Common and rare variant associations with clonal haematopoiesis phenotypes.
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
12 2022
12 2022
Historique:
received:
23
12
2021
accepted:
14
10
2022
pubmed:
1
12
2022
medline:
15
12
2022
entrez:
30
11
2022
Statut:
ppublish
Résumé
Clonal haematopoiesis involves the expansion of certain blood cell lineages and has been associated with ageing and adverse health outcomes
Identifiants
pubmed: 36450978
doi: 10.1038/s41586-022-05448-9
pii: 10.1038/s41586-022-05448-9
pmc: PMC9713173
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
301-309Subventions
Organisme : Medical Research Council
ID : MC_PC_17228
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_QA137853
Pays : United Kingdom
Commentaires et corrections
Type : CommentIn
Type : ErratumIn
Informations de copyright
© 2022. The Author(s), under exclusive licence to Springer Nature Limited.
Références
Jaiswal, S. et al. Age-related clonal hematopoiesis associated with adverse outcomes. New Engl. J. Med. 371, 2488–2498 (2014).
pubmed: 25426837
doi: 10.1056/NEJMoa1408617
Jaiswal, S. et al. Clonal hematopoiesis and risk of atherosclerotic cardiovascular disease. New Engl. J. Med. 377, 111–121 (2017).
pubmed: 28636844
doi: 10.1056/NEJMoa1701719
Jaiswal, S. & Ebert, B. L. Clonal hematopoiesis in human aging and disease. Science 366, eaan4673 (2019).
pubmed: 31672865
pmcid: 8050831
doi: 10.1126/science.aan4673
Zekavat, S. M. et al. Hematopoietic mosaic chromosomal alterations increase the risk for diverse types of infection. Nat. Med. 27, 1012–1024 (2021).
pubmed: 34099924
pmcid: 8245201
doi: 10.1038/s41591-021-01371-0
Niroula, A. et al. Distinction of lymphoid and myeloid clonal hematopoiesis. Nat. Med. 27, 1921–1927 (2021).
pubmed: 34663986
pmcid: 8621497
doi: 10.1038/s41591-021-01521-4
Bick, A. G. et al. Genetic interleukin 6 signaling deficiency attenuates cardiovascular risk in clonal hematopoiesis. Circulation 141, 124–131 (2020).
pubmed: 31707836
doi: 10.1161/CIRCULATIONAHA.119.044362
Thompson, D. J. et al. Genetic predisposition to mosaic Y chromosome loss in blood. Nature 575, 652–657 (2019).
pubmed: 31748747
pmcid: 6887549
doi: 10.1038/s41586-019-1765-3
Loh, P.-R. et al. Insights into clonal haematopoiesis from 8,342 mosaic chromosomal alterations. Nature 559, 350–355 (2018).
pubmed: 29995854
pmcid: 6054542
doi: 10.1038/s41586-018-0321-x
Akbari, P. et al. Sequencing of 640,000 exomes identifies GPR75 variants associated with protection from obesity. Science 373, eabf8683 (2021).
pubmed: 34210852
doi: 10.1126/science.abf8683
Backman, J. D. et al. Exome sequencing and analysis of 454,787 UK Biobank participants. Nature 599, 628–634 (2021).
pubmed: 34662886
pmcid: 8596853
doi: 10.1038/s41586-021-04103-z
Bick, A. G. et al. Inherited causes of clonal haematopoiesis in 97,691 whole genomes. Nature 586, 763–768 (2020).
pubmed: 33057201
pmcid: 7944936
doi: 10.1038/s41586-020-2819-2
Codd, V. et al. Polygenic basis and biomedical consequences of telomere length variation. Nat. Genet. 53, 1425–1433 (2021).
pubmed: 34611362
pmcid: 8492471
doi: 10.1038/s41588-021-00944-6
Denny, J. C. et al. PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene–disease associations. Bioinformatics 26, 1205–1210 (2010).
pubmed: 20335276
pmcid: 2859132
doi: 10.1093/bioinformatics/btq126
Nédélec, Y. et al. Genetic ancestry and natural selection drive population differences in immune responses to pathogens. Cell 167, 657–669. e21 (2016).
pubmed: 27768889
doi: 10.1016/j.cell.2016.09.025
Joehanes, R. et al. Integrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studies. Genome Biol. 18, 16 (2017).
pubmed: 28122634
pmcid: 5264466
doi: 10.1186/s13059-016-1142-6
Zhernakova, D. V. et al. Identification of context-dependent expression quantitative trait loci in whole blood. Nat. Genet. 49, 139–145 (2017).
pubmed: 27918533
doi: 10.1038/ng.3737
Võsa, U. et al. Large-scale cis-and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression. Nat. Genet. 53, 1300–1310 (2021).
pubmed: 34475573
pmcid: 8432599
doi: 10.1038/s41588-021-00913-z
Gotoh, N. et al. PARP1 V762A polymorphism affects the prognosis of myelodysplastic syndromes. Eurr. J. Haematol. 104, 526–537 (2020).
