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Nishimura A, Yokoyama K, Naruto T, Yamagishi C, Imamura T, Nakazono H, Kimura S, Ito M, Sagisaka M, Tanaka Y, Piao J, Namikawa Y, Yanagimachi M, Isoda T, Kanai A, Matsui H, Isobe T, Sato-Otsubo A, Higuchi N, Takada A, Okuno H, Saito S, Karakawa S, Kobayashi S, Hasegawa D, Fujisaki H, Hasegawa D, Koike K, Koike T, Rai S, Umeda K, Sano H, Sekinaka Y, Ogawa A, Kinoshita A, Shiba N, Miki M, Kimura F, Nakayama H, Nakazawa Y, Taga T, Taki T, Adachi S, Manabe A, Koh K, Ishida Y, Takita J, Ishikawa F, Goto H, Morio T, Mizutani S, Tojo A, Takagi M. Myeloid/natural killer (NK) cell precursor acute leukemia as a distinct leukemia type. SCIENCE ADVANCES 2023; 9:eadj4407. [PMID: 38091391 PMCID: PMC10848711 DOI: 10.1126/sciadv.adj4407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/14/2023] [Indexed: 12/18/2023]
Abstract
Myeloid/natural killer (NK) cell precursor acute leukemia (MNKPL) has been described on the basis of its unique immunophenotype and clinical phenotype. However, there is no consensus on the characteristics for identifying this disease type because of its rarity and lack of defined distinctive molecular characteristics. In this study, multiomics analysis revealed that MNKPL is distinct from acute myeloid leukemia, T cell acute lymphoblastic leukemia, and mixed-phenotype acute leukemia (MPAL), and NOTCH1 and RUNX3 activation and BCL11B down-regulation are hallmarks of MNKPL. Although NK cells have been classically considered to be lymphoid lineage-derived, the results of our single-cell analysis using MNKPL cells suggest that NK cells and myeloid cells share common progenitor cells. Treatment outcomes for MNKPL are unsatisfactory, even when hematopoietic cell transplantation is performed. Multiomics analysis and in vitro drug sensitivity assays revealed increased sensitivity to l-asparaginase and reduced levels of asparagine synthetase (ASNS), supporting the clinically observed effectiveness of l-asparaginase.
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Affiliation(s)
- Akira Nishimura
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kazuaki Yokoyama
- Department of Hematology/Oncology, Research Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takuya Naruto
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Chika Yamagishi
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Toshihiko Imamura
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Leukemia/Lymphoma Committee of Japanese Society of Pediatric Hematology and Oncology, Tokyo, Japan
| | - Hiroto Nakazono
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Shunsuke Kimura
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical Sciences, Hiroshima, Japan
| | - Mieko Ito
- Division of Hematology/Oncology, Kanagawa Children’s Medical Center, Yokohama, Japan
| | - Maiko Sagisaka
- Division of Hematology/Oncology, Kanagawa Children’s Medical Center, Yokohama, Japan
| | - Yukie Tanaka
- Research Core, Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Jinhua Piao
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yui Namikawa
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Masakatsu Yanagimachi
- Division of Hematology/Oncology, Kanagawa Children’s Medical Center, Yokohama, Japan
| | - Takeshi Isoda
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Akinori Kanai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Hirotaka Matsui
- Department of Molecular Laboratory Medicine, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Tomoya Isobe
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Aiko Sato-Otsubo
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Naoko Higuchi
- Department of Pediatrics, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Akiko Takada
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Haruna Okuno
- Department of Pediatrics, Gunma University Hospital, Maebashi, Japan
| | - Shoji Saito
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Shuhei Karakawa
- Department of Pediatrics, Hiroshima University Hospital, Hiroshima, Japan
| | - Shogo Kobayashi
- Department of Pediatric Oncology, Fukushima Medical University Hospital, Fukushima, Japan
| | - Daisuke Hasegawa
- Department of Pediatrics, St. Luke’s International Hospital, Tokyo, Japan
| | - Hiroyuki Fujisaki
- Department of Pediatric Hematology and Oncology, Osaka City General Hospital, Osaka, Japan
| | - Daiichiro Hasegawa
- Department of Hematology and Oncology, Hyogo Prefectural Kobe Children’s Hospital, Kobe, Japan
| | - Kazutoshi Koike
- Division of Pediatric Hematology and Oncology, Ibaraki Children's Hospital, Mito, Japan
| | - Takashi Koike
- Department of Pediatrics, Tokai University School of Medicine, Isehara, Japan
| | - Shinya Rai
- Department of Hematology and Rheumatology, Faculty of Medicine, Kindai University, Osakasayama, Japan
| | - Katsutsugu Umeda
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hideki Sano
- Department of Pediatric Oncology, Fukushima Medical University Hospital, Fukushima, Japan
| | - Yujin Sekinaka
- Department of Pediatrics, National Defense Medical College, Tokorozawa, Japan
| | - Atsushi Ogawa
- Department of Pediatrics, Niigata Cancer Center Hospital, Niigata, Japan
| | - Akitoshi Kinoshita
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Norio Shiba
- Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Mizuka Miki
- Department of Pediatrics, Hiroshima Red Cross Hospital and Atomic-Bomb Survivors Hospital, Hiroshima, Japan
| | - Fumihiko Kimura
- Division of Hematology, Department of Internal Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Hideki Nakayama
- Department of Pediatrics, Kyushu Cancer Center, Fukuoka, Japan
| | - Yozo Nakazawa
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Takashi Taga
- Leukemia/Lymphoma Committee of Japanese Society of Pediatric Hematology and Oncology, Tokyo, Japan
- Department of Pediatrics, Shiga University of Medical Science, Ohtsu, Japan
| | - Tomohiko Taki
- Leukemia/Lymphoma Committee of Japanese Society of Pediatric Hematology and Oncology, Tokyo, Japan
- Department of Medical Technology, Faculty of Health Sciences, Kyorin University, Tokyo, Japan
| | - Souichi Adachi
- Leukemia/Lymphoma Committee of Japanese Society of Pediatric Hematology and Oncology, Tokyo, Japan
- Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Atsushi Manabe
- Leukemia/Lymphoma Committee of Japanese Society of Pediatric Hematology and Oncology, Tokyo, Japan
- Department of Pediatrics, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Katsuyoshi Koh
- Leukemia/Lymphoma Committee of Japanese Society of Pediatric Hematology and Oncology, Tokyo, Japan
- Department of Hematology/Oncology, Saitama Children’s Medical Center, Saitama, Japan
| | - Yasushi Ishida
- Leukemia/Lymphoma Committee of Japanese Society of Pediatric Hematology and Oncology, Tokyo, Japan
- Pediatric Medical Center, Ehime Prefectural Central Hospital, Matsuyama, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fumihiko Ishikawa
- Laboratory for Human Disease Models, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Comprehensive Pathology, Tokyo Medical and Dental University University (TMDU), Tokyo, Japan
| | - Hiroaki Goto
- Division of Hematology/Oncology, Kanagawa Children’s Medical Center, Yokohama, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Shuki Mizutani
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Arinobu Tojo
- Department of Hematology/Oncology, Research Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Data Science and Faculty Affairs, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Masatoshi Takagi
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
- Leukemia/Lymphoma Committee of Japanese Society of Pediatric Hematology and Oncology, Tokyo, Japan
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Ji N, Huang W, Dang H, Xiao H, Shi Y, Guo J, Chen K, Wang J, Zou J. CBFβ is induced by spring viremia of carp virus and promotes virus replication in zebrafish. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 147:104751. [PMID: 37268261 DOI: 10.1016/j.dci.2023.104751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/04/2023]
Abstract
The core binding factor subunit beta (CBFβ) is a transcription factor that forms a complex with virial proteins to promote viral infection. In this study, we identified a CBFβ homolog from zebrafish (zfCBFβ) and characterized the biological activity. The deduced zfCBFβ protein was highly similar to orthologs from other species. The zfcbfβ gene was constitutively expressed in tissues and was induced in immune tissues after infection with spring viremia carp virus (SVCV) and stimulation with poly(I:C). Interestingly, zfcbfβ is not induced by type I interferons. Overexpression of zfcbfβ induced tnfα expression but inhibited isg15 expression. Also, overexpression of zfcbfβ significantly increased SVCV titer in the EPC cells. Co-immunoprecipitation assay revealed that zfCBFβ interacts with SVCV phosphoprotein (SVCVP) and host p53, resulting in the increased stability of zfCBFβ. Our results provide evidence that CBFβ is targeted by virus to suppress host antiviral response.
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Affiliation(s)
- Ning Ji
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Wenji Huang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Huifeng Dang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Hehe Xiao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Yanjie Shi
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Jiahong Guo
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Kangyong Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Junya Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Jun Zou
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266200, China.
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3
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Shin B, Zhou W, Wang J, Gao F, Rothenberg EV. Runx factors launch T cell and innate lymphoid programs via direct and gene network-based mechanisms. Nat Immunol 2023; 24:1458-1472. [PMID: 37563311 PMCID: PMC10673614 DOI: 10.1038/s41590-023-01585-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 07/12/2023] [Indexed: 08/12/2023]
Abstract
Runx factors are essential for lineage specification of various hematopoietic cells, including T lymphocytes. However, they regulate context-specific genes and occupy distinct genomic regions in different cell types. Here, we show that dynamic Runx binding shifts in mouse early T cell development are mostly not restricted by local chromatin state but regulated by Runx dosage and functional partners. Runx cofactors compete to recruit a limited pool of Runx factors in early T progenitor cells, and a modest increase in Runx protein availability at pre-commitment stages causes premature Runx occupancy at post-commitment binding sites. This increased Runx factor availability results in striking T cell lineage developmental acceleration by selectively activating T cell-identity and innate lymphoid cell programs. These programs are collectively regulated by Runx together with other, Runx-induced transcription factors that co-occupy Runx-target genes and propagate gene network changes.
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Affiliation(s)
- Boyoung Shin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Wen Zhou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Program in Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, CA, USA
- BillionToOne, Menlo Park, CA, USA
| | - Jue Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Program in Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, CA, USA
| | - Fan Gao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Bioinformatics Resource Center, Beckman Institute of California Institute of Technology, Pasadena, CA, USA
- Lyterian Therapeutics, South San Francisco, CA, USA
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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4
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Wong P, Foltz JA, Chang L, Neal CC, Yao T, Cubitt CC, Tran J, Kersting-Schadek S, Palakurty S, Jaeger N, Russler-Germain DA, Marin ND, Gang M, Wagner JA, Zhou AY, Jacobs MT, Foster M, Schappe T, Marsala L, McClain E, Pence P, Becker-Hapak M, Fisk B, Petti AA, Griffith OL, Griffith M, Berrien-Elliott MM, Fehniger TA. T-BET and EOMES sustain mature human NK cell identity and antitumor function. J Clin Invest 2023; 133:e162530. [PMID: 37279078 PMCID: PMC10313375 DOI: 10.1172/jci162530] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 05/19/2023] [Indexed: 06/07/2023] Open
Abstract
Since the T-box transcription factors (TFs) T-BET and EOMES are necessary for initiation of NK cell development, their ongoing requirement for mature NK cell homeostasis, function, and molecular programming remains unclear. To address this, T-BET and EOMES were deleted in unexpanded primary human NK cells using CRISPR/Cas9. Deleting these TFs compromised in vivo antitumor response of human NK cells. Mechanistically, T-BET and EOMES were required for normal NK cell proliferation and persistence in vivo. NK cells lacking T-BET and EOMES also exhibited defective responses to cytokine stimulation. Single-cell RNA-Seq revealed a specific T-box transcriptional program in human NK cells, which was rapidly lost following T-BET and EOMES deletion. Further, T-BET- and EOMES-deleted CD56bright NK cells acquired an innate lymphoid cell precursor-like (ILCP-like) profile with increased expression of the ILC-3-associated TFs RORC and AHR, revealing a role for T-box TFs in maintaining mature NK cell phenotypes and an unexpected role of suppressing alternative ILC lineages. Our study reveals the critical importance of sustained EOMES and T-BET expression to orchestrate mature NK cell function and identity.
