was categorized according to the most severe coronary artery lesion on coronary computed tomography (CT) angiography as no coronary atherosclerosis; any atherosclerosis defined as at least 1% stenosis and obstructive CAD defined as at least 50% stenosis. RESULTS In the entire population (median age 66 years, 87% men), we identified a total of 62 mutations distributed among 49 (26%) participants. The three most mutated genes were DNMT3A , TET2 , and ASXL1 , accounting for 49, 25, and 16% of mutations, respectively. Age and sex were the only variables associated with CHIP. IL-1β, IL-1Ra, IL-2, IL-6, IL-10, soluble CD14, soluble CD163 and TNF-α were not associated with CHIP, and CHIP was not associated with any atherosclerosis or with obstructive CAD in adjusted analyses. CONCLUSION In older, well treated, Scandinavian PWH, more than one in four had at least one CHIP mutation. We did not find evidence of an association between CHIP and inflammatory markers or between CHIP and CAD. CHIP is an unlikely underlying mechanism to explain the association between inflammation and CAD in treated HIV disease.
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Affiliation(s)
- Andreas D Knudsen
- Department of Infectious Diseases 8632
- Department of Cardiology, The Heart Center, Rigshospitalet, University of Copenhagen
| | | | - Thomas Benfield
- Department of Infectious Diseases, Copenhagen University Hospital - Amager and Hvidovre
| | | | | | - Lars Køber
- Department of Cardiology, The Heart Center, Rigshospitalet, University of Copenhagen
| | - Marius Trøseid
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Klaus F Kofoed
- Department of Cardiology, The Heart Center, Rigshospitalet, University of Copenhagen
- Department of Radiology, Rigshospitalet, University of Copenhagen
| | - Sisse R Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Cavan Reilly
- Division of Biostatistics, School of Public Health, University of Minnesota, MN, USA
| | - Álvaro H Borges
- Department of Infectious Disease Immunology, Statens Serum Institut
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen
| | - Kirsten Grønbæk
- Department of Hematology, Rigshospitalet, University Hospital Copenhagen, Copenhagen, Denmark
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3
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Cho JW, Cao J, Hemberg M. Joint analysis of mutational and transcriptional landscapes in human cancer reveals key perturbations during cancer evolution. Genome Biol 2024; 25:65. [PMID: 38459554 PMCID: PMC10921788 DOI: 10.1186/s13059-024-03201-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/19/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Tumors are able to acquire new capabilities, including traits such as drug resistance and metastasis that are associated with unfavorable clinical outcomes. Single-cell technologies have made it possible to study both mutational and transcriptomic profiles, but as most studies have been conducted on model systems, little is known about cancer evolution in human patients. Hence, a better understanding of cancer evolution could have important implications for treatment strategies. RESULTS Here, we analyze cancer evolution and clonal selection by jointly considering mutational and transcriptomic profiles of single cells acquired from tumor biopsies from 49 lung cancer samples and 51 samples with chronic myeloid leukemia. Comparing the two profiles, we find that each clone is associated with a preferred transcriptional state. For metastasis and drug resistance, we find that the number of mutations affecting related genes increases as the clone evolves, while changes in gene expression profiles are limited. Surprisingly, we find that mutations affecting ligand-receptor interactions with the tumor microenvironment frequently emerge as clones acquire drug resistance. CONCLUSIONS Our results show that lung cancer and chronic myeloid leukemia maintain a high clonal and transcriptional diversity, and we find little evidence in favor of clonal sweeps. This suggests that for these cancers selection based solely on growth rate is unlikely to be the dominating driving force during cancer evolution.
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Affiliation(s)
- Jae-Won Cho
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jingyi Cao
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Martin Hemberg
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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4
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Sartor O. Prostate-specific Membrane Antigen-targeted Isotope Therapy: Inherent Challenges Owing to Heterogeneity and Clonal Evolution. Eur Urol 2024; 85:205-206. [PMID: 38176993 DOI: 10.1016/j.eururo.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 12/13/2023] [Indexed: 01/06/2024]
Affiliation(s)
- Oliver Sartor
- Mayo Clinic Comprehensive Cancer Center, Rochester, MN, USA.
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5
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Reeves MQ, Balmain A. Mutations, Bottlenecks, and Clonal Sweeps: How Environmental Carcinogens and Genomic Changes Shape Clonal Evolution during Tumor Progression. Cold Spring Harb Perspect Med 2024; 14:a041388. [PMID: 38052482 PMCID: PMC10910358 DOI: 10.1101/cshperspect.a041388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
The transition from a single, initiated cell to a full-blown malignant tumor involves significant genomic evolution. Exposure to carcinogens-whether directly mutagenic or not-can drive progression toward malignancy, as can stochastic acquisition of cancer-promoting genetic events. Mouse models using both carcinogens and germline genetic manipulations have enabled precise inquiry into the evolutionary dynamics that take place as a tumor progresses from benign to malignant to metastatic stages. Tumor progression is characterized by changes in somatic point mutations and copy-number alterations, even though any single tumor can itself have a high or low burden of genomic alterations. Further, lineage-tracing, single-cell analyses and CRISPR barcoding have revealed the distinct clonal dynamics within benign and malignant tumors. Application of these tools in a range of mouse models can shed unique light on the patterns of clonal evolution that take place in both mouse and human tumors.
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Affiliation(s)
- Melissa Q Reeves
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
- Department of Pathology, University of Utah, Salt Lake City, Utah 84112, USA
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA
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6
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Bukkuri A. Modeling stress-induced responses: plasticity in continuous state space and gradual clonal evolution. Theory Biosci 2024; 143:63-77. [PMID: 38289469 DOI: 10.1007/s12064-023-00410-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 12/13/2023] [Indexed: 03/01/2024]
Abstract
Mathematical models of cancer and bacterial evolution have generally stemmed from a gene-centric framework, assuming clonal evolution via acquisition of resistance-conferring mutations and selection of their corresponding subpopulations. More recently, the role of phenotypic plasticity has been recognized and models accounting for phenotypic switching between discrete cell states (e.g., epithelial and mesenchymal) have been developed. However, seldom do models incorporate both plasticity and mutationally driven resistance, particularly when the state space is continuous and resistance evolves in a continuous fashion. In this paper, we develop a framework to model plastic and mutational mechanisms of acquiring resistance in a continuous gradual fashion. We use this framework to examine ways in which cancer and bacterial populations can respond to stress and consider implications for therapeutic strategies. Although we primarily discuss our framework in the context of cancer and bacteria, it applies broadly to any system capable of evolving via plasticity and genetic evolution.
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Affiliation(s)
- Anuraag Bukkuri
- Cancer Biology and Evolution Program and Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, USA.
- Tissue Development and Evolution Research Group, Department of Laboratory Medicine, Lund University, Lund, Sweden.
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7
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Diral E, Campochiaro C, Tomelleri A, Bergonzi GM, Pizzano U, Ponzoni M, Bongiovanni L, Ronchi P, Tresoldi C, Rigamonti S, Scarfò F, Latino GM, Rinaldi E, Bernardi M, Dagna L, Ciceri F. Case report: Cytopenias in VEXAS syndrome - a WHO 2022 based approach in a single-center cohort. Front Immunol 2024; 15:1354130. [PMID: 38333211 PMCID: PMC10850384 DOI: 10.3389/fimmu.2024.1354130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 01/08/2024] [Indexed: 02/10/2024] Open
Abstract
VEXAS syndrome is an acquired autoinflammatory disease characterized in most cases by cytopenias and macrocytic anemia. Dyshematopoiesis is a frequent finding in chronic inflammatory conditions and therefore, cytopenias are not easily classified in VEXAS patients. Here we report a series of 7 patients affected by VEXAS associated cytopenias, treated at our center. The use of NGS, together with morphological assays, integrated with the WHO 2022 criteria, allowed to identify three subsets of VEXAS associated cytopenias: ICUS (idiopathic cytopenia of uncertain significance), CCUS (clonal cytopenia of uncertain significance) at high risk of clonal evolution, and MDS. This approach could help to better understand the nature of VEXAS associated cytopenias and to guide the use of specific targeted treatments in order to achieve long lasting responses.
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Affiliation(s)
- Elisa Diral
- Unit of Hematology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Corrado Campochiaro
- Unit of Immunology, Rheumatology, Allergy and Rare Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Alessandro Tomelleri
- Unit of Immunology, Rheumatology, Allergy and Rare Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Gregorio M. Bergonzi
- Unit of Hematology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Umberto Pizzano
- Unit of Hematology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Maurilio Ponzoni
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
- Pathology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Lucia Bongiovanni
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
- Pathology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paola Ronchi
- Unit of Immunohaematology and Transfusion Medicine, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Cristina Tresoldi
- Unit of Immunohaematology and Transfusion Medicine, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Rigamonti
- Unit of Immunohaematology and Transfusion Medicine, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federico Scarfò
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
- Pathology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Gloria M. Latino
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Emma Rinaldi
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Massimo Bernardi
- Unit of Hematology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Lorenzo Dagna
- Unit of Immunology, Rheumatology, Allergy and Rare Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Fabio Ciceri
- Unit of Hematology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
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8
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Sarode GS, Sarode SC, Sharma N. Comment on " Clonal evolution of long-term expanding head and neck cancer organoid: Impact on treatment response for personalized therapeutic screening". Oral Oncol 2023; 147:106614. [PMID: 37922595 DOI: 10.1016/j.oraloncology.2023.106614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 11/07/2023]
Affiliation(s)
- Gargi S Sarode
- Department of Oral Pathology and Microbiology, Dr. D.Y. Patil Dental College & Hospital, Dr. D.Y. Patil Vidyapeeth, Pune, Maharashtra State, India
| | - Sachin C Sarode
- Department of Oral Pathology and Microbiology, Dr. D.Y. Patil Dental College & Hospital, Dr. D.Y. Patil Vidyapeeth, Pune Maharashtra State, India; Dr. D. Y. Patil Unitech Society's, Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune 411018, Maharashtra, India.
| | - Nilesh Sharma
- Cancer and Translational Research Laboratory, Dr. D.Y. Patil Biotechnology and Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Maharashtra State, Pune, India
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Russo A, Scilla KA, Mehra R, Gittens A, McCusker MG, de Miguel-Perez D, Gomez JE, Peleg A, Del Re M, Rolfo CD. Tracking Clonal Evolution of EGFR-Mutated Non-Small Cell Lung Cancer Through Liquid Biopsy: Management of C797S Acquired Mutation. Clin Lung Cancer 2023; 24:660-665. [PMID: 37487787 DOI: 10.1016/j.cllc.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/17/2023] [Accepted: 07/17/2023] [Indexed: 07/26/2023]
Affiliation(s)
- Alessandro Russo
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, Division of Hematology/Oncology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD; Department of Onco-Hematology, Papardo Hospital, Messina, Italy
| | - Katherine A Scilla
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, Division of Hematology/Oncology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD
| | - Ranee Mehra
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, Division of Hematology/Oncology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD
| | - Allison Gittens
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, Division of Hematology/Oncology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD
| | - Michael G McCusker
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, Division of Hematology/Oncology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD; Shenandoah Oncology Associates, Oncology Department, Winchester, VA
| | - Diego de Miguel-Perez
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, Division of Hematology/Oncology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD; Center for Thoracic Oncology, Tisch Cancer Institute, Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jorge E Gomez
- Center for Thoracic Oncology, Tisch Cancer Institute, Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ariel Peleg
- Center for Thoracic Oncology, Tisch Cancer Institute, Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Marzia Del Re
- Center for Thoracic Oncology, Tisch Cancer Institute, Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY; Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Christian D Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY.
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Tobias DK, Manning AK, Wessel J, Raghavan S, Westerman KE, Bick AG, Dicorpo D, Whitsel EA, Collins J, Correa A, Cupples LA, Dupuis J, Goodarzi MO, Guo X, Howard B, Lange LA, Liu S, Raffield LM, Reiner AP, Rich SS, Taylor KD, Tinker L, Wilson JG, Wu P, Carson AP, Vasan RS, Fornage M, Psaty BM, Kooperberg C, Rotter JI, Meigs J, Manson JE. Clonal Hematopoiesis of Indeterminate Potential (CHIP) and Incident Type 2 Diabetes Risk. Diabetes Care 2023; 46:1978-1985. [PMID: 37756531 PMCID: PMC10620536 DOI: 10.2337/dc23-0805] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/07/2023] [Indexed: 09/29/2023]
Abstract
OBJECTIVE Clonal hematopoiesis of indeterminate potential (CHIP) is an aging-related accumulation of somatic mutations in hematopoietic stem cells, leading to clonal expansion. CHIP presence has been implicated in atherosclerotic coronary heart disease (CHD) and all-cause mortality, but its association with incident type 2 diabetes (T2D) is unknown. We hypothesized that CHIP is associated with elevated risk of T2D. RESEARCH DESIGN AND METHODS CHIP was derived from whole-genome sequencing of blood DNA in the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine (TOPMed) prospective cohorts. We performed analysis for 17,637 participants from six cohorts, without prior T2D, cardiovascular disease, or cancer. We evaluated baseline CHIP versus no CHIP prevalence with incident T2D, including associations with DNMT3A, TET2, ASXL1, JAK2, and TP53 variants. We estimated multivariable-adjusted hazard ratios (HRs) and 95% CIs with adjustment for age, sex, BMI, smoking, alcohol, education, self-reported race/ethnicity, and combined cohorts' estimates via fixed-effects meta-analysis. RESULTS Mean (SD) age was 63.4 (11.5) years, 76% were female, and CHIP prevalence was 6.0% (n = 1,055) at baseline. T2D was diagnosed in n = 2,467 over mean follow-up of 9.8 years. Participants with CHIP had 23% (CI 1.04, 1.45) higher risk of T2D than those with no CHIP. Specifically, higher risk was for TET2 (HR 1.48; CI 1.05, 2.08) and ASXL1 (HR 1.76; CI 1.03, 2.99) mutations; DNMT3A was nonsignificant (HR 1.15; CI 0.93, 1.43). Statistical power was limited for JAK2 and TP53 analyses. CONCLUSIONS CHIP was associated with higher incidence of T2D. CHIP mutations located on genes implicated in CHD and mortality were also related to T2D, suggesting shared aging-related pathology.
