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Genome-wide association study on 13,167 individuals identifies regulators of hematopoietic stem and progenitor cell levels in human blood

Lopez de Lapuente Portilla, Aitzkoa LU ; Ekdahl, Ludvig LU ; Cafaro, Caterina LU ; Ali, Zain LU ; Miharada, Natsumi LU ; Thorleifsson, Gudmar ; Zemaitis, Kristijonas LU ; Lamarca Arrizabalaga, Antton ; Thodberg, Malte LU and Pertesi, Maroulio LU , et al. (2021)
Abstract
Understanding how hematopoietic stem and progenitor cells (HSPCs) are regulated is of central importance for the development of new therapies for blood disorders and stem cell transplantation. To date, HSPC regulation has been extensively studied in vitro and in animal models, but less is known about the mechanisms in vivo in humans. Here, in a genome-wide association study on 13,167 individuals, we identify 9 significant and 2 suggestive DNA sequence variants that influence HSPC (CD34+) levels in human blood. The identified loci associate with blood disorders, harbor known and novel HSPC genes, and affect gene expression in HSPCs. Interestingly, our strongest association maps to the PPM1H gene, encoding an evolutionarily conserved... (More)
Understanding how hematopoietic stem and progenitor cells (HSPCs) are regulated is of central importance for the development of new therapies for blood disorders and stem cell transplantation. To date, HSPC regulation has been extensively studied in vitro and in animal models, but less is known about the mechanisms in vivo in humans. Here, in a genome-wide association study on 13,167 individuals, we identify 9 significant and 2 suggestive DNA sequence variants that influence HSPC (CD34+) levels in human blood. The identified loci associate with blood disorders, harbor known and novel HSPC genes, and affect gene expression in HSPCs. Interestingly, our strongest association maps to the PPM1H gene, encoding an evolutionarily conserved serine/threonine phosphatase never previously implicated in stem cell biology. PPM1H is expressed in HSPCs, and the allele that confers higher blood CD34+ cell levels downregulates PPM1H. By functional fine-mapping, we find that this downregulation is caused by the variant rs772557-A, which abrogates a MYB transcription factor binding site in PPM1H intron 1 that is active in specific HSPC subpopulations, including hematopoietic stem cells, and interacts with the promoter by chromatin looping. Furthermore, rs772557-A selectively increases HSPC subpopulations in which the MYB site is active, and PPM1H shRNA- knockdown increased CD34+ and CD34+90+ cell proportions in umbilical cord blood cultures. Our findings represent the first large-scale association study on a stem cell trait, illuminating HSPC regulation in vivo in humans, and identifying PPM1H as a novel inhibition target that can potentially be utilized clinically to facilitate stem cell harvesting for transplantation. (Less)
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publishing date
type
Working paper/Preprint
publication status
published
subject
publisher
bioRxiv
DOI
10.1101/2021.03.31.437808
language
English
LU publication?
yes
id
93260968-6731-4ef0-9c97-c4231df55ada
date added to LUP
2021-04-21 19:13:47
date last changed
2021-12-07 09:13:09
@misc{93260968-6731-4ef0-9c97-c4231df55ada,
  abstract     = {{Understanding how hematopoietic stem and progenitor cells (HSPCs) are regulated is of central importance for the development of new therapies for blood disorders and stem cell transplantation. To date, HSPC regulation has been extensively studied in vitro and in animal models, but less is known about the mechanisms in vivo in humans. Here, in a genome-wide association study on 13,167 individuals, we identify 9 significant and 2 suggestive DNA sequence variants that influence HSPC (CD34+) levels in human blood. The identified loci associate with blood disorders, harbor known and novel HSPC genes, and affect gene expression in HSPCs. Interestingly, our strongest association maps to the PPM1H gene, encoding an evolutionarily conserved serine/threonine phosphatase never previously implicated in stem cell biology. PPM1H is expressed in HSPCs, and the allele that confers higher blood CD34+ cell levels downregulates PPM1H. By functional fine-mapping, we find that this downregulation is caused by the variant rs772557-A, which abrogates a MYB transcription factor binding site in PPM1H intron 1 that is active in specific HSPC subpopulations, including hematopoietic stem cells, and interacts with the promoter by chromatin looping. Furthermore, rs772557-A selectively increases HSPC subpopulations in which the MYB site is active, and PPM1H shRNA- knockdown increased CD34+ and CD34+90+ cell proportions in umbilical cord blood cultures. Our findings represent the first large-scale association study on a stem cell trait, illuminating HSPC regulation in vivo in humans, and identifying PPM1H as a novel inhibition target that can potentially be utilized clinically to facilitate stem cell harvesting for transplantation.}},
  author       = {{Lopez de Lapuente Portilla, Aitzkoa and Ekdahl, Ludvig and Cafaro, Caterina and Ali, Zain and Miharada, Natsumi and Thorleifsson, Gudmar and Zemaitis, Kristijonas and Lamarca Arrizabalaga, Antton and Thodberg, Malte and Pertesi, Maroulio and Dhapola, Parashar and Bao, Erik L and Niroula, Abhishek and Bali, Divya and Norddahl, Gudmundur L. and Ugidos Damboriena, Nerea and Sankaran, Vijay G and Karlsson, Göran and Thorsteinsdottir, Unnur and Larsson, Jonas and Stefánsson, Kári and Nilsson, Björn}},
  language     = {{eng}},
  month        = {{04}},
  note         = {{Preprint}},
  publisher    = {{bioRxiv}},
  title        = {{Genome-wide association study on 13,167 individuals identifies regulators of hematopoietic stem and progenitor cell levels in human blood}},
  url          = {{http://dx.doi.org/10.1101/2021.03.31.437808}},
  doi          = {{10.1101/2021.03.31.437808}},
  year         = {{2021}},
}