1
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Bhalgat AM, Taylor J. CHIPing Away at Proteomics to Find Correlations with Myeloid Neoplasms. Clin Cancer Res 2024; 30:3095-3097. [PMID: 38819216 DOI: 10.1158/1078-0432.ccr-24-0827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/18/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024]
Abstract
Plasma proteomic profiling to identify associations with myeloid neoplasm (MN) risk highlights the potential of integrating proteins and genetic biomarkers for the detection of individuals at high risk of developing MN. These proteins also offer valuable insights into biological pathways and inflammatory mechanisms involved in the progression of clonal hematopoiesis to MN. See related article by Tran et al., p. 3220.
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Affiliation(s)
- Avni M Bhalgat
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Justin Taylor
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
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2
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Coetzee SG, Hazelett DJ. MotifbreakR v2: extended capability and database integration. ARXIV 2024:arXiv:2407.03441v1. [PMID: 39010878 PMCID: PMC11247919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
MotifbreakR is a software tool that scans genetic variants against position weight matrices of transcription factors (TF) to determine the potential for the disruption of TF binding at the site of the variant. It leverages the Bioconductor suite of software packages and annotations to operate across a diverse array of genomes and motif databases. Initially developed to interrogate the effect of single nucleotide variants (common and rare SNVs) on potential TF binding sites, in motifbreakR v2, we have updated the functionality. New features include the ability to query other types of more complex genetic variants, such as short insertions and deletions (indels). This function allows modeling a more extensive array of variants that may have more significant effects on TF binding. Additionally, while TF binding is based partly on sequence preference, predictions of TF binding based on sequence preference alone can indicate many more potential binding events than observed. Adding information from DNA-binding sequencing datasets lends confidence to motif disruption prediction by demonstrating TF binding in cell lines and tissue types. Therefore, motifbreakR implements querying the ReMap2022 database for evidence that a TF matching the disrupted motif binds over the disrupting variant. Finally, in motifbreakR, in addition to the existing interface, we have implemented an R/Shiny graphical user interface to simplify and enhance access to researchers with different skill sets.
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Affiliation(s)
- Simon G Coetzee
- Department of Computational Biomedicine at Cedars-Sinai Medical Center
| | - Dennis J Hazelett
- Department of Computational Biomedicine at Cedars-Sinai Medical Center
- Cancer Prevention and Control - Samuel Oschin Cancer Center, Cedars-Sinai
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3
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Liu A, Genovese G, Zhao Y, Pirinen M, Zekavat SM, Kentistou KA, Yang Z, Yu K, Vlasschaert C, Liu X, Brown DW, Hudjashov G, Gorman BR, Dennis J, Zhou W, Momozawa Y, Pyarajan S, Tuzov V, Pajuste FD, Aavikko M, Sipilä TP, Ghazal A, Huang WY, Freedman ND, Song L, Gardner EJ, Sankaran VG, Palotie A, Ollila HM, Tukiainen T, Chanock SJ, Mägi R, Natarajan P, Daly MJ, Bick A, McCarroll SA, Terao C, Loh PR, Ganna A, Perry JRB, Machiela MJ. Genetic drivers and cellular selection of female mosaic X chromosome loss. Nature 2024; 631:134-141. [PMID: 38867047 DOI: 10.1038/s41586-024-07533-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Mosaic loss of the X chromosome (mLOX) is the most common clonal somatic alteration in leukocytes of female individuals1,2, but little is known about its genetic determinants or phenotypic consequences. Here, to address this, we used data from 883,574 female participants across 8 biobanks; 12% of participants exhibited detectable mLOX in approximately 2% of leukocytes. Female participants with mLOX had an increased risk of myeloid and lymphoid leukaemias. Genetic analyses identified 56 common variants associated with mLOX, implicating genes with roles in chromosomal missegregation, cancer predisposition and autoimmune diseases. Exome-sequence analyses identified rare missense variants in FBXO10 that confer a twofold increased risk of mLOX. Only a small fraction of associations was shared with mosaic Y chromosome loss, suggesting that distinct biological processes drive formation and clonal expansion of sex chromosome missegregation. Allelic shift analyses identified X chromosome alleles that are preferentially retained in mLOX, demonstrating variation at many loci under cellular selection. A polygenic score including 44 allelic shift loci correctly inferred the retained X chromosomes in 80.7% of mLOX cases in the top decile. Our results support a model in which germline variants predispose female individuals to acquiring mLOX, with the allelic content of the X chromosome possibly shaping the magnitude of clonal expansion.
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Affiliation(s)
- Aoxing Liu
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Yajie Zhao
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Seyedeh M Zekavat
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Katherine A Kentistou
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Zhiyu Yang
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Derek W Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Prevention Fellowship Program, Division of Cancer Prevention, National Cancer Institute, Rockville, MD, USA
| | - Georgi Hudjashov
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Bryan R Gorman
- Center for Data and Computational Sciences (C-DACS), VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
- Booz Allen Hamilton, McLean, VA, USA
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Saiju Pyarajan
- Center for Data and Computational Sciences (C-DACS), VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Valdislav Tuzov
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Fanny-Dhelia Pajuste
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Mervi Aavikko
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Timo P Sipilä
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Awaisa Ghazal
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Eugene J Gardner
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Vijay G Sankaran
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hanna M Ollila
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Taru Tukiainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Pradeep Natarajan
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Mark J Daly
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexander Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Po-Ru Loh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Andrea Ganna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - John R B Perry
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK.
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
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4
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Waterbury AL, Kwok HS, Lee C, Narducci DN, Freedy AM, Su C, Raval S, Reiter AH, Hawkins W, Lee K, Li J, Hoenig SM, Vinyard ME, Cole PA, Hansen AS, Carr SA, Papanastasiou M, Liau BB. An autoinhibitory switch of the LSD1 disordered region controls enhancer silencing. Mol Cell 2024; 84:2238-2254.e11. [PMID: 38870936 PMCID: PMC11193646 DOI: 10.1016/j.molcel.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 03/21/2024] [Accepted: 05/16/2024] [Indexed: 06/15/2024]
Abstract
Transcriptional coregulators and transcription factors (TFs) contain intrinsically disordered regions (IDRs) that are critical for their association and function in gene regulation. More recently, IDRs have been shown to promote multivalent protein-protein interactions between coregulators and TFs to drive their association into condensates. By contrast, here we demonstrate how the IDR of the corepressor LSD1 excludes TF association, acting as a dynamic conformational switch that tunes repression of active cis-regulatory elements. Hydrogen-deuterium exchange shows that the LSD1 IDR interconverts between transient open and closed conformational states, the latter of which inhibits partitioning of the protein's structured domains with TF condensates. This autoinhibitory switch controls leukemic differentiation by modulating repression of active cis-regulatory elements bound by LSD1 and master hematopoietic TFs. Together, these studies unveil alternative mechanisms by which disordered regions and their dynamic crosstalk with structured regions can shape coregulator-TF interactions to control cis-regulatory landscapes and cell fate.
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Affiliation(s)
- Amanda L Waterbury
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Hui Si Kwok
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ceejay Lee
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Domenic N Narducci
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Allyson M Freedy
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Cindy Su
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Shaunak Raval
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Andrew H Reiter
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - William Hawkins
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jiaming Li
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Samuel M Hoenig
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Anders S Hansen
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Steven A Carr
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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5
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Schiroli G, Kartha V, Duarte FM, Kristiansen TA, Mayerhofer C, Shrestha R, Earl A, Hu Y, Tay T, Rhee C, Buenrostro JD, Scadden DT. Cell of origin epigenetic priming determines susceptibility to Tet2 mutation. Nat Commun 2024; 15:4325. [PMID: 38773071 PMCID: PMC11109152 DOI: 10.1038/s41467-024-48508-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 04/30/2024] [Indexed: 05/23/2024] Open
Abstract
Hematopoietic stem cell (HSC) mutations can result in clonal hematopoiesis (CH) with heterogeneous clinical outcomes. Here, we investigate how the cell state preceding Tet2 mutation impacts the pre-malignant phenotype. Using an inducible system for clonal analysis of myeloid progenitors, we find that the epigenetic features of clones at similar differentiation status are highly heterogeneous and functionally respond differently to Tet2 mutation. Cell differentiation stage also influences Tet2 mutation response indicating that the cell of origin's epigenome modulates clone-specific behaviors in CH. Molecular features associated with higher risk outcomes include Sox4 that sensitizes cells to Tet2 inactivation, inducing dedifferentiation, altered metabolism and increasing the in vivo clonal output of mutant cells, as confirmed in primary GMP and HSC models. Our findings validate the hypothesis that epigenetic features can predispose specific clones for dominance, explaining why identical genetic mutations can result in different phenotypes.
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Affiliation(s)
- Giulia Schiroli
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Vinay Kartha
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Fabiana M Duarte
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Trine A Kristiansen
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Christina Mayerhofer
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Rojesh Shrestha
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Andrew Earl
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Yan Hu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Tristan Tay
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Catherine Rhee
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Jason D Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - David T Scadden
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
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6
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Mosley JD, Shelley JP, Dickson AL, Zanussi J, Daniel LL, Zheng NS, Bastarache L, Wei WQ, Shi M, Jarvik GP, Rosenthal EA, Khan A, Sherafati A, Kullo IJ, Walunas TL, Glessner J, Hakonarson H, Cox NJ, Roden DM, Frangakis SG, Vanderwerff B, Stein CM, Van Driest SL, Borinstein SC, Shu XO, Zawistowski M, Chung CP, Kawai VK. Clinical associations with a polygenic predisposition to benign lower white blood cell counts. Nat Commun 2024; 15:3384. [PMID: 38649760 PMCID: PMC11035609 DOI: 10.1038/s41467-024-47804-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
Polygenic variation unrelated to disease contributes to interindividual variation in baseline white blood cell (WBC) counts, but its clinical significance is uncharacterized. We investigated the clinical consequences of a genetic predisposition toward lower WBC counts among 89,559 biobank participants from tertiary care centers using a polygenic score for WBC count (PGSWBC) comprising single nucleotide polymorphisms not associated with disease. A predisposition to lower WBC counts was associated with a decreased risk of identifying pathology on a bone marrow biopsy performed for a low WBC count (odds-ratio = 0.55 per standard deviation increase in PGSWBC [95%CI, 0.30-0.94], p = 0.04), an increased risk of leukopenia (a low WBC count) when treated with a chemotherapeutic (n = 1724, hazard ratio [HR] = 0.78 [0.69-0.88], p = 4.0 × 10-5) or immunosuppressant (n = 354, HR = 0.61 [0.38-0.99], p = 0.04). A predisposition to benign lower WBC counts was associated with an increased risk of discontinuing azathioprine treatment (n = 1,466, HR = 0.62 [0.44-0.87], p = 0.006). Collectively, these findings suggest that there are genetically predisposed individuals who are susceptible to escalations or alterations in clinical care that may be harmful or of little benefit.
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Affiliation(s)
- Jonathan D Mosley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - John P Shelley
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alyson L Dickson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jacy Zanussi
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Laura L Daniel
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Neil S Zheng
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Yale School of Medicine, New Haven, CT, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mingjian Shi
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gail P Jarvik
- Department of Genome Sciences, University of Washington Medical Center, Seattle, WA, USA
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA, USA
| | - Elisabeth A Rosenthal
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA, USA
| | - Atlas Khan
- Division of Nephrology, Dept of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Alborz Sherafati
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Theresa L Walunas
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Joseph Glessner
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nancy J Cox
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Stephan G Frangakis
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Brett Vanderwerff
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - C Michael Stein
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sara L Van Driest
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Scott C Borinstein
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiao-Ou Shu
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Matthew Zawistowski
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | | | - Vivian K Kawai
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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7
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de Smith AJ, Wahlster L, Jeon S, Kachuri L, Black S, Langie J, Cato LD, Nakatsuka N, Chan TF, Xia G, Mazumder S, Yang W, Gazal S, Eng C, Hu D, Burchard EG, Ziv E, Metayer C, Mancuso N, Yang JJ, Ma X, Wiemels JL, Yu F, Chiang CWK, Sankaran VG. A noncoding regulatory variant in IKZF1 increases acute lymphoblastic leukemia risk in Hispanic/Latino children. CELL GENOMICS 2024; 4:100526. [PMID: 38537633 PMCID: PMC11019360 DOI: 10.1016/j.xgen.2024.100526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/11/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
Hispanic/Latino children have the highest risk of acute lymphoblastic leukemia (ALL) in the US compared to other racial/ethnic groups, yet the basis of this remains incompletely understood. Through genetic fine-mapping analyses, we identified a new independent childhood ALL risk signal near IKZF1 in self-reported Hispanic/Latino individuals, but not in non-Hispanic White individuals, with an effect size of ∼1.44 (95% confidence interval = 1.33-1.55) and a risk allele frequency of ∼18% in Hispanic/Latino populations and <0.5% in European populations. This risk allele was positively associated with Indigenous American ancestry, showed evidence of selection in human history, and was associated with reduced IKZF1 expression. We identified a putative causal variant in a downstream enhancer that is most active in pro-B cells and interacts with the IKZF1 promoter. This variant disrupts IKZF1 autoregulation at this enhancer and results in reduced enhancer activity in B cell progenitors. Our study reveals a genetic basis for the increased ALL risk in Hispanic/Latino children.
