1
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Li Y, Zhang Z, Yu J, Yin H, Chu X, Cao H, Tao Y, Zhang Y, Li Z, Wu S, Hu Y, Zhu F, Gao J, Wang X, Zhou B, Jiao W, Wu Y, Yang Y, Chen Y, Zhuo R, Yang Y, Zhang F, Shi L, Hu Y, Pan J, Hu S. Enhancer looping protein LDB1 modulates MYB expression in T-ALL cell lines in vitro by cooperating with master transcription factors. J Exp Clin Cancer Res 2024; 43:283. [PMID: 39385230 DOI: 10.1186/s13046-024-03199-1] [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] [Received: 01/28/2024] [Accepted: 09/20/2024] [Indexed: 10/12/2024] Open
Abstract
BACKGROUND Despite significant progress in the prognosis of pediatric T-cell acute lymphoblastic leukemia (T-ALL) in recent decades, a notable portion of children still confronts challenges such as treatment resistance and recurrence, leading to limited options and a poor prognosis. LIM domain-binding protein 1 (LDB1) has been confirmed to exert a crucial role in various physiological and pathological processes. In our research, we aim to elucidate the underlying function and mechanisms of LDB1 within the background of T-ALL. METHODS Employing short hairpin RNA (shRNA) techniques, we delineated the functional impact of LDB1 in T-ALL cell lines. Through the application of RNA-Seq, CUT&Tag, and immunoprecipitation assays, we scrutinized master transcription factors cooperating with LDB1 and identified downstream targets under LDB1 regulation. RESULTS LDB1 emerges as a critical transcription factor co-activator in cell lines derived from T-ALL. It primarily collaborates with master transcription factors (ERG, ETV6, IRF1) to cooperatively regulate the transcription of downstream target genes. Both in vitro and in vivo experiments affirm the essential fuction of LDB1 in the proliferation and survival of cell lines derived from T-ALL, with MYB identified as a significant downstream target of LDB1. CONCLUSIONS To sum up, our research establishes the pivotal fuction of LDB1 in the tumorigenesis and progression of T-ALL cell lines. Mechanistic insights reveal that LDB1 cooperates with ERG, ETV6, and IRF1 to modulate the expression of downstream effector genes. Furthermore, LDB1 controls MYB through remote enhancer modulation, providing valuable mechanistic insights into its involvement in the progression of T-ALL.
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Affiliation(s)
- Yan Li
- Children's Hospital of Soochow University, Suzhou, China
- Department of Pediatrics, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Zimu Zhang
- Institute of Pediatric Research, Children's Hospital of Soochow University, SIP, No.92 Zhongnan Street, Suzhou, 215003, China
| | - Juanjuan Yu
- Children's Hospital of Soochow University, Suzhou, China
| | - Hongli Yin
- Institute of Pediatric Research, Children's Hospital of Soochow University, SIP, No.92 Zhongnan Street, Suzhou, 215003, China
| | - Xinran Chu
- Department of Hematology, Children's Hospital of Soochow University, SIP, No.92 Zhongnan Street, Suzhou, Jiangsu, China
| | - Haibo Cao
- Department of Pediatric Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou, China
| | - Yanfang Tao
- Institute of Pediatric Research, Children's Hospital of Soochow University, SIP, No.92 Zhongnan Street, Suzhou, 215003, China
| | - Yongping Zhang
- Department of Hematology, Children's Hospital of Soochow University, SIP, No.92 Zhongnan Street, Suzhou, Jiangsu, China
| | - Zhiheng Li
- Institute of Pediatric Research, Children's Hospital of Soochow University, SIP, No.92 Zhongnan Street, Suzhou, 215003, China
| | - Shuiyan Wu
- Institute of Pediatric Research, Children's Hospital of Soochow University, SIP, No.92 Zhongnan Street, Suzhou, 215003, China
| | - Yizhou Hu
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165, Stockholm, Sweden
| | - Frank Zhu
- Department of Internal Medicine, The Ohio State University, Columbus, 43210, USA
| | - Jizhao Gao
- Department of Pediatrics, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Xiaodong Wang
- Children's Hospital of Soochow University, Suzhou, China
| | - Bi Zhou
- Children's Hospital of Soochow University, Suzhou, China
- Department of Pediatric, Suzhou Hospital of AnHui Medical University, Suzhou, 234000, China
| | - Wanyan Jiao
- Children's Hospital of Soochow University, Suzhou, China
- Department of Pediatric, Yancheng , Third People' Hospital, YanCheng, 224000, China
| | - Yumeng Wu
- Children's Hospital of Soochow University, Suzhou, China
- Department of Pediatric, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, China
| | - Yang Yang
- Institute of Pediatric Research, Children's Hospital of Soochow University, SIP, No.92 Zhongnan Street, Suzhou, 215003, China
| | - Yanling Chen
- Children's Hospital of Soochow University, Suzhou, China
| | - Ran Zhuo
- Children's Hospital of Soochow University, Suzhou, China
| | - Ying Yang
- Clinical Medicine, Guizhou Medical University, Guiyang, 550000, China
| | - Fenli Zhang
- Clinical Medicine, Guizhou Medical University, Guiyang, 550000, China
| | - Lei Shi
- Department of Medicinal Chemistry, Jiangsu Key Laboratory of Drug Design and Optimization China Pharmaceutical University, Nanjing, 210009, China
| | - Yixin Hu
- Department of Hematology, Children's Hospital of Soochow University, SIP, No.92 Zhongnan Street, Suzhou, Jiangsu, China.
| | - Jian Pan
- Institute of Pediatric Research, Children's Hospital of Soochow University, SIP, No.92 Zhongnan Street, Suzhou, 215003, China.
| | - Shaoyan Hu
- Department of Hematology, Children's Hospital of Soochow University, SIP, No.92 Zhongnan Street, Suzhou, Jiangsu, China.
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2
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Wang HY, Chen JY, Li Y, Zhang X, Liu X, Lu Y, He H, Li Y, Chen H, Liu Q, Huang Y, Jia Z, Li S, Zhang Y, Han S, Jiang S, Yang M, Zhang Y, Zhou L, Tan F, Ji Q, Meng L, Wang R, Liu Y, Liu K, Wang Q, Seim I, Zou J, Fan G, Liu S, Shao C. Single-cell RNA sequencing illuminates the ontogeny, conservation and diversification of cartilaginous and bony fish lymphocytes. Nat Commun 2024; 15:7627. [PMID: 39227568 PMCID: PMC11372145 DOI: 10.1038/s41467-024-51761-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 08/16/2024] [Indexed: 09/05/2024] Open
Abstract
Elucidating cellular architecture and cell-type evolution across species is central to understanding immune system function and susceptibility to disease. Adaptive immunity is a shared trait of the common ancestor of cartilaginous and bony fishes. However, evolutionary features of lymphocytes in these two jawed vertebrates remain unclear. Here, we present a single-cell RNA sequencing atlas of immune cells from cartilaginous (white-spotted bamboo shark) and bony (zebrafish and Chinese tongue sole) fishes. Cross-species comparisons show that the same cell types across different species exhibit similar transcriptional profiles. In the bamboo shark, we identify a phagocytic B cell population expressing several pattern recognition receptors, as well as a T cell sub-cluster co-expressing both T and B cell markers. In contrast to a division by function in the bony fishes, we show close linkage and poor functional specialization among lymphocytes in the cartilaginous fish. Our cross-species single-cell comparison presents a resource for uncovering the origin and evolution of the gnathostome immune system.
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Affiliation(s)
- Hong-Yan Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Jian-Yang Chen
- BGI Research, Qingdao, 266555, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, 266555, Shandong, China
| | - Yanan Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Xianghui Zhang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Xiang Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, 266555, China
| | - Yifang Lu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Hang He
- BGI Research, Qingdao, 266555, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, 266555, Shandong, China
| | - Yubang Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Hongxi Chen
- BGI Research, Qingdao, 266555, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, 266555, Shandong, China
| | - Qun Liu
- BGI Research, Qingdao, 266555, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, 266555, Shandong, China
| | - Yingyi Huang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Zhao Jia
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Shuo Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Yangqing Zhang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Shenglei Han
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Shuhong Jiang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Mingming Yang
- BGI Research, Qingdao, 266555, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, 266555, Shandong, China
| | - Yingying Zhang
- BGI Research, Qingdao, 266555, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, 266555, Shandong, China
| | - Li Zhou
- BGI Research, Qingdao, 266555, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, 266555, Shandong, China
| | - Fujian Tan
- BGI Research, Qingdao, 266555, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, 266555, Shandong, China
| | | | - Liang Meng
- BGI Research, Qingdao, 266555, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, 266555, Shandong, China
| | - Rui Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Yuyan Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Kaiqiang Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Qian Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, 4000, Australia
| | - Jun Zou
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Guangyi Fan
- BGI Research, Qingdao, 266555, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, 266555, Shandong, China
- BGI Research, Shenzhen, 518083, China
| | | | - Changwei Shao
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China.
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3
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Nakai R, Yokota T, Tokunaga M, Takaishi M, Yokomizo T, Sudo T, Shi H, Yasumizu Y, Okuzaki D, Kokubu C, Tanaka S, Takaoka K, Yamanishi A, Yoshida J, Watanabe H, Kondoh G, Horie K, Hosen N, Sano S, Takeda J. A newly identified gene Ahed plays essential roles in murine haematopoiesis. Nat Commun 2024; 15:5090. [PMID: 38918373 PMCID: PMC11199565 DOI: 10.1038/s41467-024-49252-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 05/29/2024] [Indexed: 06/27/2024] Open
Abstract
The development of haematopoiesis involves the coordinated action of numerous genes, some of which are implicated in haematological malignancies. However, the biological function of many genes remains elusive and unknown functional genes are likely to remain to be uncovered. Here, we report a previously uncharacterised gene in haematopoiesis, identified by screening mutant embryonic stem cells. The gene, 'attenuated haematopoietic development (Ahed)', encodes a nuclear protein. Conditional knockout (cKO) of Ahed results in anaemia from embryonic day 14.5 onward, leading to prenatal demise. Transplantation experiments demonstrate the incapacity of Ahed-deficient haematopoietic cells to reconstitute haematopoiesis in vivo. Employing a tamoxifen-inducible cKO model, we further reveal that Ahed deletion impairs the intrinsic capacity of haematopoietic cells in adult mice. Ahed deletion affects various pathways, and published databases present cancer patients with somatic mutations in Ahed. Collectively, our findings underscore the fundamental roles of Ahed in lifelong haematopoiesis, implicating its association with malignancies.
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Affiliation(s)
- Ritsuko Nakai
- Department of Haematology and Oncology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Takafumi Yokota
- Department of Haematology and Oncology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.
- Department of Haematology, Osaka International Cancer Institute, Osaka, Osaka, 541-8567, Japan.
| | - Masahiro Tokunaga
- Department of Haematology, Suita Municipal Hospital, Suita, Osaka, 564-0018, Japan
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Mikiro Takaishi
- Department of Dermatology, Kochi Medical School, Kochi University, Nankoku, Kochi, 783-8505, Japan
| | - Tomomasa Yokomizo
- Department of Microscopic and Developmental Anatomy, Tokyo Women's Medical University, Shinjuku-ku, Tokyo, 162-8666, Japan
| | - Takao Sudo
- Department of Haematology and Oncology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
- Department of Haematology, National Hospital Organisation Osaka National Hospital, Osaka, Osaka, 540-0006, Japan
| | - Henyun Shi
- Department of Haematology and Oncology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yoshiaki Yasumizu
- Department of Experimental Immunology, Immunology Frontier Research Centre, Osaka University, Suita, Osaka, 565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Daisuke Okuzaki
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, 565-0871, Japan
- Genome Information Research Centre, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Chikara Kokubu
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Sachiyo Tanaka
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Katsuyoshi Takaoka
- Developmental Genetics Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Ayako Yamanishi
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Junko Yoshida
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
- Department of Physiology II, Nara Medical University, Kashihara, Nara, 634-8521, Japan
| | - Hitomi Watanabe
- Laboratory of Animal Experiments for Regeneration, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Kyoto, 606-8507, Japan
| | - Gen Kondoh
- Laboratory of Animal Experiments for Regeneration, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Kyoto, 606-8507, Japan
| | - Kyoji Horie
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
- Department of Physiology II, Nara Medical University, Kashihara, Nara, 634-8521, Japan
| | - Naoki Hosen
- Department of Haematology and Oncology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, 565-0871, Japan
- Laboratory of Cellular Immunotherapy, World Premier International Immunology Frontier Research Centre, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Shigetoshi Sano
- Department of Dermatology, Kochi Medical School, Kochi University, Nankoku, Kochi, 783-8505, Japan
| | - Junji Takeda
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan.