doi: 10.1111/ejh.13393
Fukaya, T. et al. Conditional ablation of CD205
pubmed: 22736794
pmcid: 3396526
doi: 10.1073/pnas.1202208109
Palamarchuk, A. et al. Tcl1 protein functions as an inhibitor of de novo DNA methylation in B-cell chronic lymphocytic leukemia (CLL). Proc. Natl Acad. Sci. USA 109, 2555–2560 (2012).
pubmed: 22308499
pmcid: 3289317
doi: 10.1073/pnas.1200003109
Bulik-Sullivan, B. K. et al. LD Score regression distinguishes confounding from polygenicity in genome-wide association studies. Nat. Genet. 47, 291–295 (2015).
pubmed: 25642630
pmcid: 4495769
doi: 10.1038/ng.3211
Finucane, H. K. et al. Partitioning heritability by functional annotation using genome-wide association summary statistics. Nat. Genet. 47, 1228–1235 (2015).
pubmed: 26414678
pmcid: 4626285
doi: 10.1038/ng.3404
Sperling, A. S., Gibson, C. J. & Ebert, B. L. The genetics of myelodysplastic syndrome: from clonal haematopoiesis to secondary leukaemia. Nat. Rev. Cancer 17, 5 (2017).
pubmed: 27834397
doi: 10.1038/nrc.2016.112
Dawoud, A. A. Z., Gilbert, R. D., Tapper, W. J. & Cross, N. C. P. Clonal myelopoiesis promotes adverse outcomes in chronic kidney disease. Leukemia 36, 507–515 (2022).
pubmed: 34413458
doi: 10.1038/s41375-021-01382-3
Ostrander, E. L. et al. Divergent effects of Dnmt3a and Tet2 mutations on hematopoietic progenitor cell fitness. Stem Cell Rep. 14, 551–560 (2020).
doi: 10.1016/j.stemcr.2020.02.011
Joo, S. H., Park, J. K., Lee, E. E., Song, Y. W. & Yoon, S.-S. Changes in serum uric acid levels after allogeneic hematologic stem cell transplantation: a retrospective cohort study. Blood Res. 51, 200–203 (2016).
pubmed: 27722132
pmcid: 5054253
doi: 10.5045/br.2016.51.3.200
Reynolds, M. D. Gout and hyperuricemia associated with sickle-cell anemia. Semin. Arthritis Rheum. 12, 404–413 (1983).
pubmed: 6348953
doi: 10.1016/0049-0172(83)90020-3
McAdams-DeMarco, M. A., Maynard, J. W., Coresh, J. & Baer, A. N. Anemia and the onset of gout in a population-based cohort of adults: Atherosclerosis Risk in Communities study. Arthritis Res. Ther. 14, R193 (2012).
pubmed: 22906142
pmcid: 3580590
doi: 10.1186/ar4026
Bolton, K. L. et al. Clonal hematopoiesis is associated with risk of severe Covid-19. Nat. Commun. 12, 5975 (2021).
pubmed: 34645798
pmcid: 8514469
doi: 10.1038/s41467-021-26138-6
Kosmicki, J. A. et al. Pan-ancestry exome-wide association analyses of COVID-19 outcomes in 586,157 individuals. Am. J. Hum. Genet. 108, 1350–1355 (2021).
pubmed: 34115965
doi: 10.1016/j.ajhg.2021.05.017
Smith, M. A., McCaffrey, R. P. & Karp, J. E. The secondary leukemias: challenges and research directions. JNCI 88, 407–418 (1996).
pubmed: 8618232
doi: 10.1093/jnci/88.7.407
Fehrmann, R. S. et al. Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA. PLoS Genet. 7, e1002197 (2011).
pubmed: 21829388
pmcid: 3150446
doi: 10.1371/journal.pgen.1002197
Chaudhuri, A. R. & Nussenzweig, A. The multifaceted roles of PARP1 in DNA repair and chromatin remodelling. Nat. Rev. Mol. Cell Biol. 18, 610–621 (2017).
doi: 10.1038/nrm.2017.53
Jing, C.-B. et al. Synthetic lethal targeting of TET2-mutant hematopoietic stem and progenitor cells (HSPCs) with TOP1-targeted drugs and PARP1 inhibitors. Leukemia 34, 2992–3006 (2020).
pubmed: 32572188
doi: 10.1038/s41375-020-0927-5
Abbotts, R. et al. DNA methyltransferase inhibitors induce a BRCAness phenotype that sensitizes NSCLC to PARP inhibitor and ionizing radiation. Proc. Natl Acad. Sci. USA 116, 22609–22618 (2019).
pubmed: 31591209
pmcid: 6842607
doi: 10.1073/pnas.1903765116
Moore, K. N., Mirza, M. R. & Matulonis, U. A. The poly (ADP ribose) polymerase inhibitor niraparib: management of toxicities. Gynecol. Oncol. 149, 214–220 (2018).
pubmed: 29397193
doi: 10.1016/j.ygyno.2018.01.011
Jiang, W. et al. The receptor DEC-205 expressed by dendritic cells and thymic epithelial cells is involved in antigen processing. Nature 375, 151–155 (1995).