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Affiliation(s)
- Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA.
| | - Lara Wahlster
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Soyoung Jeon
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Susan Black
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jalen Langie
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Liam D Cato
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Tsz-Fung Chan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Guangze Xia
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Soumyaa Mazumder
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wenjian Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Steven Gazal
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Celeste Eng
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Biotherapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Donglei Hu
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Esteban González Burchard
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Biotherapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Elad Ziv
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Catherine Metayer
- School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Jun J Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiaomei Ma
- Yale School of Public Health, New Haven, CT 06520, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Fulong Yu
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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8
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Fang T, Zhang Z, Ren K, Zou L. Genetically determined telomere length as a risk factor for hematological malignancies: evidence from Mendelian randomization analysis. Aging (Albany NY) 2024; 16:4684-4698. [PMID: 38451181 PMCID: PMC10968690 DOI: 10.18632/aging.205625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/29/2024] [Indexed: 03/08/2024]
Abstract
BACKGROUND Over the past years, the exact correlation between telomere length and hematological malignancies was still not fully understood. METHODS We performed a two-sample Mendelian randomization study to investigate the causal relationship between telomere length and hematological malignancies. We selected genetic instruments associated with telomere length. The genetic associations for lymphoid and hematopoietic malignant neoplasms were obtained from the most recent publicly accessible FinnGen study R9 data. Inverse variant weighted (IVW) analysis was adopted as the primary method, and we also performed the weighted-median method and the MR-Egger, and MRPRESSO methods as sensitive analysis. RESULTS Significant associations have been observed between telomere length and primary lymphoid (IVW: OR = 1.52, P = 2.11 × 10-6), Hodgkin lymphoma (IVW: OR = 1.64, P = 0.014), non-Hodgkin lymphoma (IVW: OR = 1.70, P = 0.002), B-cell lymphoma (IVW: OR = 1.57, P = 0.015), non-follicular lymphoma (IVW: OR = 1.58, P = 1.7 × 10-3), mantle cell lymphoma (IVW: OR = 3.13, P = 0.003), lymphoid leukemia (IVW: OR = 2.56, P = 5.92E-09), acute lymphocytic leukemia (IVW: OR = 2.65, P = 0.021) and chronic lymphocytic leukemia (IVW: OR = 2.80, P = 8.21 × 10-6), along with multiple myeloma (IVW: OR = 1.85, P = 0.016). CONCLUSION This MR study found a significant association between telomere length and a wide range of hematopoietic malignancies. But no substantial impact of lymphoma and hematopoietic malignancies on telomere length has been detected.
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Affiliation(s)
- Tian Fang
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Zhihao Zhang
- Department of Breast Center, West China Hospital, Sichuan University, Chengdu, China
| | - Kexing Ren
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Liqun Zou
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
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9
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Jerez J, Santiago M. Unraveling germline predisposition in hematological neoplasms: Navigating complexity in the genomic era. Blood Rev 2024; 64:101143. [PMID: 37989620 DOI: 10.1016/j.blre.2023.101143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/14/2023] [Accepted: 11/14/2023] [Indexed: 11/23/2023]
Abstract
Genomic advancements have yielded pivotal insights into hematological neoplasms, particularly concerning germline predisposition mutations. Following the WHO 2016 revisions, dedicated segments were proposed to address these aspects. Current WHO 2022, ICC 2022, and ELN 2022 classifications recognize their significance, introducing more mutations and prompting integration into clinical practice. Approximately 5-10% of hematological neoplasm patients show germline predisposition gene mutations, rising with risk factors such as personal cancer history and familial antecedents, even in older adults. Nevertheless, technical challenges persist. Optimal DNA samples are skin fibroblast-extracted, although not universally applicable. Alternatives such as hair follicle use are explored. Moreover, the scrutiny of germline genomics mandates judicious test selection to ensure precise and accurate interpretation. Given the significant influence of genetic counseling on patient care and post-assessment procedures, there arises a demand for dedicated centers offering specialized services.
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Affiliation(s)
- Joaquín Jerez
- Hematology Department, Fundación Arturo López Pérez, Chile; Resident of Hematology, Universidad de los Andes, Chile.
| | - Marta Santiago
- Hematology Department, Hospital La Fe, 46026, Valencia, Spain; Hematology Research Group, Instituto de Investigación Sanitaria La Fe, 46026, Valencia, Spain.
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10
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Weng C, Yu F, Yang D, Poeschla M, Liggett LA, Jones MG, Qiu X, Wahlster L, Caulier A, Hussmann JA, Schnell A, Yost KE, Koblan LW, Martin-Rufino JD, Min J, Hammond A, Ssozi D, Bueno R, Mallidi H, Kreso A, Escabi J, Rideout WM, Jacks T, Hormoz S, van Galen P, Weissman JS, Sankaran VG. Deciphering cell states and genealogies of human haematopoiesis. Nature 2024; 627:389-398. [PMID: 38253266 PMCID: PMC10937407 DOI: 10.1038/s41586-024-07066-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/12/2024] [Indexed: 01/24/2024]
Abstract
The human blood system is maintained through the differentiation and massive amplification of a limited number of long-lived haematopoietic stem cells (HSCs)1. Perturbations to this process underlie diverse diseases, but the clonal contributions to human haematopoiesis and how this changes with age remain incompletely understood. Although recent insights have emerged from barcoding studies in model systems2-5, simultaneous detection of cell states and phylogenies from natural barcodes in humans remains challenging. Here we introduce an improved, single-cell lineage-tracing system based on deep detection of naturally occurring mitochondrial DNA mutations with simultaneous readout of transcriptional states and chromatin accessibility. We use this system to define the clonal architecture of HSCs and map the physiological state and output of clones. We uncover functional heterogeneity in HSC clones, which is stable over months and manifests as both differences in total HSC output and biases towards the production of different mature cell types. We also find that the diversity of HSC clones decreases markedly with age, leading to an oligoclonal structure with multiple distinct clonal expansions. Our study thus provides a clonally resolved and cell-state-aware atlas of human haematopoiesis at single-cell resolution, showing an unappreciated functional diversity of human HSC clones and, more broadly, paving the way for refined studies of clonal dynamics across a range of tissues in human health and disease.
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Affiliation(s)
- Chen Weng
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Fulong Yu
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, P.R. China
| | - Dian Yang
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Molecular Pharmacology and Therapeutics, Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Michael Poeschla
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - L Alexander Liggett
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew G Jones
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Xiaojie Qiu
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Genetics and Computer Science, BASE Research Initiative, Betty Irene Moore Children's Heart Center, Stanford University, Stanford, CA, USA
| | - Lara Wahlster
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexis Caulier
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeffrey A Hussmann
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexandra Schnell
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kathryn E Yost
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luke W Koblan
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jorge D Martin-Rufino
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joseph Min
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alessandro Hammond
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel Ssozi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Raphael Bueno
- Division of Thoracic and Cardiac Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Hari Mallidi
- Division of Thoracic and Cardiac Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Antonia Kreso
- Division of Cardiac Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Javier Escabi
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - William M Rideout
- Koch Institute For Integrative Cancer Research at MIT, MIT, Cambridge, MA, USA
| | - Tyler Jacks
- Koch Institute For Integrative Cancer Research at MIT, MIT, Cambridge, MA, USA
| | - Sahand Hormoz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Peter van Galen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute For Integrative Cancer Research at MIT, MIT, Cambridge, MA, USA.
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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11
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Guo J, Walter K, Quiros PM, Gu M, Baxter EJ, Danesh J, Di Angelantonio E, Roberts D, Guglielmelli P, Harrison CN, Godfrey AL, Green AR, Vassiliou GS, Vuckovic D, Nangalia J, Soranzo N. Inherited polygenic effects on common hematological traits influence clonal selection on JAK2 V617F and the development of myeloproliferative neoplasms. Nat Genet 2024; 56:273-280. [PMID: 38233595 PMCID: PMC10864174 DOI: 10.1038/s41588-023-01638-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 12/01/2023] [Indexed: 01/19/2024]
Abstract
Myeloproliferative neoplasms (MPNs) are chronic cancers characterized by overproduction of mature blood cells. Their causative somatic mutations, for example, JAK2V617F, are common in the population, yet only a minority of carriers develop MPN. Here we show that the inherited polygenic loci that underlie common hematological traits influence JAK2V617F clonal expansion. We identify polygenic risk scores (PGSs) for monocyte count and plateletcrit as new risk factors for JAK2V617F positivity. PGSs for several hematological traits influenced the risk of different MPN subtypes, with low PGSs for two platelet traits also showing protective effects in JAK2V617F carriers, making them two to three times less likely to have essential thrombocythemia than carriers with high PGSs. We observed that extreme hematological PGSs may contribute to an MPN diagnosis in the absence of somatic driver mutations. Our study showcases how polygenic backgrounds underlying common hematological traits influence both clonal selection on somatic mutations and the subsequent phenotype of cancer.
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Affiliation(s)
- Jing Guo
- Wellcome Sanger Institute, Hinxton, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
| | | | - Pedro M Quiros
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Muxin Gu
- Wellcome Sanger Institute, Hinxton, UK
| | - E Joanna Baxter
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - John Danesh
- Wellcome Sanger Institute, Hinxton, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Emanuele Di Angelantonio
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Fondazione Human Technopole, Milan, Italy
| | - David Roberts
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- NHS Blood and Transplant-Oxford Centre, John Radcliffe Hospital and Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Paola Guglielmelli
- Department of Experimental and Clinical Medicine, Center for Research and Innovation of Myeloproliferative Neoplasms (CRIMM), AOU Careggi, University of Florence, Florence, Italy
| | - Claire N Harrison
- Department of Haematology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | | | - Anthony R Green
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Dragana Vuckovic
- Wellcome Sanger Institute, Hinxton, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- Department of Epidemiology and Biostatistics, School of Public Health, Faculty of Medicine, Imperial College London, London, UK
| | - Jyoti Nangalia
- Wellcome Sanger Institute, Hinxton, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
- Cambridge University Hospitals NHS Trust, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
| | - Nicole Soranzo
- Wellcome Sanger Institute, Hinxton, UK.
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK.
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK.
- Fondazione Human Technopole, Milan, Italy.
- Department of Haematology, University of Cambridge, Cambridge, UK.
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12
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Zhao J, Cato LD, Arora UP, Bao EL, Bryant SC, Williams N, Jia Y, Goldman SR, Nangalia J, Erb MA, Vos SM, Armstrong SA, Sankaran VG. Inherited blood cancer predisposition through altered transcription elongation. Cell 2024; 187:642-658.e19. [PMID: 38218188 PMCID: PMC10872907 DOI: 10.1016/j.cell.2023.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 11/26/2023] [Accepted: 12/08/2023] [Indexed: 01/15/2024]
Abstract
Despite advances in defining diverse somatic mutations that cause myeloid malignancies, a significant heritable component for these cancers remains largely unexplained. Here, we perform rare variant association studies in a large population cohort to identify inherited predisposition genes for these blood cancers. CTR9, which encodes a key component of the PAF1 transcription elongation complex, is among the significant genes identified. The risk variants found in the cases cause loss of function and result in a ∼10-fold increased odds of acquiring a myeloid malignancy. Partial CTR9 loss of function expands human hematopoietic stem cells (HSCs) by increased super elongation complex-mediated transcriptional activity, which thereby increases the expression of key regulators of HSC self-renewal. By following up on insights from a human genetic study examining inherited predisposition to the myeloid malignancies, we define a previously unknown antagonistic interaction between the PAF1 and super elongation complexes. These insights could enable targeted approaches for blood cancer prevention.
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Affiliation(s)
- Jiawei Zhao
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Cancer Immunology, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, China.
| | - Liam D Cato
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Uma P Arora
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Erik L Bao
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Nicholas Williams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; UK and MRC-Wellcome Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Yuemeng Jia
- Harvard Stem Cell Institute, Cambridge, MA, USA; Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Seth R Goldman
- Nascent Transcriptomics Core, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Jyoti Nangalia
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; UK and MRC-Wellcome Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Michael A Erb
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Seychelle M Vos
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Scott A Armstrong
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA.
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13
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Xu M, Chen H, Tan T, Xie K, Xie H, Li Q. Exploring the causal association between rheumatoid arthritis and the risk of cervical cancer: a two-sample Mendelian randomization study. Arthritis Res Ther 2024; 26:35. [PMID: 38263277 PMCID: PMC10804645 DOI: 10.1186/s13075-023-03240-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024] Open
Abstract
OBJECTIVE Whether rheumatoid arthritis patients have an increased risk of cervical cancer remains controversial, and further research is needed on this clinical question. This study aims to investigate the association between rheumatoid arthritis and the susceptibility to cervical cancer by employing Mendelian randomization methodology, utilizing the extensive dataset from human genome-wide association data analysis. METHODS The publicly accessible MR base database was utilized to obtain the complete genome, relevant research findings, and summarized data pertaining to rheumatoid arthritis and cervical cancer. Genetic tool variables, specifically single-nucleotide polymorphisms closely linked to rheumatoid arthritis, were chosen for analysis. Four methods, namely inverse variance weighted analysis, weighted median analysis, weighted mode, and MR-Egger regression, were employed. Statistical analysis was conducted to explore the potential association between rheumatoid arthritis and susceptibility to cervical cancer. RESULTS The results of the inverse variance weighted analysis (OR = 1.096, 95% CI: 1.018-1.180, P = 0.015) indicate a significant causal relationship between rheumatoid arthritis and an increased risk of cervical cancer. Furthermore, the absence of horizontal pleiotropic effects (MR-Egger intercept = 0.00025, P = 0.574) and heterogeneity (QEgger = 2.239, I2Egger = 0.225, PEgger = 0.268, QIVW = 2.734, I2IVW = 0.220, PIVW = 0.999) suggests that the observed association is not influenced by confounding factors. Sensitivity analysis and other statistical methods also support the conclusion that genetic pleiotropy does not introduce bias to the findings. CONCLUSION There is a causal relationship between rheumatoid arthritis and the occurrence of cervical cancer. People with rheumatoid arthritis is one of the high-risk groups for early screening of cervical cancer. The IL-18 may play a significant role in elevating the risk of cervical cancer among rheumatoid arthritis patients.