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4
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Lemma RB, Fuglerud BM, Frampton J, Gabrielsen OS. MYB: A Key Transcription Factor in the Hematopoietic System Subject to Many Levels of Control. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:3-29. [PMID: 39017837 DOI: 10.1007/978-3-031-62731-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
MYB is a master regulator and pioneer factor highly expressed in hematopoietic progenitor cells (HPCs) where it contributes to the reprogramming processes operating during hematopoietic development. MYB plays a complex role being involved in several lineages of the hematopoietic system. At the molecular level, the MYB gene is subject to intricate regulation at many levels through several enhancer and promoter elements, through transcriptional elongation control, as well as post-transcriptional regulation. The protein is modulated by post-translational modifications (PTMs) such as SUMOylation restricting the expression of its downstream targets. Together with a range of interaction partners, cooperating transcription factors (TFs) and epigenetic regulators, MYB orchestrates a fine-tuned symphony of genes expressed during various stages of haematopoiesis. At the same time, the complex MYB system is vulnerable, being a target for unbalanced control and cancer development.
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Affiliation(s)
- Roza Berhanu Lemma
- Department of Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | | | - Jon Frampton
- Department of Cancer & Genomic Sciences, College of Medicine & Health, University of Birmingham, Edgbaston, Birmingham, UK
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5
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Xu H, Tan S, Zhao Y, Zhang L, Cao W, Li X, Tian J, Wang X, Li X, Wang F, Cao J, Zhao T. Lin - PU.1 dim GATA-1 - defines haematopoietic stem cells with long-term multilineage reconstitution activity. Cell Prolif 2023; 56:e13490. [PMID: 37147872 PMCID: PMC10623959 DOI: 10.1111/cpr.13490] [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: 02/10/2023] [Revised: 04/10/2023] [Accepted: 04/15/2023] [Indexed: 05/07/2023] Open
Abstract
Despite extensive characterization of the state and function of haematopoietic stem cells (HSCs), the use of transcription factors to define the HSC population is still limited. We show here that the HSC population in mouse bone marrow can be defined by the distinct expression levels of Spi1 and Gata1. By using a double fluorescence knock-in mouse model, PGdKI, in which the expression levels of PU.1 and GATA-1 are indicated by the expression of GFP and mCherry, respectively, we uncover that the HSCs with lymphoid and myeloid repopulating activity are specifically enriched in a Lin- PU.1dim GATA-1- (LPG) cell subset. In vivo competitive repopulation assays demonstrate that bone marrow cells gated by LPG exhibit haematopoietic reconstitution activity which is comparable to that of classical Lin- Sca1+ c-kit+ (LSK). The integrated analysis of single-cell RNA sequence data from LPG and LSK-gated cells reveals that a transcriptional network governed by core TFs contributes to regulation of HSC multipotency. These discoveries provide new clues for HSC characterization and functional study.
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Affiliation(s)
- Haoyu Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Shaojing Tan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yu Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lin Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Weiyun Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xing Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jiayi Tian
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaojing Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaoyan Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Fengchao Wang
- National Institute of Biological Sciences (NIBS)BeijingChina
| | - Jiani Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Tongbiao Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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6
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Lu L, Wang J, Fang F, Guo A, Jiang S, Tao Y, Zhang Y, Li Y, Zhang K, Zhang Z, Zhuo R, Chu X, Li X, Tian Y, Ma L, Sang X, Chen Y, Yu J, Yang Y, Cao H, Gao J, Lu J, Hu S, Pan J, He H. LMO2 promotes the development of AML through interaction with transcription co-regulator LDB1. Cell Death Dis 2023; 14:518. [PMID: 37573405 PMCID: PMC10423285 DOI: 10.1038/s41419-023-06039-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 07/20/2023] [Accepted: 08/03/2023] [Indexed: 08/14/2023]
Abstract
One of the characteristics of leukemia is that it contains multiple rearrangements of signal transduction genes and overexpression of non-mutant genes, such as transcription factors. As an important regulator of hematopoietic stem cell development and erythropoiesis, LMO2 is considered an effective carcinogenic driver in T cell lines and a marker of poor prognosis in patients with AML with normal karyotype. LDB1 is a key factor in the transformation of thymocytes into T-ALL induced by LMO2, and enhances the stability of carcinogenic related proteins in leukemia. However, the function and mechanism of LMO2 and LDB1 in AML remains unclear. Herein, the LMO2 gene was knocked down to observe its effects on proliferation, survival, and colony formation of NB4, Kasumi-1 and K562 cell lines. Using mass spectrometry and IP experiments, our results showed the presence of LMO2/LDB1 protein complex in AML cell lines, which is consistent with previous studies. Furthermore, in vitro and in vivo experiments revealed that LDB1 is essential for the proliferation and survival of AML cell lines. Analysis of RNA-seq and ChIP-Seq results showed that LDB1 could regulate apoptosis-related genes, including LMO2. In LDB1-deficient AML cell lines, the overexpression of LMO2 partially compensates for the proliferation inhibition. In summary, our findings revealed that LDB1 played an important role in AML as an oncogene, and emphasize the potential importance of the LMO2/LDB1 complex in clinical treatment of patients with AML.
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Affiliation(s)
- Lihui Lu
- Children's Hospital of Soochow University, Suzhou, 215003, China
- Department of Pediatrics, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Jianwei Wang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Fang Fang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Ailian Guo
- Department of Hematology, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Shuting Jiang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Yanfang Tao
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Yongping Zhang
- Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Yan Li
- Children's Hospital of Soochow University, Suzhou, 215003, China
- Department of Pediatrics, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Kunlong Zhang
- Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Zimu Zhang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Ran Zhuo
- Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Xinran Chu
- Department of Hematology, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Xiaolu Li
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Yuanyuan Tian
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
- Department of Hematology, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Li Ma
- Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Xu Sang
- Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Yanling Chen
- Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Juanjuan Yu
- Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Yang Yang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Haibo Cao
- Department of Pediatric Surgery, The Affiliated Hospital of Yangzhou University, Yangzhou, 225000, China
| | - Jizhao Gao
- Department of Pediatrics, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Jun Lu
- Department of Hematology, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Shaoyan Hu
- Department of Hematology, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Jian Pan
- Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou, 215003, China.
| | - Hailong He
- Department of Hematology, Children's Hospital of Soochow University, Suzhou, 215003, China.
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7
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Diacou R, Nandigrami P, Fiser A, Liu W, Ashery-Padan R, Cvekl A. Cell fate decisions, transcription factors and signaling during early retinal development. Prog Retin Eye Res 2022; 91:101093. [PMID: 35817658 PMCID: PMC9669153 DOI: 10.1016/j.preteyeres.2022.101093] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 12/30/2022]
Abstract
The development of the vertebrate eyes is a complex process starting from anterior-posterior and dorso-ventral patterning of the anterior neural tube, resulting in the formation of the eye field. Symmetrical separation of the eye field at the anterior neural plate is followed by two symmetrical evaginations to generate a pair of optic vesicles. Next, reciprocal invagination of the optic vesicles with surface ectoderm-derived lens placodes generates double-layered optic cups. The inner and outer layers of the optic cups develop into the neural retina and retinal pigment epithelium (RPE), respectively. In vitro produced retinal tissues, called retinal organoids, are formed from human pluripotent stem cells, mimicking major steps of retinal differentiation in vivo. This review article summarizes recent progress in our understanding of early eye development, focusing on the formation the eye field, optic vesicles, and early optic cups. Recent single-cell transcriptomic studies are integrated with classical in vivo genetic and functional studies to uncover a range of cellular mechanisms underlying early eye development. The functions of signal transduction pathways and lineage-specific DNA-binding transcription factors are dissected to explain cell-specific regulatory mechanisms underlying cell fate determination during early eye development. The functions of homeodomain (HD) transcription factors Otx2, Pax6, Lhx2, Six3 and Six6, which are required for early eye development, are discussed in detail. Comprehensive understanding of the mechanisms of early eye development provides insight into the molecular and cellular basis of developmental ocular anomalies, such as optic cup coloboma. Lastly, modeling human development and inherited retinal diseases using stem cell-derived retinal organoids generates opportunities to discover novel therapies for retinal diseases.
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Affiliation(s)
- Raven Diacou
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Prithviraj Nandigrami
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Andras Fiser
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Wei Liu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ruth Ashery-Padan
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ales Cvekl
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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8
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Latchmansingh KA, Wang X, Verdun RE, Marques-Piubelli ML, Vega F, You MJ, Chapman J, Lossos IS. LMO2 expression is frequent in T-lymphoblastic leukemia and correlates with survival, regardless of T-cell stage. Mod Pathol 2022; 35:1220-1226. [PMID: 35322192 PMCID: PMC9427670 DOI: 10.1038/s41379-022-01063-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 11/09/2022]
Abstract
T- lymphoblastic leukemia/lymphoma (T-LL) is an aggressive malignancy of immature T-cells with poor overall survival (OS) and in need of new therapies. LIM-domain only 2 (LMO2) is a critical regulator of hematopoietic cell development that can be overexpressed in T-LL due to chromosomal abnormalities. Deregulated LMO2 expression contributes to T-LL development by inducing block of T-cell differentiation and continuous thymocyte self-renewal. However, LMO2 expression and its biologic significance in T-LL remain largely unknown. We analyzed LMO2 expression in 100 initial and follow-up biopsies of T-LL from 67 patients, including 31 (46%) early precursor T-cell (ETP)-ALL, 26 (39%) cortical and 10 (15%) medullary type. LMO2 expression was present in 50 (74.6%) initial biopsies with an average of 87% positive tumor cells (range 30-100%). LMO2 expression in ETP, medullary and cortical T-LLs was not statistically different. In patients with biopsies after initial therapy, LMO2 expression was stable. LMO2 expression was associated with longer OS (p = 0.048) regardless of T-lymphoblast stage or other clinicopathologic features. These findings indicate that LMO2 is a promising new prognostic marker that could predict patients' outcomes and potentially be targeted for novel chemotherapy, i.e. PARP1/2 inhibitors, which have been shown to enhance chemotherapy sensitivity in LMO2 expressing diffuse large B cell lymphoma (DLBCL) tumors by decreasing DNA repair efficiency.
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Affiliation(s)
- Kerri-Ann Latchmansingh
- Department of Pathology and Laboratory Medicine, Division of Hematopathology, University of Miami/Sylvester Comprehensive Cancer Center & Jackson Memorial Hospital, Miami, FL, USA
| | - Xiaoqiong Wang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ramiro E. Verdun
- Department of Medicine, Division of Hematology, University of Miami / Sylvester Comprehensive Cancer Center & Jackson Memorial Hospital, Miami, FL, USA
| | - Mario L. Marques-Piubelli
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Francisco Vega
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - M. James You
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer Chapman
- Department of Pathology and Laboratory Medicine, Division of Hematopathology, University of Miami/Sylvester Comprehensive Cancer Center & Jackson Memorial Hospital, Miami, FL, USA
| | - Izidore S. Lossos
- Department of Medicine, Division of Hematology, University of Miami / Sylvester Comprehensive Cancer Center & Jackson Memorial Hospital, Miami, FL, USA
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9
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Chen C, Sun MA, Warzecha C, Bachu M, Dey A, Wu T, Adams PD, Macfarlan T, Love P, Ozato K. HIRA, a DiGeorge Syndrome Candidate Gene, Confers Proper Chromatin Accessibility on HSCs and Supports All Stages of Hematopoiesis. Cell Rep 2021; 30:2136-2149.e4. [PMID: 32075733 DOI: 10.1016/j.celrep.2020.01.062] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 12/05/2019] [Accepted: 01/21/2020] [Indexed: 01/22/2023] Open
Abstract
HIRA is a histone chaperone that deposits the histone variant H3.3 in transcriptionally active genes. In DiGeorge syndromes, a DNA stretch encompassing HIRA is deleted. The syndromes manifest varied abnormalities, including immunodeficiency and thrombocytopenia. HIRA is essential in mice, as total knockout (KO) results in early embryonic death. However, the role of HIRA in hematopoiesis is poorly understood. We investigate hematopoietic cell-specific Hira deletion in mice and show that it dramatically reduces bone marrow hematopoietic stem cells (HSCs), resulting in anemia, thrombocytopenia, and lymphocytopenia. In contrast, fetal hematopoiesis is normal in Hira-KO mice, although fetal HSCs lack the reconstitution capacity. Transcriptome analysis reveals that HIRA is required for expression of many transcription factors and signaling molecules critical for HSCs. ATAC-seq analysis demonstrates that HIRA establishes HSC-specific DNA accessibility, including the SPIB/PU.1 sites. Together, HIRA provides a chromatin environment essential for HSCs, thereby steering their development and survival.