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Affiliation(s)
- Pamela Wong
- Department of Medicine, Division of Oncology
| | | | - Lily Chang
- Department of Medicine, Division of Oncology
| | | | - Tony Yao
- Department of Medicine, Division of Oncology
| | | | | | | | | | | | | | | | | | | | | | | | - Mark Foster
- Department of Medicine, Division of Oncology
| | | | | | | | | | | | - Bryan Fisk
- Department of Medicine, Division of Oncology
| | | | | | | | | | - Todd A. Fehniger
- Department of Medicine, Division of Oncology
- Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
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Oei V, Chuang LSH, Matsuo J, Srivastava S, Teh M, Ito Y. RUNX3 inactivates oncogenic MYC through disruption of MYC/MAX complex and subsequent recruitment of GSK3β-FBXW7 cascade. Commun Biol 2023; 6:689. [PMID: 37400551 DOI: 10.1038/s42003-023-05037-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 06/12/2023] [Indexed: 07/05/2023] Open
Abstract
MYC is one of the most commonly dysregulated proto-oncogenes in cancer. MYC promotes cancer initiation and maintenance by regulating multiple biological processes, such as proliferation and stem cell function. Here, we show that developmental regulator RUNX3 targets MYC protein for rapid degradation through the glycogen synthase kinase-3 beta-F-box/WD repeat-containing protein 7 (GSK3β-FBXW7) proteolytic pathway. The evolutionarily conserved Runt domain of RUNX3 interacts directly with the basic helix-loop-helix leucine zipper of MYC, resulting in the disruption of MYC/MAX and MYC/MIZ-1 interactions, enhanced GSK3β-mediated phosphorylation of MYC protein at threonine-58 and its subsequent degradation via the ubiquitin-proteasomal pathway. We therefore uncover a previously unknown mode of MYC destabilization by RUNX3 and provide an explanation as to why RUNX3 inhibits early-stage cancer development in gastrointestinal and lung mouse cancer models.
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Affiliation(s)
- Vincent Oei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Graduate School, Integrative Sciences and Engineering Programme, Singapore, Singapore
| | - Linda Shyue Huey Chuang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Junichi Matsuo
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Supriya Srivastava
- Department of Medicine, National University of Singapore, Singapore, Singapore
| | - Ming Teh
- Department of Pathology, National University of Singapore, Singapore, Singapore
| | - Yoshiaki Ito
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
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Kim H, Ahn HS, Hwang N, Huh Y, Bu S, Seo KJ, Kwon SH, Lee HK, Kim JW, Yoon BK, Fang S. Epigenomic landscape exhibits interferon signaling suppression in the patient of myocarditis after BNT162b2 vaccination. Sci Rep 2023; 13:8926. [PMID: 37264110 DOI: 10.1038/s41598-023-36070-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/29/2023] [Indexed: 06/03/2023] Open
Abstract
After the outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, a novel mRNA vaccine (BNT162b2) was developed at an unprecedented speed. Although most countries have achieved widespread immunity from vaccines and infections, yet people, even who have recovered from SARS-CoV-2 infection, are recommended to receive vaccination due to their effectiveness in lowering the risk of recurrent infection. However, the BNT162b2 vaccine has been reported to increase the risk of myocarditis. To our knowledge, for the first time in this study, we tracked changes in the chromatin dynamics of peripheral blood mononuclear cells (PBMCs) in the patient who underwent myocarditis after BNT162b2 vaccination. A longitudinal study of chromatin accessibility using concurrent analysis of single-cell assays for transposase-accessible chromatin with sequencing and single-cell RNA sequencing showed downregulation of interferon signaling and upregulated RUNX2/3 activity in PBMCs. Considering BNT162b2 vaccination increases the level of interferon-α/γ in serum, our data highlight the immune responses different from the conventional responses to the vaccination, which is possibly the key to understanding the side effects of BNT162b2 vaccination.
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Affiliation(s)
- Hyeonhui Kim
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Korea
- Severance Biomedical Science Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Hyo-Suk Ahn
- Division of Cardiology, Department of Internal Medicine, The Catholic University of Korea, Uijeongbu St. Mary's Hospital, Seoul, 06591, Korea
- Catholic Research Institute for Intractable Cardiovascular Disease (CRID), College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea
| | - Nahee Hwang
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Korea
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Yune Huh
- Department of Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Seonghyeon Bu
- Division of Cardiology, Department of Internal Medicine, The Catholic University of Korea, Uijeongbu St. Mary's Hospital, Seoul, 06591, Korea
- Catholic Research Institute for Intractable Cardiovascular Disease (CRID), College of Medicine, The Catholic University of Korea, Seoul, 06591, Korea
| | - Kyung Jin Seo
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Uijeongbu St. Mary's Hospital, Seoul, South Korea
| | - Se Hwan Kwon
- Department of Radiology, Kyung Hee University Medical Center, Seoul, South Korea
| | - Hae-Kyung Lee
- Severance Biomedical Science Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Jae-Woo Kim
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Bo Kyung Yoon
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, 03722, Korea.
| | - Sungsoon Fang
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, Korea.
- Severance Biomedical Science Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, 03722, Korea.
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7
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Roy A, Chauhan S, Bhattacharya S, Jakhmola V, Tyagi K, Sachdeva A, Wasai A, Mandal S. Runt-related transcription factors in human carcinogenesis: a friend or foe? J Cancer Res Clin Oncol 2023:10.1007/s00432-023-04769-0. [PMID: 37081242 DOI: 10.1007/s00432-023-04769-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 04/08/2023] [Indexed: 04/22/2023]
Abstract
PURPOSE Cancer is one of the deadliest pathologies with more than 19 million new cases and 10 million cancer-related deaths across the globe. Despite development of advanced therapeutic interventions, cancer remains as a fatal pathology due to lack of early prognostic biomarkers, therapy resistance and requires identification of novel drug targets. METHODS Runt-related transcription factors (Runx) family controls several cellular and physiological functions including osteogenesis. Recent literatures from PubMed was mined and the review was written in comprehensive manner RESULTS: Recent literature suggests that aberrant expression of Runx contributes to tumorigenesis of many organs. Conversely, cell- and tissue-specific tumor suppressor roles of Runx are also reported. In this review, we have provided the structural/functional properties of Runx isoforms and its regulation in context of human cancer. Moreover, in an urgent need to discover novel therapeutic interventions against cancer, we comprehensively discussed the reported oncogenic and tumor suppressive roles of Runx isoforms in several tumor types and discussed the discrepancies that may have risen on Runx as a driver of malignant transformation. CONCLUSION Runx may be a novel therapeutic target against a battery of deadly human cancers.
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Affiliation(s)
- Adhiraj Roy
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India.
| | - Shivi Chauhan
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Sujata Bhattacharya
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Vibhuti Jakhmola
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Komal Tyagi
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Abha Sachdeva
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Abdul Wasai
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Sector 125, Noida, Uttar Pradesh, 201303, India
| | - Supratim Mandal
- Department of Microbiology, University of Kalyani, Kalyani, Nadia, West Bengal, 741235, India
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8
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Peng L, Renauer PA, Ye L, Yang L, Park JJ, Chow RD, Zhang Y, Lin Q, Bai M, Sanchez A, Zhang Y, Lam SZ, Chen S. Perturbomics of tumor-infiltrating NK cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532653. [PMID: 36993337 PMCID: PMC10055047 DOI: 10.1101/2023.03.14.532653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Natural killer (NK) cells are an innate immune cell type that serves at the first level of defense against pathogens and cancer. NK cells have clinical potential, however, multiple current limitations exist that naturally hinder the successful implementation of NK cell therapy against cancer, including their effector function, persistence, and tumor infiltration. To unbiasedly reveal the functional genetic landscape underlying critical NK cell characteristics against cancer, we perform perturbomics mapping of tumor infiltrating NK cells by joint in vivo AAV-CRISPR screens and single cell sequencing. We establish a strategy with AAV-SleepingBeauty(SB)- CRISPR screening leveraging a custom high-density sgRNA library targeting cell surface genes, and perform four independent in vivo tumor infiltration screens in mouse models of melanoma, breast cancer, pancreatic cancer, and glioblastoma. In parallel, we characterize single-cell transcriptomic landscapes of tumor-infiltrating NK cells, which identifies previously unexplored sub-populations of NK cells with distinct expression profiles, a shift from immature to mature NK (mNK) cells in the tumor microenvironment (TME), and decreased expression of mature marker genes in mNK cells. CALHM2, a calcium homeostasis modulator that emerges from both screen and single cell analyses, shows both in vitro and in vivo efficacy enhancement when perturbed in chimeric antigen receptor (CAR)-NK cells. Differential gene expression analysis reveals that CALHM2 knockout reshapes cytokine production, cell adhesion, and signaling pathways in CAR- NKs. These data directly and systematically map out endogenous factors that naturally limit NK cell function in the TME to offer a broad range of cellular genetic checkpoints as candidates for future engineering to enhance NK cell-based immunotherapies.
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9
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Ding Y, Harly C, Das A, Bhandoola A. Early Development of Innate Lymphoid Cells. Methods Mol Biol 2023; 2580:51-69. [PMID: 36374450 DOI: 10.1007/978-1-0716-2740-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Innate lymphoid cells (ILCs) are transcriptionally and functionally similar to T cells but lack adaptive antigen receptors. They play critical roles in early defense against pathogens. In this review, we summarize recent discoveries of ILC progenitors and discuss possible mechanisms that separate ILCs from T cells. We consider mechanisms of lineage specification in early ILC development and also examine whether differences exist between adult and fetal ILC development.
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Affiliation(s)
- Yi Ding
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA.
| | | | - Arundhoti Das
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Avinash Bhandoola
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA.
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10
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Liu C, Omilusik K, Toma C, Kurd NS, Chang JT, Goldrath AW, Wang W. Systems-level identification of key transcription factors in immune cell specification. PLoS Comput Biol 2022; 18:e1010116. [PMID: 36156073 PMCID: PMC9536753 DOI: 10.1371/journal.pcbi.1010116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 10/06/2022] [Accepted: 08/10/2022] [Indexed: 01/30/2023] Open
Abstract
Transcription factors (TFs) are crucial for regulating cell differentiation during the development of the immune system. However, the key TFs for orchestrating the specification of distinct immune cells are not fully understood. Here, we integrated the transcriptomic and epigenomic measurements in 73 mouse and 61 human primary cell types, respectively, that span the immune cell differentiation pathways. We constructed the cell-type-specific transcriptional regulatory network and assessed the global importance of TFs based on the Taiji framework, which is a method we have previously developed that can infer the global impact of TFs using integrated transcriptomic and epigenetic data. Integrative analysis across cell types revealed putative driver TFs in cell lineage-specific differentiation in both mouse and human systems. We have also identified TF combinations that play important roles in specific developmental stages. Furthermore, we validated the functions of predicted novel TFs in murine CD8+ T cell differentiation and showed the importance of Elf1 and Prdm9 in the effector versus memory T cell fate specification and Kdm2b and Tet3 in promoting differentiation of CD8+ tissue resident memory (Trm) cells, validating the approach. Thus, we have developed a bioinformatic approach that provides a global picture of the regulatory mechanisms that govern cellular differentiation in the immune system and aids the discovery of novel mechanisms in cell fate decisions.
