Regulation of lymphoid-myeloid lineage bias through regnase-1/3-mediated control of Nfkbiz

Takuya Uehata; Shinnosuke Yamada; Daisuke Ori; Alexis Vandenbon; Amir Giladi; Adam Jelinski; Yasuhiro Murakawa; Hitomi Watanabe; Kazuhiro Takeuchi; Kazunori Toratani; Takashi Mino; Hisanori Kiryu; Daron M. Standley; Tohru Tsujimura; Tomokatsu Ikawa; Gen Kondoh; Markus Landthaler; Hiroshi Kawamoto; Hans Reimer Rodewald; Ido Amit; Ryo Yamamoto; Masaki Miyazaki; Osamu Takeuchi

doi:10.1182/blood.2023020903

Regulation of lymphoid-myeloid lineage bias through regnase-1/3-mediated control of Nfkbiz

Takuya Uehata
, Shinnosuke Yamada
, Daisuke Ori
, Alexis Vandenbon
, Amir Giladi
, Adam Jelinski
, Yasuhiro Murakawa
, Hitomi Watanabe
, Kazuhiro Takeuchi
, Kazunori Toratani
, Takashi Mino
, Hisanori Kiryu
, Daron M. Standley
, Tohru Tsujimura
, Tomokatsu Ikawa
, Gen Kondoh
, Markus Landthaler
, Hiroshi Kawamoto
, Hans Reimer Rodewald
, Ido Amit

Ryo Yamamoto, Masaki Miyazaki, Osamu Takeuchi^*

^*Corresponding author for this work

Department of Systems Immunology

Research output: Contribution to journal › Article › peer-review

9 Citations (Scopus)

Abstract

Regulation of lineage biases in hematopoietic stem and progenitor cells (HSPCs) is pivotal for balanced hematopoietic output. However, little is known about the mechanism behind lineage choice in HSPCs. Here, we show that messenger RNA (mRNA) decay factors regnase-1 (Reg1; Zc3h12a) and regnase-3 (Reg3; Zc3h12c) are essential for determining lymphoid fate and restricting myeloid differentiation in HSPCs. Loss of Reg1 and Reg3 resulted in severe impairment of lymphopoiesis and a mild increase in myelopoiesis in the bone marrow. Single-cell RNA sequencing analysis revealed that Reg1 and Reg3 regulate lineage directions in HSPCs via the control of a set of myeloid-related genes. Reg1- and Reg3-mediated control of mRNA encoding Nfkbiz, a transcriptional and epigenetic regulator, was essential for balancing lymphoid/myeloid lineage output in HSPCs in vivo. Furthermore, single-cell assay for transposase-accessible chromatin sequencing analysis revealed that Reg1 and Reg3 control the epigenetic landscape on myeloid-related gene loci in early stage HSPCs via Nfkbiz. Consistently, an antisense oligonucleotide designed to inhibit Reg1- and Reg3-mediated Nfkbiz mRNA degradation primed hematopoietic stem cells toward myeloid lineages by enhancing Nfkbiz expression. Collectively, the collaboration between posttranscriptional control and chromatin remodeling by the Reg1/Reg3-Nfkbiz axis governs HSPC lineage biases, ultimately dictating the fate of lymphoid vs myeloid differentiation.

Original language	English
Pages (from-to)	243-257
Number of pages	15
Journal	Blood
Volume	143
Issue number	3
DOIs	https://doi.org/10.1182/blood.2023020903
Publication status	Published - 18 Jan 2024

Funding

The authors thank H. Miyachi, S. Kitano, R. Takeda, and S. Nagai for animal technical service; T. Maruyama for providing Nfkbiz flox mice; Y. Agata for plasmid construction of retroviral expression of human Id3, S. Yamazaki for Soluplus, T. Nagasawa, N. Chevrier, and all members of the Takeuchi laboratory for insights and suggestions. Flow cytometric analysis and cell sorting using LSRFortessa (BD Biosciences) and AriaIII (BD Biosciences) were performed at the Medical Research Support Center, Graduate School of Medicine, Kyoto University, which was supported by Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research) from Japan Agency for Medical Research and Development (AMED) (grant number JP20am0101092). Figures were created using BioRender.com. This study was supported by Japan Society for the Promotion of Science KAKENHI (18H05278, 23H00402) (O.T.) and (18K15185) (T.U.) and Core-to-Core Program (O.T.) and grant-in-aid for Scientific Research on Innovative Areas ‘Genome Science’ (221S0002, 16H06279) (T.M.). This study was also supported by AMED (grant numbers JP20gm4010002, JP21ae0121030, 23ama221327h0001) (O.T.) and the Cooperative Research Program (Joint Usage/Research Center program) of Institute for Frontier Life and Medical Sciences, Kyoto University (O.T.) and a grant-in-aid for Transformative Research Areas (A) “Material Symbiosis” (grant 20H05874) (T.U.) and ISHIZUE 2017 of Kyoto University Research Development Program (T.U.), an Office of Directors’ Research Grant provided by the Institute for Frontier Life and Medical Sciences, Kyoto University (A.V.), and the Fujiwara Memorial Foundation (T.U.). Contribution: T.U. and O.T. were in charge of experimental designs, analyses, interpretation of data, and drafting of the manuscript; S.Y. D.O. K. Toratani, and M.M. participated in the acquisition, analysis, and interpretation of data; A.J. A.G. and I.A. handled single cell RNA-sequencing (scRNA-seq) samples and performed analyses on scRNA-seq data; A.V. and K. Takeuchi. performed analysis of scRNA-seq and scATAC-seq (single-cell sequencing assay for transposase-accessible chromatin) data; Y.M. and M.L. performed HITS-CLIP (high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation) of Reg3; H. Kiryu analyzed HITS-CLIP of Reg1 and Reg3; H.W. and G.K. contributed to genetic engineering to generate multiple mouse lines; T.T. performed histological examination; T.I. and R.Y. contributed to in vitro culture of multipotent progenitors and hematopoietic stem cells, respectively; D.M.S. carried out structural modeling; T.M. M.M. R.Y. H.-R.R. and H. Kawamoto provided critical discussions and suggestions; and O.T. supervised the overall study. Publisher Copyright: © 2024 American Society of Hematology