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Affiliation(s)
- Chao Chen
- Molecular Genetics of Immunity Section, Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ming-An Sun
- Mammalian Epigenome Reprogramming Section, Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Claude Warzecha
- Hematopoiesis and Lymphocyte Biology Section, Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mahesh Bachu
- Molecular Genetics of Immunity Section, Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anup Dey
- Molecular Genetics of Immunity Section, Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tiyun Wu
- Molecular Genetics of Immunity Section, Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Todd Macfarlan
- Mammalian Epigenome Reprogramming Section, Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Love
- Hematopoiesis and Lymphocyte Biology Section, Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Keiko Ozato
- Molecular Genetics of Immunity Section, Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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10
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Ldb1 is required for Lmo2 oncogene-induced thymocyte self-renewal and T-cell acute lymphoblastic leukemia. Blood 2021; 135:2252-2265. [PMID: 32181817 DOI: 10.1182/blood.2019000794] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 02/20/2020] [Indexed: 12/18/2022] Open
Abstract
Prolonged or enhanced expression of the proto-oncogene Lmo2 is associated with a severe form of T-cell acute lymphoblastic leukemia (T-ALL), designated early T-cell precursor ALL, which is characterized by the aberrant self-renewal and subsequent oncogenic transformation of immature thymocytes. It has been suggested that Lmo2 exerts these effects by functioning as component of a multi-subunit transcription complex that includes the ubiquitous adapter Ldb1 along with b-HLH and/or GATA family transcription factors; however, direct experimental evidence for this mechanism is lacking. In this study, we investigated the importance of Ldb1 for Lmo2-induced T-ALL by conditional deletion of Ldb1 in thymocytes in an Lmo2 transgenic mouse model of T-ALL. Our results identify a critical requirement for Ldb1 in Lmo2-induced thymocyte self-renewal and thymocyte radiation resistance and for the transition of preleukemic thymocytes to overt T-ALL. Moreover, Ldb1 was also required for acquisition of the aberrant preleukemic ETP gene expression signature in immature Lmo2 transgenic thymocytes. Co-binding of Ldb1 and Lmo2 was detected at the promoters of key upregulated T-ALL driver genes (Hhex, Lyl1, and Nfe2) in preleukemic Lmo2 transgenic thymocytes, and binding of both Ldb1 and Lmo2 at these sites was reduced following Cre-mediated deletion of Ldb1. Together, these results identify a key role for Ldb1, a nonproto-oncogene, in T-ALL and support a model in which Lmo2-induced T-ALL results from failure to downregulate Ldb1/Lmo2-nucleated transcription complexes which normally function to enforce self-renewal in bone marrow hematopoietic progenitors.
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11
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Wanet A, Bassal MA, Patel SB, Marchi F, Mariani SA, Ahmed N, Zhang H, Borchiellini M, Chen S, Zhang J, Di Ruscio A, Miyake K, Tsai M, Paranjape A, Park SY, Karasuyama H, Schroeder T, Dzierzak E, Galli SJ, Tenen DG, Welner RS. E-cadherin is regulated by GATA-2 and marks the early commitment of mouse hematopoietic progenitors to the basophil and mast cell fates. Sci Immunol 2021; 6:6/56/eaba0178. [PMID: 33547048 DOI: 10.1126/sciimmunol.aba0178] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 09/09/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
E-cadherin is a calcium-dependent cell-cell adhesion molecule extensively studied for its involvement in tissue formation, epithelial cell behavior, and suppression of cancer. However, E-cadherin expression in the hematopoietic system has not been fully elucidated. Combining single-cell RNA-sequencing analyses and immunophenotyping, we revealed that progenitors expressing high levels of E-cadherin and contained within the granulocyte-monocyte progenitors (GMPs) fraction have an enriched capacity to differentiate into basophils and mast cells. We detected E-cadherin expression on committed progenitors before the expression of other reported markers of these lineages. We named such progenitors pro-BMPs (pro-basophil and mast cell progenitors). Using RNA sequencing, we observed transcriptional priming of pro-BMPs to the basophil and mast cell lineages. We also showed that GATA-2 directly regulates E-cadherin expression in the basophil and mast cell lineages, thus providing a mechanistic connection between the expression of this cell surface marker and the basophil and mast cell fate specification.
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Affiliation(s)
- Anaïs Wanet
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Mahmoud A Bassal
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Sweta B Patel
- Division of Hematology/Oncology, O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | - Samanta A Mariani
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Nouraiz Ahmed
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Haoran Zhang
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Marta Borchiellini
- Department of Health Sciences, University of Eastern Piedmont, Novara 28100, Italy.,Department of Translational Medicine, University of Eastern Piedmont, Novara 28100, Italy
| | - Sisi Chen
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Junyan Zhang
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Annalisa Di Ruscio
- Department of Translational Medicine, University of Eastern Piedmont, Novara 28100, Italy.,Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA.,Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Kensuke Miyake
- Inflammation, Infection, Immunity Laboratory, Advanced Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Mindy Tsai
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anuya Paranjape
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shin-Young Park
- Transfusion Medicine, Boston Children's Hospital and Harvard Medical School, Harvard Medical School, Boston, MA 02115, USA
| | - Hajime Karasuyama
- Inflammation, Infection, Immunity Laboratory, Advanced Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Elaine Dzierzak
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Stephen J Galli
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Microbiology and Immunology and Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daniel G Tenen
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA. .,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Robert S Welner
- Division of Hematology/Oncology, O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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12
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Guo X, Plank-Bazinet J, Krivega I, Dale RK, Dean A. Embryonic erythropoiesis and hemoglobin switching require transcriptional repressor ETO2 to modulate chromatin organization. Nucleic Acids Res 2020; 48:10226-10240. [PMID: 32960220 DOI: 10.1093/nar/gkaa736] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/19/2020] [Accepted: 09/18/2020] [Indexed: 11/14/2022] Open
Abstract
The underlying mechanism of transcriptional co-repressor ETO2 during early erythropoiesis and hemoglobin switching is unclear. We find that absence of ETO2 in mice interferes with down-regulation of PU.1 and GATA2 in the fetal liver, impeding a key step required for commitment to erythroid maturation. In human β-globin transgenic Eto2 null mice and in human CD34+ erythroid progenitor cells with reduced ETO2, loss of ETO2 results in ineffective silencing of embryonic/fetal globin gene expression, impeding hemoglobin switching during erythroid differentiation. ETO2 occupancy genome-wide occurs virtually exclusively at LDB1-complex binding sites in enhancers and ETO2 loss leads to increased enhancer activity and expression of target genes. ETO2 recruits the NuRD nucleosome remodeling and deacetylation complex to regulate histone acetylation and nucleosome occupancy in the β-globin locus control region and γ-globin gene. Loss of ETO2 elevates LDB1, MED1 and Pol II in the locus and facilitates fetal γ-globin/LCR looping and γ-globin transcription. Absence of the ETO2 hydrophobic heptad repeat region impairs ETO2-NuRD interaction and function in antagonizing γ-globin/LCR looping. Our results reveal a pivotal role for ETO2 in erythropoiesis and globin gene switching through its repressive role in the LDB1 complex, affecting the transcription factor and epigenetic environment and ultimately restructuring chromatin organization.
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Affiliation(s)
- Xiang Guo
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Building 50, Room 3154, Bethesda, MD 20892, USA
| | - Jennifer Plank-Bazinet
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Building 50, Room 3154, Bethesda, MD 20892, USA
| | - Ivan Krivega
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Building 50, Room 3154, Bethesda, MD 20892, USA
| | - Ryan K Dale
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Building 50, Room 3154, Bethesda, MD 20892, USA
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Building 50, Room 3154, Bethesda, MD 20892, USA
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13
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Jin M, Lu J, Fei X, Lu Z, Quan K, Liu Y, Chu M, Di R, Wei C, Wang H. Selection Signatures Analysis Reveals Genes Associated with High-Altitude Adaptation in Tibetan Goats from Nagqu, Tibet. Animals (Basel) 2020; 10:ani10091599. [PMID: 32911823 PMCID: PMC7552128 DOI: 10.3390/ani10091599] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/28/2020] [Accepted: 09/04/2020] [Indexed: 12/18/2022] Open
Abstract
Simple Summary In the process of domestication, goats have undergone long-term artificial and natural selection, leading to differences among goat breeds and leaving different selection traces on the genome. However, the genetic components underlying high-altitude adaptation remain largely unknown. Here, we genotyped four goat breeds using the Illumina Caprine 50K single nucleotide polymorphism (SNP) Chip. One highland breed (Tibetan goat) compared with three lowland breeds (Huanghuai goat, Taihang goat and Xinjiang goat) to identify the molecular basis of high-altitude adaptation. So, we investigated selection signatures using the di statistic of four goat breeds and some genes in Tibetan goats related to high-altitude adaptation were identified. In addition, q-PCR validated the gene expression level in Tibetan goats and Huanghuai goats. This information may be valuable for the study of the genetic uniqueness of Tibetan goats and increased understanding of the hypoxic adaptation mechanism of Tibetan goats on the plateau. Abstract Tibetan goat is an ancient breed, which inhabits the adverse conditions of the plateaus in China. To investigate the role of selection in shaping its genomes, we genotyped Tibetan goats (Nagqu Prefecture, above 4500 m) and three lowland populations (Xinjiang goats, Taihang goats and Huanghuai goats). The result of PCA, neighbor-joining (N-J) tree and model-based clustering showed that the genetic structure between the Tibetan goat and the three lowland populations has significant difference. As demonstrated by the di statistic, we found that some genes were related to the high-altitude adaptation of Tibetan goats. Functional analysis revealed that these genes were enriched in the VEGF (vascular endothelial growth factor) signaling pathway and melanoma, suggesting that nine genes (FGF2, EGFR, AKT1, PTEN, MITF, ENPEP, SIRT6, KDR, and CDC42) might have important roles in the high-altitude adaptation of Nagqu Tibetan goats. We also found that the LEPR gene was under the strongest selection (di value = 16.70), and it could induce upregulation of the hypoxic ventilatory response. In addition, five genes (LEPR, LDB1, EGFR, NOX4 and FGF2) with high di values were analyzed using q-PCR. Among them, we found that LEPR, LDB1 and FGF2 exhibited higher expression in the lungs of the Tibetan goats; LEPR, EGFR and LDB1 exhibited higher expression in the hearts of the Huanghuai goat. Our results suggest that LEPR, LDB1, EGFR and FGF2 genes may be related to the high-altitude adaptation of the goats. These findings improve our understanding of the selection of the high-altitude adaptability of the Nagqu Tibetan goats and provide new theoretical knowledge for the conservation and utilization of germplasm resources.
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Affiliation(s)
- Meilin Jin
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.J.); (X.F.); (M.C.); (R.D.)
| | - Jian Lu
- National Animal Husbandry Service, Beijing 100193, China;
| | - Xiaojuan Fei
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.J.); (X.F.); (M.C.); (R.D.)
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
| | - Kai Quan
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China;
| | - Yongbin Liu
- Inner Mongolia Academy of Animal Husbandry Science, Hohhot 010031, China;
| | - Mingxing Chu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.J.); (X.F.); (M.C.); (R.D.)
| | - Ran Di
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.J.); (X.F.); (M.C.); (R.D.)
| | - Caihong Wei
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.J.); (X.F.); (M.C.); (R.D.)
- Correspondence: (C.W.); (H.W.)
| | - Huihua Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (M.J.); (X.F.); (M.C.); (R.D.)
- Correspondence: (C.W.); (H.W.)
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14
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Steinauer N, Guo C, Zhang J. The transcriptional corepressor CBFA2T3 inhibits all- trans-retinoic acid-induced myeloid gene expression and differentiation in acute myeloid leukemia. J Biol Chem 2020; 295:8887-8900. [PMID: 32434928 PMCID: PMC7335779 DOI: 10.1074/jbc.ra120.013042] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/17/2020] [Indexed: 01/10/2023] Open
Abstract
CBFA2/RUNX1 partner transcriptional co-repressor 3 (CBFA2T3, also known as MTG16 or ETO2) is a myeloid translocation gene family protein that functions as a master transcriptional corepressor in hematopoiesis. Recently, it has been shown that CBFA2T3 maintains leukemia stem cell gene expression and promotes relapse in acute myeloid leukemia (AML). However, a role for CBFA2T3 in myeloid differentiation of AML has not been reported. Here, we show that CBFA2T3 represses retinoic acid receptor (RAR) target gene expression and inhibits all-trans-retinoic acid (ATRA)-induced myeloid differentiation of AML cells. ChIP-Seq revealed that CBFA2T3 targets the RARα/RXRα cistrome in U937 AML cells, predominantly at myeloid-specific enhancers associated with terminal differentiation. CRISPR/Cas9-mediated abrogation of CBFA2T3 resulted in spontaneous and ATRA-induced activation of myeloid-specific genes in a manner correlated with myeloid differentiation. Importantly, these effects were reversed by CBFA2T3 re-expression. Mechanistic studies showed that CBFA2T3 inhibits RAR target gene transcription by acting at an early step to regulate histone acetyltransferase recruitment, histone acetylation, and chromatin accessibility at RARα target sites, independently of the downstream, RAR-mediated steps of transcription. Finally, we validated the inhibitory effect of CBFA2T3 on RAR in multiple AML subtypes and patient samples. To our knowledge, this is the first study to show that CBFA2T3 down-regulation is both necessary and sufficient for enhancing ATRA-induced myeloid gene expression and differentiation of AML cells. Our findings suggest that CBFA2T3 can serve as a potential target for enhancing AML responsiveness to ATRA differentiation therapies.
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Affiliation(s)
- Nickolas Steinauer
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Chun Guo
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Jinsong Zhang
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri, USA.
