Activation of lineage competence in hemogenic endothelium precedes the formation of hematopoietic stem cell heterogeneity.

Jun Xia, Mengyao Liu, Caiying Zhu, Shicheng Liu, Lanlan Ai, Dongyuan Ma, Ping Zhu, Lu Wang, Feng Liu
Author Information
  1. Jun Xia: State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
  2. Mengyao Liu: 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, China.
  3. Caiying Zhu: 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, China.
  4. Shicheng Liu: State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
  5. Lanlan Ai: 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, China.
  6. Dongyuan Ma: State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
  7. Ping Zhu: 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, China. ORCID
  8. Lu Wang: 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, China. wanglu1@ihcams.ac.cn.
  9. Feng Liu: State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. liuf@ioz.ac.cn. ORCID

Abstract

Hematopoietic stem and progenitor cells (HSPCs) are considered as a heterogeneous population, but precisely when, where and how HSPC heterogeneity arises remain largely unclear. Here, using a combination of single-cell multi-omics, lineage tracing and functional assays, we show that embryonic HSPCs originate from heterogeneous hemogenic endothelial cells (HECs) during zebrafish embryogenesis. Integrated single-cell transcriptome and chromatin accessibility analysis demonstrates transcriptional heterogeneity and regulatory programs that prime lymphoid/myeloid fates at the HEC level. Importantly, spi2 HECs give rise to lymphoid/myeloid-primed HSPCs (L/M-HSPCs) and display a stress-responsive function under acute inflammation. Moreover, we uncover that Spi2 is required for the formation of L/M-HSPCs through tightly controlling the endothelial-to-hematopoietic transition program. Finally, single-cell transcriptional comparison of zebrafish and human HECs and human induced pluripotent stem cell-based hematopoietic differentiation results support the evolutionary conservation of L/M-HECs and a conserved role of SPI1 (spi2 homolog in mammals) in humans. These results unveil the lineage origin, biological function and molecular determinant of HSPC heterogeneity and lay the foundation for new strategies for induction of transplantable lineage-primed HSPCs in vitro.