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Affiliation(s)
- Cong Liu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Kyla Omilusik
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Clara Toma
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Nadia S. Kurd
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - John T. Chang
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Ananda W. Goldrath
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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11
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Wahlen S, Matthijssens F, Van Loocke W, Taveirne S, Kiekens L, Persyn E, Van Ammel E, De Vos Z, De Munter S, Matthys P, Van Nieuwerburgh F, Taghon T, Vandekerckhove B, Van Vlierberghe P, Leclercq G. The transcription factor RUNX2 drives the generation of human NK cells and promotes tissue residency. eLife 2022; 11:e80320. [PMID: 35793229 PMCID: PMC9259014 DOI: 10.7554/elife.80320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 05/26/2022] [Indexed: 12/16/2022] Open
Abstract
Natural killer (NK) cells are innate lymphocytes that eliminate virus-infected and cancer cells by cytotoxicity and cytokine secretion. In addition to circulating NK cells, distinct tissue-resident NK subsets have been identified in various organs. Although transcription factors regulating NK cell development and function have been extensively studied in mice, the role of RUNX2 in these processes has not been investigated, neither in mice nor in human. Here, by manipulating RUNX2 expression with either knockdown or overexpression in human haematopoietic stem cell-based NK cell differentiation cultures, combined with transcriptomic and ChIP-sequencing analyses, we established that RUNX2 drives the generation of NK cells, possibly through induction of IL-2Rβ expression in NK progenitor cells. Importantly, RUNX2 promotes tissue residency in human NK cells. Our findings have the potential to improve existing NK cell-based cancer therapies and can impact research fields beyond NK cell biology, since tissue-resident subsets have also been described in other lymphocyte subpopulations.
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Affiliation(s)
- Sigrid Wahlen
- Department of Diagnostic Sciences, Ghent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Filip Matthijssens
- Cancer Research Institute GhentGhentBelgium
- Department of Biomolecular Medicine, Ghent UniversityGhentBelgium
| | - Wouter Van Loocke
- Cancer Research Institute GhentGhentBelgium
- Department of Biomolecular Medicine, Ghent UniversityGhentBelgium
| | - Sylvie Taveirne
- Department of Diagnostic Sciences, Ghent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Laura Kiekens
- Department of Diagnostic Sciences, Ghent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Eva Persyn
- Department of Diagnostic Sciences, Ghent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Els Van Ammel
- Department of Diagnostic Sciences, Ghent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Zenzi De Vos
- Department of Diagnostic Sciences, Ghent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Stijn De Munter
- Department of Diagnostic Sciences, Ghent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Patrick Matthys
- Laboratory of Immunobiology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU LeuvenLeuvenBelgium
| | | | - Tom Taghon
- Department of Diagnostic Sciences, Ghent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Bart Vandekerckhove
- Department of Diagnostic Sciences, Ghent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
| | - Pieter Van Vlierberghe
- Cancer Research Institute GhentGhentBelgium
- Department of Biomolecular Medicine, Ghent UniversityGhentBelgium
| | - Georges Leclercq
- Department of Diagnostic Sciences, Ghent UniversityGhentBelgium
- Cancer Research Institute GhentGhentBelgium
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12
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Kissiov DU, Ethell A, Chen S, Wolf NK, Zhang C, Dang SM, Jo Y, Madsen KN, Paranjpe I, Lee AY, Chim B, Muljo SA, Raulet DH. Binary outcomes of enhancer activity underlie stable random monoallelic expression. eLife 2022; 11:e74204. [PMID: 35617021 PMCID: PMC9135403 DOI: 10.7554/elife.74204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 03/21/2022] [Indexed: 11/21/2022] Open
Abstract
Mitotically stable random monoallelic gene expression (RME) is documented for a small percentage of autosomal genes. We developed an in vivo genetic model to study the role of enhancers in RME using high-resolution single-cell analysis of natural killer (NK) cell receptor gene expression and enhancer deletions in the mouse germline. Enhancers of the RME NK receptor genes were accessible and enriched in H3K27ac on silent and active alleles alike in cells sorted according to allelic expression status, suggesting enhancer activation and gene expression status can be decoupled. In genes with multiple enhancers, enhancer deletion reduced gene expression frequency, in one instance converting the universally expressed gene encoding NKG2D into an RME gene, recapitulating all aspects of natural RME including mitotic stability of both the active and silent states. The results support the binary model of enhancer action, and suggest that RME is a consequence of general properties of gene regulation by enhancers rather than an RME-specific epigenetic program. Therefore, many and perhaps all genes may be subject to some degree of RME. Surprisingly, this was borne out by analysis of several genes that define different major hematopoietic lineages, that were previously thought to be universally expressed within those lineages: the genes encoding NKG2D, CD45, CD8α, and Thy-1. We propose that intrinsically probabilistic gene allele regulation is a general property of enhancer-controlled gene expression, with previously documented RME representing an extreme on a broad continuum.
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Affiliation(s)
- Djem U Kissiov
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Alexander Ethell
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Sean Chen
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Natalie K Wolf
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Chenyu Zhang
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Susanna M Dang
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Yeara Jo
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Katrine N Madsen
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Ishan Paranjpe
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Angus Y Lee
- Cancer Research Laboratory, University of California, BerkeleyBerkeleyUnited States
| | - Bryan Chim
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Stefan A Muljo
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - David H Raulet
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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13
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Fang D, Cui K, Cao Y, Zheng M, Kawabe T, Hu G, Khillan JS, Li D, Zhong C, Jankovic D, Sher A, Zhao K, Zhu J. Differential regulation of transcription factor T-bet induction during NK cell development and T helper-1 cell differentiation. Immunity 2022; 55:639-655.e7. [PMID: 35381213 PMCID: PMC9059963 DOI: 10.1016/j.immuni.2022.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 01/04/2022] [Accepted: 03/08/2022] [Indexed: 12/11/2022]
Abstract
Adaptive CD4+ T helper cells and their innate counterparts, innate lymphoid cells, utilize an identical set of transcription factors (TFs) for their differentiation and functions. However, similarities and differences in the induction of these TFs in related lymphocytes are still elusive. Here, we show that T helper-1 (Th1) cells and natural killer (NK) cells displayed distinct epigenomes at the Tbx21 locus, which encodes T-bet, a critical TF for regulating type 1 immune responses. The initial induction of T-bet in NK precursors was dependent on the NK-specific DNase I hypersensitive site Tbx21-CNS-3, and the expression of the interleukin-18 (IL-18) receptor; IL-18 induced T-bet expression through the transcription factor RUNX3, which bound to Tbx21-CNS-3. By contrast, signal transducer and activator of transcription (STAT)-binding motifs within Tbx21-CNS-12 were critical for IL-12-induced T-bet expression during Th1 cell differentiation both in vitro and in vivo. Thus, type 1 innate and adaptive lymphocytes utilize distinct enhancer elements for their development and differentiation.
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Affiliation(s)
- Difeng Fang
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Kairong Cui
- Laboratory of Epigenome Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaqiang Cao
- Laboratory of Epigenome Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mingzhu Zheng
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Microbiology and Immunology School of Medicine, Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Takeshi Kawabe
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Microbiology and Immunology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Gangqing Hu
- Laboratory of Epigenome Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
| | - Jaspal S Khillan
- Mouse Genetics and Gene Modification Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dan Li
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Clinical Laboratory, the Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China
| | - Chao Zhong
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Dragana Jankovic
- Immunoparasitology Unit, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alan Sher
- Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Keji Zhao
- Laboratory of Epigenome Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinfang Zhu
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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14
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Rawat P, Das A. Differential expression of disparate transcription factor regime holds the key for NK cell development and function modulation. Life Sci 2022; 297:120471. [DOI: 10.1016/j.lfs.2022.120471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 10/18/2022]
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15
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Saini A, Ghoneim HE, Lio CWJ, Collins PL, Oltz EM. Gene Regulatory Circuits in Innate and Adaptive Immune Cells. Annu Rev Immunol 2022; 40:387-411. [PMID: 35119910 DOI: 10.1146/annurev-immunol-101320-025949] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cell identity and function largely rely on the programming of transcriptomes during development and differentiation. Signature gene expression programs are orchestrated by regulatory circuits consisting of cis-acting promoters and enhancers, which respond to a plethora of cues via the action of transcription factors. In turn, transcription factors direct epigenetic modifications to revise chromatin landscapes, and drive contacts between distal promoter-enhancer combinations. In immune cells, regulatory circuits for effector genes are especially complex and flexible, utilizing distinct sets of transcription factors and enhancers, depending on the cues each cell type receives during an infection, after sensing cellular damage, or upon encountering a tumor. Here, we review major players in the coordination of gene regulatory programs within innate and adaptive immune cells, as well as integrative omics approaches that can be leveraged to decipher their underlying circuitry. Expected final online publication date for the Annual Review of Immunology, Volume 40 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Ankita Saini
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Hazem E Ghoneim
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Chan-Wang Jerry Lio
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Patrick L Collins
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Eugene M Oltz
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
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16
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Zhang J, Rousseaux N, Walzer T. Eomes and T‐bet, a dynamic duo regulating NK cell differentiation. Bioessays 2022; 44:e2100281. [DOI: 10.1002/bies.202100281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Jiang Zhang
- Department of Dermatology Brigham and Women's Hospital Harvard Medical School Boston Massachusetts USA
| | - Noémi Rousseaux
- CIRI Centre International de Recherche en Infectiologie CNRS, UMR5308, ENS de Lyon Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1 Lyon France
| | - Thierry Walzer
- CIRI Centre International de Recherche en Infectiologie CNRS, UMR5308, ENS de Lyon Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1 Lyon France
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17
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Vecellio M, Chen L, Cohen CJ, Cortes A, Li Y, Bonham S, Selmi C, Brown MA, Fischer R, Knight JC, Wordsworth BP. Functional Genomic Analysis of a RUNX3 Polymorphism Associated With Ankylosing Spondylitis. Arthritis Rheumatol 2021; 73:980-990. [PMID: 33369221 PMCID: PMC8251554 DOI: 10.1002/art.41628] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 09/28/2020] [Accepted: 12/15/2020] [Indexed: 12/17/2022]
Abstract
OBJECTIVE To investigate the functional consequences of the single-nucleotide polymorphism rs4648889 in a putative enhancer upstream of the RUNX3 promoter associated with susceptibility to ankylosing spondylitis (AS). METHODS Using nuclear extracts from Jurkat cells and primary human CD8+ T cells, the effects of rs4648889 on allele-specific transcription factor (TF) binding were investigated by DNA pull-down assay and quantitative mass spectrometry (qMS), with validation by electrophoretic mobility shift assay (EMSA), Western blotting of the pulled-down eluates, and chromatin immunoprecipitation (ChIP)-quantitative polymerase chain reaction (qPCR) analysis. Further functional effects were tested by small interfering RNA knockdown of the gene for interferon regulatory factor 5 (IRF5), followed by reverse transcription-qPCR (RT-qPCR) and enzyme-linked immunosorbent assay (ELISA) to measure the levels of IFNγ messenger RNA (mRNA) and protein, respectively. RESULTS In nuclear extracts from CD8+ T cells, results of qMS showed that relative TF binding to the AS-risk A allele of rs4648889 was increased 3.7-fold (P < 0.03) for Ikaros family zinc-finger protein 3 (IKZF3; Aiolos) and components of the NuRD complex, including chromodomain helicase DNA binding protein 4 (CHD4) (3.6-fold increase; P < 0.05) and retinoblastoma binding protein 4 (RBBP4) (4.1-fold increase; P < 0.03). In contrast, IRF5 bound significantly more to the AS-protective G allele compared to the AS-risk A allele (fold change 8.2; P = 0.003). Validation with Western blotting, EMSA, and ChIP-qPCR confirmed the differential allelic binding of IKZF3, CHD4, RBBP4, and IRF5. Silencing of IRF5 in CD8+ T cells increased the levels of IFNγ mRNA as measured by RT-qPCR (P = 0.03) and IFNγ protein as measured by ELISA (P = 0.02). CONCLUSION These findings suggest that the association of rs4648889 with AS reflects allele-specific binding of this enhancer-like region to certain TFs, including IRF5, IKZF3, and members of the NuRD complex. IRF5 may have crucial influences on the functions of CD8+ lymphocytes, a finding that could reveal new therapeutic targets for the management of AS.