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15
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LDB1 Enforces Stability on Direct and Indirect Oncoprotein Partners in Leukemia. Mol Cell Biol 2020; 40:MCB.00652-19. [PMID: 32229578 DOI: 10.1128/mcb.00652-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/14/2020] [Indexed: 12/22/2022] Open
Abstract
The LMO2/LDB1 macromolecular complex is critical in hematopoietic stem and progenitor cell specification and in the development of acute leukemia. This complex is comprised of core subunits of LMO2 and LDB1 as well as single-stranded DNA-binding protein (SSBP) cofactors and DNA-binding basic helix-loop-helix (bHLH) and GATA transcription factors. We analyzed the steady-state abundance and kinetic stability of LMO2 and its partners via Halo protein tagging in conjunction with variant proteins deficient in binding their respective direct protein partners. We discovered a hierarchy of protein stabilities (with half-lives in descending order) as follows: LDB1 > SSBP > LMO2 > TAL1. Importantly, LDB1 is a remarkably stable protein that confers enhanced stability upon direct and indirect partners, thereby nucleating the formation of the multisubunit protein complex. The data imply that free subunits are more rapidly degraded than those incorporated within the LMO2/LDB1 complex. Our studies provided significant insights into LMO2/LDB1 macromolecular protein complex assembly and stability, which has implications for understanding its role in blood cell formation and for therapeutically targeting this complex in human leukemias.
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16
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Wu S, Cui T, Zhang X, Tian T. A non-linear reverse-engineering method for inferring genetic regulatory networks. PeerJ 2020; 8:e9065. [PMID: 32391205 PMCID: PMC7195839 DOI: 10.7717/peerj.9065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/05/2020] [Indexed: 12/19/2022] Open
Abstract
Hematopoiesis is a highly complex developmental process that produces various types of blood cells. This process is regulated by different genetic networks that control the proliferation, differentiation, and maturation of hematopoietic stem cells (HSCs). Although substantial progress has been made for understanding hematopoiesis, the detailed regulatory mechanisms for the fate determination of HSCs are still unraveled. In this study, we propose a novel approach to infer the detailed regulatory mechanisms. This work is designed to develop a mathematical framework that is able to realize nonlinear gene expression dynamics accurately. In particular, we intended to investigate the effect of possible protein heterodimers and/or synergistic effect in genetic regulation. This approach includes the Extended Forward Search Algorithm to infer network structure (top-down approach) and a non-linear mathematical model to infer dynamical property (bottom-up approach). Based on the published experimental data, we study two regulatory networks of 11 genes for regulating the erythrocyte differentiation pathway and the neutrophil differentiation pathway. The proposed algorithm is first applied to predict the network topologies among 11 genes and 55 non-linear terms which may be for heterodimers and/or synergistic effect. Then, the unknown model parameters are estimated by fitting simulations to the expression data of two different differentiation pathways. In addition, the edge deletion test is conducted to remove possible insignificant regulations from the inferred networks. Furthermore, the robustness property of the mathematical model is employed as an additional criterion to choose better network reconstruction results. Our simulation results successfully realized experimental data for two different differentiation pathways, which suggests that the proposed approach is an effective method to infer the topological structure and dynamic property of genetic regulations.
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Affiliation(s)
- Siyuan Wu
- School of Mathematics, Monash University, Clayton, VIC, Australia
| | - Tiangang Cui
- School of Mathematics, Monash University, Clayton, VIC, Australia
| | - Xinan Zhang
- School of Mathematics and Statistics, Central China Normal University, Wuhan, PR China
| | - Tianhai Tian
- School of Mathematics, Monash University, Clayton, VIC, Australia
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17
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Renko M, Fiedler M, Rutherford TJ, Schaefer JV, Plückthun A, Bienz M. Rotational symmetry of the structured Chip/LDB-SSDP core module of the Wnt enhanceosome. Proc Natl Acad Sci U S A 2019; 116:20977-20983. [PMID: 31570581 PMCID: PMC6800368 DOI: 10.1073/pnas.1912705116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Chip/LIM-domain binding protein (LDB)-single-stranded DNA-binding protein (SSDP) (ChiLS) complex controls numerous cell-fate decisions in animal cells, by mediating transcription of developmental control genes via remote enhancers. ChiLS is recruited to these enhancers by lineage-specific LIM-domain proteins that bind to its Chip/LDB subunit. ChiLS recently emerged as the core module of the Wnt enhanceosome, a multiprotein complex that primes developmental control genes for timely Wnt responses. ChiLS binds to NPFxD motifs within Pygopus (Pygo) and the Osa/ARID1A subunit of the BAF chromatin remodeling complex, which could synergize with LIM proteins in tethering ChiLS to enhancers. Chip/LDB and SSDP both contain N-terminal dimerization domains that constitute the bulk of their structured cores. Here, we report the crystal structures of these dimerization domains, in part aided by DARPin chaperones. We conducted systematic surface scanning by structure-designed mutations, followed by in vitro and in vivo binding assays, to determine conserved surface residues required for binding between Chip/LDB, SSDP, and Pygo-NPFxD. Based on this, and on the 4:2 (SSDP-Chip/LDB) stoichiometry of ChiLS, we derive a highly constrained structural model for this complex, which adopts a rotationally symmetrical SSDP2-LDB2-SSDP2 architecture. Integrity of ChiLS is essential for Pygo binding, and our mutational analysis places the NPFxD pockets on either side of the Chip/LDB dimer, each flanked by an SSDP dimer. The symmetry and multivalency of ChiLS underpin its function as an enhancer module integrating Wnt signals with lineage-specific factors to operate context-dependent transcriptional switches that are pivotal for normal development and cancer.
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Affiliation(s)
- Miha Renko
- Medical Research Council Laboratory of Molecular Biology, CB2 0QH Cambridge, United Kingdom
| | - Marc Fiedler
- Medical Research Council Laboratory of Molecular Biology, CB2 0QH Cambridge, United Kingdom
| | - Trevor J Rutherford
- Medical Research Council Laboratory of Molecular Biology, CB2 0QH Cambridge, United Kingdom
| | - Jonas V Schaefer
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Mariann Bienz
- Medical Research Council Laboratory of Molecular Biology, CB2 0QH Cambridge, United Kingdom;
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18
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Yu X, Martella A, Kolovos P, Stevens M, Stadhouders R, Grosveld FG, Andrieu-Soler C. The dynamic emergence of GATA1 complexes identified in in vitro embryonic stem cell differentiation and in vivo mouse fetal liver. Haematologica 2019; 105:1802-1812. [PMID: 31582556 PMCID: PMC7327653 DOI: 10.3324/haematol.2019.216010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 10/03/2019] [Indexed: 01/20/2023] Open
Abstract
GATA1 is an essential transcriptional regulator of myeloid hematopoietic differentiation towards red blood cells. During erythroid differentiation, GATA1 forms different complexes with other transcription factors such as LDB1, TAL1, E2A and LMO2 ("the LDB1 complex") or with FOG1. The functions of GATA1 complexes have been studied extensively in definitive erythroid differentiation; however, the temporal and spatial formation of these complexes during erythroid development is unknown. We applied proximity ligation assay (PLA) to detect, localize and quantify individual interactions during embryonic stem cell differentiation and in mouse fetal liver (FL) tissue. We show that GATA1/LDB1 interactions appear before the proerythroblast stage and increase in a subset of the CD71+/TER119- cells to activate the terminal erythroid differentiation program in 12.5 day FL. Using Ldb1 and Gata1 knockdown FL cells, we studied the functional contribution of the GATA1/LDB1 complex during differentiation. This shows that the active LDB1 complex appears quite late at the proerythroblast stage of differentiation and confirms the power of PLA in studying the dynamic interaction of proteins in cell differentiation at the single cell level. We provide dynamic insight into the temporal and spatial formation of the GATA1 and LDB1 transcription factor complexes during hematopoietic development and differentiation.
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Affiliation(s)
- Xiao Yu
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands.,Current address: Department of Medical Microbiology, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Andrea Martella
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands.,AstraZeneca, R&D Innovative Medicines, Cambridge Science Park, Milton Road, Cambridge, UK
| | - Petros Kolovos
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands.,Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Mary Stevens
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands
| | - Ralph Stadhouders
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands.,Department of Pulmonary Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Frank G Grosveld
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands
| | - Charlotte Andrieu-Soler
- Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands .,Institut de Génétique Moléculaire Montpellier, Université de Montpellier, CNRS, Montpellier, France.,Université de Paris, Laboratoire d'excellence (LabEx) du globule rouge GR-Ex, Paris, France
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19
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Romano O, Miccio A. GATA factor transcriptional activity: Insights from genome-wide binding profiles. IUBMB Life 2019; 72:10-26. [PMID: 31574210 DOI: 10.1002/iub.2169] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/05/2019] [Indexed: 01/07/2023]
Abstract
The members of the GATA family of transcription factors have homologous zinc fingers and bind to similar sequence motifs. Recent advances in genome-wide technologies and the integration of bioinformatics data have led to a better understanding of how GATA factors regulate gene expression; GATA-factor-induced transcriptional and epigenetic changes have now been analyzed at unprecedented levels of detail. Here, we review the results of genome-wide studies of GATA factor occupancy in human and murine cell lines and primary cells (as determined by chromatin immunoprecipitation sequencing), and then discuss the molecular mechanisms underlying the mediation of transcriptional and epigenetic regulation by GATA factors.
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Affiliation(s)
- Oriana Romano
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Annarita Miccio
- Laboratory of chromatin and gene regulation during development, Imagine Institute, INSERM UMR, Paris, France.,Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris, France
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20
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Enhancer long-range contacts: The multi-adaptor protein LDB1 is the tie that binds. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:625-633. [DOI: 10.1016/j.bbagrm.2019.04.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 11/20/2022]
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21
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Agrawal P, Heimbruch KE, Rao S. Genome-Wide Maps of Transcription Regulatory Elements and Transcription Enhancers in Development and Disease. Compr Physiol 2018; 9:439-455. [PMID: 30549021 DOI: 10.1002/cphy.c180028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gene expression is regulated by numerous elements including enhancers, insulators, transcription factors, and architectural proteins. Regions of DNA distal to the transcriptional start site, called enhancers, play a central role in the temporal and tissue-specific regulation of gene expression through RNA polymerase II. The identification of enhancers and other cis regulatory elements has largely been possible due to advances in next generation sequencing technologies. Enhancers regulate gene expression through chromatin loops mediated by architectural proteins such as YY1, CTCF, the cohesin complex, and LDB1. Additionally, enhancers can be transcribed to produce noncoding RNAs termed enhancer RNAs that likely participate in transcriptional regulation. The central role of enhancers in regulating gene expression implicates them in both normal physiology but also many disease states. The importance of enhancers is evident by the suggested role of SNPs, duplications, and other alterations of enhancer function in many diseases, ranging from cancer to atherosclerosis to chronic kidney disease. Although much progress has been made in recent years, the field of enhancer biology and our knowledge of the cis regulome remains a work in progress. This review will highlight recent seminal studies which demonstrate the role of enhancers in normal physiology and disease pathogenesis. © 2019 American Physiological Society. Compr Physiol 9:439-455, 2019.
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Affiliation(s)
- Puja Agrawal
- Blood Research Institute, BloodCenter of Wisconsin, a part of Versiti, Milwaukee, Wisconsin, USA.,Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Katelyn E Heimbruch
- Blood Research Institute, BloodCenter of Wisconsin, a part of Versiti, Milwaukee, Wisconsin, USA.,Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Sridhar Rao
- Blood Research Institute, BloodCenter of Wisconsin, a part of Versiti, Milwaukee, Wisconsin, USA.,Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Pediatrics, Division of Hematology, Oncology, and Bone Marrow Transplantation, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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22
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Temporal autoregulation during human PU.1 locus SubTAD formation. Blood 2018; 132:2643-2655. [PMID: 30315124 DOI: 10.1182/blood-2018-02-834721] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 10/06/2018] [Indexed: 12/20/2022] Open
Abstract
Epigenetic control of gene expression occurs within discrete spatial chromosomal units called topologically associating domains (TADs), but the exact spatial requirements of most genes are unknown; this is of particular interest for genes involved in cancer. We therefore applied high-resolution chromosomal conformation capture sequencing to map the three-dimensional (3D) organization of the human locus encoding the key myeloid transcription factor PU.1 in healthy monocytes and acute myeloid leukemia (AML) cells. We identified a dynamic ∼75-kb unit (SubTAD) as the genomic region in which spatial interactions between PU.1 gene regulatory elements occur during myeloid differentiation and are interrupted in AML. Within this SubTAD, proper initiation of the spatial chromosomal interactions requires PU.1 autoregulation and recruitment of the chromatin-adaptor protein LDB1 (LIM domain-binding protein 1). However, once these spatial interactions have occurred, LDB1 stabilizes them independently of PU.1 autoregulation. Thus, our data support that PU.1 autoregulates its expression in a "hit-and-run" manner by initiating stable chromosomal loops that result in a transcriptionally active chromatin architecture.