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Affiliation(s)
- Deirdre K. Tobias
- Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Nutrition Department, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Alisa K. Manning
- Broad Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA
| | - Jennifer Wessel
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Department of Medicine, School of Medicine, and Diabetes Translational Research Center, Indiana University, Indianapolis, IN
| | - Sridharan Raghavan
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, and Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Kenneth E. Westerman
- Broad Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA
- Harvard Medical School, Boston, MA
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA
| | - Alexander G. Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Daniel Dicorpo
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Eric A. Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jason Collins
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Mark O. Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | | | - Leslie A. Lange
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, and Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Simin Liu
- Center for Global Cardiometabolic Health, Brown University, Providence, RI
| | - Laura M. Raffield
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Alex P. Reiner
- Department of Epidemiology, University of Washington, Seattle, WA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Kent D. Taylor
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
| | - Lesley Tinker
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
| | - James G. Wilson
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Peitao Wu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - April P. Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS
| | - Ramachandran S. Vasan
- Section of Preventive Medicine and Epidemiology, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
- University of Texas School of Public Health, San Antonio, TX
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - James Meigs
- Department of Medicine, Harvard Medical School, and Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - JoAnn E. Manson
- Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Epidemiology Department, Harvard T.H. Chan School of Public Health, Boston, MA
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Bruzos AL, Santamarina M, García-Souto D, Díaz S, Rocha S, Zamora J, Lee Y, Viña-Feás A, Quail MA, Otero I, Pequeño-Valtierra A, Temes J, Rodriguez-Castro J, Aramburu L, Vidal-Capón A, Villanueva A, Costas D, Rodríguez R, Prieto T, Tomás L, Alvariño P, Alonso J, Cao A, Iglesias D, Carballal MJ, Amaral AM, Balseiro P, Calado R, El Khalfi B, Izagirre U, de Montaudouin X, Pade NG, Probert I, Ricardo F, Ruiz P, Skazina M, Smolarz K, Pasantes JJ, Villalba A, Ning Z, Ju YS, Posada D, Demeulemeester J, Baez-Ortega A, Tubio JMC. Somatic evolution of marine transmissible leukemias in the common cockle, Cerastoderma edule. Nat Cancer 2023; 4:1575-1591. [PMID: 37783803 DOI: 10.1038/s43018-023-00641-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 08/23/2023] [Indexed: 10/04/2023]
Abstract
Transmissible cancers are malignant cell lineages that spread clonally between individuals. Several such cancers, termed bivalve transmissible neoplasia (BTN), induce leukemia-like disease in marine bivalves. This is the case of BTN lineages affecting the common cockle, Cerastoderma edule, which inhabits the Atlantic coasts of Europe and northwest Africa. To investigate the evolution of cockle BTN, we collected 6,854 cockles, diagnosed 390 BTN tumors, generated a reference genome and assessed genomic variation across 61 tumors. Our analyses confirmed the existence of two BTN lineages with hemocytic origins. Mitochondrial variation revealed mitochondrial capture and host co-infection events. Mutational analyses identified lineage-specific signatures, one of which likely reflects DNA alkylation. Cytogenetic and copy number analyses uncovered pervasive genomic instability, with whole-genome duplication, oncogene amplification and alkylation-repair suppression as likely drivers. Satellite DNA distributions suggested ancient clonal origins. Our study illuminates long-term cancer evolution under the sea and reveals tolerance of extreme instability in neoplastic genomes.
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Affiliation(s)
- Alicia L Bruzos
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Martín Santamarina
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Daniel García-Souto
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Wellcome Sanger Institute, Hinxton, UK
| | - Seila Díaz
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- ECOMARE, Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Sara Rocha
- CINBIO, Universidade de Vigo, Vigo, Spain
| | - Jorge Zamora
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Yunah Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Alejandro Viña-Feás
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | | | - Iago Otero
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Ana Pequeño-Valtierra
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Javier Temes
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Jorge Rodriguez-Castro
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Leyre Aramburu
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - André Vidal-Capón
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, Vigo, Spain
| | - Antonio Villanueva
- Centro de Investigación Mariña (CIM-ECIMAT), Universidade de Vigo, Vigo, Spain
| | - Damián Costas
- Centro de Investigación Mariña (CIM-ECIMAT), Universidade de Vigo, Vigo, Spain
| | - Rosana Rodríguez
- Centro de Investigación Mariña (CIM-ECIMAT), Universidade de Vigo, Vigo, Spain
| | - Tamara Prieto
- CINBIO, Universidade de Vigo, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
- New York Genome Center, New York, NY, USA
| | - Laura Tomás
- CINBIO, Universidade de Vigo, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Pilar Alvariño
- CINBIO, Universidade de Vigo, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Juana Alonso
- CINBIO, Universidade de Vigo, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Asunción Cao
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, Vilanova de Arousa, Spain
| | - David Iglesias
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, Vilanova de Arousa, Spain
| | - María J Carballal
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, Vilanova de Arousa, Spain
| | - Ana M Amaral
- Centro de Ciencias do Mar do Algarve (CCMAR), Universidade do Algarve, Faro, Portugal
| | - Pablo Balseiro
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- NORCE AS, Bergen, Norway
| | - Ricardo Calado
- ECOMARE, Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Bouchra El Khalfi
- Laboratory of Physiopathology, Molecular Genetics & Biotechnology, Faculty of Sciences Ain Chock, Health and Biotechnology Research Centre, Hassan II University of Casablanca, Casablanca, Morocco
| | - Urtzi Izagirre
- Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plenzia-Bitzkaia, Spain
- Cell Biology in Environmental Toxicology Research Group, University of the Basque Country (UPV/EHU), Leioa-Bizkaia, Spain
| | | | - Nicolas G Pade
- European Marine Biology Resources Centre (EMBRC-ERIC), Paris, France
| | - Ian Probert
- FR2424 Station Biologique de Roscoff, Sorbonne University/CNRS, Roscoff, France
| | - Fernando Ricardo
- ECOMARE, Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Pamela Ruiz
- Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plenzia-Bitzkaia, Spain
- Cell Biology in Environmental Toxicology Research Group, University of the Basque Country (UPV/EHU), Leioa-Bizkaia, Spain
| | - Maria Skazina
- Department of Applied Ecology, St Petersburg State University, St Petersburg, Russia
| | - Katarzyna Smolarz
- Department of Marine Ecosystem Functioning, University of Gdańsk, Gdynia, Poland
| | - Juan J Pasantes
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, Vigo, Spain
- Centro de Investigación Mariña (CIM-ECIMAT), Universidade de Vigo, Vigo, Spain
| | - Antonio Villalba
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, Vilanova de Arousa, Spain
- Research Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plenzia-Bitzkaia, Spain
- Department of Life Sciences, Universidad de Alcalá, Alcalá de Henares, Spain
| | | | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - David Posada
- CINBIO, Universidade de Vigo, Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Jonas Demeulemeester
- VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
- The Francis Crick Institute, London, UK
| | - Adrian Baez-Ortega
- Wellcome Sanger Institute, Hinxton, UK.
- Magdalene College, University of Cambridge, Cambridge, UK.
| | - Jose M C Tubio
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
- Instituto de Investigaciones Sanitarias de Santiago de Compostela (IDIS), Santiago de Compostela, Spain.
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12
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Ji J, Wan Z, Ruan J, Yang Y, Hu Q, Chen Z, Yang C, Chen M, Han B. Eltrombopag with or without Tacrolimus for relapsed/refractory acquired aplastic anaemia: a prospective randomized trial. Blood Cancer J 2023; 13:146. [PMID: 37726286 PMCID: PMC10509202 DOI: 10.1038/s41408-023-00921-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/26/2023] [Accepted: 09/01/2023] [Indexed: 09/21/2023] Open
Abstract
This trial compared eltrombopag (EPAG)+tacrolimus and EPAG monotherapy in patients with refractory/relapsed acquired aplastic anaemia (AA). Patients with refractory/relapsed AA were randomly assigned to receive either EPAG+tacrolimus or EPAG monotherapy at a ratio of 2:1. Patient response, safety, clonal evolution and survival were compared. In total, 114 patients were included in the analysis, with 76 patients receiving EPAG+tacrolimus and 38 receiving EPAG only. With a median follow-up of 18 (6-24) months, the overall response rate (ORR) for patients treated with EPAG+tacrolimus and EPAG alone was 38.2% vs. 31.6% (P = 0.490) at the 3rd month, 61.8% vs. 39.5% (P = 0.024) at the 6th month, 64.5% vs. 47.1% (P = 0.097) at the 12th month, and 60.5% vs. 34.2% (P = 0.008) at the last follow-up. The rate of each adverse event, overall survival curves (P = 0.635) and clonal evolution rate (P = 1.000) were comparable between the groups. A post hoc subgroup analysis showed that EPAG+tacrolimus could have advantage over EPAG monotherapy in terms of the ORR at the 6th month (P = 0.030)/last follow-up (P = 0.013) and the cumulative relapse-free survival (RFS) curves (P = 0.048) in patients <60 years old.
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Affiliation(s)
- Jiang Ji
- Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ziqi Wan
- Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Ruan
- Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuan Yang
- Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qinglin Hu
- Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zesong Chen
- Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chen Yang
- Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Miao Chen
- Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Bing Han
- Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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13
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Volchkov EV, Khozyainova AA, Gurzhikhanova MK, Larionova IV, Matveev VE, Evseev DA, Ignatova AK, Menyailo ME, Venyov DA, Vorobev RS, Semchenkova AA, Olshanskaya YV, Denisov EV, Maschan MA. Potential value of high-throughput single-cell DNA sequencing of Juvenile myelomonocytic leukemia: report of two cases. NPJ Syst Biol Appl 2023; 9:41. [PMID: 37684264 PMCID: PMC10491583 DOI: 10.1038/s41540-023-00303-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/14/2023] [Indexed: 09/10/2023] Open
Abstract
Juvenile myelomonocytic leukemia (JMML) is a rare myeloproliferative disease of early childhood that develops due to mutations in the genes of the RAS-signaling pathway. Next-generation high throughput sequencing (NGS) enables identification of various secondary molecular genetic events that can facilitate JMML progression and transformation into secondary acute myeloid leukemia (sAML). The methods of single-cell DNA sequencing (scDNA-seq) enable overcoming limitations of bulk NGS and exploring genetic heterogeneity at the level of individual cells, which can help in a better understanding of the mechanisms leading to JMML progression and provide an opportunity to evaluate the response of leukemia to therapy. In the present work, we applied a two-step droplet microfluidics approach to detect DNA alterations among thousands of single cells and to analyze clonal dynamics in two JMML patients with sAML transformation before and after hematopoietic stem cell transplantation (HSCT). At the time of diagnosis both of our patients harbored only "canonical" mutations in the RAS signaling pathway genes detected by targeted DNA sequencing. Analysis of samples from the time of transformation JMML to sAML revealed additional genetic events that are potential drivers for disease progression in both patients. ScDNA-seq was able to measure of chimerism level and detect a residual tumor clone in the second patient after HSCT (sensitivity of less than 0.1% tumor cells). The data obtained demonstrate the value of scDNA-seq to assess the clonal evolution of JMML to sAML, response to therapy and engraftment monitoring.
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Affiliation(s)
- E V Volchkov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology (D. Rogachev NMRCPHOI) of Ministry of Healthсare of the Russian Federation, 1, Samory Mashela St., Moscow, 117997, Russia.
- Laboratory of Single Cell Biology, Research Institute of Molecular and Cellular Medicine, RUDN University, Moscow, 117198, Russia.
| | - A A Khozyainova
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia
| | - M Kh Gurzhikhanova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology (D. Rogachev NMRCPHOI) of Ministry of Healthсare of the Russian Federation, 1, Samory Mashela St., Moscow, 117997, Russia
| | - I V Larionova
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia
| | - V E Matveev
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology (D. Rogachev NMRCPHOI) of Ministry of Healthсare of the Russian Federation, 1, Samory Mashela St., Moscow, 117997, Russia
| | - D A Evseev
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology (D. Rogachev NMRCPHOI) of Ministry of Healthсare of the Russian Federation, 1, Samory Mashela St., Moscow, 117997, Russia
| | - A K Ignatova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology (D. Rogachev NMRCPHOI) of Ministry of Healthсare of the Russian Federation, 1, Samory Mashela St., Moscow, 117997, Russia
| | - M E Menyailo
- Laboratory of Single Cell Biology, Research Institute of Molecular and Cellular Medicine, RUDN University, Moscow, 117198, Russia
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia
| | - D A Venyov
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology (D. Rogachev NMRCPHOI) of Ministry of Healthсare of the Russian Federation, 1, Samory Mashela St., Moscow, 117997, Russia
| | - R S Vorobev
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia
| | - A A Semchenkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology (D. Rogachev NMRCPHOI) of Ministry of Healthсare of the Russian Federation, 1, Samory Mashela St., Moscow, 117997, Russia
| | - Yu V Olshanskaya
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology (D. Rogachev NMRCPHOI) of Ministry of Healthсare of the Russian Federation, 1, Samory Mashela St., Moscow, 117997, Russia
| | - E V Denisov
- Laboratory of Single Cell Biology, Research Institute of Molecular and Cellular Medicine, RUDN University, Moscow, 117198, Russia
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634009, Russia
| | - M A Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology (D. Rogachev NMRCPHOI) of Ministry of Healthсare of the Russian Federation, 1, Samory Mashela St., Moscow, 117997, Russia.
