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Stonestrom AJ, Menghrajani KN, Devlin SM, Franch-Expósito S, Ptashkin RN, Patel SY, Spitzer B, Wu X, Jee J, Sánchez Vela P, Milbank JH, Shah RH, Mohanty AS, Brannon AR, Xiao W, Berger MF, Mantha S, Levine RL. High-risk and silent clonal hematopoietic genotypes in patients with nonhematologic cancer. Blood Adv 2024; 8:846-856. [PMID: 38147626 PMCID: PMC10875331 DOI: 10.1182/bloodadvances.2023011262] [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: 07/19/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/28/2023] Open
Abstract
ABSTRACT Clonal hematopoiesis (CH) identified by somatic gene variants with variant allele fraction (VAF) ≥ 2% is associated with an increased risk of hematologic malignancy. However, CH defined by a broader set of genotypes and lower VAFs is ubiquitous in older individuals. To improve our understanding of the relationship between CH genotype and risk of hematologic malignancy, we analyzed data from 42 714 patients who underwent blood sequencing as a normal comparator for nonhematologic tumor testing using a large cancer-related gene panel. We cataloged hematologic malignancies in this cohort using natural language processing and manual curation of medical records. We found that some CH genotypes including JAK2, RUNX1, and XPO1 variants were associated with high hematologic malignancy risk. Chronic disease was predicted better than acute disease suggesting the influence of length bias. To better understand the implications of hematopoietic clonality independent of mutational function, we evaluated a set of silent synonymous and noncoding mutations. We found that silent CH, particularly when multiple variants were present or VAF was high, was associated with increased risk of hematologic malignancy. We tracked expansion of CH mutations in 26 hematologic malignancies sequenced with the same platform. JAK2 and TP53 VAF consistently expanded at disease onset, whereas DNMT3A and silent CH VAFs mostly decreased. These data inform the clinical and biological interpretation of CH in the context of nonhematologic cancer.
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Affiliation(s)
- Aaron J. Stonestrom
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kamal N. Menghrajani
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sean M. Devlin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sebastià Franch-Expósito
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryan N. Ptashkin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Barbara Spitzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Xiaodi Wu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Justin Jee
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pablo Sánchez Vela
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jennifer H. Milbank
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ronak H. Shah
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Abhinita S. Mohanty
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - A. Rose Brannon
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wenbin Xiao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F. Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Simon Mantha
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ross L. Levine
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
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2
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Lasho T, Patnaik MM. Adaptive and Maladaptive Clonal Hematopoiesis in Telomere Biology Disorders. Curr Hematol Malig Rep 2024; 19:35-44. [PMID: 38095828 DOI: 10.1007/s11899-023-00719-2] [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] [Accepted: 11/24/2023] [Indexed: 01/30/2024]
Abstract
PURPOSE OF REVIEW Telomere biology disorders (TBDs) are germline-inherited conditions characterized by reduction in telomerase function, accelerated shortening of telomeres, predisposition to organ-failure syndromes, and increased risk of neoplasms, especially myeloid malignancies. In normal cells, critically short telomeres trigger apoptosis and/or cellular senescence. However, the evolutionary mechanism by which TBD-related telomerase-deficient cells can overcome this fitness constraint remains elusive. RECENT FINDINGS Preliminary data suggests the existence of adaptive somatic mosaic states characterized by variants in TBD-related genes and maladaptive somatic mosaic states that attempt to overcome hematopoietic fitness constraints by alternative methods leading to clonal hematopoiesis. TBDs are both rare and highly heterogeneous in presentation, and the association of TBD with malignant transformation is unclear. Understanding the clonal complexity and mechanisms behind TBD-associated molecular signatures that lead to somatic adaptation in the setting of defective hematopoiesis will help inform therapy and treatment for this set of diseases.
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Affiliation(s)
- Terra Lasho
- Division of Hematology, Mayo Clinic Rochester, 200 First Street SW, Rochester, MN, 55905, USA
| | - Mrinal M Patnaik
- Division of Hematology, Mayo Clinic Rochester, 200 First Street SW, Rochester, MN, 55905, USA.