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23
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Mehta C, Johnson KD, Gao X, Ong IM, Katsumura KR, McIver SC, Ranheim EA, Bresnick EH. Integrating Enhancer Mechanisms to Establish a Hierarchical Blood Development Program. Cell Rep 2018; 20:2966-2979. [PMID: 28930689 DOI: 10.1016/j.celrep.2017.08.090] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 07/30/2017] [Accepted: 08/25/2017] [Indexed: 12/20/2022] Open
Abstract
Hematopoietic development requires the transcription factor GATA-2, and GATA-2 mutations cause diverse pathologies, including leukemia. GATA-2-regulated enhancers increase Gata2 expression in hematopoietic stem/progenitor cells and control hematopoiesis. The +9.5-kb enhancer activates transcription in endothelium and hematopoietic stem cells (HSCs), and its deletion abrogates HSC generation. The -77-kb enhancer activates transcription in myeloid progenitors, and its deletion impairs differentiation. Since +9.5-/- embryos are HSC deficient, it was unclear whether the +9.5 functions in progenitors or if GATA-2 expression in progenitors solely requires -77. We further dissected the mechanisms using -77;+9.5 compound heterozygous (CH) mice. The embryonic lethal CH mutation depleted megakaryocyte-erythrocyte progenitors (MEPs). While the +9.5 suffices for HSC generation, the -77 and +9.5 must reside on one allele to induce MEPs. The -77 generated burst-forming unit-erythroid through the induction of GATA-1 and other GATA-2 targets. The enhancer circuits controlled signaling pathways that orchestrate a GATA factor-dependent blood development program.
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Affiliation(s)
- Charu Mehta
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Kirby D Johnson
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Xin Gao
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Irene M Ong
- UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53705, USA
| | - Koichi R Katsumura
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Skye C McIver
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Erik A Ranheim
- Department of Pathology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Emery H Bresnick
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.
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24
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Rossmann MP, Orkin SH, Chute JP. Hematopoietic Stem Cell Biology. Hematology 2018. [DOI: 10.1016/b978-0-323-35762-3.00009-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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25
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Stanulovic VS, Cauchy P, Assi SA, Hoogenkamp M. LMO2 is required for TAL1 DNA binding activity and initiation of definitive haematopoiesis at the haemangioblast stage. Nucleic Acids Res 2017; 45:9874-9888. [PMID: 28973433 PMCID: PMC5622341 DOI: 10.1093/nar/gkx573] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 06/27/2017] [Indexed: 02/06/2023] Open
Abstract
LMO2 is a bridging factor within a DNA binding complex and is required for definitive haematopoiesis to occur. The developmental stage of the block in haematopoietic specification is not known. We show that Lmo2−/− mouse embryonic stem cells differentiated to Flk-1+ haemangioblasts, but less efficiently to haemogenic endothelium, which only produced primitive haematopoietic progenitors. Genome-wide approaches indicated that LMO2 is required at the haemangioblast stage to position the TAL1/LMO2/LDB1 complex to regulatory elements that are important for the establishment of the haematopoietic developmental program. In the absence of LMO2, the target site recognition of TAL1 is impaired. The lack of LMO2 resulted in altered gene expression levels already at the haemangioblast stage, with transcription factor genes accounting for ∼15% of affected genes. Comparison of Lmo2−/− with Tal1−/− Flk-1+ cells further showed that TAL1 was required to initiate or sustain Lmo2 expression.
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Affiliation(s)
- Vesna S Stanulovic
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Pierre Cauchy
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Maarten Hoogenkamp
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
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26
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LDB2 inhibits proliferation and migration in liver cancer cells by abrogating HEY1 expression. Oncotarget 2017; 8:94440-94449. [PMID: 29212240 PMCID: PMC5706886 DOI: 10.18632/oncotarget.21772] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/20/2017] [Indexed: 01/09/2023] Open
Abstract
Hepatocellular carcinoma (HCC) was one of the most common cancers around the world, has very low 5-year survival rate. However, the mechanism of HCC occurrence and development is largely unknown. LDB2 belongs to the LIM-domain binding family and functions as an adaptor for transcriptional regulation. Here we found that LDB2 is downregulated in HCC samples. LDB2 has the ability to inhibit proliferation and migration of hepatocarcinoma cells. We found that the proliferation and migration abilities in HCC sample cells were impaired after LDB2 overexpression and vice versa. In mechanism, we found that LDB2 can recruit BRD7 to HEY1 promoter and then block its expression. HEY1 whose expression is upregulated in HCC acts as an oncogene. In brief, our research reveals a new regulatory mechanism for hepatocarcinoma cell proliferation and migration.
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27
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Hewitt KJ, Katsumura KR, Matson DR, Devadas P, Tanimura N, Hebert AS, Coon JJ, Kim JS, Dewey CN, Keles S, Hao S, Paulson RF, Bresnick EH. GATA Factor-Regulated Samd14 Enhancer Confers Red Blood Cell Regeneration and Survival in Severe Anemia. Dev Cell 2017; 42:213-225.e4. [PMID: 28787589 DOI: 10.1016/j.devcel.2017.07.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 05/05/2017] [Accepted: 07/11/2017] [Indexed: 12/31/2022]
Abstract
An enhancer with amalgamated E-box and GATA motifs (+9.5) controls expression of the regulator of hematopoiesis GATA-2. While similar GATA-2-occupied elements are common in the genome, occupancy does not predict function, and GATA-2-dependent genetic networks are incompletely defined. A "+9.5-like" element resides in an intron of Samd14 (Samd14-Enh) encoding a sterile alpha motif (SAM) domain protein. Deletion of Samd14-Enh in mice strongly decreased Samd14 expression in bone marrow and spleen. Although steady-state hematopoiesis was normal, Samd14-Enh-/- mice died in response to severe anemia. Samd14-Enh stimulated stem cell factor/c-Kit signaling, which promotes erythrocyte regeneration. Anemia activated Samd14-Enh by inducing enhancer components and enhancer chromatin accessibility. Thus, a GATA-2/anemia-regulated enhancer controls expression of an SAM domain protein that confers survival in anemia. We propose that Samd14-Enh and an ensemble of anemia-responsive enhancers are essential for erythrocyte regeneration in stress erythropoiesis, a vital process in pathologies, including β-thalassemia, myelodysplastic syndrome, and viral infection.
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Affiliation(s)
- Kyle J Hewitt
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Koichi R Katsumura
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Daniel R Matson
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Prithvia Devadas
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Nobuyuki Tanimura
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | | | - Joshua J Coon
- Department of Chemistry, UW-Madison, Madison, WI, USA; Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science and Department of Chemistry, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, South Korea
| | - Colin N Dewey
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Sunduz Keles
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Siyang Hao
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Robert F Paulson
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Emery H Bresnick
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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GATA3 Abundance Is a Critical Determinant of T Cell Receptor β Allelic Exclusion. Mol Cell Biol 2017; 37:MCB.00052-17. [PMID: 28320875 DOI: 10.1128/mcb.00052-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/14/2017] [Indexed: 12/30/2022] Open
Abstract
Allelic exclusion describes the essential immunological process by which feedback repression of sequential DNA rearrangements ensures that only one autosome expresses a functional T or B cell receptor. In wild-type mammals, approximately 60% of cells have recombined the DNA of one T cell receptor β (TCRβ) V-to-DJ-joined allele in a functional configuration, while the second allele has recombined only the DJ sequences; the other 40% of cells have recombined the V to the DJ segments on both alleles, with only one of the two alleles predicting a functional TCRβ protein. Here we report that the transgenic overexpression of GATA3 leads predominantly to biallelic TCRβ gene (Tcrb) recombination. We also found that wild-type immature thymocytes can be separated into distinct populations based on intracellular GATA3 expression and that GATA3LO cells had almost exclusively recombined only one Tcrb locus (that predicted a functional receptor sequence), while GATA3HI cells had uniformly recombined both Tcrb alleles (one predicting a functional and the other predicting a nonfunctional rearrangement). These data show that GATA3 abundance regulates the recombination propensity at the Tcrb locus and provide new mechanistic insight into the historic immunological conundrum for how Tcrb allelic exclusion is mediated.
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Sims EK. Chewing the Fat: A Metabolic Role for Ldb1 Beyond the Pancreas? Endocrinology 2017; 158:1113-1115. [PMID: 28609835 PMCID: PMC5460831 DOI: 10.1210/en.2017-00080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 01/20/2017] [Indexed: 11/19/2022]
Affiliation(s)
- Emily K Sims
- Department of Pediatrics and Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana 46202
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30
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Ediger BN, Lim HW, Juliana C, Groff DN, Williams LT, Dominguez G, Liu JH, Taylor BL, Walp ER, Kameswaran V, Yang J, Liu C, Hunter CS, Kaestner KH, Naji A, Li C, Sander M, Stein R, Sussel L, Won KJ, May CL, Stoffers DA. LIM domain-binding 1 maintains the terminally differentiated state of pancreatic β cells. J Clin Invest 2016; 127:215-229. [PMID: 27941246 DOI: 10.1172/jci88016] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 10/13/2016] [Indexed: 12/11/2022] Open
Abstract
The recognition of β cell dedifferentiation in type 2 diabetes raises the translational relevance of mechanisms that direct and maintain β cell identity. LIM domain-binding protein 1 (LDB1) nucleates multimeric transcriptional complexes and establishes promoter-enhancer looping, thereby directing fate assignment and maturation of progenitor populations. Many terminally differentiated endocrine cell types, however, remain enriched for LDB1, but its role is unknown. Here, we have demonstrated a requirement for LDB1 in maintaining the terminally differentiated status of pancreatic β cells. Inducible ablation of LDB1 in mature β cells impaired insulin secretion and glucose homeostasis. Transcriptomic analysis of LDB1-depleted β cells revealed the collapse of the terminally differentiated gene program, indicated by a loss of β cell identity genes and induction of the endocrine progenitor factor neurogenin 3 (NEUROG3). Lineage tracing confirmed that LDB1-depleted, insulin-negative β cells express NEUROG3 but do not adopt alternate endocrine cell fates. In primary mouse islets, LDB1 and its LIM homeodomain-binding partner islet 1 (ISL1) were coenriched at chromatin sites occupied by pancreatic and duodenal homeobox 1 (PDX1), NK6 homeobox 1 (NKX6.1), forkhead box A2 (FOXA2), and NK2 homeobox 2 (NKX2.2) - factors that co-occupy active enhancers in 3D chromatin domains in human islets. Indeed, LDB1 was enriched at active enhancers in human islets. Thus, LDB1 maintains the terminally differentiated state of β cells and is a component of active enhancers in both murine and human islets.
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31
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Simonik EA, Cai Y, Kimmelshue KN, Brantley-Sieders DM, Loomans HA, Andl CD, Westlake GM, Youngblood VM, Chen J, Yarbrough WG, Brown BT, Nagarajan L, Brandt SJ. LIM-Only Protein 4 (LMO4) and LIM Domain Binding Protein 1 (LDB1) Promote Growth and Metastasis of Human Head and Neck Cancer (LMO4 and LDB1 in Head and Neck Cancer). PLoS One 2016; 11:e0164804. [PMID: 27780223 PMCID: PMC5079595 DOI: 10.1371/journal.pone.0164804] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 10/01/2016] [Indexed: 12/18/2022] Open
Abstract
Squamous cell carcinoma of the head and neck (HNSCC) accounts for more than 300,000 deaths worldwide per year as a consequence of tumor cell invasion of adjacent structures or metastasis. LIM-only protein 4 (LMO4) and LIM-domain binding protein 1 (LDB1), two directly interacting transcriptional adaptors that have important roles in normal epithelial cell differentiation, have been associated with increased metastasis, decreased differentiation, and shortened survival in carcinoma of the breast. Here, we implicate two LDB1-binding proteins, single-stranded binding protein 2 (SSBP2) and 3 (SSBP3), in controlling LMO4 and LDB1 protein abundance in HNSCC and in regulating specific tumor cell functions in this disease. First, we found that the relative abundance of LMO4, LDB1, and the two SSBPs correlated very significantly in a panel of human HNSCC cell lines. Second, expression of these proteins in tumor primaries and lymph nodes involved by metastasis were concordant in 3 of 3 sets of tissue. Third, using a Matrigel invasion and organotypic reconstruct assay, CRISPR/Cas9-mediated deletion of LDB1 in the VU-SCC-1729 cell line, which is highly invasive of basement membrane and cellular monolayers, reduced tumor cell invasiveness and migration, as well as proliferation on tissue culture plastic. Finally, inactivation of the LDB1 gene in these cells decreased growth and vascularization of xenografted human tumor cells in vivo. These data show that LMO4, LDB1, and SSBP2 and/or SSBP3 regulate metastasis, proliferation, and angiogenesis in HNSCC and provide the first evidence that SSBPs control LMO4 and LDB1 protein abundance in a cancer context.