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Affiliation(s)
- Minxian Xu
- Department of Oncology, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, 423000, People's Republic of China
- Department of Radiation Oncology, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, 423000, Hunan Province, People's Republic of China
| | - Huan Chen
- Department of Gynecology, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, 423000, People's Republic of China
| | - Tao Tan
- Faulty of Applied Sciences, Macao Polytechnic University, Macao, 999078, People's Republic of China
| | - Kaihong Xie
- Department of Oncology, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, 423000, People's Republic of China
| | - Hui Xie
- Department of Oncology, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, 423000, People's Republic of China.
- Department of Radiation Oncology, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, 423000, Hunan Province, People's Republic of China.
| | - Qing Li
- Department of Oncology, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, 423000, People's Republic of China.
- Department of Radiation Oncology, Affiliated Hospital (Clinical College) of Xiangnan University, Chenzhou, 423000, Hunan Province, People's Republic of China.
- School of Medical Imaging, Laboratory Science and Rehabilitation, Xiangnan University, 423000, Chenzhou, Hunan Province, People's Republic of China.
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14
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Arai H, Matsui H, Chi S, Utsu Y, Masuda S, Aotsuka N, Minami Y. Germline Variants and Characteristic Features of Hereditary Hematological Malignancy Syndrome. Int J Mol Sci 2024; 25:652. [PMID: 38203823 PMCID: PMC10779750 DOI: 10.3390/ijms25010652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Due to the proliferation of genetic testing, pathogenic germline variants predisposing to hereditary hematological malignancy syndrome (HHMS) have been identified in an increasing number of genes. Consequently, the field of HHMS is gaining recognition among clinicians and scientists worldwide. Patients with germline genetic abnormalities often have poor outcomes and are candidates for allogeneic hematopoietic stem cell transplantation (HSCT). However, HSCT using blood from a related donor should be carefully considered because of the risk that the patient may inherit a pathogenic variant. At present, we now face the challenge of incorporating these advances into clinical practice for patients with myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML) and optimizing the management and surveillance of patients and asymptomatic carriers, with the limitation that evidence-based guidelines are often inadequate. The 2016 revision of the WHO classification added a new section on myeloid malignant neoplasms, including MDS and AML with germline predisposition. The main syndromes can be classified into three groups. Those without pre-existing disease or organ dysfunction; DDX41, TP53, CEBPA, those with pre-existing platelet disorders; ANKRD26, ETV6, RUNX1, and those with other organ dysfunctions; SAMD9/SAMD9L, GATA2, and inherited bone marrow failure syndromes. In this review, we will outline the role of the genes involved in HHMS in order to clarify our understanding of HHMS.
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Affiliation(s)
- Hironori Arai
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (H.A.); (S.C.)
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho, Narita 286-0041, Japan; (Y.U.); (S.M.); (N.A.)
| | - Hirotaka Matsui
- Department of Laboratory Medicine, National Cancer Center Hospital, Tsukiji, Chuoku 104-0045, Japan;
- Department of Medical Oncology and Translational Research, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8665, Japan
| | - SungGi Chi
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (H.A.); (S.C.)
| | - Yoshikazu Utsu
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho, Narita 286-0041, Japan; (Y.U.); (S.M.); (N.A.)
| | - Shinichi Masuda
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho, Narita 286-0041, Japan; (Y.U.); (S.M.); (N.A.)
| | - Nobuyuki Aotsuka
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho, Narita 286-0041, Japan; (Y.U.); (S.M.); (N.A.)
| | - Yosuke Minami
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (H.A.); (S.C.)
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15
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Li Y, Sun T, Chen J, Zhang L. Identification of Novel Risk Variants of Inflammatory Factors Related to Myeloproliferative Neoplasm: A Bidirectional Mendelian Randomization Study. Glob Med Genet 2024; 11:48-58. [PMID: 38348158 PMCID: PMC10861317 DOI: 10.1055/s-0044-1779665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024] Open
Abstract
Epidemiological and experimental evidence has linked chronic inflammation to the etiology of myeloproliferative neoplasm (MPN). However, it remains unclear whether genetic associations with specific inflammatory biomarkers are causal or due to bias. This study aimed to assess the effect of C-reactive protein (CRP) and systemic inflammatory regulators on MPN within a bidirectional Mendelian randomization design. Genetic associations with MPN were derived from a publicly available genome-wide association study (GWAS) comprising 1,086 cases and 407,155 controls of European ancestry. Additionally, data on inflammation were extracted from two GWASs focusing on CRP and cytokines. The causal relationships between exposure and outcome were explored using the inverse variance weighted (IVW) method. To confirm the final results, multiple sensitivity analyses, including MR-Egger, weighted median, and MR-pleiotropy residual sum and outlier (MR-PRESSO), were simultaneously employed. Our results suggest that lower levels of macrophage-migration inhibitory factor (IVW estimate odds ratio [OR IVW] per SD genetic cytokines change: 0.641; 95% confidence interval [CI]: 0.427-0.964; p = 0.032) and higher levels of interleukin-2 receptor α (lL2Rα, 1.377, 95% CI: 1.006-1.883; p = 0.046) are associated with an increased risk of MPN. Genetically predicted MPN is related to increased levels of RANTES (IVW estimate β: 0.043, 95% CI: 0.002-0.084; p = 0.039) and interleukin-10 (IVW estimate β: 0.030, 95% CI: 0.001-0.060; p = 0.041). This study provides evidence for a causal relationship between CRP, systemic inflammatory regulators, and MPN, and new insights into the etiology, prevention, and prognosis of MPN.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin Key Laboratory of Gene Therapy for Blood Diseases, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Tianjin, People's Republic of China
- Tianjin Institutes of Health Science, Tianjin, People's Republic of China
| | - Ting Sun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin Key Laboratory of Gene Therapy for Blood Diseases, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Tianjin, People's Republic of China
- Tianjin Institutes of Health Science, Tianjin, People's Republic of China
| | - Jia Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin Key Laboratory of Gene Therapy for Blood Diseases, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Tianjin, People's Republic of China
- Tianjin Institutes of Health Science, Tianjin, People's Republic of China
| | - Lei Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin Key Laboratory of Gene Therapy for Blood Diseases, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Tianjin, People's Republic of China
- Tianjin Institutes of Health Science, Tianjin, People's Republic of China
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
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16
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Shirbhate E, Singh V, Mishra A, Jahoriya V, Veerasamy R, Tiwari AK, Rajak H. Targeting Lysosomes: A Strategy Against Chemoresistance in Cancer. Mini Rev Med Chem 2024; 24:1449-1468. [PMID: 38343053 DOI: 10.2174/0113895575287242240129120002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/11/2024] [Accepted: 01/19/2024] [Indexed: 07/23/2024]
Abstract
Chemotherapy is still the major method of treatment for many types of cancer. Curative cancer therapy is hampered significantly by medication resistance. Acidic organelles like lysosomes serve as protagonists in cellular digestion. Lysosomes, however, are gaining popularity due to their speeding involvement in cancer progression and resistance. For instance, weak chemotherapeutic drugs of basic nature permeate through the lysosomal membrane and are retained in lysosomes in their cationic state, while extracellular release of lysosomal enzymes induces cancer, cytosolic escape of lysosomal hydrolases causes apoptosis, and so on. Drug availability at the sites of action is decreased due to lysosomal drug sequestration, which also enhances cancer resistance. This review looks at lysosomal drug sequestration mechanisms and how they affect cancer treatment resistance. Using lysosomes as subcellular targets to combat drug resistance and reverse drug sequestration is another method for overcoming drug resistance that is covered in this article. The present review has identified lysosomal drug sequestration as one of the reasons behind chemoresistance. The article delves deeper into specific aspects of lysosomal sequestration, providing nuanced insights, critical evaluations, or novel interpretations of different approaches that target lysosomes to defect cancer.
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Affiliation(s)
- Ekta Shirbhate
- Department of Pharmacy, Guru Ghasidas University, Bilaspur-495 009, (C.G.), India
| | - Vaibhav Singh
- Department of Pharmacy, Guru Ghasidas University, Bilaspur-495 009, (C.G.), India
| | - Aditya Mishra
- Department of Pharmacy, Guru Ghasidas University, Bilaspur-495 009, (C.G.), India
| | - Varsha Jahoriya
- Department of Pharmacy, Guru Ghasidas University, Bilaspur-495 009, (C.G.), India
| | - Ravichandran Veerasamy
- Faculty of Pharmacy, AIMST University, Semeling, 08100 Bedong, Kedah Darul Aman, Malaysia
| | - Amit K Tiwari
- UAMS College of Pharmacy; UAMS - University of Arkansas for Medical Sciences, (AR) USA
| | - Harish Rajak
- Department of Pharmacy, Guru Ghasidas University, Bilaspur-495 009, (C.G.), India
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17
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Cacic AM, Schulz FI, Germing U, Dietrich S, Gattermann N. Molecular and clinical aspects relevant for counseling individuals with clonal hematopoiesis of indeterminate potential. Front Oncol 2023; 13:1303785. [PMID: 38162500 PMCID: PMC10754976 DOI: 10.3389/fonc.2023.1303785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) has fascinated the medical community for some time. Discovered about a decade ago, this phenomenon links age-related alterations in hematopoiesis not only to the later development of hematological malignancies but also to an increased risk of early-onset cardiovascular disease and some other disorders. CHIP is detected in the blood and is characterized by clonally expanded somatic mutations in cancer-associated genes, predisposing to the development of hematologic neoplasms such as MDS and AML. CHIP-associated mutations often involve DNA damage repair genes and are frequently observed following prior cytotoxic cancer therapy. Genetic predisposition seems to be a contributing factor. It came as a surprise that CHIP significantly elevates the risk of myocardial infarction and stroke, and also contributes to heart failure and pulmonary hypertension. Meanwhile, evidence of mutant clonal macrophages in vessel walls and organ parenchyma helps to explain the pathophysiology. Besides aging, there are some risk factors promoting the appearance of CHIP, such as smoking, chronic inflammation, chronic sleep deprivation, and high birth weight. This article describes fundamental aspects of CHIP and explains its association with hematologic malignancies, cardiovascular disorders, and other medical conditions, while also exploring potential progress in the clinical management of affected individuals. While it is important to diagnose conditions that can lead to adverse, but potentially preventable, effects, it is equally important not to stress patients by confronting them with disconcerting findings that cannot be remedied. Individuals with diagnosed or suspected CHIP should receive counseling in a specialized outpatient clinic, where professionals from relevant medical specialties may help them to avoid the development of CHIP-related health problems. Unfortunately, useful treatments and clinical guidelines for managing CHIP are still largely lacking. However, there are some promising approaches regarding the management of cardiovascular disease risk. In the future, strategies aimed at restoration of gene function or inhibition of inflammatory mediators may become an option.
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Affiliation(s)
- Anna Maria Cacic
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
| | - Felicitas Isabel Schulz
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
| | - Ulrich Germing
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
| | - Sascha Dietrich
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
| | - Norbert Gattermann
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
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18
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Stacey SN, Zink F, Halldorsson GH, Stefansdottir L, Gudjonsson SA, Einarsson G, Hjörleifsson G, Eiriksdottir T, Helgadottir A, Björnsdottir G, Thorgeirsson TE, Olafsdottir TA, Jonsdottir I, Gretarsdottir S, Tragante V, Magnusson MK, Jonsson H, Gudmundsson J, Olafsson S, Holm H, Gudbjartsson DF, Sulem P, Helgason A, Thorsteinsdottir U, Tryggvadottir L, Rafnar T, Melsted P, Ulfarsson MÖ, Vidarsson B, Thorleifsson G, Stefansson K. Genetics and epidemiology of mutational barcode-defined clonal hematopoiesis. Nat Genet 2023; 55:2149-2159. [PMID: 37932435 PMCID: PMC10703693 DOI: 10.1038/s41588-023-01555-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/28/2023] [Indexed: 11/08/2023]
Abstract
Clonal hematopoiesis (CH) arises when a substantial proportion of mature blood cells is derived from a single hematopoietic stem cell lineage. Using whole-genome sequencing of 45,510 Icelandic and 130,709 UK Biobank participants combined with a mutational barcode method, we identified 16,306 people with CH. Prevalence approaches 50% in elderly participants. Smoking demonstrates a dosage-dependent impact on risk of CH. CH associates with several smoking-related diseases. Contrary to published claims, we find no evidence that CH is associated with cardiovascular disease. We provide evidence that CH is driven by genes that are commonly mutated in myeloid neoplasia and implicate several new driver genes. The presence and nature of a driver mutation alters the risk profile for hematological disorders. Nevertheless, most CH cases have no known driver mutations. A CH genome-wide association study identified 25 loci, including 19 not implicated previously in CH. Splicing, protein and expression quantitative trait loci were identified for CD164 and TCL1A.
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Affiliation(s)
| | | | - Gisli H Halldorsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | | | | | | | - Thorunn A Olafsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Department of Immunology, Landspitali University Hospital, Reykjavik, Iceland
| | | | | | - Magnus K Magnusson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Hilma Holm
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Agnar Helgason
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Pall Melsted
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Magnus Ö Ulfarsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Brynjar Vidarsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Department of Hematology, Landspitali University Hospital, Reykjavik, Iceland
| | | | - Kari Stefansson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
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19
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Arnold M, Stengel KR. Emerging insights into enhancer biology and function. Transcription 2023; 14:68-87. [PMID: 37312570 PMCID: PMC10353330 DOI: 10.1080/21541264.2023.2222032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/15/2023] Open
Abstract
Cell type-specific gene expression is coordinated by DNA-encoded enhancers and the transcription factors (TFs) that bind to them in a sequence-specific manner. As such, these enhancers and TFs are critical mediators of normal development and altered enhancer or TF function is associated with the development of diseases such as cancer. While initially defined by their ability to activate gene transcription in reporter assays, putative enhancer elements are now frequently defined by their unique chromatin features including DNase hypersensitivity and transposase accessibility, bidirectional enhancer RNA (eRNA) transcription, CpG hypomethylation, high H3K27ac and H3K4me1, sequence-specific transcription factor binding, and co-factor recruitment. Identification of these chromatin features through sequencing-based assays has revolutionized our ability to identify enhancer elements on a genome-wide scale, and genome-wide functional assays are now capitalizing on this information to greatly expand our understanding of how enhancers function to provide spatiotemporal coordination of gene expression programs. Here, we highlight recent technological advances that are providing new insights into the molecular mechanisms by which these critical cis-regulatory elements function in gene control. We pay particular attention to advances in our understanding of enhancer transcription, enhancer-promoter syntax, 3D organization and biomolecular condensates, transcription factor and co-factor dependencies, and the development of genome-wide functional enhancer screens.