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Johnson B, Shuai Y, Schweinsberg J, Curtius K. cloneRate: fast estimation of single-cell clonal dynamics using coalescent theory. Bioinformatics 2023; 39:btad561. [PMID: 37699006 PMCID: PMC10534056 DOI: 10.1093/bioinformatics/btad561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/25/2023] [Indexed: 09/14/2023] Open
Abstract
MOTIVATION While evolutionary approaches to medicine show promise, measuring evolution itself is difficult due to experimental constraints and the dynamic nature of body systems. In cancer evolution, continuous observation of clonal architecture is impossible, and longitudinal samples from multiple timepoints are rare. Increasingly available DNA sequencing datasets at single-cell resolution enable the reconstruction of past evolution using mutational history, allowing for a better understanding of dynamics prior to detectable disease. There is an unmet need for an accurate, fast, and easy-to-use method to quantify clone growth dynamics from these datasets. RESULTS We derived methods based on coalescent theory for estimating the net growth rate of clones using either reconstructed phylogenies or the number of shared mutations. We applied and validated our analytical methods for estimating the net growth rate of clones, eliminating the need for complex simulations used in previous methods. When applied to hematopoietic data, we show that our estimates may have broad applications to improve mechanistic understanding and prognostic ability. Compared to clones with a single or unknown driver mutation, clones with multiple drivers have significantly increased growth rates (median 0.94 versus 0.25 per year; P = 1.6×10-6). Further, stratifying patients with a myeloproliferative neoplasm (MPN) by the growth rate of their fittest clone shows that higher growth rates are associated with shorter time to MPN diagnosis (median 13.9 versus 26.4 months; P = 0.0026). AVAILABILITY AND IMPLEMENTATION We developed a publicly available R package, cloneRate, to implement our methods (Package website: https://bdj34.github.io/cloneRate/). Source code: https://github.com/bdj34/cloneRate/.
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Affiliation(s)
- Brian Johnson
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, United States
| | - Yubo Shuai
- Department of Mathematics, University of California San Diego, La Jolla, CA 92093, United States
| | - Jason Schweinsberg
- Department of Mathematics, University of California San Diego, La Jolla, CA 92093, United States
| | - Kit Curtius
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, United States
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, United States
- VA San Diego Healthcare System, San Diego, CA 92161, United States
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15
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Maffeo B, Panuzzo C, Moraca A, Cilloni D. A Leukemic Target with a Thousand Faces: The Mitochondria. Int J Mol Sci 2023; 24:13069. [PMID: 37685874 PMCID: PMC10487524 DOI: 10.3390/ijms241713069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/16/2023] [Accepted: 08/19/2023] [Indexed: 09/10/2023] Open
Abstract
In the era of personalized medicine greatly improved by molecular diagnosis and tailor-made therapies, the survival rate of acute myeloid leukemia (AML) at 5 years remains unfortunately low. Indeed, the high heterogeneity of AML clones with distinct metabolic and molecular profiles allows them to survive the chemotherapy-induced changes, thus leading to resistance, clonal evolution, and relapse. Moreover, leukemic stem cells (LSCs), the quiescent reservoir of residual disease, can persist for a long time and activate the recurrence of disease, supported by significant metabolic differences compared to AML blasts. All these points highlight the relevance to develop combination therapies, including metabolism inhibitors to improve treatment efficacy. In this review, we summarized the metabolic differences in AML blasts and LSCs, the molecular pathways related to mitochondria and metabolism are druggable and targeted in leukemia therapies, with a distinct interest for Venetoclax, which has revolutionized the therapeutic paradigms of several leukemia subtype, unfit for intensive treatment regimens.
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Affiliation(s)
| | - Cristina Panuzzo
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (B.M.); (A.M.); (D.C.)
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16
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García-Sanz R, García-Álvarez M, Medina A, Askari E, González-Calle V, Casanova M, de la Torre-Loizaga I, Escalante-Barrigón F, Bastos-Boente M, Bárez A, Vidaña-Bedera N, Alonso JM, Sarasquete ME, González M, Chillón MC, Alcoceba M, Jiménez C. Clonal architecture and evolutionary history of Waldenström's macroglobulinemia at the single-cell level. Dis Model Mech 2023; 16:dmm050227. [PMID: 37493341 PMCID: PMC10461465 DOI: 10.1242/dmm.050227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/19/2023] [Indexed: 07/27/2023] Open
Abstract
To provide insight into the subclonal architecture and co-dependency patterns of the alterations in Waldenström's macroglobulinemia (WM), we performed single-cell mutational and protein profiling of eight patients. A custom panel was designed to screen for mutations and copy number alterations at the single-cell level in samples taken from patients at diagnosis (n=5) or at disease progression (n=3). Results showed that in asymptomatic WM at diagnosis, MYD88L265P was the predominant clonal alteration; other events, if present, were secondary and subclonal to MYD88L265P. In symptomatic WM, clonal diversity was more evident, uncovering combinations of alterations that synergized to promote clonal expansion and dominance. At disease progression, a dominant clone was observed, sometimes accompanied by other less complex minor clones, which could be consistent with a clonal selection process. Clonal diversity was also reduced, probably due to the effect of treatment. Finally, we combined protein expression with mutational analysis to map somatic genotype with the immunophenotype. Our findings provide a comprehensive view of the clonality of tumor populations in WM and how clonal complexity can evolve and impact disease progression.
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Affiliation(s)
- Ramón García-Sanz
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - María García-Álvarez
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - Alejandro Medina
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - Elham Askari
- Hematology Department, Fundación Jiménez Díaz, Centro de Investigación Biomédica en Red-Cáncer, Madrid 28040, Spain
| | - Verónica González-Calle
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - María Casanova
- Hematology Department, Hospital Costa del Sol, Marbella 29603, Spain
| | - Igor de la Torre-Loizaga
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | | | - Miguel Bastos-Boente
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - Abelardo Bárez
- Hematology Department, Complejo Asistencial de Ávila, Ávila 05071, Spain
| | - Nerea Vidaña-Bedera
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - José María Alonso
- Hematology Department, Complejo Asistencial Universitario de Palencia, Palencia 34005, Spain
| | - María Eugenia Sarasquete
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - Marcos González
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - María Carmen Chillón
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - Miguel Alcoceba
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - Cristina Jiménez
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
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17
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Samur MK, Szalat R, Munshi NC. Single-cell profiling in multiple myeloma: insights, problems, and promises. Blood 2023; 142:313-324. [PMID: 37196627 PMCID: PMC10485379 DOI: 10.1182/blood.2022017145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/05/2023] [Accepted: 05/11/2023] [Indexed: 05/19/2023] Open
Abstract
In a short time, single-cell platforms have become the norm in many fields of research, including multiple myeloma (MM). In fact, the large amount of cellular heterogeneity in MM makes single-cell platforms particularly attractive because bulk assessments can miss valuable information about cellular subpopulations and cell-to-cell interactions. The decreasing cost and increasing accessibility of single-cell platform, combined with breakthroughs in obtaining multiomics data for the same cell and innovative computational programs for analyzing data, have allowed single-cell studies to make important insights into MM pathogenesis; yet, there is still much to be done. In this review, we will first focus on the types of single-cell profiling and the considerations for designing a single-cell profiling experiment. Then, we will discuss what have learned from single-cell profiling about myeloma clonal evolution, transcriptional reprogramming, and drug resistance, and about the MM microenvironment during precursor and advanced disease.
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Affiliation(s)
- Mehmet Kemal Samur
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Raphael Szalat
- Department of Hematology and Medical Oncology, Boston University Medical Center, Boston, MA
| | - Nikhil C. Munshi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- VA Boston Healthcare System, Boston, MA
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18
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Hall MWJ, Shorthouse D, Alcraft R, Jones PH, Hall BA. Mutations observed in somatic evolution reveal underlying gene mechanisms. Commun Biol 2023; 6:753. [PMID: 37468606 PMCID: PMC10356810 DOI: 10.1038/s42003-023-05136-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/11/2023] [Indexed: 07/21/2023] Open
Abstract
Highly sensitive DNA sequencing techniques have allowed the discovery of large numbers of somatic mutations in normal tissues. Some mutations confer a competitive advantage over wild-type cells, generating expanding clones that spread through the tissue. Competition between mutant clones leads to selection. This process can be considered a large scale, in vivo screen for mutations increasing cell fitness. It follows that somatic missense mutations may offer new insights into the relationship between protein structure, function and cell fitness. We present a flexible statistical method for exploring the selection of structural features in data sets of somatic mutants. We show how this approach can evidence selection of specific structural features in key drivers in aged tissues. Finally, we show how drivers may be classified as fitness-enhancing and fitness-suppressing through different patterns of mutation enrichment. This method offers a route to understanding the mechanism of protein function through in vivo mutant selection.
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Affiliation(s)
| | - David Shorthouse
- Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, University College London, Gower Street, London, WC1E 6BT, UK
| | - Rachel Alcraft
- Advanced Research Computing, University College London, London, UK
| | - Philip H Jones
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Oncology, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Benjamin A Hall
- Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, University College London, Gower Street, London, WC1E 6BT, UK.
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19
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Hoh RA, Thörnqvist L, Yang F, Godzwon M, King JJ, Lee JY, Greiff L, Boyd SD, Ohlin M. Clonal evolution and stereotyped sequences of human IgE lineages in aeroallergen-specific immunotherapy. J Allergy Clin Immunol 2023; 152:214-229. [PMID: 36828082 DOI: 10.1016/j.jaci.2023.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/22/2023] [Accepted: 02/09/2023] [Indexed: 02/24/2023]
Abstract
BACKGROUND Allergic disease reflects specific inflammatory processes initiated by interaction between allergen and allergen-specific IgE. Specific immunotherapy (SIT) is an effective long-term treatment option, but the mechanisms by which SIT provides desensitization are not well understood. OBJECTIVE Our aim was to characterize IgE sequences expressed by allergen-specific B cells over a 3-year longitudinal study of patients with aeroallergies who were undergoing SIT. METHODS Allergen-specific IgE-expressing clones were identified by using combinatorial single-chain variable fragment libraries and tracked in PBMCs and nasal biopsy samples over a 3-year period with antibody gene repertoire sequencing. The characteristics of private IgE-expressing clones were compared with those of stereotyped or "public" IgE responses to the grass pollen allergen Phleum pratense (Phl p) 2. RESULT Members of the same allergen-specific IgE lineages were observed in nasal biopsy samples and blood, and lineages detected at baseline persisted in blood and nasal biopsy samples after 3 years of SIT, including B cells that express IgE. Evidence of progressive class switch recombination to IgG subclasses was observed after 3 years of SIT. A common stereotyped Phl p 2-specific antibody heavy chain sequence was detected in multiple donors. The amino acid residues enriched in IgE-stereotyped sequences from seropositive donors were analyzed with machine learning and k-mer motif discovery. Stereotyped IgE sequences had lower overall rates of somatic hypermutation and antigen selection than did single-chain variable fragment-derived allergen-specific sequences or IgE sequences of unknown specificity. CONCLUSION Longitudinal tracking of rare circulating and tissue-resident allergen-specific IgE+ clones demonstrates persistence of allergen-specific IgE+ clones, progressive class switch recombination to IgG subtypes, and distinct maturation of a stereotyped Phl p 2 clonotype.
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Affiliation(s)
- Ramona A Hoh
- Department of Pathology, Stanford University, Stanford, Calif
| | | | - Fan Yang
- Department of Pathology, Stanford University, Stanford, Calif
| | | | - Jasmine J King
- Department of Pathology, Stanford University, Stanford, Calif
| | - Ji-Yeun Lee
- Department of Pathology, Stanford University, Stanford, Calif
| | - Lennart Greiff
- Department of Clinical Sciences, Lund University, Lund, Sweden; Department of Otorhinolaryngology, Head and Neck Surgery, Skåne University Hospital, Lund, Sweden
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, Calif; Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, Calif
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
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20
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Nabel CS, Hung YP, Kurilovich A, Lopareva A, Dias-Santagata D, Batashkov N, Tabakov D, Sorokina M, Makarov A, Sagaradze G, Butusova A, Kudryashova O, Bedniagin L, Wright CD, Shin N, Bagaev A, Postovalova E, Louissaint A. Longitudinal Molecular Analysis of Tumor Exome and Transcriptome to Evaluate Clonal Evolution and Identify Novel Therapeutic Targets in Thymoma. JCO Precis Oncol 2023; 7:e2300107. [PMID: 37437230 PMCID: PMC10581621 DOI: 10.1200/po.23.00107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/22/2023] [Accepted: 06/06/2023] [Indexed: 07/14/2023] Open
Affiliation(s)
- Christopher S. Nabel
- Department of Medicine, Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
| | - Yin P. Hung
- Harvard Medical School, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | | | | | - Dora Dias-Santagata
- Harvard Medical School, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | | | | | | | | | | | | | | | | | - Cameron D. Wright
- Harvard Medical School, Boston, MA
- Department of Surgery, Massachusetts General Hospital, Boston, MA
| | | | | | | | - Abner Louissaint
- Harvard Medical School, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Boston, MA
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21
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Momen N, Tario J, Fu K, Qian YW. Multiparameter flow cytometry and ClonoSEQ correlation to evaluate precursor B-lymphoblastic leukemia measurable residual disease. J Hematop 2023; 16:85-94. [PMID: 38175444 DOI: 10.1007/s12308-023-00544-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/03/2023] [Indexed: 01/05/2024] Open
Abstract
Measurable residual disease (MRD) detection for precursor B-lymphoblastic leukemia (B-ALL) has become the standard of care. However, the testing methodology has not been standardized. We aim to correlate COG multiparameter flow cytometry (MFC) and ClonoSEQ techniques to assess the test characteristics, to study abnormal immunophenotype for B-ALL MRD, and to observe B-ALL clonal evolution and the impact of blinatumomab therapy on MFC testing. MFC and molecular reports were retrieved from electronic medical records and data was reviewed. Included in this study were 74 bone marrow samples collected from 31 B-ALL patients at our institution between January 2021 and March 2022. COG MFC and ClonoSEQ results were concordant in 59/74 samples (80%) with positive concordant results in 12 samples (16%) and negative concordant results in 47 samples (64%). Discordant results were seen in 15/74 samples (20%), with 14 samples (19%) showing ClonoSEQ + /MFC- results and only 1 sample (1%) showing MFC + /ClonoSEQ- result. ClonoSEQ + /MFC- cases had MRD values ranging from 1 to 1400 cells/million nucleated cells with 86% of cases showing MRD values of < 100 cells/million nucleated cells. Newly identified dominant sequences were detected using ClonoSEQ in 2/31 patients (6%) during follow-up. All 14 bone marrow samples from 8 patients, who had gone through blinatumomab immunotherapy, were MRD negative by MFC, but 3 cases were MRD positive by ClonoSEQ. Our results show strong correlation between COG MFC and ClonoSEQ (r = 0.96), and both methods are complementary. Clonal evolution may occur, and blinatumomab immunotherapy may impact MFC B-ALL MRD evaluation.