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Affiliation(s)
- Elizabeth A. Simonik
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Ying Cai
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Katherine N. Kimmelshue
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Dana M. Brantley-Sieders
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Holli A. Loomans
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Claudia D. Andl
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Grant M. Westlake
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Victoria M. Youngblood
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Jin Chen
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Cell & Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, United States of America
- VA Tennessee Valley Healthcare System, Nashville, TN, United States of America
| | - Wendell G. Yarbrough
- Department of Otolaryngology and Barry Baker Laboratory for Head and Neck Oncology, Vanderbilt University School of Medicine, Nashville, TN, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Brandee T. Brown
- Department of Otolaryngology and Barry Baker Laboratory for Head and Neck Oncology, Vanderbilt University School of Medicine, Nashville, TN, United States of America
| | - Lalitha Nagarajan
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, TX, United States of America
| | - Stephen J. Brandt
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Department of Cell & Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, United States of America
- VA Tennessee Valley Healthcare System, Nashville, TN, United States of America
- * E-mail:
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32
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Zhang Y, Yu X, Sun S, Li Q, Xie Y, Li Q, Zhao Y, Pei J, Zhang W, Xue P, Zhou Z, Zhang Y. Cadmium modulates hematopoietic stem and progenitor cells and skews toward myelopoiesis in mice. Toxicol Appl Pharmacol 2016; 313:24-34. [PMID: 27771405 DOI: 10.1016/j.taap.2016.10.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/15/2016] [Accepted: 10/17/2016] [Indexed: 01/06/2023]
Abstract
The heavy metal cadmium (Cd) is known to modulate immunity and cause osteoporosis. However, how Cd influences on hematopoiesis remain largely unknown. Herein, we show that wild-type C57BL/6 (B6) mice exposed to Cd for 3months had expanded bone marrow (BM) populations of long-term hematopoietic stem cells (LT-HSCs), common myeloid progenitors (CMPs) and granulocyte-macrophage progenitors (GMPs), while having reduced populations of multipotent progenitors (MPPs) and common lymphoid progenitors (CLPs). A competitive mixed BM transplantation assay indicates that BM from Cd-treated mice had impaired LT-HSC ability to differentiate into mature cells. In accordance with increased myeloid progenitors and decreased lymphoid progenitors, the BM and spleens of Cd-treated mice had more monocytes and/or neutrophils and fewer B cells and T cells. Cd impaired the ability of the non-hematopoietic system to support LT-HSCs, in that lethally irradiated Cd-treated recipients transplanted with normal BM cells had reduced LT-HSCs after the hematopoietic system was fully reconstituted. This is consistent with reduced osteoblasts, a known critical component for HSC niche, observed in Cd-treated mice. Conversely, lethally irradiated control recipients transplanted with BM cells from Cd-treated mice had normal LT-HSC reconstitution. Furthermore, both control mice and Cd-treated mice that received Alendronate, a clinical drug used for treating osteoporosis, had BM increases of LT-HSCs. Thus, the results suggest Cd increase of LT-HSCs is due to effects on HSCs and not on osteoblasts, although, Cd causes osteoblast reduction and impaired niche function for maintaining HSCs. Furthermore, Cd skews HSCs toward myelopoiesis.
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Affiliation(s)
- Yandong Zhang
- School of Public Health and Key Laboratory of Public Health, MOE, Fudan University, Shanghai 200032, China
| | - Xinchun Yu
- School of Public Health and Key Laboratory of Public Health, MOE, Fudan University, Shanghai 200032, China
| | - Shuhui Sun
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Qian Li
- School of Public Health and Key Laboratory of Public Health, MOE, Fudan University, Shanghai 200032, China
| | - Yunli Xie
- Insititute of Brain Sciences, Fudan University, Shanghai 200032, China
| | - Qiang Li
- Putuo District Center for Disease Control and Prevention, Shanghai 200062, China
| | - Yifan Zhao
- School of Public Health and Key Laboratory of Public Health, MOE, Fudan University, Shanghai 200032, China
| | - Jianfeng Pei
- School of Public Health and Key Laboratory of Public Health, MOE, Fudan University, Shanghai 200032, China
| | - Wenmin Zhang
- School of Public Health and Key Laboratory of Public Health, MOE, Fudan University, Shanghai 200032, China
| | - Peng Xue
- School of Public Health and Key Laboratory of Public Health, MOE, Fudan University, Shanghai 200032, China
| | - Zhijun Zhou
- School of Public Health and Key Laboratory of Public Health, MOE, Fudan University, Shanghai 200032, China
| | - Yubin Zhang
- School of Public Health and Key Laboratory of Public Health, MOE, Fudan University, Shanghai 200032, China.
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Cico A, Andrieu-Soler C, Soler E. Enhancers and their dynamics during hematopoietic differentiation and emerging strategies for therapeutic action. FEBS Lett 2016; 590:4084-4104. [DOI: 10.1002/1873-3468.12424] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 09/08/2016] [Accepted: 09/12/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Alba Cico
- Inserm UMR967, CEA/DRF/iRCM; Fontenay-aux-Roses France
| | - Charlotte Andrieu-Soler
- Inserm UMR967, CEA/DRF/iRCM; Fontenay-aux-Roses France
- CNRS; Institute of Molecular Genetics (IGMM); Montpellier France
| | - Eric Soler
- Inserm UMR967, CEA/DRF/iRCM; Fontenay-aux-Roses France
- CNRS; Institute of Molecular Genetics (IGMM); Montpellier France
- Laboratory of Excellence GR-Ex; Paris France
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34
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Gueta K, David A, Cohen T, Menuchin-Lasowski Y, Nobel H, Narkis G, Li L, Love P, de Melo J, Blackshaw S, Westphal H, Ashery-Padan R. The stage-dependent roles of Ldb1 and functional redundancy with Ldb2 in mammalian retinogenesis. Development 2016; 143:4182-4192. [PMID: 27697904 DOI: 10.1242/dev.129734] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 09/20/2016] [Indexed: 12/26/2022]
Abstract
The Lim domain-binding proteins are key co-factor proteins that assemble with LIM domains of the LMO/LIM-HD family to form functional complexes that regulate cell proliferation and differentiation. Using conditional mutagenesis and comparative phenotypic analysis, we analyze the function of Ldb1 and Ldb2 in mouse retinal development, and demonstrate overlapping and specific functions of both proteins. Ldb1 interacts with Lhx2 in the embryonic retina and both Ldb1 and Ldb2 play a key role in maintaining the pool of retinal progenitor cells. This is accomplished by controlling the expression of the Vsx2 and Rax, and components of the Notch and Hedgehog signaling pathways. Furthermore, the Ldb1/Ldb2-mediated complex is essential for generation of early-born photoreceptors through the regulation of Rax and Crx. Finally, we demonstrate functional redundancy between Ldb1 and Ldb2. Ldb1 can fully compensate the loss of Ldb2 during all phases of retinal development, whereas Ldb2 alone is sufficient to sustain activity of Lhx2 in both early- and late-stage RPCs and in Müller glia. By contrast, loss of Ldb1 disrupts activity of the LIM domain factors in neuronal precursors. An intricate regulatory network exists that is mediated by Ldb1 and Ldb2, and promotes RPC proliferation and multipotency; it also controls specification of mammalian retina cells.
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Affiliation(s)
- Keren Gueta
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ahuvit David
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tsadok Cohen
- Mammalian Genes and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yotam Menuchin-Lasowski
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Hila Nobel
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ginat Narkis
- Mammalian Genes and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - LiQi Li
- Program on Genomics of Differentiation, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Love
- Program on Genomics of Differentiation, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jimmy de Melo
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Heiner Westphal
- Mammalian Genes and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ruth Ashery-Padan
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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35
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Lim CY, Wang H, Woodhouse S, Piterman N, Wernisch L, Fisher J, Göttgens B. BTR: training asynchronous Boolean models using single-cell expression data. BMC Bioinformatics 2016; 17:355. [PMID: 27600248 PMCID: PMC5012073 DOI: 10.1186/s12859-016-1235-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 09/01/2016] [Indexed: 12/25/2022] Open
Abstract
Background Rapid technological innovation for the generation of single-cell genomics data presents new challenges and opportunities for bioinformatics analysis. One such area lies in the development of new ways to train gene regulatory networks. The use of single-cell expression profiling technique allows the profiling of the expression states of hundreds of cells, but these expression states are typically noisier due to the presence of technical artefacts such as drop-outs. While many algorithms exist to infer a gene regulatory network, very few of them are able to harness the extra expression states present in single-cell expression data without getting adversely affected by the substantial technical noise present. Results Here we introduce BTR, an algorithm for training asynchronous Boolean models with single-cell expression data using a novel Boolean state space scoring function. BTR is capable of refining existing Boolean models and reconstructing new Boolean models by improving the match between model prediction and expression data. We demonstrate that the Boolean scoring function performed favourably against the BIC scoring function for Bayesian networks. In addition, we show that BTR outperforms many other network inference algorithms in both bulk and single-cell synthetic expression data. Lastly, we introduce two case studies, in which we use BTR to improve published Boolean models in order to generate potentially new biological insights. Conclusions BTR provides a novel way to refine or reconstruct Boolean models using single-cell expression data. Boolean model is particularly useful for network reconstruction using single-cell data because it is more robust to the effect of drop-outs. In addition, BTR does not assume any relationship in the expression states among cells, it is useful for reconstructing a gene regulatory network with as few assumptions as possible. Given the simplicity of Boolean models and the rapid adoption of single-cell genomics by biologists, BTR has the potential to make an impact across many fields of biomedical research. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1235-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chee Yee Lim
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK
| | - Huange Wang
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK
| | - Steven Woodhouse
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK
| | - Nir Piterman
- Department of Computer Science, University of Leicester, Leicester, UK
| | | | - Jasmin Fisher
- Microsoft Research Cambridge, Cambridge, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK.
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36
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Daly ME. Transcription factor defects causing platelet disorders. Blood Rev 2016; 31:1-10. [PMID: 27450272 DOI: 10.1016/j.blre.2016.07.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/10/2016] [Accepted: 07/12/2016] [Indexed: 01/19/2023]
Abstract
Recent years have seen increasing recognition of a subgroup of inherited platelet function disorders which are due to defects in transcription factors that are required to regulate megakaryopoiesis and platelet production. Thus, germline mutations in the genes encoding the haematopoietic transcription factors RUNX1, GATA-1, FLI1, GFI1b and ETV6 have been associated with both quantitative and qualitative platelet abnormalities, and variable bleeding symptoms in the affected patients. Some of the transcription factor defects are also associated with an increased predisposition to haematologic malignancies (RUNX1, ETV6), abnormal erythropoiesis (GATA-1, GFI1b, ETV6) and immune dysfunction (FLI1). The persistence of MYH10 expression in platelets is a surrogate marker for FLI1 and RUNX1 defects. Characterisation of the transcription factor defects that give rise to platelet function disorders, and of the genes that are differentially regulated as a result, are yielding insights into the roles of these genes in platelet formation and function.
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Affiliation(s)
- Martina E Daly
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield Medical School, Beech Hill Road, Sheffield, S10 2RX, UK.
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Abstract
Human retinoblastoma gene RB1 is the first tumor suppressor gene (TSG) isolated by positional cloning in 1986. RB is extensively studied for its ability to regulate cell cycle by binding to E2F1 and inhibiting the transcriptional activity of the latter. In human embryonic stem cells (ESCs), only a minute trace of RB is found in complex with E2F1. Increased activity of RB triggers differentiation, cell cycle arrest, and cell death. On the other hand, inactivation of the entire RB family (RB1, RBL1, and RBL2) in human ESC induces G2/M arrest and cell death. These observations indicate that both loss and overactivity of RB could be lethal for the stemness of cells. A question arises why inactive RB is required for the survival and stemness of cells? To shed some light on this question, we analyzed the RB-binding proteins. In this review we have focused on 27 RB-binding partners that may have potential roles in different aspects of stem cell biology.
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Affiliation(s)
- M Mushtaq
- Karolinska Institutet, Stockholm, Sweden
| | | | - E V Kashuba
- Karolinska Institutet, Stockholm, Sweden; R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, NASU, Kyiv, Ukraine.
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38
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Kim S, Zhao Y, Lee JM, Kim WR, Gorivodsky M, Westphal H, Geum D. Ldb1 Is Essential for the Development of Isthmic Organizer and Midbrain Dopaminergic Neurons. Stem Cells Dev 2016; 25:986-94. [PMID: 27171818 DOI: 10.1089/scd.2015.0307] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
LIM domain-binding protein 1 (Ldb1) is a nuclear cofactor that interacts with LIM homeodomain proteins to form multiprotein complexes that are important for transcription regulation. Ldb1 has been shown to play essential roles in various processes during mouse embryogenesis. To determine the role of Ldb1 in mid- and hindbrain development, we have generated a conditional mutant with a specific deletion of the Ldb1 in the Engrailed-1-expressing region of the developing mid- and hindbrain. Our study showed that the deletion impaired the expression of signaling molecules, such as fibroblast growth factor 8 (FGF8) and Wnt1, in the isthmic organizer and the expression of Shh in the ventral midbrain. The midbrain and the cerebellum were severely reduced in size, and the midbrain dopaminergic (mDA) neurons were missing in the mutant. These defects are identical to the phenotype that has been observed previously in mice with a deletion of the LIM homeodomain gene Lmx1b. Our results thus provide genetic evidence supporting that Ldb1 and Lmx1b function cooperatively to regulate mid- and hindbrain development. In addition, we found that mouse embryonic stem cells lacking Ldb1 failed to generate several types of differentiated neurons, including the mDA neurons, serotonergic neurons, cholinergic neurons, and olfactory bulb neurons, indicating an essential cell-autonomous role for Ldb1 in the development of these neurons.