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Pasupuleti SK, Ramdas B, Burns SS, Palam LR, Kanumuri R, Kumar R, Pandhiri TR, Dave UP, Yellapu NK, Zhou X, Zhang C, Sandusky GE, Yu Z, Honigberg MC, Bick AG, Griffin GK, Niroula A, Ebert BL, Paczesny S, Natarajan P, Kapur R. Obesity-induced inflammation exacerbates clonal hematopoiesis. J Clin Invest 2023; 133:e163968. [PMID: 37071471 PMCID: PMC10231999 DOI: 10.1172/jci163968] [Citation(s) in RCA: 13] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 04/07/2023] [Indexed: 04/19/2023] Open
Abstract
Characterized by the accumulation of somatic mutations in blood cell lineages, clonal hematopoiesis of indeterminate potential (CHIP) is frequent in aging and involves the expansion of mutated hematopoietic stem and progenitor cells (HSC/Ps) that leads to an increased risk of hematologic malignancy. However, the risk factors that contribute to CHIP-associated clonal hematopoiesis (CH) are poorly understood. Obesity induces a proinflammatory state and fatty bone marrow (FBM), which may influence CHIP-associated pathologies. We analyzed exome sequencing and clinical data for 47,466 individuals with validated CHIP in the UK Biobank. CHIP was present in 5.8% of the study population and was associated with a significant increase in the waist-to-hip ratio (WHR). Mouse models of obesity and CHIP driven by heterozygosity of Tet2, Dnmt3a, Asxl1, and Jak2 resulted in exacerbated expansion of mutant HSC/Ps due in part to excessive inflammation. Our results show that obesity is highly associated with CHIP and that a proinflammatory state could potentiate the progression of CHIP to more significant hematologic neoplasia. The calcium channel blockers nifedipine and SKF-96365, either alone or in combination with metformin, MCC950, or anakinra (IL-1 receptor antagonist), suppressed the growth of mutant CHIP cells and partially restored normal hematopoiesis. Targeting CHIP-mutant cells with these drugs could be a potential therapeutic approach to treat CH and its associated abnormalities in individuals with obesity.
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Affiliation(s)
| | - Baskar Ramdas
- Herman B Wells Center for Pediatric Research, Department of Pediatrics and
| | - Sarah S. Burns
- Herman B Wells Center for Pediatric Research, Department of Pediatrics and
| | | | - Rahul Kanumuri
- Herman B Wells Center for Pediatric Research, Department of Pediatrics and
| | - Ramesh Kumar
- Herman B Wells Center for Pediatric Research, Department of Pediatrics and
| | | | - Utpal P. Dave
- Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Nanda Kumar Yellapu
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Xinyu Zhou
- Department of Medical and Molecular Genetics and
| | - Chi Zhang
- Department of Medical and Molecular Genetics and
| | - George E. Sandusky
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Zhi Yu
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Michael C. Honigberg
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Alexander G. Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Gabriel K. Griffin
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Epigenomics Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Abhishek Niroula
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Benjamin L. Ebert
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sophie Paczesny
- Department of Microbiology and Immunology, Medical University of South Carolina, Charlestown, South Carolina, USA
| | - Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Reuben Kapur
- Herman B Wells Center for Pediatric Research, Department of Pediatrics and
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
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4
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Burns SS, Kumar R, Pasupuleti SK, So K, Zhang C, Kapur R. Il-1r1 drives leukemogenesis induced by Tet2 loss. Leukemia 2022; 36:2531-2534. [PMID: 35962058 PMCID: PMC9522579 DOI: 10.1038/s41375-022-01665-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 03/14/2022] [Revised: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 12/15/2022]
Affiliation(s)
- Sarah S Burns
- Medical Scientist Training Program, Indiana University-Purdue University, Indianapolis, USA
- Medical and Molecular Genetics Graduate Program, Indiana University-Purdue University, Indianapolis, USA
- The Herman B. Wells Center for Pediatric Research, Indiana University-Purdue University, Indianapolis, USA
| | - Ramesh Kumar
- The Herman B. Wells Center for Pediatric Research, Indiana University-Purdue University, Indianapolis, USA
- Department of Pediatrics, Indiana University-Purdue University, Indianapolis, USA
| | - Santhosh Kumar Pasupuleti
- The Herman B. Wells Center for Pediatric Research, Indiana University-Purdue University, Indianapolis, USA
- Department of Pediatrics, Indiana University-Purdue University, Indianapolis, USA
| | - Kaman So
- Department of Biostatistics and Health Data Science, Indiana University-Purdue University, Indianapolis, USA
| | - Chi Zhang
- Medical and Molecular Genetics Graduate Program, Indiana University-Purdue University, Indianapolis, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indiana, USA
| | - Reuben Kapur
- Medical and Molecular Genetics Graduate Program, Indiana University-Purdue University, Indianapolis, USA.