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Affiliation(s)
- Nouran Momen
- Department of Pathology, Roswell Park Cancer Institute, Basic Science Building, Room 529, Elm St & Carlton St, Buffalo, NY, 14203, USA
- Clinical & Chemical Pathology Department, Cairo University, Cairo, Egypt
| | - Joseph Tario
- Department of Pathology, Roswell Park Cancer Institute, Basic Science Building, Room 529, Elm St & Carlton St, Buffalo, NY, 14203, USA
| | - Kai Fu
- Department of Pathology, Roswell Park Cancer Institute, Basic Science Building, Room 529, Elm St & Carlton St, Buffalo, NY, 14203, USA
| | - You-Wen Qian
- Department of Pathology, Roswell Park Cancer Institute, Basic Science Building, Room 529, Elm St & Carlton St, Buffalo, NY, 14203, USA.
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22
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Xie X, Su M, Ren K, Ma X, Lv Z, Li Z, Mei Y, Ji P. Clonal hematopoiesis and bone marrow inflammation. Transl Res 2023; 255:159-170. [PMID: 36347490 DOI: 10.1016/j.trsl.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/22/2022] [Accepted: 11/01/2022] [Indexed: 11/07/2022]
Abstract
Clonal hematopoiesis (CH) occurs in hematopoietic stem cells with increased risks of progressing to hematologic malignancies. CH mutations are predominantly found in aged populations and correlate with an increased incidence of cardiovascular and other diseases. Increased lines of evidence demonstrate that CH mutations are closely related to the inflammatory bone marrow microenvironment. In this review, we summarize the recent advances in this topic starting from the discovery of CH and its mutations. We focus on the most commonly mutated and well-studied genes in CH and their contributions to the innate immune responses and inflammatory signaling, especially in the hematopoietic cells of bone marrow. We also aimed to discuss the interrelationship between inflammatory bone marrow microenvironment and CH mutations. Finally, we provide our perspectives on the challenges in the field and possible future directions to help understand the pathophysiology of CH.
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Affiliation(s)
- Xinshu Xie
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Meng Su
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Kehan Ren
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois
| | - Xuezhen Ma
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Zhiyi Lv
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Zhaofeng Li
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Yang Mei
- School of Biomedical Sciences, Hunan University, Changsha, China; Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China.
| | - Peng Ji
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois.
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23
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Al Bakir M, Huebner A, Martínez-Ruiz C, Grigoriadis K, Watkins TBK, Pich O, Moore DA, Veeriah S, Ward S, Laycock J, Johnson D, Rowan A, Razaq M, Akther M, Naceur-Lombardelli C, Prymas P, Toncheva A, Hessey S, Dietzen M, Colliver E, Frankell AM, Bunkum A, Lim EL, Karasaki T, Abbosh C, Hiley CT, Hill MS, Cook DE, Wilson GA, Salgado R, Nye E, Stone RK, Fennell DA, Price G, Kerr KM, Naidu B, Middleton G, Summers Y, Lindsay CR, Blackhall FH, Cave J, Blyth KG, Nair A, Ahmed A, Taylor MN, Procter AJ, Falzon M, Lawrence D, Navani N, Thakrar RM, Janes SM, Papadatos-Pastos D, Forster MD, Lee SM, Ahmad T, Quezada SA, Peggs KS, Van Loo P, Dive C, Hackshaw A, Birkbak NJ, Zaccaria S, Jamal-Hanjani M, McGranahan N, Swanton C. The evolution of non-small cell lung cancer metastases in TRACERx. Nature 2023; 616:534-542. [PMID: 37046095 PMCID: PMC10115651 DOI: 10.1038/s41586-023-05729-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/12/2023] [Indexed: 04/14/2023]
Abstract
Metastatic disease is responsible for the majority of cancer-related deaths1. We report the longitudinal evolutionary analysis of 126 non-small cell lung cancer (NSCLC) tumours from 421 prospectively recruited patients in TRACERx who developed metastatic disease, compared with a control cohort of 144 non-metastatic tumours. In 25% of cases, metastases diverged early, before the last clonal sweep in the primary tumour, and early divergence was enriched for patients who were smokers at the time of initial diagnosis. Simulations suggested that early metastatic divergence more frequently occurred at smaller tumour diameters (less than 8 mm). Single-region primary tumour sampling resulted in 83% of late divergence cases being misclassified as early, highlighting the importance of extensive primary tumour sampling. Polyclonal dissemination, which was associated with extrathoracic disease recurrence, was found in 32% of cases. Primary lymph node disease contributed to metastatic relapse in less than 20% of cases, representing a hallmark of metastatic potential rather than a route to subsequent recurrences/disease progression. Metastasis-seeding subclones exhibited subclonal expansions within primary tumours, probably reflecting positive selection. Our findings highlight the importance of selection in metastatic clone evolution within untreated primary tumours, the distinction between monoclonal versus polyclonal seeding in dictating site of recurrence, the limitations of current radiological screening approaches for early diverging tumours and the need to develop strategies to target metastasis-seeding subclones before relapse.
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Affiliation(s)
- Maise Al Bakir
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Ariana Huebner
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Carlos Martínez-Ruiz
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Kristiana Grigoriadis
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Sophia Ward
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Joanne Laycock
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Diana Johnson
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Maryam Razaq
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Mita Akther
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | | | - Paulina Prymas
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Antonia Toncheva
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Sonya Hessey
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Michelle Dietzen
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Emma Colliver
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Alexander M Frankell
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Abigail Bunkum
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Emilia L Lim
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Takahiro Karasaki
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Christopher Abbosh
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Crispin T Hiley
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Mark S Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Daniel E Cook
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Roberto Salgado
- Department of Pathology, ZAS Hospitals, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Emma Nye
- Experimental Histopathology, The Francis Crick Institute, London, UK
| | | | - Dean A Fennell
- University of Leicester, Leicester, UK
- University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Gillian Price
- Department of Medical Oncology, Aberdeen Royal Infirmary NHS Grampian, Aberdeen, UK
- University of Aberdeen, Aberdeen, UK
| | - Keith M Kerr
- University of Aberdeen, Aberdeen, UK
- Department of Pathology, Aberdeen Royal Infirmary NHS Grampian, Aberdeen, UK
| | - Babu Naidu
- Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Gary Middleton
- University Hospital Birmingham NHS Foundation Trust, Birmingham, UK
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Yvonne Summers
- Division of Cancer Sciences, The University of Manchester and The Christie NHS Foundation Trust, Manchester, UK
| | - Colin R Lindsay
- Division of Cancer Sciences, The University of Manchester and The Christie NHS Foundation Trust, Manchester, UK
| | - Fiona H Blackhall
- Division of Cancer Sciences, The University of Manchester and The Christie NHS Foundation Trust, Manchester, UK
| | - Judith Cave
- Department of Oncology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Kevin G Blyth
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
- Queen Elizabeth University Hospital, Glasgow, UK
| | - Arjun Nair
- Department of Radiology, University College London Hospitals, London, UK
- UCL Respiratory, Department of Medicine, University College London, London, UK
| | - Asia Ahmed
- Department of Radiology, University College London Hospitals, London, UK
| | - Magali N Taylor
- Department of Radiology, University College London Hospitals, London, UK
| | | | - Mary Falzon
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - David Lawrence
- Department of Thoracic Surgery, University College London Hospital NHS Trust, London, UK
| | - Neal Navani
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
- Department of Thoracic Medicine, University College London Hospitals, London, UK
| | - Ricky M Thakrar
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
- Department of Thoracic Medicine, University College London Hospitals, London, UK
| | - Sam M Janes
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | | | - Martin D Forster
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Siow Ming Lee
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Tanya Ahmad
- Department of Oncology, University College London Hospitals, London, UK
| | - Sergio A Quezada
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Immune Regulation and Tumour Immunotherapy Group, Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Karl S Peggs
- Department of Haematology, University College London Hospitals, London, UK
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Caroline Dive
- Cancer Research UK Manchester Institute Cancer Biomarker Centre, University of Manchester, Manchester, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Manchester, UK
| | - Allan Hackshaw
- Cancer Research UK & UCL Cancer Trials Centre, London, UK
| | - Nicolai J Birkbak
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
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24
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Sandmann S, Richter S, Jiang X, Varghese J. Reconstructing Clonal Evolution-A Systematic Evaluation of Current Bioinformatics Approaches. Int J Environ Res Public Health 2023; 20:5128. [PMID: 36982036 PMCID: PMC10049679 DOI: 10.3390/ijerph20065128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/04/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
The accurate reconstruction of clonal evolution, including the identification of newly developing, highly aggressive subclones, is essential for the application of precision medicine in cancer treatment. Reconstruction, aiming for correct variant clustering and clonal evolution tree reconstruction, is commonly performed by tedious manual work. While there is a plethora of tools to automatically generate reconstruction, their reliability, especially reasons for unreliability, are not systematically assessed. We developed clevRsim-an approach to simulate clonal evolution data, including single-nucleotide variants as well as (overlapping) copy number variants. From this, we generated 88 data sets and performed a systematic evaluation of the tools for the reconstruction of clonal evolution. The results indicate a major negative influence of a high number of clones on both clustering and tree reconstruction. Low coverage as well as an extreme number of time points usually leads to poor clustering results. An underlying branched independent evolution hampers correct tree reconstruction. A further major decline in performance could be observed for large deletions and duplications overlapping single-nucleotide variants. In summary, to explore the full potential of reconstructing clonal evolution, improved algorithms that can properly handle the identified limitations are greatly needed.
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Affiliation(s)
- Sarah Sandmann
- Institute of Medical Informatics, University of Münster, 48149 Münster, Germany
| | - Silja Richter
- Institute of Medical Informatics, University of Münster, 48149 Münster, Germany
| | - Xiaoyi Jiang
- Department of Computer Science, University of Münster, 48149 Münster, Germany
| | - Julian Varghese
- Institute of Medical Informatics, University of Münster, 48149 Münster, Germany
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25
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Haughey MJ, Bassolas A, Sousa S, Baker AM, Graham TA, Nicosia V, Huang W. First passage time analysis of spatial mutation patterns reveals sub- clonal evolutionary dynamics in colorectal cancer. PLoS Comput Biol 2023; 19:e1010952. [PMID: 36913406 PMCID: PMC10035892 DOI: 10.1371/journal.pcbi.1010952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 03/23/2023] [Accepted: 02/14/2023] [Indexed: 03/14/2023] Open
Abstract
The signature of early cancer dynamics on the spatial arrangement of tumour cells is poorly understood, and yet could encode information about how sub-clones grew within the expanding tumour. Novel methods of quantifying spatial tumour data at the cellular scale are required to link evolutionary dynamics to the resulting spatial architecture of the tumour. Here, we propose a framework using first passage times of random walks to quantify the complex spatial patterns of tumour cell population mixing. First, using a simple model of cell mixing we demonstrate how first passage time statistics can distinguish between different pattern structures. We then apply our method to simulated patterns of mutated and non-mutated tumour cell population mixing, generated using an agent-based model of expanding tumours, to explore how first passage times reflect mutant cell replicative advantage, time of emergence and strength of cell pushing. Finally, we explore applications to experimentally measured human colorectal cancer, and estimate parameters of early sub-clonal dynamics using our spatial computational model. We infer a wide range of sub-clonal dynamics, with mutant cell division rates varying between 1 and 4 times the rate of non-mutated cells across our sample set. Some mutated sub-clones emerged after as few as 100 non-mutant cell divisions, and others only after 50,000 divisions. The majority were consistent with boundary driven growth or short-range cell pushing. By analysing multiple sub-sampled regions in a small number of samples, we explore how the distribution of inferred dynamics could inform about the initial mutational event. Our results demonstrate the efficacy of first passage time analysis as a new methodology in spatial analysis of solid tumour tissue, and suggest that patterns of sub-clonal mixing can provide insights into early cancer dynamics.
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Affiliation(s)
- Magnus J. Haughey
- School of Mathematical Sciences, Queen Mary University of London, London, United Kingdom
| | - Aleix Bassolas
- School of Mathematical Sciences, Queen Mary University of London, London, United Kingdom
| | - Sandro Sousa
- School of Mathematical Sciences, Queen Mary University of London, London, United Kingdom
| | - Ann-Marie Baker
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Trevor A. Graham
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Vincenzo Nicosia
- School of Mathematical Sciences, Queen Mary University of London, London, United Kingdom
| | - Weini Huang
- School of Mathematical Sciences, Queen Mary University of London, London, United Kingdom
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26
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Lin DC. Large-scale genomic analyses reveal alterations and mechanisms underlying clonal evolution and immune evasion in esophageal cancer. Nat Commun 2023; 14:893. [PMID: 36807265 PMCID: PMC9938131 DOI: 10.1038/s41467-023-36557-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/23/2022] [Indexed: 02/19/2023] Open
Affiliation(s)
- De-Chen Lin
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA.
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA.