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Affiliation(s)
- Soojin Kim
- 1 Department of Biomedical Sciences, Korea University Medical School , Seoul, South Korea
| | - Yangu Zhao
- 2 Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland
| | - Ja-Myong Lee
- 1 Department of Biomedical Sciences, Korea University Medical School , Seoul, South Korea
| | - Woon Ryoung Kim
- 1 Department of Biomedical Sciences, Korea University Medical School , Seoul, South Korea
| | - Marat Gorivodsky
- 2 Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland
| | - Heiner Westphal
- 2 Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland
| | - Dongho Geum
- 1 Department of Biomedical Sciences, Korea University Medical School , Seoul, South Korea
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Klein RH, Stephens DN, Ho H, Chen JK, Salmans ML, Wang W, Yu Z, Andersen B. Cofactors of LIM Domains Associate with Estrogen Receptor α to Regulate the Expression of Noncoding RNA H19 and Corneal Epithelial Progenitor Cell Function. J Biol Chem 2016; 291:13271-85. [PMID: 27129775 DOI: 10.1074/jbc.m115.709386] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Indexed: 11/06/2022] Open
Abstract
Cofactors of LIM domain proteins, CLIM1 and CLIM2, are widely expressed transcriptional cofactors that are recruited to gene regulatory regions by DNA-binding proteins, including LIM domain transcription factors. In the cornea, epithelium-specific expression of a dominant negative (DN) CLIM under the keratin 14 (K14) promoter causes blistering, wounding, inflammation, epithelial hyperplasia, and neovascularization followed by epithelial thinning and subsequent epidermal-like differentiation of the corneal epithelium. The defects in corneal epithelial differentiation and cell fate determination suggest that CLIM may regulate corneal progenitor cells and the transition to differentiation. Consistent with this notion, the K14-DN-Clim corneal epithelium first exhibits increased proliferation followed by fewer progenitor cells with decreased proliferative potential. In vivo ChIP-sequencing experiments with corneal epithelium show that CLIM binds to and regulates numerous genes involved in cell adhesion and proliferation, including limbally enriched genes. Intriguingly, CLIM associates primarily with non-LIM homeodomain motifs in corneal epithelial cells, including that of estrogen receptor α. Among CLIM targets is the noncoding RNA H19 whose deregulation is associated with Silver-Russell and Beckwith-Wiedemann syndromes. We demonstrate here that H19 negatively regulates corneal epithelial proliferation. In addition to cell cycle regulators, H19 affects the expression of multiple cell adhesion genes. CLIM interacts with estrogen receptor α at the H19 locus, potentially explaining the higher expression of H19 in female than male corneas. Together, our results demonstrate an important role for CLIM in regulating the proliferative potential of corneal epithelial progenitors and identify CLIM downstream target H19 as a regulator of corneal epithelial proliferation and adhesion.
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Affiliation(s)
- Rachel Herndon Klein
- From the Departments of Biological Chemistry and Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697 and
| | | | | | | | - Michael L Salmans
- From the Departments of Biological Chemistry and Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697 and
| | - Winnie Wang
- From the Departments of Biological Chemistry and
| | - Zhengquan Yu
- From the Departments of Biological Chemistry and State Key Laboratories for AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Bogi Andersen
- From the Departments of Biological Chemistry and Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697 and Medicine and
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GATA Factor-G-Protein-Coupled Receptor Circuit Suppresses Hematopoiesis. Stem Cell Reports 2016; 6:368-82. [PMID: 26905203 PMCID: PMC4788764 DOI: 10.1016/j.stemcr.2016.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 01/11/2016] [Accepted: 01/13/2016] [Indexed: 12/20/2022] Open
Abstract
Hematopoietic stem cells (HSCs) originate from hemogenic endothelium within the aorta-gonad-mesonephros (AGM) region of the mammalian embryo. The relationship between genetic circuits controlling stem cell genesis and multi-potency is not understood. A Gata2 cis element (+9.5) enhances Gata2 expression in the AGM and induces the endothelial to HSC transition. We demonstrated that GATA-2 rescued hematopoiesis in +9.5−/− AGMs. As G-protein-coupled receptors (GPCRs) are the most common targets for FDA-approved drugs, we analyzed the GPCR gene ensemble to identify GATA-2-regulated GPCRs. Of the 20 GATA-2-activated GPCR genes, four were GATA-1-activated, and only Gpr65 expression resembled Gata2. Contrasting with the paradigm in which GATA-2-activated genes promote hematopoietic stem and progenitor cell genesis/function, our mouse and zebrafish studies indicated that GPR65 suppressed hematopoiesis. GPR65 established repressive chromatin at the +9.5 site, restricted occupancy by the activator Scl/TAL1, and repressed Gata2 transcription. Thus, a Gata2 cis element creates a GATA-2-GPCR circuit that limits positive regulators that promote hematopoiesis. GATA-2 rescues +9.5−/− AGM hematopoietic activity GATA-2 upregulates Gpr65, which encodes a negative regulator of hematopoiesis GPR65 suppresses hematopoiesis by repressing Gata2 expression GPR65 represses Gata2 expression by increasing H4K20me1, restricting Scl/TAL1 occupancy
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Krivega I, Dean A. Chromatin looping as a target for altering erythroid gene expression. Ann N Y Acad Sci 2016; 1368:31-9. [PMID: 26918894 DOI: 10.1111/nyas.13012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/04/2016] [Accepted: 01/11/2016] [Indexed: 01/07/2023]
Abstract
The β-hemoglobinopathies are the most common monogenic disorders in humans, with symptoms arising after birth when the fetal γ-globin genes are silenced and the adult β-globin gene is activated. There is a growing appreciation that genome organization and the folding of chromosomes are key determinants of gene transcription. Underlying this function is the activity of transcriptional enhancers that increase the transcription of target genes over long linear distances. To accomplish this, enhancers engage in close physical contact with target promoters through chromosome folding or looping that is orchestrated by protein complexes that bind to both sites and stabilize their interaction. We find that enhancer activity can be redirected with concomitant changes in gene transcription. Both targeting the β-globin locus control region (LCR) to the γ-globin gene in adult erythroid cells by tethering and epigenetic unmasking of a silenced γ-globin gene lead to increased frequency of LCR/γ-globin contacts and reduced LCR/β-globin contacts. The outcome of these manipulations is robust, pancellular γ-globin transcription activation with a concomitant reduction in β-globin transcription. These examples show that chromosome looping may be considered a therapeutic target for gene activation in β-thalassemia and sickle cell disease.
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Affiliation(s)
- Ivan Krivega
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
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Affeldt S, Verny L, Isambert H. 3off2: A network reconstruction algorithm based on 2-point and 3-point information statistics. BMC Bioinformatics 2016; 17 Suppl 2:12. [PMID: 26823190 PMCID: PMC4959376 DOI: 10.1186/s12859-015-0856-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Background The reconstruction of reliable graphical models from observational data is important in bioinformatics and other computational fields applying network reconstruction methods to large, yet finite datasets. The main network reconstruction approaches are either based on Bayesian scores, which enable the ranking of alternative Bayesian networks, or rely on the identification of structural independencies, which correspond to missing edges in the underlying network. Bayesian inference methods typically require heuristic search strategies, such as hill-climbing algorithms, to sample the super-exponential space of possible networks. By contrast, constraint-based methods, such as the PC and IC algorithms, are expected to run in polynomial time on sparse underlying graphs, provided that a correct list of conditional independencies is available. Yet, in practice, conditional independencies need to be ascertained from the available observational data, based on adjustable statistical significance levels, and are not robust to sampling noise from finite datasets. Results We propose a more robust approach to reconstruct graphical models from finite datasets. It combines constraint-based and Bayesian approaches to infer structural independencies based on the ranking of their most likely contributing nodes. In a nutshell, this local optimization scheme and corresponding 3off2 algorithm iteratively “take off” the most likely conditional 3-point information from the 2-point (mutual) information between each pair of nodes. Conditional independencies are thus derived by progressively collecting the most significant indirect contributions to all pairwise mutual information. The resulting network skeleton is then partially directed by orienting and propagating edge directions, based on the sign and magnitude of the conditional 3-point information of unshielded triples. The approach is shown to outperform both constraint-based and Bayesian inference methods on a range of benchmark networks. The 3off2 approach is then applied to the reconstruction of the hematopoiesis regulation network based on recent single cell expression data and is found to retrieve more experimentally ascertained regulations between transcription factors than with other available methods. Conclusions The novel information-theoretic approach and corresponding 3off2 algorithm combine constraint-based and Bayesian inference methods to reliably reconstruct graphical models, despite inherent sampling noise in finite datasets. In particular, experimentally verified interactions as well as novel predicted regulations are established on the hematopoiesis regulatory networks based on single cell expression data. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0856-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Séverine Affeldt
- Institut Curie, PSL Research University, CNRS, UMR168, 26 rue d'Ulm, Paris, 75005, France.,Sorbonne Universités, UPMC Univ Paris 06, 4, Place Jussieu, Paris, 75005, France
| | - Louis Verny
- Institut Curie, PSL Research University, CNRS, UMR168, 26 rue d'Ulm, Paris, 75005, France.,Sorbonne Universités, UPMC Univ Paris 06, 4, Place Jussieu, Paris, 75005, France
| | - Hervé Isambert
- Institut Curie, PSL Research University, CNRS, UMR168, 26 rue d'Ulm, Paris, 75005, France. .,Sorbonne Universités, UPMC Univ Paris 06, 4, Place Jussieu, Paris, 75005, France.
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Abstract
Oncogenic transcription factors are commonly activated in acute leukemias and subvert normal gene expression networks to reprogram hematopoietic progenitors into preleukemic stem cells, as exemplified by LIM-only 2 (LMO2) in T-cell acute lymphoblastic leukemia (T-ALL). Whether or not these oncoproteins interfere with other DNA-dependent processes is largely unexplored. Here, we show that LMO2 is recruited to DNA replication origins by interaction with three essential replication enzymes: DNA polymerase delta (POLD1), DNA primase (PRIM1), and minichromosome 6 (MCM6). Furthermore, tethering LMO2 to synthetic DNA sequences is sufficient to transform these sequences into origins of replication. We next addressed the importance of LMO2 in erythroid and thymocyte development, two lineages in which cell cycle and differentiation are tightly coordinated. Lowering LMO2 levels in erythroid progenitors delays G1-S progression and arrests erythropoietin-dependent cell growth while favoring terminal differentiation. Conversely, ectopic expression in thymocytes induces DNA replication and drives these cells into cell cycle, causing differentiation blockade. Our results define a novel role for LMO2 in directly promoting DNA synthesis and G1-S progression.
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Hewitt KJ, Johnson KD, Gao X, Keles S, Bresnick EH. The Hematopoietic Stem and Progenitor Cell Cistrome: GATA Factor-Dependent cis-Regulatory Mechanisms. Curr Top Dev Biol 2016; 118:45-76. [PMID: 27137654 PMCID: PMC8572122 DOI: 10.1016/bs.ctdb.2016.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Transcriptional regulators mediate the genesis and function of the hematopoietic system by binding complex ensembles of cis-regulatory elements to establish genetic networks. While thousands to millions of any given cis-element resides in a genome, how transcriptional regulators select these sites and how site attributes dictate functional output is not well understood. An instructive system to address this problem involves the GATA family of transcription factors that control vital developmental and physiological processes and are linked to multiple human pathologies. Although GATA factors bind DNA motifs harboring the sequence GATA, only a very small subset of these abundant motifs are occupied in genomes. Mechanistic studies revealed a unique configuration of a GATA factor-regulated cis-element consisting of an E-box and a downstream GATA motif separated by a short DNA spacer. GATA-1- or GATA-2-containing multiprotein complexes at these composite elements control transcription of genes critical for hematopoietic stem cell emergence in the mammalian embryo, hematopoietic progenitor cell regulation, and erythroid cell maturation. Other constituents of the complex include the basic helix-loop-loop transcription factor Scl/TAL1, its heterodimeric partner E2A, and the Lim domain proteins LMO2 and LDB1. This chapter reviews the structure/function of E-box-GATA composite cis-elements, which collectively constitute an important sector of the hematopoietic stem and progenitor cell cistrome.