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Affiliation(s)
- Matteo Vecellio
- NIHR Oxford Musculoskeletal Biomedical Research Unit, Botnar Research Centre, Nuffield Orthopaedic Centre, NIHR Oxford Comprehensive Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Liye Chen
- NIHR Oxford Musculoskeletal Biomedical Research Unit, Botnar Research Centre, Nuffield Orthopaedic Centre, NIHR Oxford Comprehensive Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Carla J Cohen
- NIHR Oxford Musculoskeletal Biomedical Research Unit, Botnar Research Centre, Nuffield Orthopaedic Centre, NIHR Oxford Comprehensive Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Adrian Cortes
- John Radcliffe Hospital, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yan Li
- The First Affiliated Hospital of Xiamen University and Xiamen University School of Medicine, Xiamen, China
| | - Sarah Bonham
- Target Discovery Institute, University of Oxford, Oxford, UK
| | - Carlo Selmi
- IRCCS Humanitas Research Hospital, Milan, Italy
| | - Matthew A Brown
- NIHR Guy's and St. Thomas' Biomedical Research Centre, London, UK, and University of Queensland, Brisbane, Queensland, Australia
| | - Roman Fischer
- Target Discovery Institute, University of Oxford, Oxford, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - B Paul Wordsworth
- NIHR Oxford Musculoskeletal Biomedical Research Unit, Botnar Research Centre, Nuffield Orthopaedic Centre, NIHR Oxford Comprehensive Biomedical Research Centre, University of Oxford, Oxford, UK
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18
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Ghaedi M, Takei F. Innate lymphoid cell development. J Allergy Clin Immunol 2021; 147:1549-1560. [PMID: 33965092 DOI: 10.1016/j.jaci.2021.03.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 12/25/2022]
Abstract
Innate lymphoid cells (ILCs) mainly reside at barrier surfaces and regulate tissue homeostasis and immunity. ILCs are divided into 3 groups, group 1 ILCs, group 2 ILCs, and group 3 ILC3, on the basis of their similar effector programs to T cells. The development of ILCs from lymphoid progenitors in adult mouse bone marrow has been studied in detail, and multiple ILC progenitors have been characterized. ILCs are mostly tissue-resident cells that develop in the perinatal period. More recently, ILC progenitors have also been identified in peripheral tissues. In this review, we discuss the stepwise transcription factor-directed differentiation of mouse ILC progenitors into mature ILCs, the critical time windows in ILC development, and the contribution of bone marrow versus tissue ILC progenitors to the pool of mature ILCs in tissues.
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Affiliation(s)
- Maryam Ghaedi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Fumio Takei
- the Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, British Columbia, Canada; Terry Fox Laboratory, B.C. Cancer, Vancouver, British Columbia, Canada.
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19
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Ye J, Chen Q, Wang R. Logical modeling of thymus and natural killer lymphocyte differentiation. J Biol Phys 2021; 47:31-47. [PMID: 33735399 DOI: 10.1007/s10867-021-09563-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/05/2021] [Indexed: 10/21/2022] Open
Abstract
Thymus (T) and natural killer (NK) lymphocytes are important barriers against diseases. Therefore, it is necessary to understand regulatory mechanisms related to the cell fate decisions involved in the production of these cells. Although some individual information related to T and NK lymphocyte cell fate decisions have been revealed, the related network and its dynamical characteristics still have not been well understood. By integrating individual information and comparing with experimental data, we construct a comprehensive regulatory network and a logical model related to T and NK lymphocyte differentiation. We aim to explore possible mechanisms of how each lineage differentiation is realized by systematically screening individual perturbations. When determining the perturbation strategies, the state transition can be used to identify the roles of specific genes in cell type selection and reprogramming. In agreement with experimental observations, the dynamics of the model correctly restates the cell differentiation processes from common lymphoid progenitors to CD4+ T cells, CD8+ T cells, and NK cells. Our analysis reveals that some specific perturbations can give rise to directional cell differentiation or reprogramming. We test our in silico results by using known experimental observations. The integrated network and the logical model presented here might be a good candidate for providing qualitative mechanisms of cell fate specification involved in T and NK lymphocyte cell fate decisions.
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Affiliation(s)
- Jianting Ye
- Department of Mathematics, Shanghai University, Shanghai, China
| | - Qingxi Chen
- Department of Mathematics, Shanghai University, Shanghai, China
| | - Ruiqi Wang
- Department of Mathematics, Shanghai University, Shanghai, China.
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20
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Dybska E, Adams AT, Duclaux-Loras R, Walkowiak J, Nowak JK. Waiting in the wings: RUNX3 reveals hidden depths of immune regulation with potential implications for inflammatory bowel disease. Scand J Immunol 2021; 93:e13025. [PMID: 33528856 DOI: 10.1111/sji.13025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 01/11/2021] [Accepted: 01/27/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Complex interactions between the environment and the mucosal immune system underlie inflammatory bowel disease (IBD). The involved cytokine signalling pathways are modulated by a number of transcription factors, one of which is runt-related transcription factor 3 (RUNX3). OBJECTIVE To systematically review the immune roles of RUNX3 in immune regulation, with a focus on the context of IBD. METHODS Relevant articles and reviews were identified through a Scopus search in April 2020. Information was categorized by immune cell types, analysed and synthesized. IBD transcriptome data sets and FANTOM5 regulatory networks were processed in order to complement the literature review. RESULTS The available evidence on the immune roles of RUNX3 allowed for its description in twelve cell types: intraepithelial lymphocyte, Th1, Th2, Th17, Treg, double-positive T, cytotoxic T, B, dendritic, innate lymphoid, natural killer and macrophages. In the gut, the activity of RUNX3 is multifaceted and context-dependent: it may promote homeostasis or exacerbated reactions via cytokine signalling and regulation of receptor expression. RUNX3 is mostly engaged in pathways involving ThPOK, T-bet, IFN-γ, TGF-β/IL-2Rβ, GATA/CBF-β, SMAD/p300 and a number of miRNAs. RUNX3 targets relevant to IBD may include RAG1, OSM and IL-17B. Moreover, in IBD RUNX3 expression correlates positively with GZMM, and negatively with IFNAR1, whereas in controls, it strongly associates with TGFBR3. CONCLUSIONS Dysregulation of RUNX3, mostly in the form of deficiency, likely contributes to IBD pathogenesis. More clinical research is needed to examine RUNX3 in IBD.
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Affiliation(s)
- Emilia Dybska
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Alex T Adams
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Rémi Duclaux-Loras
- INSERM U1111, Centre International de Recherche en Infectiologie, Université Claude Bernard Lyon 1, Lyon, France
| | - Jarosław Walkowiak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Jan K Nowak
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
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21
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Beaulieu AM. Transcriptional and epigenetic regulation of memory NK cell responses. Immunol Rev 2021; 300:125-133. [PMID: 33491231 DOI: 10.1111/imr.12947] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/28/2020] [Accepted: 12/31/2020] [Indexed: 12/14/2022]
Abstract
Natural killer (NK) cells are cytotoxic innate lymphocytes with key roles in host protection against viruses and malignancy. Notwithstanding their historical classification as innate immune cells, NK cells are now understood to have some capacity to mount memory or memory-like immune responses in which effector cells undergo antigen-driven expansion and give rise to long-lived memory cells with enhanced functionality. Understanding how antigen-specific effector and memory NK responses are regulated is an important and active area of research in the field. Here, we discuss key transcription factors and epigenetic processes involved in antigen-specific effector and memory NK cell differentiation.
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Affiliation(s)
- Aimee M Beaulieu
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers - The State University of New Jersey, Newark, NJ, USA.,Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers - The State University of New Jersey, Newark, NJ, USA
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22
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Yang C, Malarkannan S. Transcriptional Regulation of NK Cell Development by mTOR Complexes. Front Cell Dev Biol 2020; 8:566090. [PMID: 33240877 PMCID: PMC7683515 DOI: 10.3389/fcell.2020.566090] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/16/2020] [Indexed: 11/13/2022] Open
Abstract
The mechanistic target of Rapamycin (mTOR) is essential for multiple cellular processes. The unique roles of mTOR complex 1 (mTORC1) or mTOR2 in regulating immune functions are emerging. NK cells are the major lymphocyte subset of innate immunity, and their development and effector functions require metabolic reprogramming. Recent studies demonstrate that in NK cells, conditionally disrupting the formation of mTORC1 or mTOR complex 2 (mTORC2) alters their development significantly. Transcriptomic profiling of NK cells at the single-cell level demonstrates that mTORC1 was critical for the early developmental progression, while mTORC2 regulated the terminal maturation. In this review, we summarize the essential roles of mTOR complexes in NK development and functions.
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Affiliation(s)
- Chao Yang
- Laboratory of Molecular Immunology and Immunotherapy, Versiti Blood Research Institute, Milwaukee, WI, United States.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Subramaniam Malarkannan
- Laboratory of Molecular Immunology and Immunotherapy, Versiti Blood Research Institute, Milwaukee, WI, United States.,Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, United States
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23
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Hosokawa H, Romero-Wolf M, Yang Q, Motomura Y, Levanon D, Groner Y, Moro K, Tanaka T, Rothenberg EV. Cell type-specific actions of Bcl11b in early T-lineage and group 2 innate lymphoid cells. J Exp Med 2020; 217:jem.20190972. [PMID: 31653691 PMCID: PMC7037248 DOI: 10.1084/jem.20190972] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/16/2019] [Accepted: 09/27/2019] [Indexed: 01/16/2023] Open
Abstract
Bcl11b binds to distinctive genomic regions with different partners and regulates completely different target genes in pro-T and ILC2 cells. Despite these divergences in Bcl11b function, a shared enhancer supports initial Bcl11b locus opening in both pro-T and ILC2 lineages. The zinc finger transcription factor, Bcl11b, is expressed in T cells and group 2 innate lymphoid cells (ILC2s) among hematopoietic cells. In early T-lineage cells, Bcl11b directly binds and represses the gene encoding the E protein antagonist, Id2, preventing pro-T cells from adopting innate-like fates. In contrast, ILC2s co-express both Bcl11b and Id2. To address this contradiction, we have directly compared Bcl11b action mechanisms in pro-T cells and ILC2s. We found that Bcl11b binding to regions across the genome shows distinct cell type–specific motif preferences. Bcl11b occupies functionally different sites in lineage-specific patterns and controls totally different sets of target genes in these cell types. In addition, Bcl11b bears cell type–specific post-translational modifications and organizes different cell type–specific protein complexes. However, both cell types use the same distal enhancer region to control timing of Bcl11b activation. Therefore, although pro-T cells and ILC2s both need Bcl11b for optimal development and function, Bcl11b works substantially differently in these two cell types.
