1
|
Hu M, Alkhairy S, Lee I, Pillich RT, Fong D, Smith K, Bachelder R, Ideker T, Pratt D. Evaluation of large language models for discovery of gene set function. ArXiv 2024:arXiv:2309.04019v2. [PMID: 37731657 PMCID: PMC10508824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Gene set analysis is a mainstay of functional genomics, but it relies on curated databases of gene functions that are incomplete. Here we evaluate five Large Language Models (LLMs) for their ability to discover the common biological functions represented by a gene set, substantiated by supporting rationale, citations and a confidence assessment. Benchmarking against canonical gene sets from the Gene Ontology, GPT-4 confidently recovered the curated name or a more general concept (73% of cases), while benchmarking against random gene sets correctly yielded zero confidence. Gemini-Pro and Mixtral-Instruct showed ability in naming but were falsely confident for random sets, whereas Llama2-70b had poor performance overall. In gene sets derived from 'omics data, GPT-4 identified novel functions not reported by classical functional enrichment (32% of cases), which independent review indicated were largely verifiable and not hallucinations. The ability to rapidly synthesize common gene functions positions LLMs as valuable 'omics assistants.
Collapse
Affiliation(s)
- Mengzhou Hu
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Sahar Alkhairy
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Ingoo Lee
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Rudolf T. Pillich
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Dylan Fong
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Kevin Smith
- Department of Physics, University of California San Diego, La Jolla, California, USA
| | - Robin Bachelder
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Dexter Pratt
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| |
Collapse
|
2
|
Xie L, Tao Y, Shen Z, Deng H, Duan X, Xue Y, Chen D, Li Y. Congenital asplenia impairs heme-iron recycling during erythropoiesis in zebrafish. Developmental & Comparative Immunology 2024; 151:105108. [PMID: 38040044 DOI: 10.1016/j.dci.2023.105108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/13/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
The spleen is postulated to be a hematopoietic tissue in adult fish; however, clear evidence is still lacking to define its role in hematopoietic activity. In our previous study, a congenitally asplenic zebrafish was generated though gene editing, which provided a new perspective for studying the role of fish spleen in hematopoiesis. In this study, HSC-regulated and erythrocyte marker genes, such as gata1a, gata2, klf1, hbaa1, hbaa2, hbba1 and hbba2 were significantly reduced in congenitally asplenic zebrafish when compared with wild-type (WT). Subsequently, we conducted the transcriptome profiles of whole kidneys from WT and congenitally asplenic zebrafish to explore the possible molecular mechanisms underlying the impaired erythropoiesis caused by congenital asplenia. Our results demonstrated that congenital asplenia might impair heme-iron recycling during erythropoiesis, as evidenced by significant down-regulation of genes associated with iron acquisition (tfr1a, tfa, steap3 and slc25a37) and heme biosynthesis and transport (alas2, fech, uros, urod, copx, ppox and abcb10) in congenitally asplenic zebrafish. In addition, the down-regulation of hemopoiesis-related GO terms, including heme binding, tetrapyrrole binding, iron ion binding, heme metabolic process, heme biosynthetic process, erythrocyte differentiation, iron ion homeostasis and hemoglobin metabolic process confirmed the impaired erythropoiesis induced by congenital asplenia. Our study provides an in-depth understanding of spleen function in regulating heme-iron homeostasis during hematopoiesis, thereby providing valuable insights into pathological responses in splenectomized or congenitally asplenic patients.
Collapse
Affiliation(s)
- Lang Xie
- National Agricultural Science Observing and Experimental Station of Chongqing, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, Hubei, 430223, China; Aquaculture Engineering Technology Research Center of Southwest University, College of Fisheries, Southwest University, Chongqing, 400715, China
| | - Yixi Tao
- Aquaculture Engineering Technology Research Center of Southwest University, College of Fisheries, Southwest University, Chongqing, 400715, China
| | - Ziwei Shen
- National Agricultural Science Observing and Experimental Station of Chongqing, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, Hubei, 430223, China
| | - Huatang Deng
- National Agricultural Science Observing and Experimental Station of Chongqing, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, Hubei, 430223, China
| | - Xinbin Duan
- National Agricultural Science Observing and Experimental Station of Chongqing, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, Hubei, 430223, China
| | - Yang Xue
- Chongqing Fisheries Technical Extension Center, Chongqing, 400020, China
| | - Daqing Chen
- National Agricultural Science Observing and Experimental Station of Chongqing, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, Hubei, 430223, China
| | - Yun Li
- Aquaculture Engineering Technology Research Center of Southwest University, College of Fisheries, Southwest University, Chongqing, 400715, China.