- The Herman B. Wells Center for Pediatric Research, Indiana University-Purdue University, Indianapolis, USA.
- Department of Pediatrics, Indiana University-Purdue University, Indianapolis, USA.
- Molecular Biology and Biochemistry, Indiana University School of Medicine, Indiana, USA.
- Medical and Molecular Genetics, Indiana University School of Medicine, Indiana, USA.
- Microbiology and Immunology, Indiana University School of Medicine, Indiana, USA.
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5
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Abraham IE, Rauscher GH, Patel AA, Pearse WB, Rajakumar P, Burkart M, Aleem A, Dave A, Bharadwaj S, Paydary K, Acevedo-Mendez M, Goparaju K, Gomez R, Carlson K, Tsai SB, Quigley JG, Galvin JP, Zia M, Larson ML, Berg S, Stock W, Altman JK, Khan I. Structural racism is a mediator of disparities in acute myeloid leukemia outcomes. Blood 2022; 139:2212-2226. [PMID: 35061876 PMCID: PMC9710198 DOI: 10.1182/blood.2021012830] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [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: 06/08/2021] [Accepted: 01/03/2022] [Indexed: 12/15/2022] Open
Abstract
Non-Hispanic Black (NHB) and Hispanic patients with acute myeloid leukemia (AML) have higher mortality rates than non-Hispanic White (NHW) patients despite more favorable genetics and younger age. A discrete survival analysis was performed on 822 adult patients with AML from 6 urban cancer centers and revealed inferior survival among NHB (hazard ratio [HR] = 1.59; 95% confidence interval [CI]: 1.15, 2.22) and Hispanic (HR = 1.25; 95% CI: 0.88, 1.79) patients compared with NHW patients. A multilevel analysis of disparities was then conducted to investigate the contribution of neighborhood measures of structural racism on racial/ethnic differences in survival. Census tract disadvantage and affluence scores were individually calculated. Mediation analysis of hazard of leukemia death between groups was examined across 6 composite variables: structural racism (census tract disadvantage, affluence, and segregation), tumor biology (European Leukemia Network risk and secondary leukemia), health care access (insurance and clinical trial enrollment), comorbidities, treatment patterns (induction intensity and transplant utilization), and intensive care unit (ICU) admission during induction chemotherapy. Strikingly, census tract measures accounted for nearly all of the NHB-NHW and Hispanic-NHW disparity in leukemia death. Treatment patterns, including induction intensity and allogeneic transplant, and treatment complications, as assessed by ICU admission during induction chemotherapy, were additional mediators of survival disparities in AML. This is the first study to formally test mediators for observed disparities in AML survival and highlights the need to investigate the mechanisms by which structural racism interacts with known prognostic and treatment factors to influence leukemia outcomes.