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Affiliation(s)
- Mirjam Arnold
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kristy R. Stengel
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- Montefiore Einstein Cancer Center, Albert Einstein College of Medicine-Montefiore Health System, Bronx, NY, USA
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, USA
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20
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Seetharam SM, Liu Y, Wu J, Fechter L, Murugesan K, Maecker H, Gotlib J, Zehnder J, Paulmurugan R, Krishnan A. Enkurin: a novel marker for myeloproliferative neoplasms from platelet, megakaryocyte, and whole blood specimens. Blood Adv 2023; 7:5433-5445. [PMID: 37315179 PMCID: PMC10509670 DOI: 10.1182/bloodadvances.2022008939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/10/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023] Open
Abstract
Impaired protein homeostasis, though well established in age-related disorders, has been recently linked with the pathogenesis of myeloproliferative neoplasms (MPNs). However, little is known about MPN-specific modulators of proteostasis, thus impeding our ability for increased mechanistic understanding and discovery of additional therapeutic targets. Loss of proteostasis, in itself, is traced to dysregulated mechanisms in protein folding and intracellular calcium signaling at the endoplasmic reticulum (ER). Here, using ex vivo and in vitro systems (including CD34+ cultures from patient bone marrow and healthy cord/peripheral blood specimens), we extend our prior data from platelet RNA sequencing in patients with MPN and discover select proteostasis-associated markers at RNA and/or protein levels in each of platelet, parent megakaryocyte, and whole blood specimens. Importantly, we identify a novel role in MPNs for enkurin (ENKUR), a calcium mediator protein originally implicated only in spermatogenesis. Our data reveal consistent ENKUR downregulation at both RNA and protein levels across specimens from patients with MPN and experimental models (including upon treatment with thapsigargin, an agent that causes protein misfolding in the ER by selective loss of calcium), with a concomitant upregulation of a cell cycle marker, CDC20. Silencing of ENKUR using short hairpin RNA in CD34+-derived megakaryocytes further confirms this association with CDC20 at both RNA and protein levels and indicates a likely role for the PI3K/Akt pathway. Together, our work sheds light on enkurin as a novel marker of MPN pathogenesis and indicates further mechanistic investigation into a role for dysregulated calcium homeostasis and ER and protein folding stress in MPN transformation.
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Affiliation(s)
| | - Yi Liu
- Department of Radiology, Stanford University, Stanford, CA
| | - Jason Wu
- High-Throughput Bioscience Center and Stanford Genomics, Stanford University School of Medicine, Stanford, CA
| | - Lenn Fechter
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | | | - Holden Maecker
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA
| | - Jason Gotlib
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - James Zehnder
- Department of Pathology, Stanford University, Stanford, CA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | | | - Anandi Krishnan
- Department of Pathology, Stanford University, Stanford, CA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
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21
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Brown DW, Cato LD, Zhao Y, Nandakumar SK, Bao EL, Gardner EJ, Hubbard AK, DePaulis A, Rehling T, Song L, Yu K, Chanock SJ, Perry JRB, Sankaran VG, Machiela MJ. Shared and distinct genetic etiologies for different types of clonal hematopoiesis. Nat Commun 2023; 14:5536. [PMID: 37684235 PMCID: PMC10491829 DOI: 10.1038/s41467-023-41315-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
Clonal hematopoiesis (CH)-age-related expansion of mutated hematopoietic clones-can differ in frequency and cellular fitness by CH type (e.g., mutations in driver genes (CHIP), gains/losses and copy-neutral loss of chromosomal segments (mCAs), and loss of sex chromosomes). Co-occurring CH raises questions as to their origin, selection, and impact. We integrate sequence and genotype array data in up to 482,378 UK Biobank participants to demonstrate shared genetic architecture across CH types. Our analysis suggests a cellular evolutionary trade-off between different types of CH, with LOY occurring at lower rates in individuals carrying mutations in established CHIP genes. We observed co-occurrence of CHIP and mCAs with overlap at TET2, DNMT3A, and JAK2, in which CHIP precedes mCA acquisition. Furthermore, individuals carrying overlapping CH had high risk of future lymphoid and myeloid malignancies. Finally, we leverage shared genetic architecture of CH traits to identify 15 novel loci associated with leukemia risk.
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Affiliation(s)
- Derek W Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Prevention Fellowship Program, Division of Cancer Prevention, National Cancer Institute, Rockville, MD, USA
| | - Liam D Cato
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Yajie Zhao
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Satish K Nandakumar
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Albert Einstein Cancer Center, Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Bronx, NY, 10461, USA
| | - Erik L Bao
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Eugene J Gardner
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Aubrey K Hubbard
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Alexander DePaulis
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Thomas Rehling
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - John R B Perry
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK.
- Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK.
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
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22
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Liu J, Osman AEG, Bolton K, Godley LA. Germline predisposition to clonal hematopoiesis. Leuk Res 2023; 132:107344. [PMID: 37421681 DOI: 10.1016/j.leukres.2023.107344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/13/2023] [Accepted: 06/17/2023] [Indexed: 07/10/2023]
Abstract
We now recognize that with aging, hematopoietic stem and progenitor cells (HSPCs) acquire mutations that confer a fitness advantage and clonally expand in a process now termed clonal hematopoiesis (CH). Because CH predisposes to a variety of health problems, including cancers, cardiovascular diseases, and inflammatory conditions, there is intense interest in the inherited alleles associated with the development of CH. DNA variants near TERT, SMC4, KPNA4, IL12A, CD164, and ATM confer the strongest associations. In this review, we discuss our current state of knowledge regarding germline predisposition to CH.
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Affiliation(s)
- Jie Liu
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Afaf E G Osman
- Division of Hematology and Hematologic Malignancies, University of Utah, Salt Lake City, UT, USA
| | - Kelly Bolton
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Lucy A Godley
- Division of Hematology/Oncology, Department of Medicine, and the Robert H. Lurie Cancer Center, Northwestern University, Chicago, IL, USA.
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23
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Morishita S, Komatsu N. Diagnosis- and Prognosis-Related Gene Alterations in BCR::ABL1-Negative Myeloproliferative Neoplasms. Int J Mol Sci 2023; 24:13008. [PMID: 37629188 PMCID: PMC10455804 DOI: 10.3390/ijms241613008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
BCR::ABL1-negative myeloproliferative neoplasms (MPNs) are a group of hematopoietic malignancies in which somatic mutations are acquired in hematopoietic stem/progenitor cells, resulting in an abnormal increase in blood cells in peripheral blood and fibrosis in bone marrow. Mutations in JAK2, MPL, and CALR are frequently found in BCR::ABL1-negative MPNs, and detecting typical mutations in these three genes has become essential for the diagnosis of BCR::ABL1-negative MPNs. Furthermore, comprehensive gene mutation and expression analyses performed using massively parallel sequencing have identified gene mutations associated with the prognosis of BCR::ABL1-negative MPNs such as ASXL1, EZH2, IDH1/2, SRSF2, and U2AF1. Furthermore, single-cell analyses have partially elucidated the effect of the order of mutation acquisition on the phenotype of BCR::ABL1-negative MPNs and the mechanism of the pathogenesis of BCR::ABL1-negative MPNs. Recently, specific CREB3L1 overexpression has been identified in megakaryocytes and platelets in BCR::ABL1-negative MPNs, which may be promising for the development of diagnostic applications. In this review, we describe the genetic mutations found in BCR::ABL1-negative MPNs, including the results of analyses conducted by our group.
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Affiliation(s)
- Soji Morishita
- Development of Therapies against MPNs, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
- Advanced Hematology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkuo-ku, Tokyo 113-8421, Japan
| | - Norio Komatsu
- Development of Therapies against MPNs, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
- Advanced Hematology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkuo-ku, Tokyo 113-8421, Japan
- PharmaEssentia Japan, Akasaka Center Building 12 Fl, 1-3-13 Motoakasaka, Minato-ku, Tokyo 107-0051, Japan
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24
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Stuckey R, Bilbao-Sieyro C, Segura-Díaz A, Gómez-Casares MT. Molecular Studies for the Early Detection of Philadelphia-Negative Myeloproliferative Neoplasms. Int J Mol Sci 2023; 24:12700. [PMID: 37628880 PMCID: PMC10454334 DOI: 10.3390/ijms241612700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
JAK2 V617F is the predominant driver mutation in patients with Philadelphia-negative myeloproliferative neoplasms (MPN). JAK2 mutations are also frequent in clonal hematopoiesis of indeterminate potential (CHIP) in otherwise "healthy" individuals. However, the period between mutation acquisition and MPN diagnosis (known as latency) varies widely between individuals, with JAK2 mutations detectable several decades before diagnosis and even from birth in some individuals. Here, we will review the current evidence on the biological factors, such as additional mutations and chronic inflammation, which influence clonal expansion and may determine why some JAK2-mutated individuals will progress to an overt neoplasm during their lifetime while others will not. We will also introduce several germline variants that predispose individuals to CHIP (as well as MPN) identified from genome-wide association studies. Finally, we will explore possible mutation screening or interventions that could help to minimize MPN-associated cardiovascular complications or even delay malignant progression.
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Affiliation(s)
- Ruth Stuckey
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrín, 35019 Las Palmas de Gran Canaria, Spain; (R.S.); (C.B.-S.); (A.S.-D.)
| | - Cristina Bilbao-Sieyro
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrín, 35019 Las Palmas de Gran Canaria, Spain; (R.S.); (C.B.-S.); (A.S.-D.)
- Morphology Department, Universidad de Las Palmas de Gran Canaria, 35016 Las Palmas de Gran Canaria, Spain
| | - Adrián Segura-Díaz
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrín, 35019 Las Palmas de Gran Canaria, Spain; (R.S.); (C.B.-S.); (A.S.-D.)
| | - María Teresa Gómez-Casares
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrín, 35019 Las Palmas de Gran Canaria, Spain; (R.S.); (C.B.-S.); (A.S.-D.)
- Department of Medical Sciences, Universidad de Las Palmas de Gran Canaria, 35016 Las Palmas de Gran Canaria, Spain
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25
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Sikking MA, Stroeks SLVM, Waring OJ, Henkens MTHM, Riksen NP, Hoischen A, Heymans SRB, Verdonschot JAJ. Clonal Hematopoiesis of Indeterminate Potential From a Heart Failure Specialist's Point of View. J Am Heart Assoc 2023; 12:e030603. [PMID: 37489738 PMCID: PMC10492961 DOI: 10.1161/jaha.123.030603] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/06/2023] [Indexed: 07/26/2023]
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is a common bone marrow abnormality induced by age-related DNA mutations, which give rise to proinflammatory immune cells. These immune cells exacerbate atherosclerotic cardiovascular disease and may induce or accelerate heart failure. The mechanisms involved are complex but point toward a central role for proinflammatory macrophages and an inflammasome-dependent immune response (IL-1 [interleukin-1] and IL-6 [interleukin-6]) in the atherosclerotic plaque or directly in the myocardium. Intracardiac inflammation may decrease cardiac function and induce cardiac fibrosis, even in the absence of atherosclerotic cardiovascular disease. The pathophysiology and consequences of CHIP may differ among implicated genes as well as subgroups of patients with heart failure, based on cause (ischemic versus nonischemic) and ejection fraction (reduced ejection fraction versus preserved ejection fraction). Evidence is accumulating that CHIP is associated with cardiovascular mortality in ischemic and nonischemic heart failure with reduced ejection fraction and involved in the development of heart failure with preserved ejection fraction. CHIP and corresponding inflammatory pathways provide a highly potent therapeutic target. Randomized controlled trials in patients with well-phenotyped heart failure, where readily available anti-inflammatory therapies are used to intervene with clonal hematopoiesis, may pave the way for a new area of heart failure treatment. The first clinical trials that target CHIP are already registered.