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27
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Kanwal J, Maqbool O, Basit HA, Sindhu MA, Inoue K. Historical perspective of code clone refactorings in evolving software. PLoS One 2022; 17:e0277216. [PMID: 36454895 PMCID: PMC9714808 DOI: 10.1371/journal.pone.0277216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 10/24/2022] [Indexed: 12/04/2022] Open
Abstract
Cloning in software is generally perceived as a threat to its maintenance and that is why it needs to be managed properly. Understanding clones from a historical perspective is essential for effective clone management. Analysis of code refactorings performed on clones in previous releases will help developers in taking decisions about clone refactoring in future releases. In this paper we perform a longitudinal study on the evolution of clone refactorings in various versions of five software systems. To perform a systematic study on clone refactoring evolution, we define clone evolution patterns for studying refactorings in a formal notation. Our results show that only a small proportion of code clones are refactored between the versions and most of the refactorings are inconsistent within clone classes. Moreover, clone refactorings may cause clone removal. Analysis of the source code of refactored clones reveals similar reasons of inconsistent refactorings and clone removal for five Java systems. This analysis will help in devising appropriate strategies for managing clone refactorings in software and hence provide foundation for devising better clone management tools.
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Affiliation(s)
- Jaweria Kanwal
- Software Engineering Dept., National University of Moderns Languages, Islamabad, Pakistan
- Computer Science Dept., Quaid-i-Azam University, Islamabad, Pakistan
- * E-mail:
| | - Onaiza Maqbool
- Computer Science Dept., Quaid-i-Azam University, Islamabad, Pakistan
| | - Hamid Abdul Basit
- College of Computer and Information Sciences, Prince Sultan University, Riyadh, Saudi Arabia
| | | | - Katsuro Inoue
- Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
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28
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Rovira-Clavé X, Drainas AP, Jiang S, Bai Y, Baron M, Zhu B, Dallas AE, Lee MC, Chu TP, Holzem A, Ayyagari R, Bhattacharya D, McCaffrey EF, Greenwald NF, Markovic M, Coles GL, Angelo M, Bassik MC, Sage J, Nolan GP. Spatial epitope barcoding reveals clonal tumor patch behaviors. Cancer Cell 2022; 40:1423-1439.e11. [PMID: 36240778 PMCID: PMC9673683 DOI: 10.1016/j.ccell.2022.09.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/22/2022] [Accepted: 09/21/2022] [Indexed: 01/09/2023]
Abstract
Intratumoral heterogeneity is a seminal feature of human tumors contributing to tumor progression and response to treatment. Current technologies are still largely unsuitable to accurately track phenotypes and clonal evolution within tumors, especially in response to genetic manipulations. Here, we developed epitopes for imaging using combinatorial tagging (EpicTags), which we coupled to multiplexed ion beam imaging (EpicMIBI) for in situ tracking of barcodes within tissue microenvironments. Using EpicMIBI, we dissected the spatial component of cell lineages and phenotypes in xenograft models of small cell lung cancer. We observed emergent properties from mixed clones leading to the preferential expansion of clonal patches for both neuroendocrine and non-neuroendocrine cancer cell states in these models. In a tumor model harboring a fraction of PTEN-deficient cancer cells, we observed a non-autonomous increase of clonal patch size in PTEN wild-type cancer cells. EpicMIBI facilitates in situ interrogation of cell-intrinsic and cell-extrinsic processes involved in intratumoral heterogeneity.
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Affiliation(s)
- Xavier Rovira-Clavé
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Alexandros P Drainas
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Sizun Jiang
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Yunhao Bai
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Maya Baron
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Bokai Zhu
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Alec E Dallas
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Myung Chang Lee
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Theresa P Chu
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Alessandra Holzem
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Ramya Ayyagari
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Debadrita Bhattacharya
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Erin F McCaffrey
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Noah F Greenwald
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Maxim Markovic
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Garry L Coles
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julien Sage
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA 94305, USA.
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29
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Miller PG, Fell GG, Foy BH, Scherer AK, Gibson CJ, Sperling AS, Burugula BB, Nakao T, Uddin MM, Warren H, Bry L, Pozdnyakova O, Frigault MJ, Bick AG, Neuberg D, Higgins JM, Mansour MK, Natarajan P, Kim AS, Kitzman JO, Ebert BL. Clonal hematopoiesis of indeterminate potential and risk of death from COVID-19. Blood 2022; 140:1993-1997. [PMID: 36096050 PMCID: PMC9474399 DOI: 10.1182/blood.2022018052] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/05/2022] [Indexed: 01/07/2023] Open
Abstract
Two Letters to Blood address the risks of COVID-19 in populations with precursors of hematological disease. In the first article, Miller and colleagues report on whether clonal hematopoiesis of intermediate potential (CHIP) is associated with adverse outcomes with COVID-19, finding no association between CHIP and 28-day mortality while providing data indirectly linking IL-6 signaling and patient outcomes. In the second article, Ho and colleagues investigate the outcomes of patients with monoclonal gammopathy of undetermined significance (MGUS) with COVID-19, reporting that one-fourth had a severe infection and that on multivariable analysis, adverse outcomes are more likely if immunoparesis is present.
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Affiliation(s)
- Peter G Miller
- Center for Cancer Research and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA
| | - Geoffrey G Fell
- Department of Data Sciences, Dana Farber Cancer Institute, Boston, MA
| | - Brody H Foy
- Department of Pathology & Center for Systems Biology, Massachusetts General Hospital, Boston, MA
- Department of Systems Biology, Harvard Medical School, Boston, MA
| | - Allison K Scherer
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | | | - Adam S Sperling
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Bala B Burugula
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
| | - Tetsushi Nakao
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Division of Cardiology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Md M Uddin
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Hailey Warren
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA
| | - Lynn Bry
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Olga Pozdnyakova
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Matthew J Frigault
- Center for Cancer Research and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Alex G Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Donna Neuberg
- Department of Data Sciences, Dana Farber Cancer Institute, Boston, MA
| | - John M Higgins
- Department of Pathology & Center for Systems Biology, Massachusetts General Hospital, Boston, MA
- Department of Systems Biology, Harvard Medical School, Boston, MA
| | - Michael K Mansour
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Pradeep Natarajan
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Jacob O Kitzman
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
| | - Benjamin L Ebert
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Howard Hughes Medical Institute, Bethesda, MD
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30
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Zhou Y, Shalhoub R, Rogers SN, Yu S, Gu M, Fabre MA, Quiros PM, Shin TH, Diangson A, Deng W, Anand S, Lu W, Cullen M, Godfrey AL, Preller J, Hadjadj J, Jouanguy E, Cobat A, Abel L, Rieux-Laucat F, Terrier B, Fischer A, Novik L, Gordon IJ, Strom L, Gaudinski MR, Lisco A, Sereti I, Gniadek TJ, Biondi A, Bonfanti P, Imberti L, Dalgard CL, Zhang Y, Dobbs K, Su HC, Notarangelo LD, Wu CO, Openshaw PJ, Semple MG, Mallat Z, Baillie K, Dunbar CE, Vassiliou GS. Clonal hematopoiesis is not significantly associated with COVID-19 disease severity. Blood 2022; 140:1650-1655. [PMID: 35839449 PMCID: PMC9293387 DOI: 10.1182/blood.2022015721] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/28/2022] [Indexed: 11/25/2022] Open
Affiliation(s)
- Yifan Zhou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ruba Shalhoub
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
| | - Stephanie N. Rogers
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Shiqin Yu
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - Muxin Gu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Margarete A. Fabre
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Pedro M. Quiros
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tae-Hoon Shin
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Republic of Korea
| | - Arch Diangson
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
| | - Wenhan Deng
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
| | - Shubha Anand
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
| | - Wenhua Lu
- East Genomic Laboratory Hub, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Matthew Cullen
- East Genomic Laboratory Hub, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Anna L. Godfrey
- Haematopathology and Oncology Diagnostics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jacobus Preller
- John Farman Intensive Care Unit, Cambridge University Hospital, Cambridge, UK
| | - Jerome Hadjadj
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, Assistance Publique-Hôpitaux de Paris, APHP.CUP, Hôpital Cochin, Paris Cité University, Paris, France
| | - Emmanuelle Jouanguy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Frederic Rieux-Laucat
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Université de Paris, Institut Imagine, INSERM UMR 1163, Paris, France
| | - Benjamin Terrier
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, Assistance Publique-Hôpitaux de Paris, APHP.CUP, Hôpital Cochin, Paris Cité University, Paris, France
| | - Alain Fischer
- Université de Paris, Institut Imagine, and Paediatric Immuno-Haematology and Rheumatology Department, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Collège de France, Paris, France
| | - Lara Novik
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Ingelise J. Gordon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Larisa Strom
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Martin R. Gaudinski
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Andrea Lisco
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Irini Sereti
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Thomas J. Gniadek
- Department of Pathology and Laboratory Medicine, NorthShore University Health System, Evanston, IL
| | - Andrea Biondi
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, Italy
| | - Paolo Bonfanti
- Department of Infectious Diseases, San Gerardo Hospital-University of Milano-Bicocca, Monza, Italy
| | - Luisa Imberti
- CREA Laboratory (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Clifton L. Dalgard
- Primer, Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Kerry Dobbs
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Helen C. Su
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Luigi D. Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - COVID-STORM Clinicians
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Republic of Korea
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
- East Genomic Laboratory Hub, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
- Haematopathology and Oncology Diagnostics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- John Farman Intensive Care Unit, Cambridge University Hospital, Cambridge, UK
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, Assistance Publique-Hôpitaux de Paris, APHP.CUP, Hôpital Cochin, Paris Cité University, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Université de Paris, Institut Imagine, INSERM UMR 1163, Paris, France
- Université de Paris, Institut Imagine, and Paediatric Immuno-Haematology and Rheumatology Department, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Collège de France, Paris, France
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, NorthShore University Health System, Evanston, IL
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, Italy
- Department of Infectious Diseases, San Gerardo Hospital-University of Milano-Bicocca, Monza, Italy
- CREA Laboratory (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
- Primer, Uniformed Services University of the Health Sciences, Bethesda, MD
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- National Heart and Lung Institute, Imperial College London, Chelsea, London, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
- INSERM U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - NIAID Immune Response to COVID Group
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Republic of Korea
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
- East Genomic Laboratory Hub, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
- Haematopathology and Oncology Diagnostics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- John Farman Intensive Care Unit, Cambridge University Hospital, Cambridge, UK
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, Assistance Publique-Hôpitaux de Paris, APHP.CUP, Hôpital Cochin, Paris Cité University, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Université de Paris, Institut Imagine, INSERM UMR 1163, Paris, France
- Université de Paris, Institut Imagine, and Paediatric Immuno-Haematology and Rheumatology Department, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Collège de France, Paris, France
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, NorthShore University Health System, Evanston, IL
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, Italy
- Department of Infectious Diseases, San Gerardo Hospital-University of Milano-Bicocca, Monza, Italy
- CREA Laboratory (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
- Primer, Uniformed Services University of the Health Sciences, Bethesda, MD
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- National Heart and Lung Institute, Imperial College London, Chelsea, London, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
- INSERM U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - The ISARIC4C Investigators
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Jeju National University, Jeju, Republic of Korea
- Cancer Molecular Diagnostics Laboratory, University of Cambridge, Cambridge, UK
- East Genomic Laboratory Hub, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
- Haematopathology and Oncology Diagnostics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- John Farman Intensive Care Unit, Cambridge University Hospital, Cambridge, UK
- Department of Internal Medicine, National Reference Center for Rare Systemic Autoimmune Diseases, Assistance Publique-Hôpitaux de Paris, APHP.CUP, Hôpital Cochin, Paris Cité University, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Université de Paris, Institut Imagine, INSERM UMR 1163, Paris, France
- Université de Paris, Institut Imagine, and Paediatric Immuno-Haematology and Rheumatology Department, Necker-Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Collège de France, Paris, France
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- HIV Pathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, NorthShore University Health System, Evanston, IL
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, Italy
- Department of Infectious Diseases, San Gerardo Hospital-University of Milano-Bicocca, Monza, Italy
- CREA Laboratory (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
- Primer, Uniformed Services University of the Health Sciences, Bethesda, MD
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- National Institute of Allergy and Infectious Diseases Clinical Genomics Program, NIH, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- National Heart and Lung Institute, Imperial College London, Chelsea, London, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
- INSERM U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Colin O. Wu
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD
| | - Peter J.M. Openshaw
- National Heart and Lung Institute, Imperial College London, Chelsea, London, UK
| | - Malcolm G. Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Ziad Mallat
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
- INSERM U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Cynthia E. Dunbar
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health (NIH), Bethesda, MD
| | - George S. Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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31
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Lucas CHG, Davidson CJ, Alashari M, Putnam AR, Whipple NS, Bruggers CS, Mendez JS, Cheshier SH, Walker JB, Ramani B, Cadwell CR, Sullivan DV, Lu R, Mirchia K, Van Ziffle J, Devine P, Goldschmidt E, Hervey-Jumper SL, Gupta N, Oberheim Bush NA, Raleigh DR, Bollen A, Tihan T, Pekmezci M, Solomon DA, Phillips JJ, Perry A. Targeted Next-Generation Sequencing Reveals Divergent Clonal Evolution in Components of Composite Pleomorphic Xanthoastrocytoma-Ganglioglioma. J Neuropathol Exp Neurol 2022; 81:650-657. [PMID: 35703914 PMCID: PMC9297094 DOI: 10.1093/jnen/nlac044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Composite pleomorphic xanthoastrocytoma-ganglioglioma (PXA-GG) is an extremely rare central nervous system neoplasm with 2 distinct but intermingled components. Whether this tumor represents a "collision tumor" of separate neoplasms or a monoclonal neoplasm with divergent evolution is poorly understood. Clinicopathologic studies and capture-based next generation sequencing were performed on extracted DNA from all available PXA-GG at 2 medical centers. Five PXA-GG were diagnosed in 1 male and 4 female patients ranging from 13 to 25 years in age. Four arose within the cerebral hemispheres; 1 presented in the cerebellar vermis. DNA was sufficient for analysis in 4 PXA components and 3 GG components. Four paired PXA and GG components harbored BRAF p.V600E hotspot mutations. The 4 sequenced PXA components demonstrated CDKN2A homozygous deletion by sequencing with loss of p16 (protein product of CDKN2A) expression by immunohistochemistry, which was intact in all assessed GG components. The PXA components also demonstrated more frequent copy number alterations relative to paired GG components. In one PXA-GG, shared chromosomal copy number alterations were identified in both components. Our findings support divergent evolution of the PXA and GG components from a common BRAF p.V600E-mutant precursor lesion, with additional acquisition of CDKN2A homozygous deletion in the PXA component as is typically seen in conventional PXA.