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Affiliation(s)
| | - Garth H. Rauscher
- Division of Epidemiology and Biostatistics UIC, University of Illinois Cancer Center, Chicago, IL
| | - Anand Ashwin Patel
- Department of Medicine, Section of Hematology-Oncology, University of Chicago, Chicago, IL
| | - William B. Pearse
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Priya Rajakumar
- Division of Hematology, Oncology and Stem Cell Transplant, Rush University Medical Center, Chicago, IL
| | - Madelyn Burkart
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Ahmed Aleem
- Division of Hematology and Oncology, Loyola University Medical Center, Maywood, IL
| | - Ami Dave
- Division of Hematology, Oncology and Stem Cell Transplant, Rush University Medical Center, Chicago, IL
| | - Sushma Bharadwaj
- Division of Hematology and Oncology, John H. Stroger, Jr. Hospital of Cook County, Chicago, IL; and
| | - Koosha Paydary
- Division of Hematology and Oncology, John H. Stroger, Jr. Hospital of Cook County, Chicago, IL; and
| | - Maria Acevedo-Mendez
- Division of Epidemiology and Biostatistics UIC, University of Illinois Cancer Center, Chicago, IL
| | - Krishna Goparaju
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Richard Gomez
- Division of Hematology and Oncology, Loyola University Medical Center, Maywood, IL
| | - Kylie Carlson
- Division of Hematology and Oncology, Loyola University Medical Center, Maywood, IL
| | - Stephanie B. Tsai
- Division of Hematology and Oncology, Loyola University Medical Center, Maywood, IL
| | - John G. Quigley
- Division of Hematology and Oncology UIC, University of Illinois Cancer Center, Chicago, IL
| | - John P. Galvin
- Division of Epidemiology and Biostatistics UIC, University of Illinois Cancer Center, Chicago, IL
| | - Maryam Zia
- Division of Hematology and Oncology, John H. Stroger, Jr. Hospital of Cook County, Chicago, IL; and
| | - Melissa L. Larson
- Division of Hematology, Oncology and Stem Cell Transplant, Rush University Medical Center, Chicago, IL
| | - Stephanie Berg
- Division of Hematology and Oncology, Loyola University Medical Center, Maywood, IL
| | - Wendy Stock
- Department of Medicine, Section of Hematology-Oncology, University of Chicago, Chicago, IL
| | - Jessica K. Altman
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Irum Khan
- Division of Hematology and Oncology UIC, University of Illinois Cancer Center, Chicago, IL
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6
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Liu X, Sato N, Shimosato Y, Wang TW, Denda T, Chang YH, Yabushita T, Fujino T, Asada S, Tanaka Y, Fukuyama T, Enomoto Y, Ota Y, Sakamoto T, Kitamura T, Goyama S. CHIP-associated mutant ASXL1 in blood cells promotes solid tumor progression. Cancer Sci 2022; 113:1182-1194. [PMID: 35133065 PMCID: PMC8990791 DOI: 10.1111/cas.15294] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/23/2022] [Accepted: 01/28/2022] [Indexed: 11/30/2022] Open
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is an age‐associated phenomenon characterized by clonal expansion of blood cells harboring somatic mutations in hematopoietic genes, including DNMT3A, TET2, and ASXL1. Clinical evidence suggests that CHIP is highly prevalent and associated with poor prognosis in solid‐tumor patients. However, whether blood cells with CHIP mutations play a causal role in promoting the development of solid tumors remained unclear. Using conditional knock‐in mice that express CHIP‐associated mutant Asxl1 (Asxl1‐MT), we showed that expression of Asxl1‐MT in T cells, but not in myeloid cells, promoted solid‐tumor progression in syngeneic transplantation models. We also demonstrated that Asxl1‐MT–expressing blood cells accelerated the development of spontaneous mammary tumors induced by MMTV‐PyMT. Intratumor analysis of the mammary tumors revealed the reduced T‐cell infiltration at tumor sites and programmed death receptor‐1 (PD‐1) upregulation in CD8+ T cells in MMTV‐PyMT/Asxl1‐MT mice. In addition, we found that Asxl1‐MT induced T‐cell dysregulation, including aberrant intrathymic T‐cell development, decreased CD4/CD8 ratio, and naïve‐memory imbalance in peripheral T cells. These results indicate that Asxl1‐MT perturbs T‐cell development and function, which contributes to creating a protumor microenvironment for solid tumors. Thus, our findings raise the possibility that ASXL1‐mutated blood cells exacerbate solid‐tumor progression in ASXL1‐CHIP carriers.