All Science Journal Classification (ASJC) codes

Biochemistry
Immunology
Hematology
Cell Biology

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Uehata, T., Yamada, S., Ori, D., Vandenbon, A., Giladi, A., Jelinski, A., Murakawa, Y., Watanabe, H., Takeuchi, K., Toratani, K., Mino, T., Kiryu, H., Standley, D. M., Tsujimura, T., Ikawa, T., Kondoh, G., Landthaler, M., Kawamoto, H., Rodewald, H. R., ... Takeuchi, O. (2024). Regulation of lymphoid-myeloid lineage bias through regnase-1/3-mediated control of Nfkbiz. Blood, 143(3), 243-257. https://doi.org/10.1182/blood.2023020903

@article{f88a657339b64ec5bef261f9e08d7e3c,

title = "Regulation of lymphoid-myeloid lineage bias through regnase-1/3-mediated control of Nfkbiz",

abstract = "Regulation of lineage biases in hematopoietic stem and progenitor cells (HSPCs) is pivotal for balanced hematopoietic output. However, little is known about the mechanism behind lineage choice in HSPCs. Here, we show that messenger RNA (mRNA) decay factors regnase-1 (Reg1; Zc3h12a) and regnase-3 (Reg3; Zc3h12c) are essential for determining lymphoid fate and restricting myeloid differentiation in HSPCs. Loss of Reg1 and Reg3 resulted in severe impairment of lymphopoiesis and a mild increase in myelopoiesis in the bone marrow. Single-cell RNA sequencing analysis revealed that Reg1 and Reg3 regulate lineage directions in HSPCs via the control of a set of myeloid-related genes. Reg1- and Reg3-mediated control of mRNA encoding Nfkbiz, a transcriptional and epigenetic regulator, was essential for balancing lymphoid/myeloid lineage output in HSPCs in vivo. Furthermore, single-cell assay for transposase-accessible chromatin sequencing analysis revealed that Reg1 and Reg3 control the epigenetic landscape on myeloid-related gene loci in early stage HSPCs via Nfkbiz. Consistently, an antisense oligonucleotide designed to inhibit Reg1- and Reg3-mediated Nfkbiz mRNA degradation primed hematopoietic stem cells toward myeloid lineages by enhancing Nfkbiz expression. Collectively, the collaboration between posttranscriptional control and chromatin remodeling by the Reg1/Reg3-Nfkbiz axis governs HSPC lineage biases, ultimately dictating the fate of lymphoid vs myeloid differentiation.",

author = "Takuya Uehata and Shinnosuke Yamada and Daisuke Ori and Alexis Vandenbon and Amir Giladi and Adam Jelinski and Yasuhiro Murakawa and Hitomi Watanabe and Kazuhiro Takeuchi and Kazunori Toratani and Takashi Mino and Hisanori Kiryu and Standley, \{Daron M.\} and Tohru Tsujimura and Tomokatsu Ikawa and Gen Kondoh and Markus Landthaler and Hiroshi Kawamoto and Rodewald, \{Hans Reimer\} and Ido Amit and Ryo Yamamoto and Masaki Miyazaki and Osamu Takeuchi",

year = "2024",

month = jan,

day = "18",

doi = "10.1182/blood.2023020903",

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volume = "143",

pages = "243--257",

journal = "Blood",

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Uehata, T, Yamada, S, Ori, D, Vandenbon, A, Giladi, A, Jelinski, A, Murakawa, Y, Watanabe, H, Takeuchi, K, Toratani, K, Mino, T, Kiryu, H, Standley, DM, Tsujimura, T, Ikawa, T, Kondoh, G, Landthaler, M, Kawamoto, H, Rodewald, HR, Amit, I, Yamamoto, R, Miyazaki, M & Takeuchi, O 2024, 'Regulation of lymphoid-myeloid lineage bias through regnase-1/3-mediated control of Nfkbiz', Blood, vol. 143, no. 3, pp. 243-257. https://doi.org/10.1182/blood.2023020903

