Institute of Biomedical Research and InnovationDepartment of Hematology-Oncology

Research Overview

Understanding and Targeting the Dysregulated Pathways in Malignant or Aged Hematopoiesis

We pursue undetermined mechanisms for developing and sustaining malignant and/or aged hematopoiesis, mainly focusing on post-transcriptional regulation (e.g., pre-mRNA splicing, RNA modification, RNA transport, and translation initiation), cancer-specific metabolic pathways (e.g., ferroptosis), and extrinsic support by the bone marrow (BM) microenvironment. Using novel animal models, high-throughput screening, and patient-derived data, we will explore here-to-fore unrecognized characteristics of malignant and/or aged hematopoiesis and develop a mechanism-based therapeutic approach for malignant and/or aged hematopoiesis.

NEWS

12.25 2023

“BRD9 determines the cell fate of hematopoietic stem cells by regulating chromatin state” published in Nature Communications on December 16, 2023

07.18 2023

“SETBP1 is dispensable for normal and malignant hematopoiesis” Published at Leukemia

07.01 2022

“Aberrant EVI1 splicing contributes to EVI1-rearranged leukemia” Published at Blood

05.10 2022

“MDS cells impair osteolineage differentiation of MSCs via extracellular vesicles to suppress normal hematopoiesis” Published at Cell Reports

04.09 2021

“Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition” Published at Nature Genetics

Member

  • Professor
  • Daichi
    Inoue
Twitter
@DaichiInoue5(External link)
E-mail
d-inoue★fbri.org
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  • Koutarou
    Nishimura
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  • Hiromi
    Yamazaki
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  • Yasutaka
    Hayashi

    1. Masaki Nomura

    1. Miki Fukumoto

    2. Yui Koike

    3. Hiromi Ito

    1. Atsushi Tanaka

    2. Muran Xiao

    3. Yifan Zhang

    4. Weijia Zang

    5. Yumi Aoyama

    6. Wataru Saika

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  • Research focus
  • Publications

Research focus

Cancer cells depend on differential programs for their proliferation, metabolism, and self-renewal than normal cells. Although these are partially attributed to genetic mutations in cancer cells, precise mechanisms largely remain unsolved. In addition, intrinsic and extrinsic pathways are necessary to sustain cancer stemness. Here, we aim to better understand cancers (mainly myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML)), particularly focusing on the following aspects:

(1) Oncogenic mechanisms based on aberrant post-transcriptional regulation
As we understand as "Central dogma", the genetic information on DNA is converted to pre-mRNA and proteins via multiple biological steps, including transcription, RNA processing (e.g., splicing), translation, and post-translational modification. We have reported that genetic information is distorted in various cancers, including hematologic malignancies, in the process of "post-transcriptional regulation," including splicing (Inoue et al. Nature 2019, Inoue et al. Nature Genetics 2021, Tanaka et al. Blood 2022) and RNA modification. For example, the mutations in SF3B1 (the most commonly mutated splicing factor in cancer) lead to the aberrant splicing of the pre-mRNA of BRD9, a central component of the newly-identified chromatin remodeling complex, thereby inducing a disturbed differentiation program (Inoue et al. Nature. 2019, Xiao et al. unpublished data) (Fig. 1). We have also reported that dysregulation of "minor introns" contained only in ~700 evolutionarily significant genes leads to aberrant RAS pathway activation (Inoue et al. Nature Genetics 2021) (Fig. 2). Motivated by these findings, we have performed multiple screening and demonstrated that the regulators in RNA methylation/transport as well as RNA splicing are essential for malignant transformation (Fig. 3). Thus, specific aims in this field are as follows:
  1. - Determine the role of BRD9 in normal and malignant hematopoiesis
  2. - Elucidate the functional connection between minor intron splicing and stemness
  3. - Clarify how malignant hematopoietic stem cells (HSCs) depend on distinct RNA methylation and transport system
  4. - Explore the therapeutic strategies against RNA methylation enzymes and Nuclear Pore Complex (NPC) in AML