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Affiliation(s)
- Xiaoxiao Liu
- Division of Molecular Oncology, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Naru Sato
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yuko Shimosato
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Teh-Wei Wang
- Division of Cancer Cell Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tamami Denda
- Department of Pathology, The Institute of Medical Science Research Hospital, The University of Tokyo, Tokyo, Japan
| | - Yu-Hsuan Chang
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tomohiro Yabushita
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takeshi Fujino
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shuhei Asada
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,The Institute of Laboratory Animals, Tokyo Women's Medical University, Tokyo, Japan
| | - Yosuke Tanaka
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tomofusa Fukuyama
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yutaka Enomoto
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yasunori Ota
- Department of Pathology, The Institute of Medical Science Research Hospital, The University of Tokyo, Tokyo, Japan
| | - Takeharu Sakamoto
- Department of Cancer Biology, Institute of Biomedical Science, Kansai Medical University, Osaka, Japan
| | - Toshio Kitamura
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Susumu Goyama
- Division of Molecular Oncology, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
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7
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Abstract
The genetic information of human cells is stored in the context of chromatin, which is subjected to DNA methylation and various histone modifications. Such a 'language' of chromatin modification constitutes a fundamental means of gene and (epi)genome regulation, underlying a myriad of cellular and developmental processes. In recent years, mounting evidence has demonstrated that miswriting, misreading or mis-erasing of the modification language embedded in chromatin represents a common, sometimes early and pivotal, event across a wide range of human cancers, contributing to oncogenesis through the induction of epigenetic, transcriptomic and phenotypic alterations. It is increasingly clear that cancer-related metabolic perturbations and oncohistone mutations also directly impact chromatin modification, thereby promoting cancerous transformation. Phase separation-based deregulation of chromatin modulators and chromatin structure is also emerging to be an important underpinning of tumorigenesis. Understanding the various molecular pathways that underscore a misregulated chromatin language in cancer, together with discovery and development of more effective drugs to target these chromatin-related vulnerabilities, will enhance treatment of human malignancies.
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Affiliation(s)
- Shuai Zhao
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics and Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics and Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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8
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Mellid S, Coloma J, Calsina B, Monteagudo M, Roldán-Romero JM, Santos M, Leandro-García LJ, Lanillos J, Martínez-Montes ÁM, Rodríguez-Antona C, Montero-Conde C, Martínez-López J, Ayala R, Matias-Guiu X, Robledo M, Cascón A. Novel DNMT3A Germline Variant in a Patient with Multiple Paragangliomas and Papillary Thyroid Carcinoma. Cancers (Basel) 2020; 12:E3304. [PMID: 33182397 DOI: 10.3390/cancers12113304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 12/15/2022] Open
Abstract
Simple Summary The use of next generation technologies has helped to unravel the genetics of rare inherited diseases, facilitating the discovery of new susceptibility genes. Nonetheless, the sequencing of all protein-coding genes of an individual may lead to doubtful assignments of causality for non-pathological variants, so it is mandatory to perform comprehensive studies and screening of additional patients for new mutations. Here we describe a novel DNMT3A germline variant identified by whole-exome sequencing in a patient with multiple paragangliomas and papillary thyroid carcinoma. The increased methylation of DNMT3A target genes observed in the proband’s sample points towards a gain-of-function effect of the variant, contrasting with the inactivation caused by loss-of-function alterations commonly seen in other neoplasia and in patients with Tatton-Brown-Rahman syndrome. This finding stresses the diverse molecular outcomes and suggests a heterogeneous phenotypic spectrum related to DNMT3A germline variants. Abstract Over the past few years, next generation technologies have been applied to unravel the genetics of rare inherited diseases, facilitating the discovery of new susceptibility genes. We recently found germline DNMT3A gain-of-function variants in two patients with head and neck paragangliomas causing a characteristic hypermethylated DNA profile. Here, whole-exome sequencing identifies a novel germline DNMT3A variant (p.Gly332Arg) in a patient with bilateral carotid paragangliomas, papillary thyroid carcinoma and idiopathic intellectual disability. The variant, located in the Pro-Trp-Trp-Pro (PWWP) domain of the protein involved in chromatin targeting, affects a residue mutated in papillary thyroid tumors and located between the two residues found mutated in microcephalic dwarfism patients. Structural modelling of the variant in the DNMT3A PWWP domain predicts that the interaction with H3K36me3 will be altered. An increased methylation of DNMT3A target genes, compatible with a gain-of-function effect of the alteration, was observed in saliva DNA from the proband and in one independent acute myeloid leukemia sample carrying the same p.Gly332Arg variant. Although further studies are needed to support a causal role of DNMT3A variants in paraganglioma, the description of a new DNMT3A alteration in a patient with multiple clinical features suggests a heterogeneous phenotypic spectrum related to DNMT3A germline variants.