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Affiliation(s)
- Calixto-Hope G Lucas
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | | | - Mouied Alashari
- Division of Pediatric Pathology, Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Angelica R Putnam
- Division of Pediatric Pathology, Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Nicholas S Whipple
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Carol S Bruggers
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Joe S Mendez
- Department of Neurosurgery, University of Utah/Huntsman Cancer Institute, Salt Lake City, Utah, USA
| | - Samuel H Cheshier
- Division of Pediatric Neurosurgery, Department of Neurosurgery, Huntsman Cancer Institute, University of Utah, Intermountain Primary Children's Hospital, Salt Lake City, Utah, USA
| | | | - Biswarathan Ramani
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Cathryn R Cadwell
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Daniel V Sullivan
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Rufei Lu
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Kanish Mirchia
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Jessica Van Ziffle
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Clinical Cancer Genomics Laboratory, University of California, San Francisco, San Francisco, California, USA
| | - Patrick Devine
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Clinical Cancer Genomics Laboratory, University of California, San Francisco, San Francisco, California, USA
| | - Ezequiel Goldschmidt
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Shawn L Hervey-Jumper
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Nalin Gupta
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
- Department of Pediatrics, University of California, San Francisco, San Francisco, USA
| | - Nancy Ann Oberheim Bush
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - David R Raleigh
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California, USA
| | - Andrew Bollen
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Tarik Tihan
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Melike Pekmezci
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - David A Solomon
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Arie Perry
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
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32
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Cheng P, Lan Y, Liao J, Zhao E, Yan H, Xu L, A S, Ping Y, Xu J. Systematic investigation of the prognostic impact of clonal status of somatic mutations across multiple cancer types. Genomics 2022; 114:110412. [PMID: 35714828 DOI: 10.1016/j.ygeno.2022.110412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 05/15/2022] [Accepted: 06/10/2022] [Indexed: 11/18/2022]
Abstract
Tumors are genetically heterogeneous and many mutations are actually present in subclonal populations. The clonal status of mutations is valuable for accurate prognosis, clinical management. The aim of this study was to identify the clonal status of somatic mutations and systematically evaluate their prognostic values across various cancer types. We totally identified 227 clonal and 432 subclonal mutations contributed to prognosis and demonstrated the importance of clonal status in improving mutation-related clinical guidance. We further developed a customized multi-step approach to identify gene-specific prognostic patterns of clonal status at pan-cancer level and found some cancer-specific prognostic patterns. The 'subclonal-dependent risk' subpattern was one of the most common subpatterns, it usually accompanied by high genomic in-stability and high extent of intra-tumor heterogeneity and could be used to improve the accuracy of prognostic analysis. Our results revealed the importance of clonal status, especially subclonal mutation in clinical survival.
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Affiliation(s)
- Peng Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yujia Lan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Jianlong Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Erjie Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Haoteng Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China; Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Suru A
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yanyan Ping
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China.
| | - Jinyuan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China.
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33
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Affiliation(s)
- Christian Umkehrer
- Cancer Cell Signaling, Boehringer-Ingelheim RCV GmbH & Co KG, Vienna, Austria.
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34
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Schenck RO, Brosula G, West J, Leedham S, Shibata D, Anderson AR. Gattaca: Base-Pair Resolution Mutation Tracking for Somatic Evolution Studies using Agent-based Models. Mol Biol Evol 2022; 39:msac058. [PMID: 35298641 PMCID: PMC9034688 DOI: 10.1093/molbev/msac058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Research over the past two decades has made substantial inroads into our understanding of somatic mutations. Recently, these studies have focused on understanding their presence in homeostatic tissue. In parallel, agent-based mechanistic models have emerged as an important tool for understanding somatic mutation in tissue; yet no common methodology currently exists to provide base-pair resolution data for these models. Here, we present Gattaca as the first method for introducing and tracking somatic mutations at the base-pair resolution within agent-based models that typically lack nuclei. With nuclei that incorporate human reference genomes, mutational context, and sequence coverage/error information, Gattaca is able to realistically evolve sequence data, facilitating comparisons between in silico cell tissue modeling with experimental human somatic mutation data. This user-friendly method, incorporated into each in silico cell, allows us to fully capture somatic mutation spectra and evolution.
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Affiliation(s)
- Ryan O. Schenck
- Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX37BN, United Kingdom
| | - Gabriel Brosula
- Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Jeffrey West
- Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Simon Leedham
- Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Darryl Shibata
- Department of Pathology, University of Southern California, Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Alexander R.A. Anderson
- Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
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35
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Nichols MM, Cook JR, Bosler DS, Rogers HJ, Philip JKSS, Jogenpally NR, Reynolds JP, Robertson S, Cotta CV. Myeloid Sarcoma Involving the Testis in Adults: Clonal Evolution of Acute Myeloid Leukemia. Appl Immunohistochem Mol Morphol 2022; 30:e32-e39. [PMID: 35001036 DOI: 10.1097/pai.0000000000001007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 12/10/2021] [Indexed: 11/25/2022]
Abstract
To describe the clinical, histologic, immunophenotypic, and genetic characteristics of myeloid sarcoma (MS) diagnosed in the testes of adults, 3 cases were identified, and information on their presentation, clinical features, treatment, and outcome was retrieved from the medical records. In addition, histologic, immunophenotypic, and molecular characteristics were reviewed. This showed that all patients had a previous history of acute myeloid leukemia (AML), in 2 cases diagnosed >10 years before the testicular lesions. In 1 case, there was bilateral involvement, while in 2, involvement was unilateral. The neoplastic cells showed evidence of cytogenetic/molecular clonal evolution in all cases, 1 of which also had significant immunophenotypic changes. A mutational profile including NPM1 p.Trp288Cysfs*12, IDH1 p.Arg132His NRAS p.Gly12Asp was seen in 2 of the 3 cases. Concurrent bone marrow involvement by a myeloid neoplasm was diagnosed in 2 patients, in 1, there was AML in the second 8% blasts. These patients progressed rapidly after MS and had a dismal outcome. The patient with no concurrent bone marrow disease had a favorable outcome. In conclusion, MS involving the testes of adults is a rare event, and it may represent the clonal evolution of AML.
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Affiliation(s)
- Meredith M Nichols
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH
| | - James R Cook
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH
| | - David S Bosler
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH
| | - Heesun J Rogers
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH
| | | | | | - Jordan P Reynolds
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH
| | - Scott Robertson
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH
| | - Claudiu V Cotta
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH
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36
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Kotagiri P, Mescia F, Rae WM, Bergamaschi L, Tuong ZK, Turner L, Hunter K, Gerber PP, Hosmillo M, Hess C, Clatworthy MR, Goodfellow IG, Matheson NJ, McKinney EF, Wills MR, Gupta RK, Bradley JR, Bashford-Rogers RJM, Lyons PA, Smith KGC. B cell receptor repertoire kinetics after SARS-CoV-2 infection and vaccination. Cell Rep 2022; 38:110393. [PMID: 35143756 PMCID: PMC8801326 DOI: 10.1016/j.celrep.2022.110393] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/28/2021] [Accepted: 01/24/2022] [Indexed: 11/24/2022] Open
Abstract
B cells are important in immunity to both severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection and vaccination, but B cell receptor (BCR) repertoire development in these contexts has not been compared. We analyze serial samples from 171 SARS-CoV-2-infected individuals and 63 vaccine recipients and find the global BCR repertoire differs between them. Following infection, immunoglobulin (Ig)G1/3 and IgA1 BCRs increase, somatic hypermutation (SHM) decreases, and, in severe disease, IgM and IgA clones are expanded. In contrast, after vaccination, the proportion of IgD/M BCRs increase, SHM is unchanged, and expansion of IgG clones is prominent. VH1-24, which targets the N-terminal domain (NTD) and contributes to neutralization, is expanded post infection except in the most severe disease. Infection generates a broad distribution of SARS-CoV-2-specific clones predicted to target the spike protein, while a more focused response after vaccination mainly targets the spike's receptor-binding domain. Thus, the nature of SARS-CoV-2 exposure differentially affects BCR repertoire development, potentially informing vaccine strategies.
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Affiliation(s)
- Prasanti Kotagiri
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK.
| | - Federica Mescia
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - William M Rae
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Laura Bergamaschi
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Zewen K Tuong
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK; Cellular Genetics, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1RQ, UK
| | - Lorinda Turner
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Kelvin Hunter
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Pehuén P Gerber
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Myra Hosmillo
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Christoph Hess
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK; Department of Biomedicine, University and University Hospital Basel, Basel 4031, Switzerland; Botnar Research Centre for Child Health (BRCCH) University Basel and ETH Zurich, Basel 4059, Switzerland
| | - Menna R Clatworthy
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK; Cellular Genetics, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1RQ, UK
| | - Ian G Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Nicholas J Matheson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK; NHS Blood and Transplant, Cambridge CB2 1PT, UK
| | - Eoin F McKinney
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Mark R Wills
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - John R Bradley
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | | | - Paul A Lyons
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK.
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK.
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37
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Lapin M, Huang HJ, Chagani S, Javle M, Shroff RT, Pant S, Gouda MA, Raina A, Madwani K, Holley VR, Call SG, Dustin DJ, Lanman RB, Meric-Bernstam F, Raymond VM, Kwong LN, Janku F. Monitoring of Dynamic Changes and Clonal Evolution in Circulating Tumor DNA From Patients With IDH-Mutated Cholangiocarcinoma Treated With Isocitrate Dehydrogenase Inhibitors. JCO Precis Oncol 2022; 6:e2100197. [PMID: 35171660 PMCID: PMC8865526 DOI: 10.1200/po.21.00197] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/25/2021] [Accepted: 01/06/2022] [Indexed: 12/21/2022] Open
Abstract
PURPOSE IDH mutations occur in about 30% of patients with cholangiocarcinoma. Analysis of mutations in circulating tumor DNA (ctDNA) can be performed by droplet digital polymerase chain reaction (ddPCR). The analysis of ctDNA is a feasible approach to detect IDH mutations. METHODS We isolated ctDNA from the blood of patients with IDH-mutated advanced cholangiocarcinoma collected at baseline, on therapy, and at progression to isocitrate dehydrogenase (IDH) inhibitors. RESULTS Of 31 patients with IDH1R132 (n = 26) or IDH2R172 mutations (n = 5) in the tumor, IDH mutations were detected in 84% of ctDNA samples analyzed by ddPCR and in 83% of ctDNA samples analyzed by next-generation sequencing (NGS). Patients with a low variant allele frequency of ctDNA detected by NGS at baseline had a longer median time to treatment failure compared to patients with high variant allele frequency of ctDNA (3.6 v 1.5 months; P = .008). Patients with a decrease in IDH-mutated ctDNA on therapy by ddPCR compared with no change/increase had a trend to a longer median survival (P = .07). Most frequent emergent alterations in ctDNA by NGS at progression were ARID1A (n = 3) and TP53 mutations (n = 3). CONCLUSION Detection of IDH mutations in ctDNA in patients with advanced cholangiocarcinoma is feasible, and dynamic changes in ctDNA can correspond with the clinical course and clonal evolution.
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Affiliation(s)
- Morten Lapin
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
- Department of Hematology and Oncology, Stavanger University Hospital, Stavanger, Norway
| | - Helen J. Huang
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sharmeen Chagani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Milind Javle
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Rachna T. Shroff
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
- Division of Hematology/Oncology, University of Arizona Cancer Center, Tucson, AZ
| | - Shubham Pant
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Mohamed A. Gouda
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Anjali Raina
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kiran Madwani
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Veronica R. Holley
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - S. Greg Call
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Derek J. Dustin
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Lawrence N. Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Filip Janku
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
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38
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Dawoud AAZ, Gilbert RD, Tapper WJ, Cross NCP. Clonal myelopoiesis promotes adverse outcomes in chronic kidney disease. Leukemia 2022; 36:507-515. [PMID: 34413458 PMCID: PMC8807385 DOI: 10.1038/s41375-021-01382-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 12/18/2022]
Abstract
We sought to determine the relationship between age-related clonal hematopoiesis (CH) and chronic kidney disease (CKD). CH, defined as mosaic chromosome abnormalities (mCA) and/or driver mutations was identified in 5449 (2.9%) eligible UK Biobank participants (n = 190,487 median age = 58 years). CH was negatively associated with glomerular filtration rate estimated from cystatin-C (eGFR.cys; β = -0.75, P = 2.37 × 10-4), but not with eGFR estimated from creatinine, and was specifically associated with CKD defined by eGFR.cys < 60 (OR = 1.02, P = 8.44 × 10-8). In participants without prevalent myeloid neoplasms, eGFR.cys was associated with myeloid mCA (n = 148, β = -3.36, P = 0.01) and somatic driver mutations (n = 3241, β = -1.08, P = 6.25 × 10-5) associated with myeloid neoplasia (myeloid CH), specifically mutations in CBL, TET2, JAK2, PPM1D and GNB1 but not DNMT3A or ASXL1. In participants with no history of cardiovascular disease or myeloid neoplasms, myeloid CH increased the risk of adverse outcomes in CKD (HR = 1.6, P = 0.002) compared to those without myeloid CH. Mendelian randomisation analysis provided suggestive evidence for a causal relationship between CH and CKD (P = 0.03). We conclude that CH, and specifically myeloid CH, is associated with CKD defined by eGFR.cys. Myeloid CH promotes adverse outcomes in CKD, highlighting the importance of the interaction between intrinsic and extrinsic factors to define the health risk associated with CH.