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Affiliation(s)
- Hiroyuki Hosokawa
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA.,Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Maile Romero-Wolf
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Qi Yang
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY
| | - Yasutaka Motomura
- Laboratory for Innate Immune Systems, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Laboratory for Innate Immune Systems, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | | | | | - Kazuyo Moro
- Laboratory for Innate Immune Systems, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Laboratory for Innate Immune Systems, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan.,Agency for Medical Research and Development - Core Research for Evolutionary Medical Science and Technology (AMED-CREST), Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA
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24
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Stokic-Trtica V, Diefenbach A, Klose CSN. NK Cell Development in Times of Innate Lymphoid Cell Diversity. Front Immunol 2020; 11:813. [PMID: 32733432 PMCID: PMC7360798 DOI: 10.3389/fimmu.2020.00813] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 04/08/2020] [Indexed: 12/31/2022] Open
Abstract
After being described in the 1970s as cytotoxic cells that do not require MHC-dependent pre-activation, natural killer (NK) cells remained the sole member of innate lymphocytes for decades until lymphoid tissue-inducer cells in the 1990s and helper-like innate lymphoid lineages from 2008 onward completed the picture of innate lymphoid cell (ILC) diversity. Since some of the ILC members, such as ILC1s and CCR6- ILC3s, share specific markers previously used to identify NK cells, these findings provoked the question of how to delineate the development of NK cell and helper-like ILCs and how to properly identify and genetically interfere with NK cells. The description of eomesodermin (EOMES) as a lineage-specifying transcription factor of NK cells provided a candidate that may serve as a selective marker for the genetic targeting and identification of NK cells. Unlike helper-like ILCs, NK cell activation is, to a large degree, regulated by the engagement of activating and inhibitory surface receptors. NK cell research has revealed some elegant mechanisms of immunosurveillance, coined "missing-self" and "induced-self" recognition, thus complementing "non-self recognition", which is predominantly utilized by adaptive lymphocytes and myeloid cells. Notably, the balance of activating and inhibitory signals perceived by surface receptors can be therapeutically harnessed for anti-tumor immunity mediated by NK cells. This review aims to summarize the similarities and the differences in development, function, localization, and phenotype of NK cells and helper-like ILCs, with the purpose to highlight the unique feature of NK cell development and regulation.
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Affiliation(s)
- Vladislava Stokic-Trtica
- Department of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Max-Planck Institute for Infection Biology, Berlin, Germany
| | - Andreas Diefenbach
- Department of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany.,Mucosal and Developmental Immunology, Deutsches Rheuma-Forschungszentrum, Berlin, Germany
| | - Christoph S N Klose
- Department of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
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25
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Chauvin JM, Ka M, Pagliano O, Menna C, Ding Q, DeBlasio R, Sanders C, Hou J, Li XY, Ferrone S, Davar D, Kirkwood JM, Johnston RJ, Korman AJ, Smyth MJ, Zarour HM. IL15 Stimulation with TIGIT Blockade Reverses CD155-mediated NK-Cell Dysfunction in Melanoma. Clin Cancer Res 2020; 26:5520-5533. [PMID: 32591463 DOI: 10.1158/1078-0432.ccr-20-0575] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/03/2020] [Accepted: 06/22/2020] [Indexed: 01/05/2023]
Abstract
PURPOSE Natural killer (NK) cells play a critical role in tumor immunosurveillance. Multiple activating and inhibitory receptors (IR) regulate NK-cell-mediated tumor control. The IR T-cell immunoglobulin and ITIM domain (TIGIT) and its counter-receptor CD226 exert opposite effects on NK-cell-mediated tumor reactivity. EXPERIMENTAL DESIGN We evaluated the frequency, phenotype, and functions of NK cells freshly isolated from healthy donors and patients with melanoma with multiparameter flow cytometry. We assessed TIGIT and CD226 cell surface expression and internalization upon binding to CD155. We evaluated the role of IL15 and TIGIT blockade in increasing NK-cell-mediated cytotoxicity in vitro and in two mouse models. RESULTS NK cells are present at low frequencies in metastatic melanoma, are dysfunctional, and downregulate both TIGIT and CD226 expression. As compared with TIGIT- NK cells, TIGIT+ NK cells exhibit higher cytotoxic capacity and maturation, but paradoxically lower cytotoxicity against CD155+ MHC class I-deficient melanoma cells. Membrane bound CD155 triggers CD226 internalization and degradation, resulting in decreased NK-cell-mediated tumor reactivity. IL15 increases TIGIT and CD226 gene expression by tumor-infiltrating NK cells (TiNKs) and, together with TIGIT blockade, increases NK-cell-mediated melanoma cytotoxicity in vitro and decreases tumor metastasis in two mouse melanoma models. Specific deletion of TIGIT on transferred NK cells enhances the antimetastatic activity of IL15, while CD226 blockade decreases the effects of IL15 and TIGIT blockade. CONCLUSIONS Our findings support the development of novel combinatorial immunotherapy with IL15 and TIGIT blockade to promote NK-cell-mediated destruction of MHC class I-deficient melanoma, which are refractory to CD8+ T-cell-mediated immunity.See related commentary by Pietra et al., p. 5274.
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Affiliation(s)
- Joe-Marc Chauvin
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania
| | - Mignane Ka
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania
| | - Ornella Pagliano
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania
| | - Carmine Menna
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania
| | - Quanquan Ding
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania
| | - Richelle DeBlasio
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania
| | - Cindy Sanders
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania
| | - Jiajie Hou
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xian-Yang Li
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Soldano Ferrone
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Diwakar Davar
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania
| | - John M Kirkwood
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania
| | - Robert J Johnston
- Biologics Discovery California, Bristol-Myers Squibb, Redwood City, California
| | - Alan J Korman
- Biologics Discovery California, Bristol-Myers Squibb, Redwood City, California
| | - Mark J Smyth
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Hassane M Zarour
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania. .,Department of Immunology, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania
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26
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Transcriptional Regulation of Natural Killer Cell Development and Functions. Cancers (Basel) 2020; 12:cancers12061591. [PMID: 32560225 PMCID: PMC7352776 DOI: 10.3390/cancers12061591] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/30/2020] [Accepted: 06/13/2020] [Indexed: 02/08/2023] Open
Abstract
Natural killer (NK) cells are the major lymphocyte subset of the innate immune system. Their ability to mediate anti-tumor cytotoxicity and produce cytokines is well-established. However, the molecular mechanisms associated with the development of human or murine NK cells are not fully understood. Knowledge is being gained about the environmental cues, the receptors that sense the cues, signaling pathways, and the transcriptional programs responsible for the development of NK cells. Specifically, a complex network of transcription factors (TFs) following microenvironmental stimuli coordinate the development and maturation of NK cells. Multiple TFs are involved in the development of NK cells in a stage-specific manner. In this review, we summarize the recent advances in the understandings of TFs involved in the regulation of NK cell development, maturation, and effector function, in the aspects of their mechanisms, potential targets, and functions.
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27
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Hantisteanu S, Dicken Y, Negreanu V, Goldenberg D, Brenner O, Leshkowitz D, Lotem J, Levanon D, Groner Y. Runx3 prevents spontaneous colitis by directing the differentiation of anti-inflammatory mononuclear phagocytes. PLoS One 2020; 15:e0233044. [PMID: 32453801 PMCID: PMC7250423 DOI: 10.1371/journal.pone.0233044] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/27/2020] [Indexed: 12/23/2022] Open
Abstract
Mice deficient in the transcription factor Runx3 develop a multitude of immune system defects, including early onset colitis. This paper demonstrates that Runx3 is expressed in colonic mononuclear phagocytes (MNP), including resident macrophages (RM) and dendritic cell subsets (cDC2). Runx3 deletion in MNP causes early onset colitis due to their impaired maturation. Mechanistically, the resulting MNP subset imbalance leads to up-regulation of pro-inflammatory genes as occurs in IL10R-deficient RM. In addition, RM and cDC2 display a marked decrease in expression of anti-inflammatory/TGF β-regulated genes and β-catenin signaling associated genes, respectively. MNP transcriptome and ChIP-seq data analysis suggest that a significant fraction of genes affected by Runx3 loss are direct Runx3 targets. Collectively, Runx3 imposes intestinal immune tolerance by regulating maturation of colonic anti-inflammatory MNP, befitting the identification of RUNX3 as a genome-wide associated risk gene for various immune-related diseases in humans, including gastrointestinal tract diseases such as Crohn’s disease and celiac.
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Affiliation(s)
- Shay Hantisteanu
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Yosef Dicken
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Varda Negreanu
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Dalia Goldenberg
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Ori Brenner
- Veterinary Resources, The Weizmann Institute of Science, Rehovot, Israel
| | - Dena Leshkowitz
- Bioinformatics Unit, The Weizmann Institute of Science, Rehovot, Israel
| | - Joseph Lotem
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Ditsa Levanon
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Yoram Groner
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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28
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Seo W, Taniuchi I. The Roles of RUNX Family Proteins in Development of Immune Cells. Mol Cells 2020; 43:107-113. [PMID: 31926543 PMCID: PMC7057832 DOI: 10.14348/molcells.2019.0291] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 12/12/2019] [Indexed: 02/04/2023] Open
Abstract
The Runt-related transcription factors (RUNX) transcription factors have been known for their critical roles in numerous developmental processes and diseases such as autoimmune disorders and cancer. Especially, RUNX proteins are best known for their roles in hematopoiesis, particularly during the development of T cells. As scientists discover more types of new immune cells, the functional diversity of RUNX proteins also has been increased over time. Furthermore, recent research has revealed complicated transcriptional networks involving RUNX proteins by the current technical advances. Databases established by next generation sequencing data analysis has identified ever increasing numbers of potential targets for RUNX proteins and other transcription factors. Here, we summarize diverse functions of RUNX proteins mainly on lymphoid lineage cells by incorporating recent discoveries.