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Wang J, Dao FT, Yang L, Qin YZ. Characterization of somatic mutation-associated microenvironment signatures in acute myeloid leukemia patients based on TCGA analysis. Sci Rep 2020; 10:19037. [PMID: 33149230 DOI: 10.1038/s41598-020-76048-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/21/2020] [Indexed: 01/05/2023] Open
Abstract
Recurrent genetic mutations occur in acute myeloid leukemia (AML) and have been incorporated into risk stratification to predict the prognoses of AML patients. The bone marrow microenvironment plays a critical role in the development and progression of AML. However, the characteristics of the genetic mutation-associated microenvironment have not been comprehensively identified to date. In this study, we obtained the gene expression profiles of 173 AML patients from The Cancer Genome Atlas (TCGA) database and calculated their immune and stromal scores by applying the ESTIMATE algorithm. Immune scores were significantly associated with OS and cytogenetic risk. Next, we categorized the intermediate and poor cytogenetic risk patients into individual-mutation and wild-type groups according to RUNX1, ASXL1, TP53, FLT3-ITD, NPM1 and biallelic CEBPA mutation status. The relationships between the immune microenvironment and each genetic mutation were investigated by identifying differentially expressed genes (DEGs) and conducting functional enrichment analyses of them. Significant immune- and stromal-relevant DEGs associated with each mutation were identified, and most of the DEGs (from the FLT3-ITD, NPM1 and biallelic CEBPA mutation groups) were validated in the GSE14468 cohort downloaded from the Gene Expression Omnibus (GEO) database. In summary, we identified key immune- and stromal-relevant gene signatures associated with genetic mutations in AML, which may provide new biomarkers for risk stratification and personalized immunotherapy.
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10
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SanMiguel JM, Young K, Trowbridge JJ. Hand in hand: intrinsic and extrinsic drivers of aging and clonal hematopoiesis. Exp Hematol 2020; 91:1-9. [PMID: 32991978 DOI: 10.1016/j.exphem.2020.09.197] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 12/17/2022]
Abstract
Over the past 25 years, the importance of hematopoietic stem cell (HSC) aging in overall hematopoietic and immune system health span has been appreciated. Much work has been done in model organisms to understand the intrinsic dysregulation that occurs in HSCs during aging, with the goal of identifying modifiable mechanisms that represent the proverbial "fountain of youth." Much more recently, the discovery of somatic mutations that are found to provide a selective advantage to HSCs and accumulate in the hematopoietic system during aging, termed clonal hematopoiesis (CH), inspires revisiting many of these previously defined drivers of HSC aging in the context of these somatic mutations. To truly understand these processes and develop a holistic picture of HSC aging, ongoing and future studies must include investigation of the critical changes that occur in the HSC niche or bone marrow microenvironment with aging, as increasing evidence supports that these HSC-extrinsic alterations provide necessary inflammation, signaling pathway activation or repression, and other selective pressures to favor HSC aging-associated phenotypes and CH. Here, we provide our perspectives based on the past 8 years of our own laboratory's investigations into these mechanisms and chart a path for integrative studies that, in our opinion, will provide an ideal opportunity to discover HSC and hematopoietic health span-extending interventions. This path includes examining when and how aging-associated HSC-intrinsic and HSC-extrinsic changes accumulate over time in different individuals and developing new models to track and test relevant HSC-extrinsic changes, complementary to innovative HSC lineage tracing systems that have recently been developed.
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