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Affiliation(s)
| | - Rodney D Gilbert
- Faculty of Medicine, University of Southampton, Southampton, UK
- Southampton Children's Hospital, Southampton, UK
| | | | - Nicholas C P Cross
- Faculty of Medicine, University of Southampton, Southampton, UK.
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK.
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39
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Öztürk S, Paul Y, Afzal S, Gil-Farina I, Jauch A, Bruch PM, Kalter V, Hanna B, Arseni L, Roessner PM, Schmidt M, Stilgenbauer S, Dietrich S, Lichter P, Zapatka M, Seiffert M. Longitudinal analyses of CLL in mice identify leukemia-related clonal changes including a Myc gain predicting poor outcome in patients. Leukemia 2022; 36:464-475. [PMID: 34417556 PMCID: PMC8807396 DOI: 10.1038/s41375-021-01381-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 02/07/2023]
Abstract
Chronic lymphocytic leukemia (CLL) is a B-cell malignancy mainly occurring at an advanced age with no single major genetic driver. Transgenic expression of TCL1 in B cells leads after a long latency to a CLL-like disease in aged Eµ-TCL1 mice suggesting that TCL1 overexpression is not sufficient for full leukemic transformation. In search for secondary genetic events and to elucidate the clonal evolution of CLL, we performed whole exome and B-cell receptor sequencing of longitudinal leukemia samples of Eµ-TCL1 mice. We observed a B-cell receptor stereotypy, as described in patients, confirming that CLL is an antigen-driven disease. Deep sequencing showed that leukemia in Eµ-TCL1 mice is mostly monoclonal. Rare oligoclonality was associated with inability of tumors to develop disease upon adoptive transfer in mice. In addition, we identified clonal changes and a sequential acquisition of mutations with known relevance in CLL, which highlights the genetic similarities and therefore, suitability of the Eµ-TCL1 mouse model for progressive CLL. Among them, a recurrent gain of chromosome 15, where Myc is located, was identified in almost all tumors in Eµ-TCL1 mice. Interestingly, amplification of 8q24, the chromosomal region containing MYC in humans, was associated with worse outcome of patients with CLL.
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Affiliation(s)
- Selcen Öztürk
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yashna Paul
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Saira Afzal
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center (DKFZ), Heidelberg, Germany
- GeneWerk GmbH, Heidelberg, Germany
| | - Irene Gil-Farina
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center (DKFZ), Heidelberg, Germany
- GeneWerk GmbH, Heidelberg, Germany
| | - Anna Jauch
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Peter-Martin Bruch
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Verena Kalter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bola Hanna
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lavinia Arseni
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp M Roessner
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manfred Schmidt
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center (DKFZ), Heidelberg, Germany
- GeneWerk GmbH, Heidelberg, Germany
| | | | - Sascha Dietrich
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Seiffert
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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40
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Azimzade Y. Invasion front dynamics of interactive populations in environments with barriers. Sci Rep 2022; 12:826. [PMID: 35039586 PMCID: PMC8764055 DOI: 10.1038/s41598-022-04806-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/03/2022] [Indexed: 11/20/2022] Open
Abstract
Invading populations normally comprise different subpopulations that interact while trying to overcome existing barriers against their way to occupy new areas. However, the majority of studies so far only consider single or multiple population invasion into areas where there is no resistance against the invasion. Here, we developed a model to study how cooperative/competitive populations invade in the presence of a physical barrier that should be degraded during the invasion. For one dimensional (1D) environment, we found that a Langevin equation as [Formula: see text] describing invasion front position. We then obtained how [Formula: see text] and [Formula: see text] depend on population interactions and environmental barrier intensity. In two dimensional (2D) environment, for the average interface position movements we found a Langevin equation as [Formula: see text]. Similar to the 1D case, we calculate how [Formula: see text] and [Formula: see text] respond to population interaction and environmental barrier intensity. Finally, the study of invasion front morphology through dynamic scaling analysis showed that growth exponent, [Formula: see text], depends on both population interaction and environmental barrier intensity. Saturated interface width, [Formula: see text], versus width of the 2D environment (L) also exhibits scaling behavior. Our findings show revealed that competition among subpopulations leads to more rough invasion fronts. Considering the wide range of shreds of evidence for clonal diversity in cancer cell populations, our findings suggest that interactions between such diverse populations can potentially participate in the irregularities of tumor border.
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Affiliation(s)
- Youness Azimzade
- Department of Physics, University of Tehran, Tehran, 14395-547, Iran.
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41
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Fu X, Zhao Y, Lopez JI, Rowan A, Au L, Fendler A, Hazell S, Xu H, Horswell S, Shepherd STC, Spencer CE, Spain L, Byrne F, Stamp G, O'Brien T, Nicol D, Augustine M, Chandra A, Rudman S, Toncheva A, Furness AJS, Pickering L, Kumar S, Koh DM, Messiou C, Dafydd DA, Orton MR, Doran SJ, Larkin J, Swanton C, Sahai E, Litchfield K, Turajlic S, Bates PA. Spatial patterns of tumour growth impact clonal diversification in a computational model and the TRACERx Renal study. Nat Ecol Evol 2022; 6:88-102. [PMID: 34949820 PMCID: PMC8752443 DOI: 10.1038/s41559-021-01586-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 10/07/2021] [Indexed: 11/16/2022]
Abstract
Genetic intra-tumour heterogeneity fuels clonal evolution, but our understanding of clinically relevant clonal dynamics remain limited. We investigated spatial and temporal features of clonal diversification in clear cell renal cell carcinoma through a combination of modelling and real tumour analysis. We observe that the mode of tumour growth, surface or volume, impacts the extent of subclonal diversification, enabling interpretation of clonal diversity in patient tumours. Specific patterns of proliferation and necrosis explain clonal expansion and emergence of parallel evolution and microdiversity in tumours. In silico time-course studies reveal the appearance of budding structures before detectable subclonal diversification. Intriguingly, we observe radiological evidence of budding structures in early-stage clear cell renal cell carcinoma, indicating that future clonal evolution may be predictable from imaging. Our findings offer a window into the temporal and spatial features of clinically relevant clonal evolution.
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Affiliation(s)
- Xiao Fu
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
| | - Yue Zhao
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jose I Lopez
- Department of Pathology, Cruces University Hospital, Biocruces-Bizkaia Institute, Barakaldo, Spain
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Lewis Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
| | - Annika Fendler
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Steve Hazell
- Department of Pathology, the Royal Marsden NHS Foundation Trust, London, UK
| | - Hang Xu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Stuart Horswell
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Scott T C Shepherd
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
| | - Charlotte E Spencer
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
| | - Lavinia Spain
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
| | - Fiona Byrne
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Gordon Stamp
- Experimental Histopathology Laboratory, The Francis Crick Institute, London, UK
| | - Tim O'Brien
- Urology Centre, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - David Nicol
- Department of Urology, the Royal Marsden NHS Foundation Trust, London, UK
| | - Marcellus Augustine
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Ashish Chandra
- Department of Pathology, Guy's and St. Thomas NHS Foundation Trust, London, UK
| | - Sarah Rudman
- Department of Medical Oncology, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | | | - Andrew J S Furness
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
| | - Lisa Pickering
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
| | - Santosh Kumar
- Division of Radiotherapy and Imaging, Institute of Cancer Research, Sutton, UK
| | - Dow-Mu Koh
- Division of Radiotherapy and Imaging, Institute of Cancer Research, Sutton, UK
- Department of Radiology, Royal Marsden Hospital, London, UK
| | - Christina Messiou
- Division of Radiotherapy and Imaging, Institute of Cancer Research, Sutton, UK
- Department of Radiology, Royal Marsden Hospital, London, UK
| | | | - Matthew R Orton
- Artificial Intelligence Imaging Hub, Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Simon J Doran
- Division of Radiotherapy and Imaging, Institute of Cancer Research, Sutton, UK
| | - James Larkin
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals, London, UK
| | - Erik Sahai
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK.
| | - Kevin Litchfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK.
| | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK.
- Renal and Skin Units, The Royal Marsden Hospital, London, UK.
| | - Paul A Bates
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK.
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42
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Furukawa Y. [Treatment strategies for multiple myeloma based on molecular pathogenesis]. Rinsho Ketsueki 2022; 63:1167-1179. [PMID: 36198542 DOI: 10.11406/rinketsu.63.1167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
It is well documented that multiple myeloma (MM) originates in a single plasma cell transformed by chromosome 14q translocations or chromosomal hyperdiploidy and evolves with the accumulation of point mutations of driver genes and/or cytogenetic abnormalities. Furthermore, disease progression is accomplished by branching patterns of subclonal evolution from reservoir clones with a propagating potential and/or the emergence of minor clones, which already exist at premalignant stages and outcompete other clones through selective pressure mainly by therapeutic agents. Each subclone harbors novel mutations and distinct phenotypes, including drug sensitivities. Generally, mature clones are highly sensitive to proteasome inhibitors (PIs), whereas immature clones are resistant to PIs although could be eradicated by immunomodulatory drugs (IMiDs). The branching evolution is a result of the fitness of different clones to the microenvironment and their evasion of immune surveillance; therefore, IMiDs are effective for MM with this pattern of evolution. In contrast, ∼20% of MM evolve neutrally in the context of strong oncogenic drivers, including high-risk IgH translocations, and are relatively resistant to IMiDs. Treatment strategies considering the genomic landscape and the pattern of clonal evolution may further improve the treatment outcome of MM.
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Affiliation(s)
- Yusuke Furukawa
- Division of Stem Cell Regulation, Center for Molecular Medicine, Jichi Medical University
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43
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Zaimoku Y, Patel BA, Adams SD, Shalhoub R, Groarke EM, Lee AAC, Kajigaya S, Feng X, Rios OJ, Eager H, Alemu L, Quinones Raffo D, Wu CO, Flegel WA, Young NS. HLA associations, somatic loss of HLA expression, and clinical outcomes in immune aplastic anemia. Blood 2021; 138:2799-2809. [PMID: 34724566 PMCID: PMC8718630 DOI: 10.1182/blood.2021012895] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/18/2021] [Indexed: 01/01/2023] Open
Abstract
Immune aplastic anemia (AA) features somatic loss of HLA class I allele expression on bone marrow cells, consistent with a mechanism of escape from T-cell-mediated destruction of hematopoietic stem and progenitor cells. The clinical significance of HLA abnormalities has not been well characterized. We examined the somatic loss of HLA class I alleles and correlated HLA loss and mutation-associated HLA genotypes with clinical presentation and outcomes after immunosuppressive therapy in 544 AA patients. HLA class I allele loss was detected in 92 (22%) of the 412 patients tested, in whom there were 393 somatic HLA gene mutations and 40 instances of loss of heterozygosity. Most frequently affected was HLA-B*14:02, followed by HLA-A*02:01, HLA-B*40:02, HLA-B*08:01, and HLA-B*07:02. HLA-B*14:02, HLA-B*40:02, and HLA-B*07:02 were also overrepresented in AA. High-risk clonal evolution was correlated with HLA loss, HLA-B*14:02 genotype, and older age, which yielded a valid prediction model. In 2 patients, we traced monosomy 7 clonal evolution from preexisting clones harboring somatic mutations in HLA-A*02:01 and HLA-B*40:02. Loss of HLA-B*40:02 correlated with higher blood counts. HLA-B*07:02 and HLA-B*40:01 genotypes and their loss correlated with late-onset of AA. Our results suggest the presence of specific immune mechanisms of molecular pathogenesis with clinical implications. HLA genotyping and screening for HLA loss may be of value in the management of immune AA. This study was registered at clinicaltrials.gov as NCT00001964, NCT00061360, NCT00195624, NCT00260689, NCT00944749, NCT01193283, and NCT01623167.
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Affiliation(s)
- Yoshitaka Zaimoku
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Bhavisha A Patel
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Sharon D Adams
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD; and
| | - Ruba Shalhoub
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Emma M Groarke
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Audrey Ai Chin Lee
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD; and
| | - Sachiko Kajigaya
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Xingmin Feng
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Olga Julia Rios
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Holly Eager
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Lemlem Alemu
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Diego Quinones Raffo
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Colin O Wu
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Willy A Flegel
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD; and
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
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44
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Benard BA, Leak LB, Azizi A, Thomas D, Gentles AJ, Majeti R. Clonal architecture predicts clinical outcomes and drug sensitivity in acute myeloid leukemia. Nat Commun 2021; 12:7244. [PMID: 34903734 PMCID: PMC8669028 DOI: 10.1038/s41467-021-27472-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/17/2021] [Indexed: 12/17/2022] Open
Abstract
The impact of clonal heterogeneity on disease behavior or drug response in acute myeloid leukemia remains poorly understood. Using a cohort of 2,829 patients, we identify features of clonality associated with clinical features and drug sensitivities. High variant allele frequency for 7 mutations (including NRAS and TET2) associate with dismal prognosis; elevated GATA2 variant allele frequency correlates with better outcomes. Clinical features such as white blood cell count and blast percentage correlate with the subclonal abundance of mutations such as TP53 and IDH1. Furthermore, patients with cohesin mutations occurring before NPM1, or transcription factor mutations occurring before splicing factor mutations, show shorter survival. Surprisingly, a branched pattern of clonal evolution is associated with superior clinical outcomes. Finally, several mutations (including NRAS and IDH1) predict drug sensitivity based on their subclonal abundance. Together, these results demonstrate the importance of assessing clonal heterogeneity with implications for prognosis and actionable biomarkers for therapy.