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Affiliation(s)
- Maurits A. Sikking
- Department of CardiologyCardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center (MUMC)Maastrichtthe Netherlands
| | - Sophie L. V. M. Stroeks
- Department of CardiologyCardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center (MUMC)Maastrichtthe Netherlands
| | - Olivia J. Waring
- Department of PathologyCardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center (MUMC)Maastrichtthe Netherlands
| | - Michiel T. H. M. Henkens
- Department of PathologyCardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center (MUMC)Maastrichtthe Netherlands
- Netherlands Heart Institute (NLHI)Utrechtthe Netherlands
| | - Niels P. Riksen
- Department of Internal MedicineRadboud University Medical CenterNijmegenthe Netherlands
| | - Alexander Hoischen
- Department of Human GeneticsRadboud University Medical CenterNijmegenthe Netherlands
| | - Stephane R. B. Heymans
- Department of CardiologyCardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center (MUMC)Maastrichtthe Netherlands
- Department of Cardiovascular ResearchUniversity of LeuvenBelgium
| | - Job A. J. Verdonschot
- Department of CardiologyCardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Center (MUMC)Maastrichtthe Netherlands
- Department of Clinical GeneticsMaastricht University Medical Center (MUMC)Maastrichtthe Netherlands
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26
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Hermouet S. Mutations, inflammation and phenotype of myeloproliferative neoplasms. Front Oncol 2023; 13:1196817. [PMID: 37284191 PMCID: PMC10239955 DOI: 10.3389/fonc.2023.1196817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/09/2023] [Indexed: 06/08/2023] Open
Abstract
Knowledge on the myeloproliferative neoplasms (MPNs) - polycythemia vera (PV), essential thrombocythemia (ET), primary myelofibrosis (PMF) - has accumulated since the discovery of the JAK/STAT-activating mutations associated with MPNs: JAK2V617F, observed in PV, ET and PMF; and the MPL and CALR mutations, found in ET and PMF. The intriguing lack of disease specificity of these mutations, and of the chronic inflammation associated with MPNs, triggered a quest for finding what precisely determines that MPN patients develop a PV, ET or PMF phenoptype. The mechanisms of action of MPN-driving mutations, and concomitant mutations (ASXL1, DNMT3A, TET2, others), have been extensively studied, as well as the role played by these mutations in inflammation, and several pathogenic models have been proposed. In parallel, different types of drugs have been tested in MPNs (JAK inhibitors, interferons, hydroxyurea, anagrelide, azacytidine, combinations of those), some acting on both JAK2 and inflammation. Yet MPNs remain incurable diseases. This review aims to present current, detailed knowledge on the pathogenic mechanisms specifically associated with PV, ET or PMF that may pave the way for the development of novel, curative therapies.
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Affiliation(s)
- Sylvie Hermouet
- Nantes Université, INSERM, Immunology and New Concepts in ImmunoTherapy, INCIT, UMR 1302, Nantes, France
- Laboratoire d'Hématologie, CHU Nantes, Nantes, France
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27
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Wu B, Chen X, Pan X, Deng X, Li S, Wang Z, Wang J, Liao D, Xu J, Chen M, Zhao C, Xue Z, Wang Y, Niu T, Lin J, Chen L, Liu Y, Chen C. Single-cell transcriptome analyses reveal critical roles of RNA splicing during leukemia progression. PLoS Biol 2023; 21:e3002088. [PMID: 37130348 PMCID: PMC10154039 DOI: 10.1371/journal.pbio.3002088] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 03/21/2023] [Indexed: 05/04/2023] Open
Abstract
Leukemogenesis is proposed to be a multistep process by which normal hematopoietic stem and progenitor cells are transformed into full-blown leukemic cells, the details of which are not fully understood. Here, we performed serial single-cell transcriptome analyses of preleukemic and leukemic cells (PLCs) and constructed the cellular and molecular transformation trajectory in a Myc-driven acute myeloid leukemia (AML) model in mice, which represented the transformation course in patients. We found that the Myc targets were gradually up-regulated along the trajectory. Among them were splicing factors, which showed stage-specific prognosis for AML patients. Furthermore, we dissected the detailed gene network of a tipping point for hematopoietic stem and progenitor cells (HSPCs) to generate initiating PLCs, which was characterized by dramatically increased splicing factors and unusual RNA velocity. In the late stage, PLCs acquired explosive heterogeneity through RNA alternative splicing. Among them, the Hsp90aa1hi subpopulation was conserved in both human and mouse AML and associated with poor prognosis. Exon 4 skipping of Tmem134 was identified in these cells. While the exon skipping product Tmem134β promoted the cell cycle, full-length Tmem134α delayed tumorigenesis. Our study emphasized the critical roles of RNA splicing in the full process of leukemogenesis.
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Affiliation(s)
- Baohong Wu
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xuelan Chen
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiangyu Pan
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xintong Deng
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Shujun Li
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhongwang Wang
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jian Wang
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Dan Liao
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jing Xu
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Mei Chen
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chengjian Zhao
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
| | - Zhihong Xue
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
| | - Yuan Wang
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
| | - Ting Niu
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jingwen Lin
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
| | - Lu Chen
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Yu Liu
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
| | - Chong Chen
- Department of Hematology and Institute of Hematology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
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28
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Harris Z, Kaizer H, Wei A, Karantanos T, Williams DM, Chaturvedi S, Jain T, Resar L, Moliterno AR, Braunstein EM. Characterization of myeloproliferative neoplasms in the paediatric and young adult population. Br J Haematol 2023; 201:449-458. [PMID: 36647302 PMCID: PMC10121873 DOI: 10.1111/bjh.18650] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 12/30/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023]
Abstract
The aim of this study was to compare the genomic features and clinical outcomes between paediatric and young adult patients (PAYA, <40 years) and older adults (OA, ≥40 years) with myeloproliferative neoplasms (MPN) to gain insight into pathogenesis, disease prognosis and management. Of 630 MPN patients, 171 (27%) were PAYA with an average age at diagnosis of 31 years. Females were more prevalent in PAYA than OA (71% vs 58%; p = 0.002), and PAYA more frequently presented with essential thrombocytosis (ET) at diagnosis (67% vs 39%; p < 0.001). The presence of a JAK2 somatic mutation was higher in OA (80.4% vs 64.3%; p < 0.001), while a CALR mutation or lack of any traditional driver mutation was more common in PAYA (20.5% vs 10.5%; p = 0.001, 8.8% vs 3.7%; p = 0.01 respectively). Venous thrombosis was more common in PAYA compared to OA (19.8% vs 10.7%; p = 0.002). PAYA had a higher prevalence of familial MPN and familial cancer predisposition, and two PAYA patients harboured pathogenic germline JAK2 lesions. PAYA demonstrated longer survival from diagnosis than OA (median not reached vs 13 years), while disease transformation was less frequent (19.3% vs 37.9%).
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Affiliation(s)
- Zoey Harris
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Hannah Kaizer
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Aria Wei
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Theodoros Karantanos
- Division of Hematological Malignancies, Department of Medical Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205
| | - Donna M Williams
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Shruti Chaturvedi
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Tania Jain
- Division of Hematological Malignancies, Department of Medical Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205
| | - Linda Resar
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Alison R. Moliterno
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Evan M. Braunstein
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
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29
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Ji X, Hong J, Yang W, Yao M, Wang J, Jiang G, Wang Y, Li C, Lin J, Mou H, Li C, Li S, Chen Y, Shi M, Wang W, Lu F, Wu H, Zhao X, Qi Y, Yan S. GSTP1-mediated S-glutathionylation of Pik3r1 is a redox hub that inhibits osteoclastogenesis through regulating autophagic flux. Redox Biol 2023; 61:102635. [PMID: 36870110 PMCID: PMC9995948 DOI: 10.1016/j.redox.2023.102635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 02/11/2023] [Indexed: 03/03/2023] Open
Abstract
Glutathione S-transferase P1(GSTP1) is known for its transferase and detoxification activity. Based on disease-phenotype genetic associations, we found that GSTP1 might be associated with bone mineral density through Mendelian randomization analysis. Therefore, this study was performed both in vitro cellular and in vivo mouse model to determine how GSTP1 affects bone homeostasis. In our research, GSTP1 was revealed to upregulate the S-glutathionylation level of Pik3r1 through Cys498 and Cys670, thereby decreasing its phosphorylation, further controlling the alteration of autophagic flux via the Pik3r1-AKT-mTOR axis, and lastly altering osteoclast formation in vitro. In addition, knockdown and overexpression of GSTP1 in vivo also altered bone loss outcomes in the OVX mice model. In general, this study identified a new mechanism by which GSTP1 regulates osteoclastogenesis, and it is evident that the cell fate of osteoclasts is controlled by GSTP1-mediated S-glutathionylation via a redox-autophagy cascade.
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Affiliation(s)
- Xiaoxiao Ji
- Department of Orthopedic Surgery, The Fourth Affiliated Hospital, International Institutes of Medicine, Zhejiang University School of Medicine, Yiwu, Zhejiang, PR China; Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province, PR China; Orthopedics Research Institute of Zhejiang University, Hangzhou City, Zhejiang Province, PR China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou City, Zhejiang Province, PR China
| | - Jianqiao Hong
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province, PR China; Orthopedics Research Institute of Zhejiang University, Hangzhou City, Zhejiang Province, PR China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou City, Zhejiang Province, PR China
| | - Weinan Yang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province, PR China; Orthopedics Research Institute of Zhejiang University, Hangzhou City, Zhejiang Province, PR China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou City, Zhejiang Province, PR China
| | - Minjun Yao
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province, PR China; Orthopedics Research Institute of Zhejiang University, Hangzhou City, Zhejiang Province, PR China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou City, Zhejiang Province, PR China
| | - Jie Wang
- Department of Orthopedic Surgery, The Fourth Affiliated Hospital, International Institutes of Medicine, Zhejiang University School of Medicine, Yiwu, Zhejiang, PR China; Orthopedics Research Institute of Zhejiang University, Hangzhou City, Zhejiang Province, PR China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou City, Zhejiang Province, PR China
| | - Guangyao Jiang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province, PR China; Orthopedics Research Institute of Zhejiang University, Hangzhou City, Zhejiang Province, PR China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou City, Zhejiang Province, PR China
| | - Yibo Wang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province, PR China; Orthopedics Research Institute of Zhejiang University, Hangzhou City, Zhejiang Province, PR China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou City, Zhejiang Province, PR China
| | - Congsun Li
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province, PR China; Orthopedics Research Institute of Zhejiang University, Hangzhou City, Zhejiang Province, PR China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou City, Zhejiang Province, PR China
| | - Jiyan Lin
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province, PR China; Orthopedics Research Institute of Zhejiang University, Hangzhou City, Zhejiang Province, PR China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou City, Zhejiang Province, PR China
| | - Haochen Mou
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province, PR China; Orthopedics Research Institute of Zhejiang University, Hangzhou City, Zhejiang Province, PR China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou City, Zhejiang Province, PR China
| | - Chaozhong Li
- College of Computer Science, Sichuan University, Chengdu, PR China
| | - Sihao Li
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province, PR China; Orthopedics Research Institute of Zhejiang University, Hangzhou City, Zhejiang Province, PR China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou City, Zhejiang Province, PR China
| | - Yazhou Chen
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province, PR China; Orthopedics Research Institute of Zhejiang University, Hangzhou City, Zhejiang Province, PR China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou City, Zhejiang Province, PR China
| | - Minming Shi
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province, PR China; Orthopedics Research Institute of Zhejiang University, Hangzhou City, Zhejiang Province, PR China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou City, Zhejiang Province, PR China
| | - Wei Wang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province, PR China; Orthopedics Research Institute of Zhejiang University, Hangzhou City, Zhejiang Province, PR China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou City, Zhejiang Province, PR China
| | - Fei Lu
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province, PR China
| | - Haobo Wu
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province, PR China; Orthopedics Research Institute of Zhejiang University, Hangzhou City, Zhejiang Province, PR China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou City, Zhejiang Province, PR China.
| | - Xiang Zhao
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province, PR China; Orthopedics Research Institute of Zhejiang University, Hangzhou City, Zhejiang Province, PR China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou City, Zhejiang Province, PR China.
| | - Yiying Qi
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province, PR China; Orthopedics Research Institute of Zhejiang University, Hangzhou City, Zhejiang Province, PR China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou City, Zhejiang Province, PR China.
| | - Shigui Yan
- Department of Orthopedic Surgery, The Fourth Affiliated Hospital, International Institutes of Medicine, Zhejiang University School of Medicine, Yiwu, Zhejiang, PR China; Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province, PR China; Orthopedics Research Institute of Zhejiang University, Hangzhou City, Zhejiang Province, PR China; Key Laboratory of Motor System Disease Research and Precision Therapy of Zhejiang Province, Hangzhou City, Zhejiang Province, PR China.
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30
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How J, Garcia JS, Mullally A. Biology and therapeutic targeting of molecular mechanisms in MPNs. Blood 2023; 141:1922-1933. [PMID: 36534936 PMCID: PMC10163317 DOI: 10.1182/blood.2022017416] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Myeloproliferative neoplasms (MPNs) are clonal hematopoietic stem cell disorders characterized by activated Janus kinase (JAK)-signal transducer and activator of transcription signaling. As a result, JAK inhibitors have been the standard therapy for treatment of patients with myelofibrosis (MF). Although currently approved JAK inhibitors successfully ameliorate MPN-related symptoms, they are not known to substantially alter the MF disease course. Similarly, in essential thrombocythemia and polycythemia vera, treatments are primarily aimed at reducing the risk of cardiovascular and thromboembolic complications, with a watchful waiting approach often used in patients who are considered to be at a lower risk for thrombosis. However, better understanding of MPN biology has led to the development of rationally designed therapies, with the goal of not only addressing disease complications but also potentially modifying disease course. We review the most recent data elucidating mechanisms of disease pathogenesis and highlight emerging therapies that target MPN on several biologic levels, including JAK2-mutant MPN stem cells, JAK and non-JAK signaling pathways, mutant calreticulin, and the inflammatory bone marrow microenvironment.