References

  1. Bioinformatics. 2014 Aug 1;30(15):2114-20 [PMID: 24695404]
  2. J Exp Med. 2017 Oct 2;214(10):2817-2827 [PMID: 28830909]
  3. Nat Protoc. 2010 Mar;5(3):516-35 [PMID: 20203668]
  4. Nat Methods. 2015 Apr;12(4):357-60 [PMID: 25751142]
  5. Nature. 2019 Oct;574(7778):365-371 [PMID: 31597962]
  6. Nat Cell Biol. 2016 Jan;18(1):21-32 [PMID: 26619147]
  7. Immunity. 2019 Jun 18;50(6):1439-1452.e5 [PMID: 31178352]
  8. Nat Immunol. 2003 Dec;4(12):1238-46 [PMID: 14608381]
  9. Dev Cell. 2020 Oct 26;55(2):133-149.e6 [PMID: 32810442]
  10. Nat Protoc. 2014 Jan;9(1):171-81 [PMID: 24385147]
  11. Nature. 2017 May 25;545(7655):439-445 [PMID: 28514438]
  12. Blood. 2013 Jul 18;122(3):367-75 [PMID: 23591790]
  13. Blood. 2005 Dec 1;106(12):3803-10 [PMID: 16099879]
  14. J Exp Med. 2017 Nov 6;214(11):3347-3360 [PMID: 28931624]
  15. Blood. 2021 Jul 8;138(1):23-33 [PMID: 33763704]
  16. Trends Cell Biol. 2018 Dec;28(12):976-986 [PMID: 29935893]
  17. Nature. 2021 Mar;591(7849):281-287 [PMID: 33568815]
  18. Trends Immunol. 2017 May;38(5):345-357 [PMID: 28216309]
  19. Nature. 2007 Jun 21;447(7147):1007-11 [PMID: 17581586]
  20. Dev Biol. 2021 Jul;475:156-164 [PMID: 33689804]
  21. Cell Res. 2015 May;25(5):634-7 [PMID: 25849248]
  22. Dev Cell. 2014 Dec 8;31(5):640-53 [PMID: 25490269]
  23. Trends Cell Biol. 2016 Mar;26(3):202-214 [PMID: 26526106]
  24. Nature. 2010 Mar 4;464(7285):108-11 [PMID: 20154733]
  25. PLoS Pathog. 2018 Jun 8;14(6):e1007063 [PMID: 29883484]
  26. OMICS. 2012 May;16(5):284-7 [PMID: 22455463]
  27. Cell Res. 2015 Oct;25(10):1093-107 [PMID: 26358189]
  28. Dev Dyn. 2007 Nov;236(11):3088-99 [PMID: 17937395]
  29. Exp Hematol. 2005 Feb;33(2):131-43 [PMID: 15676205]
  30. Cell Res. 2017 Aug;27(8):1065-1068 [PMID: 28452344]
  31. Development. 2009 Feb;136(4):647-54 [PMID: 19168679]
  32. Cell Stem Cell. 2012 Jun 14;10(6):690-697 [PMID: 22704509]
  33. Development. 2022 Oct 1;149(19): [PMID: 36178053]
  34. Nat Methods. 2017 Oct;14(10):979-982 [PMID: 28825705]
  35. Nature. 2018 Jan 24;553(7689):418-426 [PMID: 29364285]
  36. Dev Biol. 2002 Aug 15;248(2):307-18 [PMID: 12167406]
  37. Genes Dev. 2014 Dec 1;28(23):2597-612 [PMID: 25395663]
  38. Nature. 2022 Jun;606(7915):747-753 [PMID: 35705805]
  39. Nat Cell Biol. 2018 Jun;20(6):721-734 [PMID: 29802404]
  40. Cell. 2008 Feb 22;132(4):631-44 [PMID: 18295580]
  41. EMBO J. 2017 Oct 16;36(20):2987-2997 [PMID: 28882847]
  42. Nat Methods. 2018 May;15(5):359-362 [PMID: 29608555]
  43. Nat Cell Biol. 2017 Jan 31;19(2):142 [PMID: 28139650]
  44. Int J Biochem Cell Biol. 2008;40(1):22-7 [PMID: 17374502]
  45. Cell Death Differ. 1999 Jul;6(7):599-608 [PMID: 10453070]
  46. Stem Cells Transl Med. 2015 Apr;4(4):309-19 [PMID: 25713465]
  47. Blood Cells Mol Dis. 2013 Dec;51(4):248-55 [PMID: 23927967]
  48. Dev Dyn. 1995 Jul;203(3):253-310 [PMID: 8589427]
  49. Elife. 2020 Jan 06;9: [PMID: 31904340]
  50. Immunity. 2020 Nov 17;53(5):934-951.e9 [PMID: 33159854]
  51. Nat Biotechnol. 2018 Jun;36(5):411-420 [PMID: 29608179]
  52. Cell. 1990 Apr 6;61(1):113-24 [PMID: 2180582]
  53. Nature. 2017 Sep 14;549(7671):273-276 [PMID: 28869969]
  54. Cell Res. 2008 Jun;18(6):677-85 [PMID: 18504458]
  55. Cell Stem Cell. 2015 Jun 4;16(6):712-24 [PMID: 26004780]
  56. Cell. 2014 Nov 20;159(5):1070-1085 [PMID: 25416946]
  57. Cold Spring Harb Symp Quant Biol. 1999;64:13-20 [PMID: 11232277]
  58. Nature. 2022 Apr;604(7906):534-540 [PMID: 35418685]
  59. Mol Cell. 2010 May 28;38(4):576-89 [PMID: 20513432]
  60. Development. 2014 Oct;141(20):4018-30 [PMID: 25252941]
  61. Blood. 2012 Jul 12;120(2):314-22 [PMID: 22668850]
  62. Dev Cell. 2005 Jan;8(1):97-108 [PMID: 15621533]
  63. EMBO J. 2020 Apr 15;39(8):e104270 [PMID: 32149421]
  64. BMC Bioinformatics. 2008 Dec 29;9:559 [PMID: 19114008]
  65. Cell. 2019 Jun 13;177(7):1888-1902.e21 [PMID: 31178118]
  66. Science. 2020 Dec 4;370(6521):1186-1191 [PMID: 33273096]
  67. Cell Rep. 2021 Sep 14;36(11):109703 [PMID: 34525360]
  68. Mol Cell Biol. 2005 Dec;25(23):10338-51 [PMID: 16287849]
  69. Proc Natl Acad Sci U S A. 2009 Aug 11;106(32):13365-70 [PMID: 19628697]
  70. Nat Commun. 2019 Apr 3;10(1):1523 [PMID: 30944313]
  71. Nat Neurosci. 2010 Nov;13(11):1354-6 [PMID: 20935642]
  72. Blood. 2015 Feb 12;125(7):1098-106 [PMID: 25540193]
  73. Cell Rep. 2021 Sep 14;36(11):109675 [PMID: 34525376]
  74. Development. 2013 Oct;140(19):3977-85 [PMID: 24046317]
  75. Cell Stem Cell. 2018 May 3;22(5):627-638 [PMID: 29727678]
  76. Proc Natl Acad Sci U S A. 2021 Apr 6;118(14): [PMID: 33785593]
  77. Nature. 2017 May 25;545(7655):432-438 [PMID: 28514439]
  78. Dev Biol. 2006 Nov 15;299(2):551-62 [PMID: 16999953]
  79. Nat Cell Biol. 2017 Oct;19(10):1153-1163 [PMID: 28920953]
  80. Nat Commun. 2020 Aug 28;11(1):4318 [PMID: 32859930]
  81. Nature. 2022 Sep;609(7928):779-784 [PMID: 36104564]
  82. Cell Res. 2013 Apr;23(4):465-72 [PMID: 23528705]
  83. Dev Cell. 2021 Mar 8;56(5):627-640.e5 [PMID: 33651979]
  84. Development. 2016 Jun 15;143(12):2103-10 [PMID: 27151951]

MeSH Term

Animals
Humans
Hemangioblasts
Zebrafish
Hematopoiesis
Induced Pluripotent Stem Cells
Hematopoietic Stem Cells
Cell Differentiation
Cell Lineage
Mammals

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