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Affiliation(s)
- Wooseok Seo
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama 30-0045, Japan
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama 30-0045, Japan
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29
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Valero-Pacheco N, Beaulieu AM. Transcriptional Regulation of Mouse Tissue-Resident Natural Killer Cell Development. Front Immunol 2020; 11:309. [PMID: 32161593 PMCID: PMC7052387 DOI: 10.3389/fimmu.2020.00309] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/07/2020] [Indexed: 12/11/2022] Open
Abstract
Natural killer (NK) cells are cytotoxic innate lymphocytes that are well-known for their ability to kill infected or malignant cells. Beyond their roles in tumor surveillance and anti-pathogen defense, more recent studies have highlighted key roles for NK cells in a broad range of biological processes, including metabolic homeostasis, immunomodulation of T cells, contact hypersensitivity, and pregnancy. Consistent with the breadth and diversity of these functions, it is now appreciated that NK cells are a heterogeneous population, comprised of specialized and sometimes tissue-specific subsets with distinct phenotypes and effector functions. Indeed, in addition to the conventional NK cells (cNKs) that are abundant and have been well-studied in the blood and spleen, distinct subsets of tissue-resident NK cells (trNKs) and "helper" Group 1 innate lymphoid cells (ILC1s) have now been described in multiple organs and tissues, including the liver, uterus, thymus, adipose tissue, and skin, among others. The cNK, trNK, and/or helper ILC1 populations that co-exist in these various tissues exhibit both common and distinct developmental requirements, suggesting that a combination of lineage-, subset-, and tissue-specific differentiation processes may contribute to the unique functional properties of these various populations. Here, we provide an overview of the transcriptional regulatory pathways known to instruct the development and differentiation of cNK, trNK, and helper ILC1 populations in specific tissues in mice.
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Affiliation(s)
- Nuriban Valero-Pacheco
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers – The State University of New Jersey, Newark, NJ, United States
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers – The State University of New Jersey, Newark, NJ, United States
| | - Aimee M. Beaulieu
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers – The State University of New Jersey, Newark, NJ, United States
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers – The State University of New Jersey, Newark, NJ, United States
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30
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Abstract
Specification of multipotent blood precursor cells in postnatal mice to become committed T-cell precursors involves a gene regulatory network of several interacting but functionally distinct modules. Many links of this network have been defined by perturbation tests and by functional genomics. However, using the network model to predict real-life kinetics of the commitment process is still difficult, partly due to the tenacity of repressive chromatin states, and to the ability of transcription factors to affect each other's binding site choices through competitive recruitment to alternative sites ("coregulator theft"). To predict kinetics, future models will need to incorporate mechanistic information about chromatin state change dynamics and more sophisticated understanding of the proteomics and cooperative DNA site choices of transcription factor complexes.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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31
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Mevel R, Draper JE, Lie-A-Ling M, Kouskoff V, Lacaud G. RUNX transcription factors: orchestrators of development. Development 2019; 146:dev148296. [PMID: 31488508 DOI: 10.1242/dev.148296] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
RUNX transcription factors orchestrate many different aspects of biology, including basic cellular and developmental processes, stem cell biology and tumorigenesis. In this Primer, we introduce the molecular hallmarks of the three mammalian RUNX genes, RUNX1, RUNX2 and RUNX3, and discuss the regulation of their activities and their mechanisms of action. We then review their crucial roles in the specification and maintenance of a wide array of tissues during embryonic development and adult homeostasis.
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Affiliation(s)
- Renaud Mevel
- Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Alderley Edge, Macclesfield SK10 4TG, UK
| | - Julia E Draper
- Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Alderley Edge, Macclesfield SK10 4TG, UK
| | - Michael Lie-A-Ling
- Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Alderley Edge, Macclesfield SK10 4TG, UK
| | - Valerie Kouskoff
- Division of Developmental Biology & Medicine, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Georges Lacaud
- Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Alderley Edge, Macclesfield SK10 4TG, UK
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32
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Almeida FF, Jacquelot N, Belz GT. Deconstructing deployment of the innate immune lymphocyte army for barrier homeostasis and protection. Immunol Rev 2019; 286:6-22. [PMID: 30294966 PMCID: PMC6446816 DOI: 10.1111/imr.12709] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/16/2018] [Indexed: 12/30/2022]
Abstract
The study of the immune system has shifted from a purely dichotomous separation between the innate and adaptive arms to one that is now highly complex and reshaping our ideas of how steady‐state health is assured. It is now clear that immune cells do not neatly fit into these two streams and immune homeostasis depends on continual dialogue between multiple lineages of the innate (including dendritic cells, innate lymphoid cells, and unconventional lymphocytes) and adaptive (T and B lymphocytes) arms together with a finely tuned synergy between the host and microbes which is essential to ensure immune homeostasis. Innate lymphoid cells are critical players in this new landscape. Here, we discuss recent studies that have elucidated in detail the development of ILCs from their earliest progenitors and examine factors that influence their identification and ability to drive immune homeostasis and long‐term immune protection.
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Affiliation(s)
- Francisca F Almeida
- Division of Molecular Immunology, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Nicolas Jacquelot
- Division of Molecular Immunology, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Gabrielle T Belz
- Division of Molecular Immunology, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
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33
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RUNX family: Oncogenes or tumor suppressors (Review). Oncol Rep 2019; 42:3-19. [PMID: 31059069 PMCID: PMC6549079 DOI: 10.3892/or.2019.7149] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/11/2019] [Indexed: 02/07/2023] Open
Abstract
Runt-related transcription factor (RUNX) proteins belong to a transcription factors family known as master regulators of important embryonic developmental programs. In the last decade, the whole family has been implicated in the regulation of different oncogenic processes and signaling pathways associated with cancer. Furthermore, a suppressor tumor function has been also reported, suggesting the RUNX family serves key role in all different types of cancer. In this review, the known biological characteristics, specific regulatory abilities and experimental evidence of RUNX proteins will be analyzed to demonstrate their oncogenic potential and tumor suppressor abilities during oncogenic processes, suggesting their importance as biomarkers of cancer. Additionally, the importance of continuing with the molecular studies of RUNX proteins' and its dual functions in cancer will be underlined in order to apply it in the future development of specific diagnostic methods and therapies against different types of cancer.
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Ebihara T, Taniuchi I. Transcription Factors in the Development and Function of Group 2 Innate Lymphoid Cells. Int J Mol Sci 2019; 20:ijms20061377. [PMID: 30893794 PMCID: PMC6470746 DOI: 10.3390/ijms20061377] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 12/18/2022] Open
Abstract
Group 2 innate lymphoid cells (ILC2s) are tissue-resident cells and are a major source of innate TH2 cytokine secretion upon allergen exposure or parasitic-worm infection. Accumulating studies have revealed that transcription factors, including GATA-3, Bcl11b, Gfi1, RORα, and Ets-1, play a role in ILC2 differentiation. Recent reports have further revealed that the characteristics and functions of ILC2 are influenced by the physiological state of the tissues. Specifically, the type of inflammation strongly affects the ILC2 phenotype in tissues. Inhibitory ILC2s, memory-like ILC2s, and ex-ILC2s with ILC1 features acquire their characteristic properties following exposure to their specific inflammatory environment. We have recently reported a new ILC2 population, designated as exhausted-like ILC2s, which emerges after a severe allergic inflammation. Exhausted-like ILC2s are featured with low reactivity and high expression of inhibitory receptors. Therefore, for a more comprehensive understanding of ILC2 function and differentiation, we review the recent knowledge of transcriptional regulation of ILC2 differentiation and discuss the roles of the Runx transcription factor in controlling the emergence of exhausted-like ILC2s. The concept of exhausted-like ILC2s sheds a light on a new aspect of ILC2 biology in allergic diseases.
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Affiliation(s)
- Takashi Ebihara
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
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Fauteux-Daniel S, Faure F, Marotel M, Geary C, Daussy C, Sun JC, Walzer T. Styk1 expression is a hallmark of murine NK cells and other NK1.1 + subsets but is dispensable for NK-cell development and effector functions. Eur J Immunol 2019; 49:677-685. [PMID: 30690705 DOI: 10.1002/eji.201847721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 11/29/2018] [Accepted: 01/24/2019] [Indexed: 02/01/2023]
Abstract
To gain insight into the biology of NK cells, others and we previously identified the NK-cell signature, defined as the set of transcripts which expression is highly enriched in these cells compared to other immune subtypes. The transcript encoding the Serine/threonine/tyrosine kinase 1 (Styk1) is part of this signature. However, the role of Styk1 in the immune system is unknown. Here, we report the generation of a novel transgenic mouse model, in which Styk1 expression is invalidated and replaced by an EGFP reporter cassette. We demonstrated that Styk1 expression is a hallmark of NK cells and other NK1.1 expressing cells such as liver type 1 innate lymphoid cells (ILC1) and NK1.1+ γδ T cells. Styk1 expression is maintained by IL-15 in NK cells and negatively correlates with the expression of educating NK-cell receptors. Analysis of phosphorylation levels of mTOR substrates suggested that Styk1 could moderately contribute to the activity of the PI3K/Akt/mTOR pathway. However, Styk1-deficient NK cells develop normally and have normal in vitro and in vivo effector functions. Thus Styk1 expression is a hallmark of NK cells, ILC1 and NK1.1+ T cells but is dispensable for their development and immune functions.
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Affiliation(s)
- Sébastien Fauteux-Daniel
- CIRI, Centre International de Recherche en Infectiologie - International Center for Infectiology Research, Lyon, France.,Inserm, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,CNRS, UMR5308, Lyon, France
| | - Fabrice Faure
- CIRI, Centre International de Recherche en Infectiologie - International Center for Infectiology Research, Lyon, France.,Inserm, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,CNRS, UMR5308, Lyon, France
| | - Marie Marotel
- CIRI, Centre International de Recherche en Infectiologie - International Center for Infectiology Research, Lyon, France.,Inserm, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,CNRS, UMR5308, Lyon, France
| | - Clair Geary
- Department of Immunology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cécile Daussy
- CIRI, Centre International de Recherche en Infectiologie - International Center for Infectiology Research, Lyon, France.,Inserm, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,CNRS, UMR5308, Lyon, France
| | - Joseph C Sun
- Department of Immunology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thierry Walzer
- CIRI, Centre International de Recherche en Infectiologie - International Center for Infectiology Research, Lyon, France.,Inserm, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,CNRS, UMR5308, Lyon, France
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CD226 regulates natural killer cell antitumor responses via phosphorylation-mediated inactivation of transcription factor FOXO1. Proc Natl Acad Sci U S A 2018; 115:E11731-E11740. [PMID: 30504141 PMCID: PMC6294892 DOI: 10.1073/pnas.1814052115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
CD226 is an important activating receptor involved in mediating natural killer (NK) cell responses against tumors, but how CD226 exerts control over NK cell function is not fully understood. CD226 belongs to the poliovirus receptor (PVR)-nectin family that includes TIGIT and CD96, with TIGIT garnering much attention as a key checkpoint in T cell and NK cell antitumor responses and as an immunotherapy target. Thus, it is imperative to determine how CD226 counteracts the actions of TIGIT and CD96 with which it competes for binding to its ligands such as CD155 (PVR). We demonstrate that CD226 engagement of CD155 is required for phosphorylation of transcription factor FOXO1, resulting in inactivation of its negative regulatory control over NK cell effector function. Natural killer (NK) cell recognition of tumor cells is mediated through activating receptors such as CD226, with suppression of effector functions often controlled by negative regulatory transcription factors such as FOXO1. Here we show that CD226 regulation of NK cell cytotoxicity is facilitated through inactivation of FOXO1. Gene-expression analysis of NK cells isolated from syngeneic tumors grown in wild-type or CD226-deficient mice revealed dysregulated expression of FOXO1-regulated genes in the absence of CD226. In vitro cytotoxicity and stimulation assays demonstrated that CD226 is required for optimal killing of tumor target cells, with engagement of its ligand CD155 resulting in phosphorylation of FOXO1. CD226 deficiency or anti-CD226 antibody blockade impaired cytotoxicity with concomitant compromised inactivation of FOXO1. Furthermore, inhibitors of FOXO1 phosphorylation abrogated CD226-mediated signaling and effector responses. These results define a pathway by which CD226 exerts control of NK cell responses against tumors.