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Affiliation(s)
- Joan How
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Jacqueline S. Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Ann Mullally
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute, Cambridge, MA
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31
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Luque Paz D, Kralovics R, Skoda RC. Genetic basis and molecular profiling in myeloproliferative neoplasms. Blood 2023; 141:1909-1921. [PMID: 36347013 PMCID: PMC10646774 DOI: 10.1182/blood.2022017578] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/03/2022] [Accepted: 11/03/2022] [Indexed: 11/11/2022] Open
Abstract
BCR::ABL1-negative myeloproliferative neoplasms (MPNs) are clonal diseases originating from a single hematopoietic stem cell that cause excessive production of mature blood cells. The 3 subtypes, that is, polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF), are diagnosed according to the World Health Organization (WHO) and international consensus classification (ICC) criteria. Acquired gain-of-function mutations in 1 of 3 disease driver genes (JAK2, CALR, and MPL) are the causative events that can alone initiate and promote MPN disease without requiring additional cooperating mutations. JAK2-p.V617F is present in >95% of PV patients, and also in about half of the patients with ET or PMF. ET and PMF are also caused by mutations in CALR or MPL. In ∼10% of MPN patients, those referred to as being "triple negative," none of the known driver gene mutations can be detected. The common theme between the 3 driver gene mutations and triple-negative MPN is that the Janus kinase-signal transducer and activator of transcription (JAK/STAT) signaling pathway is constitutively activated. We review the recent advances in our understanding of the early events after the acquisition of a driver gene mutation. The limiting factor that determines the frequency at which MPN disease develops with a long latency is not the acquisition of driver gene mutations, but rather the expansion of the clone. Factors that control the conversion from clonal hematopoiesis to MPN disease include inherited predisposition, presence of additional mutations, and inflammation. The full extent of knowledge of the mutational landscape in individual MPN patients is now increasingly being used to predict outcome and chose the optimal therapy.
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Affiliation(s)
- Damien Luque Paz
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, CRCI2NA, Angers, France
| | - Robert Kralovics
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Radek C. Skoda
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Basel, Switzerland
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32
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Moliterno AR, Kaizer H, Reeves BN. JAK2 V617F allele burden in polycythemia vera: burden of proof. Blood 2023; 141:1934-1942. [PMID: 36745865 PMCID: PMC10163319 DOI: 10.1182/blood.2022017697] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/09/2023] [Accepted: 01/23/2023] [Indexed: 02/08/2023] Open
Abstract
Polycythemia vera (PV) is a hematopoietic stem cell neoplasm defined by activating somatic mutations in the JAK2 gene and characterized clinically by overproduction of red blood cells, platelets, and neutrophils; a significant burden of disease-specific symptoms; high rates of vascular events; and evolution to a myelofibrosis phase or acute leukemia. The JAK2V617F variant allele frequency (VAF) is a key determinant of outcomes in PV, including thrombosis and myelofibrotic progression. Here, we critically review the dynamic role of JAK2V617F mutation burden in the pathogenesis and natural history of PV, the suitability of JAK2V617F VAF as a diagnostic and prognostic biomarker, and the utility of JAK2V617F VAF reduction in PV treatment.
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Affiliation(s)
- Alison R. Moliterno
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Hannah Kaizer
- Division of Hematology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Brandi N. Reeves
- Division of Hematology, Department of Medicine, Blood Research Center, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC
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33
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Mendez LM, Patnaik MM. Clonal Hematopoiesis: Origins and determinants of evolution. Leuk Res 2023; 129:107076. [PMID: 37075557 DOI: 10.1016/j.leukres.2023.107076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/22/2023] [Accepted: 04/10/2023] [Indexed: 04/21/2023]
Abstract
The accrual of somatic mutations is a byproduct of aging. When a clone bearing a somatic genetic alteration, conferring comparative competitive advantage, displays sufficient outgrowth to become detectable amongst an otherwise polyclonal background in the hematopoietic system, this is called clonal hematopoiesis (CH). Somatic genetic alterations observed in CH include point mutations in cancer related genes, mosaic chromosomal alterations or a combination of these. Interestingly, clonal hematopoiesis (CH) can also occur with somatic variants in genes without a known role in cancer and in the absence of a somatic genetic alteration through a process that has been described as 'genetic drift'. Clonal hematopoiesis of indeterminate significance (CHIP), is age-related and defined by the presence of somatic point mutations in cancer related genes, in the absence of cytopenias or a diagnosis of hematologic neoplasm, with a variant allele fraction ≥ 2 %. Remarkably, the increased mortality associated with CHIP is largely due to cardiovascular disease. Subsequently, CHIP has been associated with a myriad of age-related conditions such as Alzheimer's Disease, osteoporosis, CVA and COPD. CHIP is associated with an increased risk of hematologic malignancies, particularly myeloid neoplasms, with the risk rising with increasing clone size and clonal complexity. Mechanisms regulating clonal evolution and progression to hematologic malignancies remain to be defined. However, observations on context specific CH arising in the setting of bone marrow failure states, or on exposure to chemotherapy and radiation therapy, suggest that CH reflects context specific selection pressures and constraint-escape mechanisms.
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Affiliation(s)
- Lourdes M Mendez
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center and Smilow Cancer Hospital, Yale University School of Medicine, CT, USA
| | - Mrinal M Patnaik
- Division of Hematology, Department of Medicine, Mayo Clinic, MN, USA.
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34
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Clarke ML, Lemma RB, Walton DS, Volpe G, Noyvert B, Gabrielsen OS, Frampton J. MYB insufficiency disrupts proteostasis in hematopoietic stem cells, leading to age-related neoplasia. Blood 2023; 141:1858-1870. [PMID: 36603185 PMCID: PMC10646772 DOI: 10.1182/blood.2022019138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 01/07/2023] Open
Abstract
MYB plays a key role in gene regulation throughout the hematopoietic hierarchy and is critical for the maintenance of normal hematopoietic stem cells (HSC). Acquired genetic dysregulation of MYB is involved in the etiology of a number of leukemias, although inherited noncoding variants of the MYB gene are a susceptibility factor for many hematological conditions, including myeloproliferative neoplasms (MPN). The mechanisms that connect variations in MYB levels to disease predisposition, especially concerning age dependency in disease initiation, are completely unknown. Here, we describe a model of Myb insufficiency in mice that leads to MPN, myelodysplasia, and leukemia in later life, mirroring the age profile of equivalent human diseases. We show that this age dependency is intrinsic to HSC, involving a combination of an initial defective cellular state resulting from small effects on the expression of multiple genes and a progressive accumulation of further subtle changes. Similar to previous studies showing the importance of proteostasis in HSC maintenance, we observed altered proteasomal activity and elevated proliferation indicators, followed by elevated ribosome activity in young Myb-insufficient mice. We propose that these alterations combine to cause an imbalance in proteostasis, potentially creating a cellular milieu favoring disease initiation.
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Affiliation(s)
- Mary L. Clarke
- Institute of Cancer & Genomic Sciences, College of Medical & Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Roza B. Lemma
- Department of Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - David S. Walton
- Institute of Cancer & Genomic Sciences, College of Medical & Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Giacomo Volpe
- Institute of Cancer & Genomic Sciences, College of Medical & Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Boris Noyvert
- Institute of Cancer & Genomic Sciences, College of Medical & Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- CRUK Birmingham Centre and Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom
| | | | - Jon Frampton
- Institute of Cancer & Genomic Sciences, College of Medical & Dental Sciences, University of Birmingham, Birmingham, United Kingdom
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35
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Wong WJ, Emdin C, Bick AG, Zekavat SM, Niroula A, Pirruccello JP, Dichtel L, Griffin G, Uddin MM, Gibson CJ, Kovalcik V, Lin AE, McConkey ME, Vromman A, Sellar RS, Kim PG, Agrawal M, Weinstock J, Long MT, Yu B, Banerjee R, Nicholls RC, Dennis A, Kelly M, Loh PR, McCarroll S, Boerwinkle E, Vasan RS, Jaiswal S, Johnson AD, Chung RT, Corey K, Levy D, Ballantyne C, Ebert BL, Natarajan P. Clonal haematopoiesis and risk of chronic liver disease. Nature 2023; 616:747-754. [PMID: 37046084 PMCID: PMC10405350 DOI: 10.1038/s41586-023-05857-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/16/2023] [Indexed: 04/14/2023]
Abstract
Chronic liver disease is a major public health burden worldwide1. Although different aetiologies and mechanisms of liver injury exist, progression of chronic liver disease follows a common pathway of liver inflammation, injury and fibrosis2. Here we examined the association between clonal haematopoiesis of indeterminate potential (CHIP) and chronic liver disease in 214,563 individuals from 4 independent cohorts with whole-exome sequencing data (Framingham Heart Study, Atherosclerosis Risk in Communities Study, UK Biobank and Mass General Brigham Biobank). CHIP was associated with an increased risk of prevalent and incident chronic liver disease (odds ratio = 2.01, 95% confidence interval (95% CI) [1.46, 2.79]; P < 0.001). Individuals with CHIP were more likely to demonstrate liver inflammation and fibrosis detectable by magnetic resonance imaging compared to those without CHIP (odds ratio = 1.74, 95% CI [1.16, 2.60]; P = 0.007). To assess potential causality, Mendelian randomization analyses showed that genetic predisposition to CHIP was associated with a greater risk of chronic liver disease (odds ratio = 2.37, 95% CI [1.57, 3.6]; P < 0.001). In a dietary model of non-alcoholic steatohepatitis, mice transplanted with Tet2-deficient haematopoietic cells demonstrated more severe liver inflammation and fibrosis. These effects were mediated by the NLRP3 inflammasome and increased levels of expression of downstream inflammatory cytokines in Tet2-deficient macrophages. In summary, clonal haematopoiesis is associated with an elevated risk of liver inflammation and chronic liver disease progression through an aberrant inflammatory response.
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Affiliation(s)
- Waihay J Wong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Connor Emdin
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Alexander G Bick
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Seyedeh M Zekavat
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Yale University School of Medicine, New Haven, CT, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Abhishek Niroula
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - James P Pirruccello
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Division of Cardiology, University of California San Francisco, San Francisco, CA, USA
| | - Laura Dichtel
- Neuroendocrine Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Gabriel Griffin
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Md Mesbah Uddin
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Christopher J Gibson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Veronica Kovalcik
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amy E Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Marie E McConkey
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amelie Vromman
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Rob S Sellar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Haematology, UCL Cancer Institute, London, UK
| | - Peter G Kim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Mridul Agrawal
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joshua Weinstock
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Michelle T Long
- Section of Gastroenterology, Boston Medical Center, Boston University School of Medicine, Boston, MA, USA
| | - Bing Yu
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | | | | | | | - Po-Ru Loh
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Steve McCarroll
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ramachandran S Vasan
- The University of Texas School of Public Health San Antonio, San Antonio, TX, USA
- Framingham Heart Study of the NHLBI and Boston University School of Medicine, Framingham, MA, USA
- The University of Texas Health Science Center, San Antonio, TX, USA
| | - Siddhartha Jaiswal
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Andrew D Johnson
- Population Sciences Branch, National Heart, Lung, and Blood Institute, Framingham, MA, USA
| | - Raymond T Chung
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Liver Center, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kathleen Corey
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Liver Center, Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Daniel Levy
- Framingham Heart Study of the NHLBI and Boston University School of Medicine, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christie Ballantyne
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Pradeep Natarajan
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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36
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Cato LD, Li R, Lu HY, Yu F, Wissman M, Mkumbe BS, Ekwattanakit S, Deelen P, Mwita L, Sangeda R, Suksangpleng T, Riolueang S, Bronson PG, Paul DS, Kawabata E, Astle WJ, Aguet F, Ardlie K, de Lapuente Portilla AL, Kang G, Zhang Y, Nouraie SM, Gordeuk VR, Gladwin MT, Garrett ME, Ashley-Koch A, Telen MJ, Custer B, Kelly S, Dinardo CL, Sabino EC, Loureiro P, Carneiro-Proietti AB, Maximo C, Méndez A, Hammerer-Lercher A, Sheehan VA, Weiss MJ, Franke L, Nilsson B, Butterworth AS, Viprakasit V, Nkya S, Sankaran VG. Genetic regulation of fetal hemoglobin across global populations. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.24.23287659. [PMID: 36993312 PMCID: PMC10055601 DOI: 10.1101/2023.03.24.23287659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Human genetic variation has enabled the identification of several key regulators of fetal-to-adult hemoglobin switching, including BCL11A, resulting in therapeutic advances. However, despite the progress made, limited further insights have been obtained to provide a fuller accounting of how genetic variation contributes to the global mechanisms of fetal hemoglobin (HbF) gene regulation. Here, we have conducted a multi-ancestry genome-wide association study of 28,279 individuals from several cohorts spanning 5 continents to define the architecture of human genetic variation impacting HbF. We have identified a total of 178 conditionally independent genome-wide significant or suggestive variants across 14 genomic windows. Importantly, these new data enable us to better define the mechanisms by which HbF switching occurs in vivo. We conduct targeted perturbations to define BACH2 as a new genetically-nominated regulator of hemoglobin switching. We define putative causal variants and underlying mechanisms at the well-studied BCL11A and HBS1L-MYB loci, illuminating the complex variant-driven regulation present at these loci. We additionally show how rare large-effect deletions in the HBB locus can interact with polygenic variation to influence HbF levels. Our study paves the way for the next generation of therapies to more effectively induce HbF in sickle cell disease and β-thalassemia.