pubmed: 7753172
doi: 10.1038/375151a0
Kato, M. et al. Expression of human DEC-205 (CD205) multilectin receptor on leukocytes. Int. Immunol. 18, 857–869 (2006).
pubmed: 16581822
doi: 10.1093/intimm/dxl022
Kim, P. G. et al. Dnmt3a-mutated clonal hematopoiesis promotes osteoporosis. J. Exp. Med. 218, e20211872 (2021).
pubmed: 34698806
pmcid: 8552148
doi: 10.1084/jem.20211872
Van Hout, C. V. et al. Exome sequencing and characterization of 49,960 individuals in the UK Biobank. Nature 586, 749–756 (2020).
pubmed: 33087929
pmcid: 7759458
doi: 10.1038/s41586-020-2853-0
Ferreira, R. C. et al. Functional IL6R 358Ala allele impairs classical IL-6 receptor signaling and influences risk of diverse inflammatory diseases. PLoS Genet. 9, e1003444 (2013).
pubmed: 23593036
pmcid: 3617094
doi: 10.1371/journal.pgen.1003444
Szustakowski, J. D. et al. Advancing human genetics research and drug discovery through exome sequencing of the UK Biobank. Nat. Genet. 53, 942–948 (2021).
pubmed: 34183854
doi: 10.1038/s41588-021-00885-0
Benjamin, D. et al. Calling Somatic SNVs and Indels with Mutect2. Preprint at bioRxiv https://doi.org/10.1101/861054 (2019).
Karczewski, K. J. et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434–443 (2020).
pubmed: 32461654
pmcid: 7334197
doi: 10.1038/s41586-020-2308-7
Pich, O., Reyes-Salazar, I., Gonzalez-Perez, A. & Lopez-Bigas, N. Discovering the drivers of clonal hematopoiesis. Nat. Commun. 13, 4267 (2022).
pubmed: 35871184
pmcid: 9308779
doi: 10.1038/s41467-022-31878-0
Costello, M. et al. Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation. Nucleic Acids Res. 41, e67 (2013).
pubmed: 23303777
pmcid: 3616734
doi: 10.1093/nar/gks1443
Mbatchou, J. et al. Computationally efficient whole-genome regression for quantitative and binary traits. Nat. Genet. 53, 1097–1103 (2021).
pubmed: 34017140
doi: 10.1038/s41588-021-00870-7
Taliun, D. et al. Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. Nature 590, 290–299 (2021).
pubmed: 33568819
pmcid: 7875770
doi: 10.1038/s41586-021-03205-y
Watanabe, K., Taskesen, E., Van Bochoven, A. & Posthuma, D. Functional mapping and annotation of genetic associations with FUMA. Nat. Commun. 8, 1826 (2017).
pubmed: 29184056
pmcid: 5705698
doi: 10.1038/s41467-017-01261-5
Zhong, H. & Prentice, R. L. Correcting “winner’s curse” in odds ratios from genomewide association findings for major complex human diseases. Genet. Epidemiol. 34, 78–91 (2010).
pubmed: 19639606
pmcid: 2796696
Ghosh, A., Zou, F. & Wright, F. A. Estimating odds ratios in genome scans: an approximate conditional likelihood approach. Am. J. Hum. Genet. 82, 1064–1074 (2008).
pubmed: 18423522
pmcid: 2665019
doi: 10.1016/j.ajhg.2008.03.002
Privé, F., Vilhjálmsson, B. J., Aschard, H. & Blum, M. G. Making the most of clumping and thresholding for polygenic scores. Am. J. Hum. Genet. 105, 1213–1221 (2019).
pubmed: 31761295
pmcid: 6904799
doi: 10.1016/j.ajhg.2019.11.001
Yang, J. et al. Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits. Nat. Genet. 44, 369–375 (2012).
pubmed: 22426310
pmcid: 3593158
doi: 10.1038/ng.2213
Benner, C. et al. FINEMAP: efficient variable selection using summary data from genome-wide association studies. Bioinformatics 32, 1493–1501 (2016).
pubmed: 26773131
pmcid: 4866522
doi: 10.1093/bioinformatics/btw018
Kikushige, Y. et al. Self-renewing hematopoietic stem cell is the primary target in pathogenesis of human chronic lymphocytic leukemia. Cancer Cell 20, 246–259 (2011).
pubmed: 21840488
doi: 10.1016/j.ccr.2011.06.029
Quivoron, C. et al. TET2 inactivation results in pleiotropic hematopoietic abnormalities in mouse and is a recurrent event during human lymphomagenesis. Cancer Cell 20, 25–38 (2011).
pubmed: 21723201
doi: 10.1016/j.ccr.2011.06.003
Couronné, L., Bastard, C. & Bernard, O. A. TET2 and DNMT3A mutations in human T-cell lymphoma. New Engl. J. Med. 366, 95–96 (2012).
pubmed: 22216861
doi: 10.1056/NEJMc1111708
Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).
pubmed: 17701901
pmcid: 1950838
doi: 10.1086/519795