(2) Targeting BRD9 for AML treatment and developing a synthetic lethal approach in SF3B1-mutated cancer
Our studies have shown that BRD9 is a promising therapeutic target in various AMLs and rare leukemia with BRD9 translocation by altering three-dimensional chromatin structure. We are applying degraders of BRD9 protein and BRD9 bromodomain inhibitors to pre-clinical models. At the same time, through the efforts in CRISPR-based screening, we are pursuing a synthetic lethal target with BRD9, whose expression is dramatically downregulated in SF3B1-mutated cancer.

(3) Generation of pre-clinical models of poor-prognostic leukemia to elucidate the underlying mechanisms
Over the past 20 years, we have major advances in AML treatment in several subpopulations; however, AMLs without specific treatment still have dismal outcomes. We conduct functional analysis of those AMLs, particularly focusing on AMLs with inversion or translocation of chromosome 3 (inv(3)/t(3;3)) where EVI1 is highly upregulated due to the "enhancer hijacking" and AMLs with SETBP1 or TP53 mutation. We recently demonstrated that frequent SF3B1 mutations in inv(3)/t(3;3) leukemia generate a novel EVI1 isoform with an aberrant second Zinc finger domain, leading to the altered DNA binding preference of EVI1 (Tanaka et al. Blood 2022) (Fig. 4). We are now investigating the specific pathways and molecules that SETBP1 and TP53 mutated AML cells highly depend on by utilizing faithful mimicked animal models and high-throughput technologies such as CRISPR screening.

(4) Clarify how impaired HSCs and BM microenvironment affect each other
A multicellular system of the BM supports HSCs. Thus, HSCs are subject to extrinsic control by mesenchymal stem cells (MSCs), vascular endothelial cells, and osteolineage cells. It has long remained unresolved how MDS cells, which are less proliferative than normal HSCs, inhibit normal hematopoiesis and eventually dominate the BM space. We recently demonstrated that impaired osteolineage differentiation of MSCs plays a pivotal role in the unresolved question in MDS. Specifically, microRNAs transferred by extracellular vesicles from MDS disrupt the BM microenvironment supporting normal HSCs through suppressing an osteolineage differentiation of the normal MSCs (Hayashi et al. Cell Reports 2022) (Fig. 5). We are now pursuing another unrecognized mechanism which can explain the undesired intercellular communication among normal HSCs, modified BM microenvironment, and MDS/AML cells.

(5) Understanding biological effects of "ferroptosis" in AML cells and aged BM for novel therapies
There has been accumulating evidence that various types of cell death physiologically occur. We are particularly paying attention to cell death called "ferroptosis" with iron-dependent lipid peroxidation in aged BM and HSCs. Our data show that normal HSCs and MDS/AML cells have distinct mechanisms for overcoming ferroptosis, which can be applied to the novel therapeutic approach. For this purpose, we investigate how MDS/AML cells behave differently in anti-oxidative machinery, amino acid metabolism, and iron/heme metabolism. Of note, such mechanisms are regulated by the BM microenvironment, motivating us to examine the mediators between HSCs and niche cells.