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Affiliation(s)
- Kyle J. Hewitt
- University of Wisconsin School of Medicine and Public Health, Department of Cell and Regenerative Biology, Carbone Cancer Center, Madison, WI 53705,UW-Madison Blood Research Program
| | - Kirby D. Johnson
- University of Wisconsin School of Medicine and Public Health, Department of Cell and Regenerative Biology, Carbone Cancer Center, Madison, WI 53705,UW-Madison Blood Research Program
| | - Xin Gao
- University of Wisconsin School of Medicine and Public Health, Department of Cell and Regenerative Biology, Carbone Cancer Center, Madison, WI 53705,UW-Madison Blood Research Program
| | - Sunduz Keles
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health
| | - Emery H. Bresnick
- University of Wisconsin School of Medicine and Public Health, Department of Cell and Regenerative Biology, Carbone Cancer Center, Madison, WI 53705,UW-Madison Blood Research Program,Corresponding author:
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LMO2 Oncoprotein Stability in T-Cell Leukemia Requires Direct LDB1 Binding. Mol Cell Biol 2015; 36:488-506. [PMID: 26598604 DOI: 10.1128/mcb.00901-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/16/2015] [Indexed: 12/24/2022] Open
Abstract
LMO2 is a component of multisubunit DNA-binding transcription factor complexes that regulate gene expression in hematopoietic stem and progenitor cell development. Enforced expression of LMO2 causes leukemia by inducing hematopoietic stem cell-like features in T-cell progenitor cells, but the biochemical mechanisms of LMO2 function have not been fully elucidated. In this study, we systematically dissected the LMO2/LDB1-binding interface to investigate the role of this interaction in T-cell leukemia. Alanine scanning mutagenesis of the LIM interaction domain of LDB1 revealed a discrete motif, R(320)LITR, required for LMO2 binding. Most strikingly, coexpression of full-length, wild-type LDB1 increased LMO2 steady-state abundance, whereas coexpression of mutant proteins deficient in LMO2 binding compromised LMO2 stability. These mutant LDB1 proteins also exerted dominant negative effects on growth and transcription in diverse leukemic cell lines. Mass spectrometric analysis of LDB1 binding partners in leukemic lines supports the notion that LMO2/LDB1 function in leukemia occurs in the context of multisubunit complexes, which also protect the LMO2 oncoprotein from degradation. Collectively, these data suggest that the assembly of LMO2 into complexes, via direct LDB1 interaction, is a potential molecular target that could be exploited in LMO2-driven leukemias resistant to existing chemotherapy regimens.
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A Systems Approach Identifies Essential FOXO3 Functions at Key Steps of Terminal Erythropoiesis. PLoS Genet 2015; 11:e1005526. [PMID: 26452208 PMCID: PMC4599908 DOI: 10.1371/journal.pgen.1005526] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 08/24/2015] [Indexed: 12/26/2022] Open
Abstract
Circulating red blood cells (RBCs) are essential for tissue oxygenation and homeostasis. Defective terminal erythropoiesis contributes to decreased generation of RBCs in many disorders. Specifically, ineffective nuclear expulsion (enucleation) during terminal maturation is an obstacle to therapeutic RBC production in vitro. To obtain mechanistic insights into terminal erythropoiesis we focused on FOXO3, a transcription factor implicated in erythroid disorders. Using an integrated computational and experimental systems biology approach, we show that FOXO3 is essential for the correct temporal gene expression during terminal erythropoiesis. We demonstrate that the FOXO3-dependent genetic network has critical physiological functions at key steps of terminal erythropoiesis including enucleation and mitochondrial clearance processes. FOXO3 loss deregulated transcription of genes implicated in cell polarity, nucleosome assembly and DNA packaging-related processes and compromised erythroid enucleation. Using high-resolution confocal microscopy and imaging flow cytometry we show that cell polarization is impaired leading to multilobulated Foxo3-/- erythroblasts defective in nuclear expulsion. Ectopic FOXO3 expression rescued Foxo3-/- erythroblast enucleation-related gene transcription, enucleation defects and terminal maturation. Remarkably, FOXO3 ectopic expression increased wild type erythroblast maturation and enucleation suggesting that enhancing FOXO3 activity may improve RBCs production. Altogether these studies uncover FOXO3 as a novel regulator of erythroblast enucleation and terminal maturation suggesting FOXO3 modulation might be therapeutic in disorders with defective erythroid maturation. Red blood cells (RBCs) are highly specialized cells that transport oxygen throughout the body and are essential for survival. However, RBCs have a limited lifespan and need to be replenished continuously by stem cells in the bone marrow. Mammalian RBCs are unique in that in order to fully mature they exclude their nucleus and other organelles. Mechanisms involved in these processes are not well understood at the molecular level. Defects in any of the these processes may lead to red blood cell defects, a decreased capacity to transport oxygen and/or a block in red blood cell production in vitro. Therefore, understanding how these processes are regulated at the molecular level can lead to promising new therapies for red blood cell defects and improved methods of generating red blood cells in a dish. Here, using an integrated computational and experimental biology approach, we found that the nuclear factor FOXO3 is a crucial regulator of red blood cell production by coordinating the expression of many of the genes specific for terminal maturation of red blood cells. Furthermore we found that FOXO3 can even increase the production of normal red blood cells in culture raising the possibility that enhancing FOXO3 may have a therapeutic use. Our studies identify FOXO3 as a novel regulator of RBC enucleation and terminal erythropoiesis.
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47
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Fiedler M, Graeb M, Mieszczanek J, Rutherford TJ, Johnson CM, Bienz M. An ancient Pygo-dependent Wnt enhanceosome integrated by Chip/LDB-SSDP. eLife 2015; 4:e09073. [PMID: 26312500 PMCID: PMC4571689 DOI: 10.7554/elife.09073] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/26/2015] [Indexed: 12/15/2022] Open
Abstract
TCF/LEF factors are ancient context-dependent enhancer-binding proteins that are activated by β-catenin following Wnt signaling. They control embryonic development and adult stem cell compartments, and their dysregulation often causes cancer. β-catenin-dependent transcription relies on the NPF motif of Pygo proteins. Here, we use a proteomics approach to discover the Chip/LDB-SSDP (ChiLS) complex as the ligand specifically binding to NPF. ChiLS also recognizes NPF motifs in other nuclear factors including Runt/RUNX2 and Drosophila ARID1, and binds to Groucho/TLE. Studies of Wnt-responsive dTCF enhancers in the Drosophila embryonic midgut indicate how these factors interact to form the Wnt enhanceosome, primed for Wnt responses by Pygo. Together with previous evidence, our study indicates that ChiLS confers context-dependence on TCF/LEF by integrating multiple inputs from lineage and signal-responsive factors, including enhanceosome switch-off by Notch. Its pivotal function in embryos and stem cells explain why its integrity is crucial in the avoidance of cancer.
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Affiliation(s)
- Marc Fiedler
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Michael Graeb
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Juliusz Mieszczanek
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Trevor J Rutherford
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Christopher M Johnson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Mariann Bienz
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, United Kingdom
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48
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Gu W, Monteiro R, Zuo J, Simões FC, Martella A, Andrieu-Soler C, Grosveld F, Sauka-Spengler T, Patient R. A novel TGFβ modulator that uncouples R-Smad/I-Smad-mediated negative feedback from R-Smad/ligand-driven positive feedback. PLoS Biol 2015; 13:e1002051. [PMID: 25665164 PMCID: PMC4321984 DOI: 10.1371/journal.pbio.1002051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/17/2014] [Indexed: 01/17/2023] Open
Abstract
As some of the most widely utilised intercellular signalling molecules, transforming growth factor β (TGFβ) superfamily members play critical roles in normal development and become disrupted in human disease. Establishing appropriate levels of TGFβ signalling involves positive and negative feedback, which are coupled and driven by the same signal transduction components (R-Smad transcription factor complexes), but whether and how the regulation of the two can be distinguished are unknown. Genome-wide comparison of published ChIP-seq datasets suggests that LIM domain binding proteins (Ldbs) co-localise with R-Smads at a substantial subset of R-Smad target genes including the locus of inhibitory Smad7 (I-Smad7), which mediates negative feedback for TGFβ signalling. We present evidence suggesting that zebrafish Ldb2a binds and directly activates the I-Smad7 gene, whereas it binds and represses the ligand gene, Squint (Sqt), which drives positive feedback. Thus, the fine tuning of TGFβ signalling derives from positive and negative control by Ldb2a. Expression of ldb2a is itself activated by TGFβ signals, suggesting potential feed-forward loops that might delay the negative input of Ldb2a to the positive feedback, as well as the positive input of Ldb2a to the negative feedback. In this way, precise gene expression control by Ldb2a enables an initial build-up of signalling via a fully active positive feedback in the absence of buffering by the negative feedback. In Ldb2a-deficient zebrafish embryos, homeostasis of TGFβ signalling is perturbed and signalling is stably enhanced, giving rise to excess mesoderm and endoderm, an effect that can be rescued by reducing signalling by the TGFβ family members, Nodal and BMP. Thus, Ldb2a is critical to the homeostatic control of TGFβ signalling and thereby embryonic patterning.
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Affiliation(s)
- Wenchao Gu
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Rui Monteiro
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- BHF Centre of Research Excellence, Oxford, United Kingdom
| | - Jie Zuo
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Filipa Costa Simões
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Andrea Martella
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Charlotte Andrieu-Soler
- INSERM U872, Université René Descartes Sorbonne Paris Cité, Team 17, Centre de Recherche des Cordeliers, Paris, France
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Tatjana Sauka-Spengler
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Roger Patient
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- BHF Centre of Research Excellence, Oxford, United Kingdom
- * E-mail:
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49
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Plautz CZ, Zirkle BE, Deshotel MJ, Grainger RM. Early stages of induction of anterior head ectodermal properties in Xenopus embryos are mediated by transcriptional cofactor ldb1. Dev Dyn 2014; 243:1606-18. [PMID: 25258326 DOI: 10.1002/dvdy.24193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 09/02/2014] [Accepted: 09/22/2014] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Specific molecules involved in early inductive signaling from anterior neural tissue to the placodal ectoderm to establish a lens-forming bias, as well as their regulatory factors, remain largely unknown. In this study, we sought to identify and characterize these molecules. RESULTS Using an expression cloning strategy to isolate genes with lens-inducing activity, we identified the transcriptional cofactor ldb1. This, together with evidence for its nuclear dependence, suggests its role as a regulatory factor, not a direct signaling molecule. We propose that ldb1 mediates induction of early lens genes in our functional assay by transcriptional activation of lens-inducing signals. Gain-of-function assays demonstrate that the inductive activity of the anterior neural plate on head ectodermal structures can be augmented by ldb1. Loss-of-function assays show that knockdown of ldb1 leads to decreased expression of early lens and retinal markers and subsequently to defects in eye development. CONCLUSIONS The functional cloning, expression pattern, overexpression, and knockdown data show that an ldb1-regulated mechanism acts as an early signal for Xenopus lens induction.
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Affiliation(s)
- Carol Zygar Plautz
- Shepherd University, Department of Biology, Shepherdstown, West Virginia
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50
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Li J, Kurasawa Y, Wang Y, Clise-Dwyer K, Klumpp SA, Liang H, Tailor RC, Raymond AC, Estrov Z, Brandt SJ, Davis RE, Zweidler-McKay P, Amin HM, Nagarajan L. Requirement for ssbp2 in hematopoietic stem cell maintenance and stress response. THE JOURNAL OF IMMUNOLOGY 2014; 193:4654-62. [PMID: 25238756 DOI: 10.4049/jimmunol.1300337] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Transcriptional mechanisms governing hematopoietic stem cell (HSC) quiescence, self-renewal, and differentiation are not fully understood. Sequence-specific ssDNA-binding protein 2 (SSBP2) is a candidate acute myelogenous leukemia (AML) suppressor gene located at chromosome 5q14. SSBP2 binds the transcriptional adaptor protein Lim domain-binding protein 1 (LDB1) and enhances LDB1 stability to regulate gene expression. Notably, Ldb1 is essential for HSC specification during early development and maintenance in adults. We previously reported shortened lifespan and greater susceptibility to B cell lymphomas and carcinomas in Ssbp2(-/-) mice. However, whether Ssbp2 plays a regulatory role in normal HSC function and leukemogenesis is unknown. In this study, we provide several lines of evidence to demonstrate a requirement for Ssbp2 in the function and transcriptional program of hematopoietic stem and progenitor cells (HSPCs) in vivo. We found that hematopoietic tissues were hypoplastic in Ssbp2(-/-) mice, and the frequency of lymphoid-primed multipotent progenitor cells in bone marrow was reduced. Other significant features of these mice were delayed recovery from 5-fluorouracil treatment and diminished multilineage reconstitution in lethally irradiated bone marrow recipients. Dramatic reduction of Notch1 transcripts and increased expression of transcripts encoding the transcription factor E2a and its downstream target Cdkn1a also distinguished Ssbp2(-/-) HSPCs from wild-type HSPCs. Finally, a tendency toward coordinated expression of SSBP2 and the AML suppressor NOTCH1 in a subset of the Cancer Genome Atlas AML cases suggested a role for SSBP2 in AML pathogenesis. Collectively, our results uncovered a critical regulatory function for SSBP2 in HSPC gene expression and function.
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Affiliation(s)
- June Li
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Yasuhiro Kurasawa
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Yang Wang
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Karen Clise-Dwyer
- Department of Stem Cell Transplantation, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Sherry A Klumpp
- Department of Veterinary Medicine and Surgery, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Hong Liang
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Ramesh C Tailor
- Department of Radiation Physics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Aaron C Raymond
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030; Graduate Program in Genes and Development, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Zeev Estrov
- Department of Leukemia, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Stephen J Brandt
- Department of Medicine, Vanderbilt University, Nashville, TN 37232; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232; Department of Cancer Biology, Vanderbilt University, Nashville, TN 37232; Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN 37232
| | - Richard E Davis
- Department of Lymphoma and Myeloma, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Patrick Zweidler-McKay
- Division of Pediatrics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Hesham M Amin
- Department of Hematopathology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030; and
| | - Lalitha Nagarajan
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030; Graduate Program in Genes and Development, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030; Department of Leukemia, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030; Graduate Program in Human Molecular Genetics, Center for Stem Cell and Developmental Biology, and Center for Cancer Genetics and Genomics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
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