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Brillantes M, Beaulieu AM. Transcriptional control of natural killer cell differentiation. Immunology 2018; 156:111-119. [PMID: 30450565 DOI: 10.1111/imm.13017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/24/2018] [Accepted: 10/24/2018] [Indexed: 01/01/2023] Open
Abstract
Natural killer (NK) cells are highly specialized cytotoxic lymphocytes that provide protection against pathogens and malignant cells. They develop from common lymphoid progenitors via a multi-stage lineage commitment and differentiation process that gives rise to mature NK cells with potent cytotoxic functionality. Although generally considered cells of the innate immune system, recent studies have demonstrated that NK cells have the capacity to mount immune responses with features of adaptive immunity, including robust antigen-specific clonal-like expansion and the generation of long-lived memory cells that mediate enhanced recall responses. Here, we discuss specific transcription factors that have been shown to commonly and uniquely regulate NK cell development and effector and memory responses in experimental mouse models.
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Affiliation(s)
- Marc Brillantes
- Rutgers Graduate School of Biomedical Sciences, Rutgers - The State University of New Jersey, Newark, NJ, USA
| | - Aimee M Beaulieu
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers - The State University of New Jersey, Newark, NJ, USA.,Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers - The State University of New Jersey, Newark, NJ, USA
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38
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Xu ZY, Zhou C, Zhang KF, Zheng YP. Identification of key genes in Ankylosing spondylitis. Immunol Lett 2018; 204:60-66. [PMID: 30321561 DOI: 10.1016/j.imlet.2018.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 03/15/2018] [Accepted: 03/18/2018] [Indexed: 11/24/2022]
Abstract
Ankylosing spondylitis (AS) is a common form of seronegative spondyloarthritis. We had identified differentially expressed genes (DEGs) in AS based on our previous RNA-sequencing results. Our study aimed to identify key genes in AS by integrated microarray analysis. In this present study, we identified 1328 DEGs between AS and normal control by using integrated analysis of two datasets derived from the Gene Expression Omnibus (GEO) database. Functional annotation of DEGs were performed. Pathways in cancer, Pancreatic cancer and Natural killer cell mediated cytotoxicity were significantly enriched pathways for DEGs. Based on the shared DEGs of AS in both integrated analysis and our previous RNA-sequencing results, we constructed the protein and protein interaction (PPI) network. BIRC2, MAPILC3A and MAGED1 were hub proteins. Validation of gene expression by qRT-PCR were performed and the results were consistent with our integrated analysis generally. Our finding provided new clues for understanding the mechanism of AS.
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Affiliation(s)
- Zhong-Yang Xu
- Department of Orthopaedics, Jining NO.1 People's Hospital, China; Department of Orthopaedics, Sandong University Qilu Hospital, China
| | - Chao Zhou
- Department of Orthopaedics, Sandong University Qilu Hospital, China
| | - Ke-Feng Zhang
- Department of Orthopaedics, Jining NO.1 People's Hospital, China
| | - Yan-Ping Zheng
- Department of Orthopaedics, Sandong University Qilu Hospital, China.
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Yin S, Yu J, Hu B, Lu C, Liu X, Gao X, Li W, Zhou L, Wang J, Wang D, Lu L, Wang L. Runx3 Mediates Resistance to Intracellular Bacterial Infection by Promoting IL12 Signaling in Group 1 ILC and NCR+ILC3. Front Immunol 2018; 9:2101. [PMID: 30258450 PMCID: PMC6144956 DOI: 10.3389/fimmu.2018.02101] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/24/2018] [Indexed: 12/20/2022] Open
Abstract
Innate lymphoid cells (ILCs) are the most recently identified family of the innate immune system and are hypothesized to modulate immune functions prior to the generation of adaptive immune responses. Subsets of ILCs reside in the mucosa and regulate immune responses to external pathogens; however, their role and the mechanism by which they protect against intracellular bacterial infection is not completely understood. In this report, using S. typhimurium and L. monocytogenes, we found that the levels of group 1 ILCs and NCR+ ILC3s were increased upon infection and that these increases were associated with Runt-related transcription factor 3 (Runx3) expression. Runx3 fl/fl PLZF-cre mice were much more sensitive to infection with the intracellular bacterial pathogens S. typhimurium and L. monocytogenes partially due to abnormal Group 1 ILC and NCR+ILC3 function. We also found that Runx3 directly binds to the Il12Rβ2 promoter and intron 8 to accelerate the expression of Il12Rβ2 and modulates IFNγ secretion triggered by the IL12/ STAT4 axis. Therefore, we demonstrate that Runx3 influences group 1 ILC- and NCR+ILC3-mediated immune protection against intracellular bacterial infections of both the gut and liver.
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Affiliation(s)
- Shengxia Yin
- Institute of Immunology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Jingjing Yu
- Institute of Immunology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Bian Hu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Chenyu Lu
- Institute of Immunology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Xia Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Department of Laboratory Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xianzhi Gao
- Institute of Immunology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Wei Li
- Laboraty Animal Center, Zhejiang University, Hangzhou, China
| | - Lina Zhou
- Institute of Immunology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Jianli Wang
- Institute of Immunology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Di Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China
| | - Linrong Lu
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China
| | - Lie Wang
- Institute of Immunology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China.,Laboraty Animal Center, Zhejiang University, Hangzhou, China
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40
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Held W, Jeevan-Raj B, Charmoy M. Transcriptional regulation of murine natural killer cell development, differentiation and maturation. Cell Mol Life Sci 2018; 75:3371-3379. [PMID: 29959459 PMCID: PMC11105435 DOI: 10.1007/s00018-018-2865-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/13/2018] [Accepted: 06/27/2018] [Indexed: 01/20/2023]
Abstract
Natural killer (NK) cells are innate cytotoxic effector cells that play important protective roles against certain pathogens as well as against pathogen-infected and transformed host cells. NK cells continuously arise from adult bone marrow-resident haematopoietic progenitors. Their generation can be sub-divided into three phases. The early NK cell development phase from multipotent common lymphoid progenitors occurs at least in part in common with that of additional members of a family of innate lymphoid cells, for which NK cells are the founding member. An intermediate phase of NK cell differentiation is characterized by the acquisition of IL-15 responsiveness and lineage-defining properties such as the transcription of genes coding for cytotoxic effector molecules. This is followed by a late maturation phase during which NK cells lose homeostatic expansion and increase effector capacity. These three phases are regulated by multiple stage-specific but not NK cell-specific transcription factors. This review summarizes the NK cell developmental and maturation processes and their transcriptional regulation with an emphasis on data derived from genetically modified mouse models.
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Affiliation(s)
- Werner Held
- Department of Oncology UNIL CHUV, University of Lausanne, Ch. des Boveresses 155, 1066, Epalinges, Switzerland.
| | - Beena Jeevan-Raj
- Department of Oncology UNIL CHUV, University of Lausanne, Ch. des Boveresses 155, 1066, Epalinges, Switzerland
| | - Mélanie Charmoy
- Department of Oncology UNIL CHUV, University of Lausanne, Ch. des Boveresses 155, 1066, Epalinges, Switzerland
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41
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Liquitaya-Montiel AJ, Mendoza L. Dynamical Analysis of the Regulatory Network Controlling Natural Killer Cells Differentiation. Front Physiol 2018; 9:1029. [PMID: 30116200 PMCID: PMC6082967 DOI: 10.3389/fphys.2018.01029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/11/2018] [Indexed: 12/22/2022] Open
Abstract
Many disease fighting strategies have focused on the generation of NK cells, since they constitute the main immune barrier against cancer and intracellular pathogens such as viruses. Therefore, a predictive model for the development of NK cells would constitute a useful tool to test several hypotheses regarding the production of these cells during both physiological and pathological conditions. Here, we present a boolean network model that reproduces experimental results reported on the literature regarding the progressive stages of the development of NK cells in wild-type and mutant backgrounds. The model allows for the simulation of different conditions, including extracellular micro-environment as well as the simulation of genetic alterations. It also describes how NK cell differentiation depends on a molecular regulatory network that controls the specification of lymphoid lineages, such as T and B cells, which share a common progenitor with NKs. Furthermore, the study shows that the structure of the regulatory network strongly determines the stability of the expression patterns against perturbations.
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Affiliation(s)
- Adhemar J. Liquitaya-Montiel
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Programa de Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Luis Mendoza
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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42
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Monomethylarsonous acid: Induction of DNA damage and oxidative stress in mouse natural killer cells at environmentally-relevant concentrations. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2018; 832-833:1-6. [DOI: 10.1016/j.mrgentox.2018.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/21/2018] [Accepted: 05/21/2018] [Indexed: 12/11/2022]
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Rapp M, Lau CM, Adams NM, Weizman OE, O'Sullivan TE, Geary CD, Sun JC. Core-binding factor β and Runx transcription factors promote adaptive natural killer cell responses. Sci Immunol 2018; 2:2/18/eaan3796. [PMID: 29222089 DOI: 10.1126/sciimmunol.aan3796] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 09/12/2017] [Accepted: 11/02/2017] [Indexed: 01/03/2023]
Abstract
Natural killer (NK) cells are innate lymphocytes that have features of adaptive immunity such as clonal expansion and generation of long-lived memory. Interleukin-12 (IL-12) signaling through its downstream transcription factor signal transducer and activator of transcription 4 (STAT4) is required for the generation of memory NK cells after expansion. We identify gene loci that are highly enriched for STAT4 binding using chromatin immunoprecipitation sequencing for STAT4 and the permissive histone mark H3K4me3 in activated NK cells. We found that promoter regions of Runx1 and Runx3 are targets of STAT4 and that STAT4 binding during NK cell activation induces epigenetic modifications of Runx gene loci resulting in increased expression. Furthermore, specific ablation of Runx1, Runx3, or their binding partner Cbfb in NK cells resulted in defective clonal expansion and memory formation during viral infection, with evidence for Runx1-mediated control of a cell cycle program. Thus, our study reveals a mechanism whereby STAT4-mediated epigenetic control of individual Runx transcription factors promotes the adaptive behavior of antiviral NK cells.
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Affiliation(s)
- Moritz Rapp
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Colleen M Lau
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nicholas M Adams
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Orr-El Weizman
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Timothy E O'Sullivan
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Clair D Geary
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. .,Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY 10065, USA
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44
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Schöneberg T, Meister J, Knierim AB, Schulz A. The G protein-coupled receptor GPR34 - The past 20 years of a grownup. Pharmacol Ther 2018; 189:71-88. [PMID: 29684466 DOI: 10.1016/j.pharmthera.2018.04.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Research on GPR34, which was discovered in 1999 as an orphan G protein-coupled receptor of the rhodopsin-like class, disclosed its physiologic relevance only piece by piece. Being present in all recent vertebrate genomes analyzed so far it seems to improve the fitness of species although it is not essential for life and reproduction as GPR34-deficient mice demonstrate. However, closer inspection of macrophages and microglia, where it is mainly expressed, revealed its relevance in immune cell function. Recent data clearly demonstrate that GPR34 function is required to arrest microglia in the M0 homeostatic non-phagocytic phenotype. Herein, we summarize the current knowledge on its evolution, genomic and structural organization, physiology, pharmacology and relevance in human diseases including neurodegenerative diseases and cancer, which accumulated over the last 20 years.