Publications and Activities

  1. Chen S, Vedula RS, Cuevas-Navarro A, Lu B, Hogg SJ, Wang E, Benbarche S, Knorr K, Kim WJ, Stanley RF, Cho H, Erickson C, Singer M, Cui D, Tittley S, Durham BH, Pavletich TS, Fiala E, Walsh MF, Inoue D, Monette S, Taylor J, Rosen N, McCormick F, Lindsley RC, Castel P, Abdel-Wahab O. Impaired proteolysis of non-canonical RAS proteins drives clonal hematopoietic transformation. Cancer Discov. 2022 Oct 5;12(10):2434-2453.
  2. Nishimura K, Yamazaki H, Zang W, Inoue D. Dysregulated Minor Intron Splicing in Cancer. Cancer Sci. 2022 Sep;113(9):2934-2942.
  3. Tanaka A, Nakano AT, Nomura M, Yamazaki H, Bewersdorf JP, Lazaro RM, Hogg S, Liu B, Penson A, Yokoyama A, Zang W, Havermans M, Koizumi M, Hayashi Y, Cho H, Kanai A, Lee SC, Xiao M, Koike Y, Zhang Y, Fukumoto M, Aoyama Y, Konuma T, Kunimoto H, Inaba T, Nakajima H, Honda H, Kawamoto H, Delwel R, Abdel-Wahab O, Inoue D. Aberrant EVI1 splicing contributes to EVI1-rearranged leukemia. Blood, 2022 Jun 16:blood.2021015325. doi: 10.1182/blood.2021015325. Online ahead of print.
  4. Tanaka A, Nakano AT, Nomura M, Yamazaki H, Bewersdorf JP, Lazaro RM, Hogg S, Liu B, Penson A, Yokoyama A, Zang W, Havermans M, Koizumi M, Hayashi Y, Cho H, Kanai A, Lee SC, Xiao M, Koike Y, Zhang Y, Fukumoto M, Aoyama Y, Konuma T, Kunimoto H, Inaba T, Nakajima H, Honda H, Kawamoto H, Delwel R, Abdel-Wahab O, Inoue D. Aberrant EVI1 splicing contributes to EVI1-rearranged leukemia. Blood, 2022 Aug 25;140(8):875-888.
  5. Inoue D, Polaski JT, Taylor J, Castel P, Chen S, Kobayashi S, Hogg SJ, Hayashi Y, Bello Pineda JM, Ettaib EM, Erickson C, Knorr K, Fukumoto M, Yamazaki H, Tanaka A, Fukui C, Lu XL, Durham BH, Liu B, Wang E, Mehta S, Zakheim D, Grippa R, Penson A, Chew GL, McCormick F, Bradley RK, Abdel-Wahab O. Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition. Nat Genetics, 2021 May;53(5):707-718.
  6. Rahmani NE, Ramachandra N, Sahu S, Gitego N, Lopez A, Pradhan K, Bhagat TD, Gordon-Mitchell S, Pena BR, Kazemi M, Rao K, Giricz O, Maqbool SB, Olea R, Zhao Y, Zhang J, Dolatshad H, Tittrea V, Tatwavedi D, Singh S, Lee J, Sun T, Steidl U, Shastri A, Inoue D, Abdel-Wahab O, Pellagatti A, Gavathiotis E, Boultwood J, Verma A. Blood Cancer J, 2021 Sep 21;11(9):157.
  7. Trivedi G, Inoue D, Zhang L. Targeting low-risk myelodysplastic syndrome with novel therapeutic strategies. Trends Mol Med. 2021 Oct;27(10):990-999.
  8. Fujino T, Goyama S, Sugiura Y, Inoue D, Asada S, Yamasaki S, Matsumoto A, Yamaguchi K, Isobe Y, Tsuchiya A, Shikata S, Sato N, Morinaga H, Fukuyama T, Tanaka Y, Fukushima T, Takeda R, Yamamoto K, Honda H, Nishimura E, Furukawa Y, Shibata T, Abdel-Wahab O, Suematsu M, Kitamura T. Mutant ASXL1 induces age-related expansion of phenotypic hematopoietic stem cells through activation of Akt/mTOR pathway. Nat Commun, Mar 23;12(1):1826. doi: 10.1038/s41467-021-22053-y..