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Affiliation(s)
- Liam D. Cato
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rick Li
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Henry Y. Lu
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Fulong Yu
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Mariel Wissman
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Baraka S. Mkumbe
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Biochemistry, Muhimbili University of Health and Allied Science, Dar es Salaam, Tanzania
- Department of Artificial Intelligence and Innovative Medicine, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Supachai Ekwattanakit
- Siriraj Thalassemia Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Patrick Deelen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - Liberata Mwita
- Department of Pharmaceutical Microbiology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Raphael Sangeda
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Pharmaceutical Microbiology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Thidarat Suksangpleng
- Siriraj Thalassemia Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Suchada Riolueang
- Siriraj Thalassemia Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Paola G. Bronson
- R&D Translational Biology, Biogen, Cambridge, Massachusetts, USA
| | - Dirk S. Paul
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
| | - Emily Kawabata
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - William J. Astle
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- NHS Blood and Transplant, Cambridge, UK
| | - Francois Aguet
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kristin Ardlie
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Guolian Kang
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yingze Zhang
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Seyed Mehdi Nouraie
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Victor R. Gordeuk
- Division of Hematology and Oncology, Department of Medicine, Comprehensive Sickle Cell Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Mark T. Gladwin
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Melanie E. Garrett
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Allison Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Marilyn J. Telen
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Brian Custer
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, UCSF, San Francisco, California, USA
| | - Shannon Kelly
- Vitalant Research Institute, San Francisco, California, USA
- Division of Pediatric Hematology, UCSF Benioff Children's Hospital, Oakland, California, USA
| | - Carla Luana Dinardo
- Fundacao Pro-Sangue Hemocentro de Sao Paulo, Sao Paulo, Brazil
- Institute of Tropical Medicine, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Ester C. Sabino
- Institute of Tropical Medicine, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | | | | | | | | | | | - Adriana Méndez
- Institute of Laboratory Medicine, Cantonal Hospital Aarau, 5000 Aarau, Switzerland
| | | | - Vivien A. Sheehan
- Aflac Cancer & Blood Disorders Center, Children's Healthcare of Atlanta & Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Lude Franke
- Oncode Institute, Amsterdam, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Björn Nilsson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
- Department of Laboratory Medicine, Lund University, 221 84 Lund, Sweden
| | - Adam S. Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Vip Viprakasit
- Siriraj Thalassemia Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Siana Nkya
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Biochemistry, Muhimbili University of Health and Allied Science, Dar es Salaam, Tanzania
- Tanzania Human Genetics Organisation, Tanzania
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Biochemistry, Muhimbili University of Health and Allied Science
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37
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Gundry M, Sankaran VG. Hacking hematopoiesis - emerging tools for examining variant effects. Dis Model Mech 2023; 16:288409. [PMID: 36826849 PMCID: PMC9983777 DOI: 10.1242/dmm.049857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Hematopoiesis is a continuous process of blood and immune cell production. It is orchestrated by thousands of gene products that respond to extracellular signals by guiding cell fate decisions to meet the needs of the organism. Although much of our knowledge of this process comes from work in model systems, we have learned a great deal from studies on human genetic variation. Considerable insight has emerged from studies on presumed monogenic blood disorders, which continue to provide key insights into the mechanisms critical for hematopoiesis. Furthermore, the emergence of large-scale biobanks and cohorts has uncovered thousands of genomic loci associated with blood cell traits and diseases. Some of these blood cell trait-associated loci act as modifiers of what were once thought to be monogenic blood diseases. However, most of these loci await functional validation. Here, we discuss the validation bottleneck and emerging methods to more effectively connect variant to function. In particular, we highlight recent innovations in genome editing, which have paved the path forward for high-throughput functional assessment of loci. Finally, we discuss existing barriers to progress, including challenges in manipulating the genomes of primary hematopoietic cells.
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Affiliation(s)
- Michael Gundry
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Author for correspondence ()
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38
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Braunstein EM, Imada E, Pasca S, Wang S, Chen H, Alba C, Hupalo DN, Wilkerson M, Dalgard CL, Ghannam J, Liu Y, Marchionni L, Moliterno A, Hourigan CS, Gondek LP. Recurrent germline variant in ATM associated with familial myeloproliferative neoplasms. Leukemia 2023; 37:627-635. [PMID: 36543879 DOI: 10.1038/s41375-022-01797-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Genetic predisposition (familial risk) in the myeloproliferative neoplasms (MPNs) is more common than the risk observed in most other cancers, including breast, prostate, and colon. Up to 10% of MPNs are considered to be familial. Recent genome-wide association studies have identified genomic loci associated with an MPN diagnosis. However, the identification of variants with functional contributions to the development of MPN remains limited. In this study, we have included 630 MPN patients and whole genome sequencing was performed in 64 individuals with familial MPN to uncover recurrent germline predisposition variants. Both targeted and unbiased filtering of single nucleotide variants (SNVs) was performed, with a comparison to 218 individuals with MPN unselected for familial status. This approach identified an ATM L2307F SNV occurring in nearly 8% of individuals with familial MPN. Structural protein modeling of this variant suggested stabilization of inactive ATM dimer, and alteration of the endogenous ATM locus in a human myeloid cell line resulted in decreased phosphorylation of the downstream tumor suppressor CHEK2. These results implicate ATM, and the DNA-damage response pathway, in predisposition to MPN.
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Affiliation(s)
- Evan M Braunstein
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.,Division of Hematology, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Eddie Imada
- Division of Computational and Systems Pathology, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sergiu Pasca
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Shiyu Wang
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Hang Chen
- Division of Hematology, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD, USA.,Committee on Genetics, Genomics and Systems Biology, Biological Sciences Division, University of Chicago, Chicago, IL, USA
| | - Camille Alba
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.,The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Dan N Hupalo
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Matthew Wilkerson
- Department of Anatomy Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Clifton L Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Department of Anatomy Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jack Ghannam
- Laboratory of Myeloid Malignancies, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yujia Liu
- Department of Biochemistry and Molecular Biology, Biological Sciences Division, University of Chicago, Chicago, IL, USA
| | - Luigi Marchionni
- Division of Computational and Systems Pathology, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alison Moliterno
- Division of Hematology, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Christopher S Hourigan
- Laboratory of Myeloid Malignancies, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lukasz P Gondek
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
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39
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Zhao J, Jia Y, Mahmut D, Deik AA, Jeanfavre S, Clish CB, Sankaran VG. Human hematopoietic stem cell vulnerability to ferroptosis. Cell 2023; 186:732-747.e16. [PMID: 36803603 PMCID: PMC9978939 DOI: 10.1016/j.cell.2023.01.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 11/20/2022] [Accepted: 01/12/2023] [Indexed: 02/18/2023]
Abstract
Hematopoietic stem cells (HSCs) have a number of unique physiologic adaptations that enable lifelong maintenance of blood cell production, including a highly regulated rate of protein synthesis. Yet, the precise vulnerabilities that arise from such adaptations have not been fully characterized. Here, inspired by a bone marrow failure disorder due to the loss of the histone deubiquitinase MYSM1, characterized by selectively disadvantaged HSCs, we show how reduced protein synthesis in HSCs results in increased ferroptosis. HSC maintenance can be fully rescued by blocking ferroptosis, despite no alteration in protein synthesis rates. Importantly, this selective vulnerability to ferroptosis not only underlies HSC loss in MYSM1 deficiency but also characterizes a broader liability of human HSCs. Increasing protein synthesis rates via MYSM1 overexpression makes HSCs less susceptible to ferroptosis, more broadly illustrating the selective vulnerabilities that arise in somatic stem cell populations as a result of physiologic adaptations.
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Affiliation(s)
- Jiawei Zhao
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yuemeng Jia
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Dilnar Mahmut
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amy A Deik
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah Jeanfavre
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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40
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Liu A, Genovese G, Zhao Y, Pirinen M, Zekavat MM, Kentistou K, Yang Z, Yu K, Vlasschaert C, Liu X, Brown DW, Hudjashov G, Gorman B, Dennis J, Zhou W, Momozawa Y, Pyarajan S, Tuzov V, Pajuste FD, Aavikko M, Sipilä TP, Ghazal A, Huang WY, Freedman N, Song L, Gardner EJ, Sankaran VG, Palotie A, Ollila HM, Tukiainen T, Chanock SJ, Mägi R, Natarajan P, Daly MJ, Bick A, McCarroll SA, Terao C, Loh PR, Ganna A, Perry JRB, Machiela MJ. Population analyses of mosaic X chromosome loss identify genetic drivers and widespread signatures of cellular selection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.28.23285140. [PMID: 36778285 PMCID: PMC9915812 DOI: 10.1101/2023.01.28.23285140] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Mosaic loss of the X chromosome (mLOX) is the most commonly occurring clonal somatic alteration detected in the leukocytes of women, yet little is known about its genetic determinants or phenotypic consequences. To address this, we estimated mLOX in >900,000 women across eight biobanks, identifying 10% of women with detectable X loss in approximately 2% of their leukocytes. Out of 1,253 diseases examined, women with mLOX had an elevated risk of myeloid and lymphoid leukemias and pneumonia. Genetic analyses identified 49 common variants influencing mLOX, implicating genes with established roles in chromosomal missegregation, cancer predisposition, and autoimmune diseases. Complementary exome-sequence analyses identified rare missense variants in FBXO10 which confer a two-fold increased risk of mLOX. A small fraction of these associations were shared with mosaic Y chromosome loss in men, suggesting different biological processes drive the formation and clonal expansion of sex chromosome missegregation events. Allelic shift analyses identified alleles on the X chromosome which are preferentially retained, demonstrating that variation at many loci across the X chromosome is under cellular selection. A novel polygenic score including 44 independent X chromosome allelic shift loci correctly inferred the retained X chromosomes in 80.7% of mLOX cases in the top decile. Collectively our results support a model where germline variants predispose women to acquiring mLOX, with the allelic content of the X chromosome possibly shaping the magnitude of subsequent clonal expansion.
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Affiliation(s)
- Aoxing Liu
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally: Aoxing Liu, Giulio Genovese, Yajie Zhao
| | - Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- These authors contributed equally: Aoxing Liu, Giulio Genovese, Yajie Zhao
| | - Yajie Zhao
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- These authors contributed equally: Aoxing Liu, Giulio Genovese, Yajie Zhao
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Publich Health, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Maryam M Zekavat
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Katherine Kentistou
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Zhiyu Yang
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Derek W Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Prevention Fellowship Program, Division of Cancer Prevention, National Cancer Institute, Rockville, MD, USA
| | - Georgi Hudjashov
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Bryan Gorman
- Center for Data and Computational Sciences (C-DACS), VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
- Booz Allen Hamilton, McLean, VA, USA
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Saiju Pyarajan
- Center for Data and Computational Sciences (C-DACS), VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Vlad Tuzov
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Fanny-Dhelia Pajuste
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Mervi Aavikko
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Timo P Sipilä
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Awaisa Ghazal
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Neal Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Eugene J Gardner
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Vijay G Sankaran
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Hanna M Ollila
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center of Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Taru Tukiainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Pradeep Natarajan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Center of Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Mark J Daly
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Alexander Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Po-Ru Loh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- These authors jointly supervised this work: Po-Ru Loh, Andrea Ganna, John R.B. Perry, Mitchell J. Machiela
| | - Andrea Ganna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- These authors jointly supervised this work: Po-Ru Loh, Andrea Ganna, John R.B. Perry, Mitchell J. Machiela
| | - John R B Perry
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- These authors jointly supervised this work: Po-Ru Loh, Andrea Ganna, John R.B. Perry, Mitchell J. Machiela
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- These authors jointly supervised this work: Po-Ru Loh, Andrea Ganna, John R.B. Perry, Mitchell J. Machiela
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41
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O'Sullivan JM, Mead AJ, Psaila B. Single-cell methods in myeloproliferative neoplasms: old questions, new technologies. Blood 2023; 141:380-390. [PMID: 36322938 DOI: 10.1182/blood.2021014668] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/14/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022] Open
Abstract
Myeloproliferative neoplasms (MPN) are a group of clonal stem cell-derived hematopoietic malignancies driven by aberrant Janus kinase-signal transducer and activator of transcription proteins (JAK/STAT) signaling. Although these are genetically simple diseases, MPNs are phenotypically heterogeneous, reflecting underlying intratumoral heterogeneity driven by the interplay of genetic and nongenetic factors. Their evolution is determined by factors that enable certain cellular subsets to outcompete others. Therefore, techniques that resolve cellular heterogeneity at the single-cell level are ideally placed to provide new insights into MPN biology. With these insights comes the potential to uncover new approaches to predict the clinical course and treat these cancers, ultimately improving outcomes for patients. MPNs present a particularly tractable model of cancer evolution, because most patients present in an early disease phase and only a small proportion progress to aggressive disease. Therefore, it is not surprising that many groundbreaking technological advances in single-cell omics have been pioneered by their application in MPNs. In this review article, we explore how single-cell approaches have provided transformative insights into MPN disease biology, which are broadly applicable across human cancers, and discuss how these studies might be swiftly translated into clinical pathways and may eventually underpin precision medicine.
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Affiliation(s)
- Jennifer Mary O'Sullivan
- Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Adam J Mead
- Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Bethan Psaila
- Medical Research Council Molecular Haematology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
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42
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Mosale Seetharam S, Liu Y, Wu J, Fechter L, Murugesan K, Maecker H, Gotlib J, Zehnder J, Paulmurugan R, Krishnan A. Enkurin: A novel marker for myeloproliferative neoplasms from platelet, megakaryocyte, and whole blood specimens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.07.523111. [PMID: 36712071 PMCID: PMC9881897 DOI: 10.1101/2023.01.07.523111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Impaired protein homeostasis, though well established in age-related disorders, has been linked in recent research with the pathogenesis of myeloproliferative neoplasms (MPNs). As yet, however, little is known about MPN-specific modulators of proteostasis, thus impeding our ability for increased mechanistic understanding and discovery of additional therapeutic targets. Loss of proteostasis, in itself, is traced to dysregulated mechanisms in protein folding and intracellular calcium signaling at the endoplasmic reticulum (ER). Here, using ex vivo and in vitro systems (including CD34 + cultures from patient bone marrow, and healthy cord/peripheral blood specimens), we extend our prior data from MPN patient platelet RNA sequencing, and discover select proteostasis-associated markers at RNA and/or protein levels in each of platelets, parent megakaryocytes, and whole blood specimens. Importantly, we identify a novel role in MPNs for enkurin ( ENKUR ), a calcium mediator protein, implicated originally only in spermatogenesis. Our data reveal consistent ENKUR downregulation at both RNA and protein levels across MPN patient specimens and experimental models, with a concomitant upregulation of a cell cycle marker, CDC20 . Silencing of ENKUR by shRNA in CD34 + derived megakaryocytes further confirm this association with CDC20 at both RNA and protein levels; and indicate a likely role for the PI3K/Akt pathway. The inverse association of ENKUR and CDC20 expression was further confirmed upon treatment with thapsigargin (an agent that causes protein misfolding in the ER by selective loss of calcium) in both megakaryocyte and platelet fractions at RNA and protein levels. Together, our work sheds light on enkurin as a novel marker of MPN pathogenesis beyond the genetic alterations; and indicates further mechanistic investigation into a role for dysregulated calcium homeostasis, and ER and protein folding stress in MPN transformation. VISUAL ABSTRACT Key Points Enkurin, a calcium adaptor protein, is identified as a novel marker of pathogenesis in MPNs.MPN megakaryocyte and platelet expression of enkurin at RNA and protein levels is inversely associated with a cell differentiation cycle gene, CDC20.Likely role for dysregulated calcium homeostasis, and ER and protein folding stress in MPN transformation.