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Affiliation(s)
- Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany.
| | - Jaroslawna Meister
- Molecular Signaling Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, United States
| | - Alexander Bernd Knierim
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany; Leipzig University Medical Center, IFB AdiposityDiseases, 04103 Leipzig, Germany
| | - Angela Schulz
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
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45
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MiR-544 promotes immune escape through downregulation of NCR1/NKp46 via targeting RUNX3 in liver cancer. Cancer Cell Int 2018; 18:52. [PMID: 29636640 PMCID: PMC5883289 DOI: 10.1186/s12935-018-0542-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 03/14/2018] [Indexed: 02/06/2023] Open
Abstract
Objective To study the potential role of miR-544 in the immune escape mechanism of hepatoma cells. Methods Natural killer (NK) cells were collected from healthy volunteers and patients with liver cancer. Interleukin (IL)-2 activated-NK-92 cells were transfected with miR-544 inhibitor/mimic or NC/pre-NC in HepG2 co-culture system. NK-92 cells were treated with control, IL-2, IL-2 + pre-NC, IL-2 + miR-544 mimic, IL-2 + miR-544 mimic + pcDNA and IL-2 + miR-544 mimic + pcDNA-runt-related transcription factor 3 (RUNX3) groups. Mice models of liver cancer were well established. Expression of miR-544, natural cytotoxicity receptor 1 (NCR1) and RUNX3 were evaluated by quantitative real-time PCR and western blotting. Flow cytometry and ELISA were used to determine NK cell cytotoxicity and the levels of INF-γ, respectively. Results MiR-544 was upregulated while NCR1 and RUNX3 was downregulated in NK cells of patients with liver cancer. The levels of IFN-γ and miR-544 expression were increased and decreased in IL-2 activated-NK cells, respectively. Inversely, miR-544 overexpression inhibited NK cell cytotoxicity by downregulating IFN-γ. However, miR-544 directly targeted RUNX3 and negatively regulated NCR1. Furthermore, miR-544 promoted immune escape of hepatoma cells in vivo and in vitro. Conclusion miR-544 promoted the immune escape of liver cancer cells by downregulating NCR1 via targeting RUNX3.
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Su W, Du L, Liu S, Deng J, Cao Q, Yuan G, Kijlstra A, Yang P. ERAP1/ERAP2 and RUNX3 polymorphisms are not associated with ankylosing spondylitis susceptibility in Chinese Han. Clin Exp Immunol 2018; 193:95-102. [PMID: 29480940 PMCID: PMC6038008 DOI: 10.1111/cei.13121] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2018] [Indexed: 02/01/2023] Open
Abstract
Previous studies show that endoplasmic reticulum‐associated aminopeptidase (ERAP1/ERAP2) and runt‐related transcription factor 3 (RUNX3) gene polymorphisms are associated with AS (ankylosing spondylitis) in European Caucasians. However, contradictory results were reported in different Asian populations. The purpose of this study was to determine whether eleven candidate single nucleotide polymorphisms (SNPs) in ERAP1/ERAP2 and six in RUNX3 genes confer susceptibility to AS with or without acute anterior uveitis (AAU) [AS+AAU+ or AS+AAU–] in Chinese Han. Therefore, a case–control association study was performed in 882 AS+AAU–, 884 AS+AAU+ and 1727 healthy controls. Genotyping was performed using the iPLEXGold genotyping assay. A meta‐analysis was performed to assess the association of polymorphisms of ERAP1 with AS susceptibility in Asian populations. No association was found between SNPs of ERAP1/ERAP2/RUNX3 and susceptibility of AS with or without AAU. A case–control study between patients with human leucocyte antigen HLA‐B27‐positive and healthy controls also failed to demonstrate an association of the tested SNP with AS with or without AAU. Moreover, a meta‐analysis showed that there was no association of rs30187, rs27037, rs27980, rs27434 and rs27582 in ERAP1 with AS in Chinese Han. Taken together, 17 SNPs in ERAP1/ERAP2 and RUNX3 genes did not confer disease susceptibility to AS in Chinese Han.
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Affiliation(s)
- W Su
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - L Du
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - S Liu
- Rheumatology Department of the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - J Deng
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - Q Cao
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - G Yuan
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - A Kijlstra
- University Eye Clinic, Maastricht, Maastricht, the Netherlands
| | - P Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
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47
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Zhang J, Marotel M, Fauteux-Daniel S, Mathieu AL, Viel S, Marçais A, Walzer T. T-bet and Eomes govern differentiation and function of mouse and human NK cells and ILC1. Eur J Immunol 2018; 48:738-750. [PMID: 29424438 DOI: 10.1002/eji.201747299] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 12/14/2017] [Accepted: 02/06/2018] [Indexed: 11/08/2022]
Abstract
T-bet and Eomes are T-box transcription factors that drive the differentiation and function of cytotoxic lymphocytes such as NK cells. Their DNA-binding domains are highly similar, suggesting redundant transcriptional activity. However, while these transcription factors have different patterns of expression, the phenotype of loss-of-function mouse models suggests that they play distinct roles in the development of NK cells and other innate lymphoid cells (ILCs). Recent technological advances using reporter mice and conditional knockouts were fundamental in defining the regulation and function of these factors at steady state and during pathological conditions such as various types of cancer or infection. Here, we review these recent developments, focusing on NK cells as prototypical cytotoxic lymphocytes and their development, and also discuss parallels between NK cells and T cells. We also examine the role of T-bet and Eomes in human NK cells and ILC1s. Considering divergent findings on mouse and human ILC1s, we propose that NK cells are defined by coexpression of T-bet and Eomes, while ILC1s express only one of these factors, either T-bet or Eomes, depending on the tissue or the species.
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Affiliation(s)
- Jiang Zhang
- CIRI, Centre International de Recherche en Infectiologie-International Center for Infectiology Research, Inserm, U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France.,Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Marie Marotel
- CIRI, Centre International de Recherche en Infectiologie-International Center for Infectiology Research, Inserm, U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France
| | - Sébastien Fauteux-Daniel
- CIRI, Centre International de Recherche en Infectiologie-International Center for Infectiology Research, Inserm, U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France
| | - Anne-Laure Mathieu
- CIRI, Centre International de Recherche en Infectiologie-International Center for Infectiology Research, Inserm, U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France
| | - Sébastien Viel
- CIRI, Centre International de Recherche en Infectiologie-International Center for Infectiology Research, Inserm, U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France.,Laboratoire d'Immunologie, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, 69495, Pierre-Bénite, France
| | - Antoine Marçais
- CIRI, Centre International de Recherche en Infectiologie-International Center for Infectiology Research, Inserm, U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France
| | - Thierry Walzer
- CIRI, Centre International de Recherche en Infectiologie-International Center for Infectiology Research, Inserm, U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France
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48
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Beyond genome-wide scan: Association of a cis-regulatory NCR3 variant with mild malaria in a population living in the Republic of Congo. PLoS One 2017; 12:e0187818. [PMID: 29121672 PMCID: PMC5679660 DOI: 10.1371/journal.pone.0187818] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/26/2017] [Indexed: 12/15/2022] Open
Abstract
Linkage studies have revealed a linkage of mild malaria to chromosome 6p21 that contains the NCR3 gene encoding a natural killer cell receptor, whereas NCR3-412G>C (rs2736191) located in its promoter region was found to be associated with malaria in Burkina Faso. Here we confirmed the association of rs2736191 with mild malaria in a Congolese cohort and investigated its potential cis-regulatory effect. Luciferase assay results indicated that rs2736191-G allele had a significantly increased promoter activity compared to rs2736191-C allele. Furthermore, EMSAs demonstrated an altered binding of two nuclear protein complexes to the rs2736191-C allele in comparison to rs2736191-G allele. Finally, after in silico identification of transcription factor candidates, pull-down western blot experiments confirmed that both STAT4 and RUNX3 bind the region encompassing rs2736191 with a higher affinity for the G allele. To our knowledge, this is the first report that explored the functional role of rs2736191. These results support the hypothesis that genetic variation within natural killer cell receptors alters malaria resistance in humans.
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49
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Appel E, Weissmann S, Salzberg Y, Orlovsky K, Negreanu V, Tsoory M, Raanan C, Feldmesser E, Bernstein Y, Wolstein O, Levanon D, Groner Y. An ensemble of regulatory elements controls Runx3 spatiotemporal expression in subsets of dorsal root ganglia proprioceptive neurons. Genes Dev 2017; 30:2607-2622. [PMID: 28007784 PMCID: PMC5204353 DOI: 10.1101/gad.291484.116] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 11/16/2016] [Indexed: 12/11/2022]
Abstract
Appel et al. defined the genomic transcription unit encompassing regulatory elements (REs) that mediate the tissue-specific expression of Runx3. Then, using transgenic mice expressing BAC reporters spanning the Runx3 locus, they discovered three REs that cross-talk with promoter-2 (P2) to drive TrkC neuron-specific Runx3 transcription. The Runx3 transcription factor is essential for development and diversification of the dorsal root ganglia (DRGs) TrkC sensory neurons. In Runx3-deficient mice, developing TrkC neurons fail to extend central and peripheral afferents, leading to cell death and disruption of the stretch reflex circuit, resulting in severe limb ataxia. Despite its central role, the mechanisms underlying the spatiotemporal expression specificities of Runx3 in TrkC neurons were largely unknown. Here we first defined the genomic transcription unit encompassing regulatory elements (REs) that mediate the tissue-specific expression of Runx3. Using transgenic mice expressing BAC reporters spanning the Runx3 locus, we discovered three REs—dubbed R1, R2, and R3—that cross-talk with promoter-2 (P2) to drive TrkC neuron-specific Runx3 transcription. Deletion of single or multiple elements either in the BAC transgenics or by CRISPR/Cas9-mediated endogenous ablation established the REs’ ability to promote and/or repress Runx3 expression in developing sensory neurons. Our analysis reveals that an intricate combinatorial interplay among the three REs governs Runx3 expression in distinct subtypes of TrkC neurons while concomitantly extinguishing its expression in non-TrkC neurons. These findings provide insights into the mechanism regulating cell type-specific expression and subtype diversification of TrkC neurons in developing DRGs.
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Affiliation(s)
- Elena Appel
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Sarit Weissmann
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Yehuda Salzberg
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, 7610001, Israel.,Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Kira Orlovsky
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Varda Negreanu
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Michael Tsoory
- Department of Veterinary Resources, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Calanit Raanan
- Department of Veterinary Resources, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ester Feldmesser
- Life Science Core Facilities, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Yael Bernstein
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Orit Wolstein
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ditsa Levanon
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Yoram Groner
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, 7610001, Israel
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50
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Development of innate lymphoid cells. Nat Immunol 2017; 17:775-82. [PMID: 27328007 DOI: 10.1038/ni.3481] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/04/2016] [Indexed: 12/13/2022]
Abstract
Innate lymphoid cells (ILCs) are a family of immune effector cells that have important roles in host defense, metabolic homeostasis and tissue repair but can also contribute to inflammatory diseases such as asthma and colitis. These cells can be categorized into three groups on the basis of the transcription factors that direct their function and the cytokines they produce, which parallel the effector functions of T lymphocytes. The hierarchy of cell-fate-restriction events that occur as common lymphoid progenitors become committed to each of the ILC lineages further underscores the relationship between these innate immune cells and T lymphocytes. In this Review we discuss the developmental program of ILCs and transcription factors that guide ILC lineage specification and commitment.
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