  9. HHEX promotes myeloid transformation in cooperation with mutant ASXL1. Takeda R, Asada S, Park SJ, Yokoyama A, Becker HJ, Kanai A, Visconte V, Hershberger CE, Hayashi Y, Yonezawa T, Tamura M, Fukushima T, Tanaka Y, Fukuyama T, Matsumoto A, Yamasaki S, Nakai K, Yamazaki S, Inaba T, Shibata T, Inoue D, Honda H, Goyama S, Maciejewski JP, Kitamura T. Blood, 2020 Oct 1;136(14):1670-1684.
  10. Inoue D, Chew GL, Liu B, Michel BC, Pangallo J, D’Avino AR, Hitchman T, North K, Lee SC, Bitner L, Ariele B, Moore AR, Yoshimi A, Hoyos LE, Cho H, Penson A, Lu SX, Taylor J, Chen Y, Kadoch C, Abdel-Wahab O, Bradley RK. Spliceosomal disruption of the non-canonical BAF complex in cancer. Nature, 2019 Oct;574(7778):432-436.
  11. Yoshimi A, Lin KT, Wiseman DH, Rahman MA, Pastore1 A, Intlekofer AM, Wang B, Lee SCW, Micol JB, Zhang XJ, Inoue D, Thompson CB, Levine RL, Bradley RK, Abdel-Wahab O. Coordinated Alterations in RNA Splicing and Epigenetic Regulation Drive Leukemogenesis. Nature, 2019 Oct;574(7777):273-277.
  12. Trivedi G, Inoue D, Chen C, Bitner L, Chung YR, Justin T, Gönen M, Wess J, Abdel-Wahab O, and Zhang L. Muscarinic acetylcholine receptor regulates self-renewal of early erythroid progenitors. Sci Transl Med. 2019 Sep 25;11(511).
  13. 12. Taylor J, Sendino M, Gorelick AN, Pastore A, Chang MT, Penson AV, Gavrila EI, Stewart C, Melnik EM, Herrejon Chavez F, Bitner L, Yoshimi A, Lee SC, Inoue D, Liu B, Zhang XJ, Mato AR, Dogan A, Kharas MG, Chen Y, Wang D, Soni RK, Hendrickson RC, Prieto G, Rodriguez JA, Taylor BS, Abdel-Wahab O. Altered nuclear export signal recognition as a driver of oncogenesis. Cancer Discov, 2019 Oct;9(10):1452-1467.
  14. Wang E, Lu SX, Pastore A, Chen X, Imig J, Chun-Wei Lee S, Hockemeyer K, Ghebrechristos YE, Yoshimi A, Inoue D, Ki M, Cho H, Bitner L, Kloetgen A, Lin KT, Uehara T, Owa T, Tibes R, Krainer AR, Abdel-Wahab O, Aifantis I. Targeting an RNA-Binding Protein Network in Acute Myeloid Leukemia. Cancer Cell. 2019 Mar 18;35(3):369-384.
  15. Saika M, Inoue D, Nagase R, Sato N, Tsuchiya A, Yabushita T, Kitamura T, Goyama S. ASXL1 and SETBP1 mutations promote leukaemogenesis by repressing TGFβ pathway genes through histone deacetylation. Sci Rep. 2018 Oct 26;8(1):15873.
  16. Lee SC, North K, Kim E, Jang E, Obeng E, Lu SX, Liu B, Inoue D, Yoshimi A, Ki M, Yeo M, Zhang XJ, Kim MK, Cho H, Chung YR, Taylor J, Durham BH, Kim YJ, Pastore A, Monette S, Palacino J, Seiler M, Buonamici S, Smith PG, Ebert BL, Bradley RK, Abdel-Wahab O. Synthetic Lethal and Convergent Biological Effects of Cancer-Associated Spliceosomal Gene Mutations. Cancer Cell. 2018 Aug 34(2):225-241.
  17. Asada S, Goyama S, InoueD, Shikata S, Takeda R, Fukushima T, Yonezawa T, Fujino T, Hayashi Y, Kawabata KC, Fukuyama T, Tanaka Y, Yokoyama A, Yamazaki S, Kozuka-Hata H, Oyama M, Kojima S, Kawazu M, Mano H, Kitamura T. Mutant ASXL1 cooperates with BAP1 to promote myeloid leukaemogenesis. Nat Commun. 2018 Jul16;9(1):2733.