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Affiliation(s)
- Brooks A Benard
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA
- Cancer Biology Program, Stanford University, Stanford, CA, USA
| | - Logan B Leak
- Cancer Biology Program, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Armon Azizi
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA
| | - Daniel Thomas
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Andrew J Gentles
- Department of Medicine (Biomedical Informatics/Quantitative Sciences unit), Stanford University, Stanford, CA, USA
| | - Ravindra Majeti
- Department of Medicine, Division of Hematology, Cancer Institute, Stanford University, Stanford, CA, USA.
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45
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Simundza J. Probing clonal dynamics with single-cell genomics. Nat Cancer 2021; 2:1289. [PMID: 35121909 DOI: 10.1038/s43018-021-00311-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
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46
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Hill W, Caswell DR, Swanton C. Capturing cancer evolution using genetically engineered mouse models (GEMMs). Trends Cell Biol 2021; 31:1007-1018. [PMID: 34400045 DOI: 10.1016/j.tcb.2021.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/11/2021] [Accepted: 07/15/2021] [Indexed: 12/17/2022]
Abstract
Initiating from a single cell, cancer undergoes clonal evolution, leading to a high degree of intratumor heterogeneity (ITH). The arising genetic heterogeneity between cancer cells is influenced by exogenous and endogenous forces that shape the composition of clones within tumors. Preclinical mouse models have provided a valuable tool for understanding cancer, helping to build a fundamental understanding of tumor initiation, progression, and metastasis. Until recently, genetically engineered mouse models (GEMMS) of cancer had lacked the genetic diversity found in human tumors, in which evolution may be driven by long-term carcinogen exposure and DNA damage. However, advances in sequencing technology and in our understanding of the drivers of genetic instability have given us the knowledge to generate new mouse models, offering an approach to functionally explore mechanisms of tumor evolution.
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Affiliation(s)
- William Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Deborah R Caswell
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, University College London, London, UK; University College London Hospitals NHS Trust, London, UK.
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47
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Schmelz K, Toedling J, Huska M, Cwikla MC, Kruetzfeldt LM, Proba J, Ambros PF, Ambros IM, Boral S, Lodrini M, Chen CY, Burkert M, Guergen D, Szymansky A, Astrahantseff K, Kuenkele A, Haase K, Fischer M, Deubzer HE, Hertwig F, Hundsdoerfer P, Henssen AG, Schwarz RF, Schulte JH, Eggert A. Spatial and temporal intratumour heterogeneity has potential consequences for single biopsy-based neuroblastoma treatment decisions. Nat Commun 2021; 12:6804. [PMID: 34815394 PMCID: PMC8611017 DOI: 10.1038/s41467-021-26870-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 10/18/2021] [Indexed: 01/12/2023] Open
Abstract
Intratumour heterogeneity is a major cause of treatment failure in cancer. We present in-depth analyses combining transcriptomic and genomic profiling with ultra-deep targeted sequencing of multiregional biopsies in 10 patients with neuroblastoma, a devastating childhood tumour. We observe high spatial and temporal heterogeneity in somatic mutations and somatic copy-number alterations which are reflected on the transcriptomic level. Mutations in some druggable target genes including ALK and FGFR1 are heterogeneous at diagnosis and/or relapse, raising the issue whether current target prioritization and molecular risk stratification procedures in single biopsies are sufficiently reliable for therapy decisions. The genetic heterogeneity in gene mutations and chromosome aberrations observed in deep analyses from patient courses suggest clonal evolution before treatment and under treatment pressure, and support early emergence of metastatic clones and ongoing chromosomal instability during disease evolution. We report continuous clonal evolution on mutational and copy number levels in neuroblastoma, and detail its implications for therapy selection, risk stratification and therapy resistance.
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Affiliation(s)
- Karin Schmelz
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- The German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Joern Toedling
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- The German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matt Huska
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Maja C Cwikla
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | | | - Jutta Proba
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Peter F Ambros
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090, Vienna, Austria
| | - Inge M Ambros
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090, Vienna, Austria
| | - Sengül Boral
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Marco Lodrini
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- The German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Celine Y Chen
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- Experimental and Clinical Research Center (ECRC) of the Charité and Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Martin Burkert
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Dennis Guergen
- Experimental Pharmacology and Oncology Berlin-Buch GmbH (EPO), Berlin, Germany
| | | | | | - Annette Kuenkele
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- The German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Kerstin Haase
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- The German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, Medical Faculty, University Children's Hospital of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Hedwig E Deubzer
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- The German Cancer Research Center (DKFZ), Heidelberg, Germany
- Experimental and Clinical Research Center (ECRC) of the Charité and Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Falk Hertwig
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany
- The German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Hundsdoerfer
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- Helios Klinikum Berlin-Buch, Berlin, Germany
| | - Anton G Henssen
- Charité-Universitätsmedizin Berlin, Berlin, Germany.
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany.
- The German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
- Experimental and Clinical Research Center (ECRC) of the Charité and Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
- Berlin Institute of Health (BIH), Berlin, Germany.
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
- BIFOLD-Berlin Institute for the Foundations of Learning and Data, Berlin, Germany.
| | - Johannes H Schulte
- Charité-Universitätsmedizin Berlin, Berlin, Germany.
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany.
- The German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Berlin Institute of Health (BIH), Berlin, Germany.
| | - Angelika Eggert
- Charité-Universitätsmedizin Berlin, Berlin, Germany.
- The German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany.
- The German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Berlin Institute of Health (BIH), Berlin, Germany.
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48
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Bachireddy P, Azizi E, Burdziak C, Nguyen VN, Ennis CS, Maurer K, Park CY, Choo ZN, Li S, Gohil SH, Ruthen NG, Ge Z, Keskin DB, Cieri N, Livak KJ, Kim HT, Neuberg DS, Soiffer RJ, Ritz J, Alyea EP, Pe'er D, Wu CJ. Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy. Cell Rep 2021; 37:109992. [PMID: 34758319 PMCID: PMC9035342 DOI: 10.1016/j.celrep.2021.109992] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 06/23/2021] [Accepted: 10/21/2021] [Indexed: 01/06/2023] Open
Abstract
To elucidate mechanisms by which T cells eliminate leukemia, we study donor lymphocyte infusion (DLI), an established immunotherapy for relapsed leukemia. We model T cell dynamics by integrating longitudinal, multimodal data from 94,517 bone marrow-derived single T cell transcriptomes in addition to chromatin accessibility and single T cell receptor sequencing from patients undergoing DLI. We find that responsive tumors are defined by enrichment of late-differentiated T cells before DLI and rapid, durable expansion of early differentiated T cells after treatment, highly similar to "terminal" and "precursor" exhausted subsets, respectively. Resistance, in contrast, is defined by heterogeneous T cell dysfunction. Surprisingly, early differentiated T cells in responders mainly originate from pre-existing and novel clonotypes recruited to the leukemic microenvironment, rather than the infusion. Our work provides a paradigm for analyzing longitudinal single-cell profiling of scenarios beyond adoptive cell therapy and introduces Symphony, a Bayesian approach to infer regulatory circuitry underlying T cell subsets, with broad relevance to exhaustion antagonists across cancers.
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Affiliation(s)
- Pavan Bachireddy
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA; Department of Hematopoietic Biology & Malignancy, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Cancer Prevention and Research Institute of Texas (CPRIT) Scholar in Cancer Research, Austin, TX 78701, USA.
| | - Elham Azizi
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Biomedical Engineering and Irving Institute for Cancer Dynamics, Columbia University, New York, NY 10027, USA.
| | - Cassandra Burdziak
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Vinhkhang N Nguyen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Christina S Ennis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Katie Maurer
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Cameron Y Park
- Department of Biomedical Engineering and Irving Institute for Cancer Dynamics, Columbia University, New York, NY 10027, USA
| | - Zi-Ning Choo
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Shuqiang Li
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Satyen H Gohil
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Neil G Ruthen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Zhongqi Ge
- Department of Hematopoietic Biology & Malignancy, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Derin B Keskin
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nicoletta Cieri
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Haesook T Kim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Robert J Soiffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Edwin P Alyea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Parker Institute of Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Catherine J Wu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA.
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49
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Röcken C, Amallraja A, Halske C, Opasic L, Traulsen A, Behrens HM, Krüger S, Liu A, Haag J, Egberts JH, Rosenstiel P, Meißner T. Multiscale heterogeneity in gastric adenocarcinoma evolution is an obstacle to precision medicine. Genome Med 2021; 13:177. [PMID: 34749812 PMCID: PMC8576943 DOI: 10.1186/s13073-021-00975-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Cancer is a somatic evolutionary disease and adenocarcinomas of the stomach and gastroesophageal junction (GC) may serve as a two-dimensional model of cancer expansion, in which tumor subclones are not evenly mixed during tumor progression but rather spatially separated and diversified. We hypothesize that precision medicine efforts are compromised when clinical decisions are based on a single-sample analysis, which ignores the mechanisms of cancer evolution and resulting intratumoral heterogeneity. Using multiregional whole-exome sequencing, we investigated the effect of somatic evolution on intratumoral heterogeneity aiming to shed light on the evolutionary biology of GC. METHODS The study comprised a prospective discovery cohort of 9 and a validation cohort of 463 GCs. Multiregional whole-exome sequencing was performed using samples form 45 primary tumors and 3 lymph node metastases (range 3-10 tumor samples/patient) of the discovery cohort. RESULTS In total, the discovery cohort harbored 16,537 non-synonymous mutations. Intratumoral heterogeneity of somatic mutations and copy number variants were present in all tumors of the discovery cohort. Of the non-synonymous mutations, 53-91% were not present in each patient's sample; 399 genes harbored 2-4 different non-synonymous mutations in the same patient; 175 genes showed copy number variations, the majority being heterogeneous, including CD274 (PD-L1). Multi-sample tree-based analyses provided evidence for branched evolution being most complex in a microsatellite instable GC. The analysis of the mode of evolution showed a high degree of heterogeneity in deviation from neutrality within each tumor. We found evidence of parallel evolution and evolutionary trajectories: different mutations of SMAD4 aligned with different subclones and were found only in TP53 mutant GCs. CONCLUSIONS Neutral and non-neutral somatic evolution shape the mutational landscape in GC along its lateral expansions. It leads to complex spatial intratumoral heterogeneity, where lymph node metastases may stem from different areas of the primary tumor, synchronously. Our findings may have profound effects on future patient management. They illustrate the risk of mis-interpreting tumor genetics based on single-sample analysis and open new avenues for an evolutionary classification of GC, i.e., the discovery of distinct evolutionary trajectories which can be utilized for precision medicine.
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Affiliation(s)
- Christoph Röcken
- Department of Pathology, Christian-Albrechts-University, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Arnold-Heller-Str. 3, Haus U33, D-24105, Kiel, Germany.
- Institute for Clinical Molecular Biology, Christian-Albrechts-University, 24105, Kiel, Germany.
| | - Anu Amallraja
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, Sioux Falls, USA
| | - Christine Halske
- Department of Pathology, Christian-Albrechts-University, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Arnold-Heller-Str. 3, Haus U33, D-24105, Kiel, Germany
| | - Luka Opasic
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Arne Traulsen
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Hans-Michael Behrens
- Department of Pathology, Christian-Albrechts-University, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Arnold-Heller-Str. 3, Haus U33, D-24105, Kiel, Germany
| | - Sandra Krüger
- Department of Pathology, Christian-Albrechts-University, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Arnold-Heller-Str. 3, Haus U33, D-24105, Kiel, Germany
| | - Anne Liu
- Department of Pathology, Christian-Albrechts-University, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Arnold-Heller-Str. 3, Haus U33, D-24105, Kiel, Germany
| | - Jochen Haag
- Department of Pathology, Christian-Albrechts-University, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Arnold-Heller-Str. 3, Haus U33, D-24105, Kiel, Germany
| | - Jan-Hendrik Egberts
- Department of General Surgery, Visceral, Thoracic, Transplantation and Pediatric Surgery, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Kiel, Germany
| | - Philip Rosenstiel
- Department of General Surgery, Visceral, Thoracic, Transplantation and Pediatric Surgery, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Kiel, Germany
| | - Tobias Meißner
- Institute for Clinical Molecular Biology, Christian-Albrechts-University, 24105, Kiel, Germany
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50
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Batta K, Bossenbroek HM, Pemmaraju N, Wilks DP, Chasty R, Dennis M, Milne P, Collin M, Beird HC, Taylor J, Patnaik MM, Cargo CA, Somervaille TCP, Wiseman DH. Divergent clonal evolution of blastic plasmacytoid dendritic cell neoplasm and chronic myelomonocytic leukemia from a shared TET2-mutated origin. Leukemia 2021; 35:3299-3303. [PMID: 33833384 PMCID: PMC8550946 DOI: 10.1038/s41375-021-01228-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/15/2021] [Accepted: 03/11/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Kiran Batta
- Epigenetics of Haematopoiesis Laboratory, Division of Cancer Sciences, The University of Manchester, Manchester, UK.
| | - Hasse M Bossenbroek
- Epigenetics of Haematopoiesis Laboratory, Division of Cancer Sciences, The University of Manchester, Manchester, UK
| | - Naveen Pemmaraju
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Deepti P Wilks
- Haematological Malignancies Biobank, Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Richard Chasty
- Department of Haematology, The Christie NHS Foundation Trust, Manchester, UK
| | - Mike Dennis
- Department of Haematology, The Christie NHS Foundation Trust, Manchester, UK
| | - Paul Milne
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, UK
- Northern Centre for Cancer Care, Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle-upon-Tyne, UK
| | - Matthew Collin
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, UK
- Northern Centre for Cancer Care, Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle-upon-Tyne, UK
| | - Hannah C Beird
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Justin Taylor
- Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Catherine A Cargo
- Haematological Malignancy Diagnostics Service, St James' University Hospital, Leeds, UK
| | - Tim C P Somervaille
- Department of Haematology, The Christie NHS Foundation Trust, Manchester, UK
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
| | - Daniel H Wiseman
- Epigenetics of Haematopoiesis Laboratory, Division of Cancer Sciences, The University of Manchester, Manchester, UK.
- Department of Haematology, The Christie NHS Foundation Trust, Manchester, UK.
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