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Affiliation(s)
| | - Yi Liu
- Department of Radiology, Stanford University, Stanford, CA
| | - Jason Wu
- High-Throughput Bioscience Center (HTBC), Stanford University School of Medicine, Stanford, CA
| | - Lenn Fechter
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | | | - Holden Maecker
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA
| | - Jason Gotlib
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - James Zehnder
- Department of Pathology, Stanford University, Stanford, CA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | | | - Anandi Krishnan
- Department of Pathology, Stanford University, Stanford, CA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
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43
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Voit RA, Tao L, Yu F, Cato LD, Cohen B, Fleming TJ, Antoszewski M, Liao X, Fiorini C, Nandakumar SK, Wahlster L, Teichert K, Regev A, Sankaran VG. A genetic disorder reveals a hematopoietic stem cell regulatory network co-opted in leukemia. Nat Immunol 2023; 24:69-83. [PMID: 36522544 PMCID: PMC9810535 DOI: 10.1038/s41590-022-01370-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 10/25/2022] [Indexed: 12/23/2022]
Abstract
The molecular regulation of human hematopoietic stem cell (HSC) maintenance is therapeutically important, but limitations in experimental systems and interspecies variation have constrained our knowledge of this process. Here, we have studied a rare genetic disorder due to MECOM haploinsufficiency, characterized by an early-onset absence of HSCs in vivo. By generating a faithful model of this disorder in primary human HSCs and coupling functional studies with integrative single-cell genomic analyses, we uncover a key transcriptional network involving hundreds of genes that is required for HSC maintenance. Through our analyses, we nominate cooperating transcriptional regulators and identify how MECOM prevents the CTCF-dependent genome reorganization that occurs as HSCs differentiate. We show that this transcriptional network is co-opted in high-risk leukemias, thereby enabling these cancers to acquire stem cell properties. Collectively, we illuminate a regulatory network necessary for HSC self-renewal through the study of a rare experiment of nature.
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Affiliation(s)
- Richard A Voit
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Liming Tao
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Fulong Yu
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Liam D Cato
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Blake Cohen
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Travis J Fleming
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mateusz Antoszewski
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaotian Liao
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Claudia Fiorini
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Satish K Nandakumar
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Albert Einstein Cancer Center, Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Bronx, NY, USA
| | - Lara Wahlster
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kristian Teichert
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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Rolles B, Mullally A. Molecular Pathogenesis of Myeloproliferative Neoplasms. Curr Hematol Malig Rep 2022; 17:319-329. [PMID: 36336766 DOI: 10.1007/s11899-022-00685-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2022] [Indexed: 11/09/2022]
Abstract
PURPOSE OF REVIEW Myeloproliferative neoplasms (MPNs) are chronic hematological malignancies characterized by increased proliferation of MPN stem and myeloid progenitor cells with or without bone marrow fibrosis that typically lead to increased peripheral blood cell counts. The genetic and cytogenetic alterations that initiate and drive the development of MPNs have largely been defined, and we summarize these here. RECENT FINDINGS In recent years, advances in understanding the pathogenesis of MPNs have defined a long-preclinical phase in JAK2-mutant MPN, identified genetic loci associated with MPN predisposition and uncovered mechanistic insights in CALR-mutant MPN. The integration of molecular genetics into prognostic risk models is well-established in myelofibrosis and ongoing studies are interrogating the prognostic implications of concomitant mutations in ET and PV. Despite all these advances, the field is deficient in clonally selective therapies to effectively target the MPN clone at any stage of disease, from pre-clinical to advanced. Although the biological understanding of the pathogenesis of MPNs has progressed quickly, substantial knowledge gaps remain, including in the molecular mechanisms underlying MPN progression and myelofibrotic transformation. An ongoing goal for the MPN field is to translate advances in biological understanding to improved treatments for patients.
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Affiliation(s)
- Benjamin Rolles
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Institutes of Medicine Building, Room 738, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Ann Mullally
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Institutes of Medicine Building, Room 738, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA. .,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Broad Institute, Cambridge, MA, USA.
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45
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Lansdorp PM. Telomeres, Telomerase and Cancer. Arch Med Res 2022; 53:741-746. [PMID: 36334946 DOI: 10.1016/j.arcmed.2022.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/05/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
Abstract
Telomeres and telomerase play a crucial role in human aging and cancer. Three "drivers" of human aging can be identified. The developmental program encoded in DNA is the primary determinant of lifespan. Faithful execution of the developmental program requires stability of the (epi-)genome which is challenged throughout life by damage to DNA as well as epigenetic 'scars' from error-free DNA repair and stochastic errors made during the establishment and maintenance of the "epigenome". Over time (epi-)mutations accumulate, compromising cellular function and causing (pre-)malignant alterations. Damage to the genome and epigenome can be considered the second "driver" of aging. A third driver of the aging process, important to suppress tumors in long-lived animals, is caused by progressive loss of telomeric DNA. Telomere erosion protects against cancer early in life but limits cell renewal late in life, in agreement with the Antagonistic Pleiotropy theory on the evolutionary origin of aging. Malignant tumors arise when mutations and/or epimutations in cells (clock 2) corrupt the developmental program (clock 1) as well as tumor suppression by telomere erosion (clock 3). In cancer cells clock 3 is typically inactivated by loss of p53 as well as increased expression of telomerase. Taken together, aging in humans can be described by the ticking of three clocks: the clock that directs development, the accumulation of (epi-)mutations over time and the telomere clock that limits the number of cell divisions in normal stem and immune cells.
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Affiliation(s)
- Peter M Lansdorp
- Terry Fox Laboratory, BC Cancer Research Institute, Vancouver, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada.
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46
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Koutsogiannaki S, Hou L, Okuno T, Shibamura-Fujiogi M, Luo HR, Yuki K. αDβ2 as a novel target of experimental polymicrobial sepsis. Front Immunol 2022; 13:1059996. [PMID: 36466931 PMCID: PMC9716080 DOI: 10.3389/fimmu.2022.1059996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 10/17/2022] [Indexed: 11/19/2022] Open
Abstract
Since sepsis was defined three decades ago, it has been a target of intensive study. However, there is no specific sepsis treatment available, with its high mortality and morbidity. αDβ2 (CD11d/CD18) is one of the four β2 integrin members. Its role in sepsis has been limitedly studied. Using an experimental polymicrobial sepsis model, we found that the deficiency of αDβ2 was associated with less lung injury and better outcome, which was in sharp contrast to other β2 integrin member αLβ2 (CD11a/CD18), and αMβ2 (CD11b/CD18). This phenotype was supported by a reduction of bacterial loads in αDβ2 knockout mice. Further analysis showed that the deficiency of αDβ2 led to a reduction of neutrophil cell death as well as an increase in neutrophil phagocytosis in both murine and human systems. Our data showed a unique role of αDβ2 among the β2 integrin members, which would serve as a potential target to improve the outcome of sepsis.
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47
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The Contribution of JAK2 46/1 Haplotype in the Predisposition to Myeloproliferative Neoplasms. Int J Mol Sci 2022; 23:ijms232012582. [PMID: 36293440 PMCID: PMC9604447 DOI: 10.3390/ijms232012582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/13/2022] [Accepted: 10/15/2022] [Indexed: 11/17/2022] Open
Abstract
Haplotype 46/1 (GGCC) consists of a set of genetic variations distributed along chromosome 9p.24.1, which extend from the Janus Kinase 2 gene to Insulin like 4. Marked by four jointly inherited variants (rs3780367, rs10974944, rs12343867, and rs1159782), this haplotype has a strong association with the development of BCR-ABL1-negative myeloproliferative neoplasms (MPNs) because it precedes the acquisition of the JAK2V617F variant, a common genetic alteration in individuals with these hematological malignancies. It is also described as one of the factors that increases the risk of familial MPNs by more than five times, 46/1 is associated with events related to inflammatory dysregulation, splenomegaly, splanchnic vein thrombosis, Budd–Chiari syndrome, increases in RBC count, platelets, leukocytes, hematocrit, and hemoglobin, which are characteristic of MPNs, as well as other findings that are still being elucidated and which are of great interest for the etiopathological understanding of these hematological neoplasms. Considering these factors, the present review aims to describe the main findings and discussions involving the 46/1 haplotype, and highlights the molecular and immunological aspects and their relevance as a tool for clinical practice and investigation of familial cases.
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48
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Sankaran VG, Weissman JS, Zon LI. Cellular barcoding to decipher clonal dynamics in disease. Science 2022; 378:eabm5874. [PMID: 36227997 PMCID: PMC10111813 DOI: 10.1126/science.abm5874] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Cellular barcodes are distinct DNA sequences that enable one to track specific cells across time or space. Recent advances in our ability to detect natural or synthetic cellular barcodes, paired with single-cell readouts of cell state, have markedly increased our knowledge of clonal dynamics and genealogies of the cells that compose a variety of tissues and organs. These advances hold promise to redefine our view of human disease. Here, we provide an overview of cellular barcoding approaches, discuss applications to gain new insights into disease mechanisms, and provide an outlook on future applications. We discuss unanticipated insights gained through barcoding in studies of cancer and blood cell production and describe how barcoding can be applied to a growing array of medical fields, particularly with the increasing recognition of clonal contributions in human diseases.
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Affiliation(s)
- Vijay G Sankaran
- Division of Hematology and Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Leonard I Zon
- Division of Hematology and Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Harvard Stem Cell Institute, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Stem Cell Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
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Germline-somatic JAK2 interactions are associated with clonal expansion in myelofibrosis. Nat Commun 2022; 13:5284. [PMID: 36075929 PMCID: PMC9458655 DOI: 10.1038/s41467-022-32986-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 08/25/2022] [Indexed: 12/13/2022] Open
Abstract
Myelofibrosis is a rare myeloproliferative neoplasm (MPN) with high risk for progression to acute myeloid leukemia. Our integrated genomic analysis of up to 933 myelofibrosis cases identifies 6 germline susceptibility loci, 4 of which overlap with previously identified MPN loci. Virtual karyotyping identifies high frequencies of mosaic chromosomal alterations (mCAs), with enrichment at myelofibrosis GWAS susceptibility loci and recurrently somatically mutated MPN genes (e.g., JAK2). We replicate prior MPN associations showing germline variation at the 9p24.1 risk haplotype confers elevated risk of acquiring JAK2V617F mutations, demonstrating with long-read sequencing that this relationship occurs in cis. We also describe recurrent 9p24.1 large mCAs that selectively retained JAK2V617F mutations. Germline variation associated with longer telomeres is associated with increased myelofibrosis risk. Myelofibrosis cases with high-frequency JAK2 mCAs have marked reductions in measured telomere length – suggesting a relationship between telomere biology and myelofibrosis clonal expansion. Our results advance understanding of the germline-somatic interaction at JAK2 and implicate mCAs involving JAK2 as strong promoters of clonal expansion of those mutated clones. Myelofibrosis is a risk factor for the development of Acute Myeloid Leukaemia. Here, the authors carry out an integrated genomic investigation of 933 myelofibrosis patients, and identified interactions between germline and somatic variation in patients who required haematopoietic cell transplantation.
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Cytokine pathway variants modulate platelet production: IFNA16 is a thrombocytosis susceptibility locus in humans. Blood Adv 2022; 6:4884-4900. [PMID: 35381074 PMCID: PMC9631663 DOI: 10.1182/bloodadvances.2021005648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 03/09/2022] [Indexed: 02/08/2023] Open
Abstract
Inflammatory stimuli have divergent effects on peripheral platelet counts, although the mechanisms of thrombocytopenic and thrombocytotic responses remain poorly understood. A candidate gene approach targeting 326 polymorphic genes enriched in thrombopoietic and cytokine signaling pathways was applied to identify single nucleotide variants (SNVs) implicated in enhanced platelet responses in cohorts with reactive thrombocytosis (RT) or essential (myeloproliferative neoplasm [MPN]) thrombocytosis (ET). Cytokine profiles incorporating a 15-member subset, pathway topology, and functional interactive networks were distinct between ET and RT, consistent with distinct regulatory pathways of exaggerated thrombopoiesis. Genetic studies using aggregate (ET + RT) or ET-restricted cohorts identified associations with 2 IFNA16 (interferon-α16) SNVs, and the ET associations were validated in a second independent cohort (P = .0002). Odds ratio of the combined ET cohort (n = 105) was 4.92, restricted to the JAK2V617F-negative subset (odds ratio, 5.01). ET substratification analysis by variant IFNA16 exhibited a statistically significant increase in IFN-α16 levels (P = .002) among 16 quantifiable cytokines. Recombinantly expressed variant IFN-α16 encompassing 3 linked non-synonymous SNVs (E65H95P133) retained comparable antiviral and pSTAT signaling profiles as native IFN-α16 (V65D95A133) or IFN-α2, although both native and variant IFN-α16 showed stage-restricted differences (compared with IFN-α2) of IFN-regulated genes in CD34+-stimulated megakaryocytes. These data implicate IFNA16 (IFN-α16 gene product) as a putative susceptibility locus (driver) within the broader disrupted cytokine network evident in MPNs, and they provide a framework for dissecting functional interactive networks regulating stress or MPN thrombopoiesis.
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