  18. Taylor J, Pavlick D, Yoshimi A, Marcelus C, Chung SS, Hechtman JF, Benayed R, Cocco E, Durham BH, Bitner L, Inoue D, Chung YR, Mullaney K, Watts JM, Diamond EL, Albacker LA, Mughal TI, Ebata K, Tuch BB, Ku N, Scaltriti M, Roshal M, Arcila M, Ali S, Hyman DM, Park JH, Abdel-Wahab O. Oncogenic TRK fusions are amenable to inhibition in hematologic malignancies. J Clin Invest. 2018 Aug 31;128(9):3819-3825.
  19. Nagase R, Inoue D (co-first and Corresponding author), Pastore A, Fujino T, Hou HA, Yamasaki N, Goyama S, Saika M, Kanai A, Sera Y, Horikawa S, Ota Y, Asada S, Hayashi Y, Kawabata KC, Takeda R, Tien HF, Honda H, Abdel-Wahab O, Kitamura T. Expression of mutant Asxl1 perturbs hematopoiesis and promotes susceptibility to leukemic transformation. J Exp Med. 2018 Jun 215(6):1729-1747.
  20. Inoue D (Corresponding author), Fujino T, Sheridan P, Zhang YZ, Nagase R, Horikawa S, Li Z, Matsui H, Kanai A, Saika M, Yamaguchi R, Kozuka-Hata H, Kawabata KC, Yokoyama A, Goyama S, Inaba T, Imoto S, Miyano S, Xu M, Yang FC, Oyama M, Kitamura T. A novel ASXL1-OGT axis plays roles in H3K4 methylation and tumor suppression in myeloid malignancies. Leukemia. 2018 Jun 32(6):1327-1337.
  21. Kawabata KC, Hayashi Y, Inoue D, Meguro H, Sakurai H, Fukuyama T, Tanaka Y, Asada S, Fukushima T, Nagase R, Takeda R, Harada Y, Kitaura J, Goyama S, Harada H, Aburatani H, Kitamura T. High expression of ABCG2 induced by EZH2 disruption plays pivotal roles in MDS pathogenesis. Leukemia. 2018 Feb 32(2):419-428.
  22. Inoue D, Fujino T, Kitamura T. ASXL1 as a critical regulator of epigenetic marks and therapeutic potential of mutated cells. LOncotarget. 2018 Oct 16;9(81):35203-35204.
  23. Micol JB, Pastore A, Inoue D (co-first author), Duployez N, Kim E, Lee SC, Durham BH, Chung YR, Cho H, Zhang XJ, Yoshimi A, Krivtsov A, Koche R, Solary E, Sinha A, Preudhomme C, Abdel-Wahab O. ASXL2 is essential for haematopoiesis and acts as a haploinsufficient tumour suppressor in leukemia. Nat Commun. 2017 May 18;8:15429, 2017.
  24. Inoue D, Abdel-Wahab O. Modeling SF3B1 Mutations in Cancer: Advances, Challenges, and Opportunities. Cancer Cell. 2016 Sep 12;30(3):371-373.
  25. Inoue D, Bradley RK, Abdel-Wahab O. Spliceosomal gene mutations in myelodysplasia: molecular links to clonal abnormalities of hematopoiesis. Genes Dev. 2016 May 1;30(9):989-1001.

Major Awards in Recent Years

(Daichi Inoue)

  1. • UJA outstanding publication award, United Japanese Researchers Around the World
  2. • Inoue Research Award, Inoue Foundation for Science
  3. • Institute of Biomedical Research and Innovation Director's Award, Foundation for Biomedical Research and Innovation at Kobe
  4. • Foundation for Biomedical Research and Innovation at Kobe President's Award, Foundation for Biomedical Research and Innovation at Kobe
  5. • ASH (American Society of Hematology) Global Research Award, American Society of Hematology
  6. • Kirin-ji Award, Kirin Juku 2021
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