TY - JOUR

T1 - Regulation of lymphoid-myeloid lineage bias through regnase-1/3-mediated control of Nfkbiz

AU - Uehata, Takuya

AU - Yamada, Shinnosuke

AU - Ori, Daisuke

AU - Vandenbon, Alexis

AU - Giladi, Amir

AU - Jelinski, Adam

AU - Murakawa, Yasuhiro

AU - Watanabe, Hitomi

AU - Takeuchi, Kazuhiro

AU - Toratani, Kazunori

AU - Mino, Takashi

AU - Kiryu, Hisanori

AU - Standley, Daron M.

AU - Tsujimura, Tohru

AU - Ikawa, Tomokatsu

AU - Kondoh, Gen

AU - Landthaler, Markus

AU - Kawamoto, Hiroshi

AU - Rodewald, Hans Reimer

AU - Amit, Ido

AU - Yamamoto, Ryo

AU - Miyazaki, Masaki

AU - Takeuchi, Osamu

PY - 2024/1/18

Y1 - 2024/1/18

N2 - Regulation of lineage biases in hematopoietic stem and progenitor cells (HSPCs) is pivotal for balanced hematopoietic output. However, little is known about the mechanism behind lineage choice in HSPCs. Here, we show that messenger RNA (mRNA) decay factors regnase-1 (Reg1; Zc3h12a) and regnase-3 (Reg3; Zc3h12c) are essential for determining lymphoid fate and restricting myeloid differentiation in HSPCs. Loss of Reg1 and Reg3 resulted in severe impairment of lymphopoiesis and a mild increase in myelopoiesis in the bone marrow. Single-cell RNA sequencing analysis revealed that Reg1 and Reg3 regulate lineage directions in HSPCs via the control of a set of myeloid-related genes. Reg1- and Reg3-mediated control of mRNA encoding Nfkbiz, a transcriptional and epigenetic regulator, was essential for balancing lymphoid/myeloid lineage output in HSPCs in vivo. Furthermore, single-cell assay for transposase-accessible chromatin sequencing analysis revealed that Reg1 and Reg3 control the epigenetic landscape on myeloid-related gene loci in early stage HSPCs via Nfkbiz. Consistently, an antisense oligonucleotide designed to inhibit Reg1- and Reg3-mediated Nfkbiz mRNA degradation primed hematopoietic stem cells toward myeloid lineages by enhancing Nfkbiz expression. Collectively, the collaboration between posttranscriptional control and chromatin remodeling by the Reg1/Reg3-Nfkbiz axis governs HSPC lineage biases, ultimately dictating the fate of lymphoid vs myeloid differentiation.

AB - Regulation of lineage biases in hematopoietic stem and progenitor cells (HSPCs) is pivotal for balanced hematopoietic output. However, little is known about the mechanism behind lineage choice in HSPCs. Here, we show that messenger RNA (mRNA) decay factors regnase-1 (Reg1; Zc3h12a) and regnase-3 (Reg3; Zc3h12c) are essential for determining lymphoid fate and restricting myeloid differentiation in HSPCs. Loss of Reg1 and Reg3 resulted in severe impairment of lymphopoiesis and a mild increase in myelopoiesis in the bone marrow. Single-cell RNA sequencing analysis revealed that Reg1 and Reg3 regulate lineage directions in HSPCs via the control of a set of myeloid-related genes. Reg1- and Reg3-mediated control of mRNA encoding Nfkbiz, a transcriptional and epigenetic regulator, was essential for balancing lymphoid/myeloid lineage output in HSPCs in vivo. Furthermore, single-cell assay for transposase-accessible chromatin sequencing analysis revealed that Reg1 and Reg3 control the epigenetic landscape on myeloid-related gene loci in early stage HSPCs via Nfkbiz. Consistently, an antisense oligonucleotide designed to inhibit Reg1- and Reg3-mediated Nfkbiz mRNA degradation primed hematopoietic stem cells toward myeloid lineages by enhancing Nfkbiz expression. Collectively, the collaboration between posttranscriptional control and chromatin remodeling by the Reg1/Reg3-Nfkbiz axis governs HSPC lineage biases, ultimately dictating the fate of lymphoid vs myeloid differentiation.

UR - https://www.scopus.com/pages/publications/85181759820

U2 - 10.1182/blood.2023020903

DO - 10.1182/blood.2023020903

M3 - Article

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AN - SCOPUS:85181759820

SN - 0006-4971

VL - 143

SP - 243

EP - 257

JO - Blood

JF - Blood

IS - 3

ER -

Regulation of lymphoid-myeloid lineage bias through regnase-1/3-mediated control of Nfkbiz

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