| |
Collapse
|
3
|
Quotti Tubi L, Canovas Nunes S, Mandato E, Pizzi M, Vitulo N, D’Agnolo M, Colombatti R, Martella M, Boaro MP, Doriguzzi Breatta E, Fregnani A, Spinello Z, Nabergoj M, Filhol O, Boldyreff B, Albiero M, Fadini GP, Gurrieri C, Vianello F, Semenzato G, Manni S, Trentin L, Piazza F. CK2β Regulates Hematopoietic Stem Cell Biology and Erythropoiesis. Hemasphere 2023; 7:e978. [PMID: 38026791 PMCID: PMC10673422 DOI: 10.1097/hs9.0000000000000978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/25/2023] [Indexed: 12/01/2023] Open
Abstract
The Ser-Thr kinase CK2 plays important roles in sustaining cell survival and resistance to stress and these functions are exploited by different types of blood tumors. Yet, the physiological involvement of CK2 in normal blood cell development is poorly known. Here, we discovered that the β regulatory subunit of CK2 is critical for normal hematopoiesis in the mouse. Fetal livers of conditional CK2β knockout embryos showed increased numbers of hematopoietic stem cells associated to a higher proliferation rate compared to control animals. Both hematopoietic stem and progenitor cells (HSPCs) displayed alterations in the expression of transcription factors involved in cell quiescence, self-renewal, and lineage commitment. HSPCs lacking CK2β were functionally impaired in supporting both in vitro and in vivo hematopoiesis as demonstrated by transplantation assays. Furthermore, KO mice developed anemia due to a reduced number of mature erythroid cells. This compartment was characterized by dysplasia, proliferative defects at early precursor stage, and apoptosis at late-stage erythroblasts. Erythroid cells exhibited a marked compromise of signaling cascades downstream of the cKit and erythropoietin receptor, with a defective activation of ERK/JNK, JAK/STAT5, and PI3K/AKT pathways and perturbations of several transcriptional programs as demonstrated by RNA-Seq analysis. Moreover, we unraveled an unforeseen molecular mechanism whereby CK2 sustains GATA1 stability and transcriptional proficiency. Thus, our work demonstrates new and crucial functions of CK2 in HSPC biology and in erythropoiesis.
Collapse
Affiliation(s)
- Laura Quotti Tubi
- Department of Medicine, Division of Hematology, University of Padova, Italy
- Laboratory of Normal and Malignant Hematopoiesis and Pathobiology of Myeloma and Lymphoma. Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Sara Canovas Nunes
- Laboratory of Normal and Malignant Hematopoiesis and Pathobiology of Myeloma and Lymphoma. Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Elisa Mandato
- Laboratory of Normal and Malignant Hematopoiesis and Pathobiology of Myeloma and Lymphoma. Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marco Pizzi
- Department of Medicine, Cytopathology and Surgical Pathology Unit, University of Padova, Italy
| | - Nicola Vitulo
- Department of Biotechnology, University of Verona, Italy
| | - Mirco D’Agnolo
- Department of Women’s and Child’s Health, University of Padova, Italy
| | | | | | - Maria Paola Boaro
- Department of Women’s and Child’s Health, University of Padova, Italy
| | - Elena Doriguzzi Breatta
- Department of Medicine, Division of Hematology, University of Padova, Italy
- Laboratory of Normal and Malignant Hematopoiesis and Pathobiology of Myeloma and Lymphoma. Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Anna Fregnani
- Department of Medicine, Division of Hematology, University of Padova, Italy
- Laboratory of Normal and Malignant Hematopoiesis and Pathobiology of Myeloma and Lymphoma. Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Zaira Spinello
- Department of Medicine, Division of Hematology, University of Padova, Italy
- Laboratory of Normal and Malignant Hematopoiesis and Pathobiology of Myeloma and Lymphoma. Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Mitja Nabergoj
- Hematology Service, Institut Central des Hôpitaux (ICH), Hôpital du Valais, Sion, Switzerland
| | - Odile Filhol
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1036, Institute de Reserches en Technologies et Sciences pour le Vivant/Biologie du Cancer et de l’Infection, Grenoble, France
| | | | - Mattia Albiero
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Italy
- Veneto Institute of Molecular Medicine, Experimental Diabetology Lab, Padova, Italy
| | - Gian Paolo Fadini
- Veneto Institute of Molecular Medicine, Experimental Diabetology Lab, Padova, Italy
- Department of Medicine, University of Padova, Italy
| | - Carmela Gurrieri
- Department of Medicine, Division of Hematology, University of Padova, Italy
- Laboratory of Normal and Malignant Hematopoiesis and Pathobiology of Myeloma and Lymphoma. Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Fabrizio Vianello
- Department of Medicine, Division of Hematology, University of Padova, Italy
- Laboratory of Normal and Malignant Hematopoiesis and Pathobiology of Myeloma and Lymphoma. Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Gianpietro Semenzato
- Department of Medicine, Division of Hematology, University of Padova, Italy
- Laboratory of Normal and Malignant Hematopoiesis and Pathobiology of Myeloma and Lymphoma. Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Sabrina Manni
- Department of Medicine, Division of Hematology, University of Padova, Italy
- Laboratory of Normal and Malignant Hematopoiesis and Pathobiology of Myeloma and Lymphoma. Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Livio Trentin
- Department of Medicine, Division of Hematology, University of Padova, Italy
- Laboratory of Normal and Malignant Hematopoiesis and Pathobiology of Myeloma and Lymphoma. Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Francesco Piazza
- Department of Medicine, Division of Hematology, University of Padova, Italy
- Laboratory of Normal and Malignant Hematopoiesis and Pathobiology of Myeloma and Lymphoma. Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| |
Collapse
|
4
|
Hu M, Alkhairy S, Lee I, Pillich RT, Bachelder R, Ideker T, Pratt D. Evaluation of large language models for discovery of gene set function. Res Sq 2023:rs.3.rs-3270331. [PMID: 37790547 PMCID: PMC10543283 DOI: 10.21203/rs.3.rs-3270331/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Gene set analysis is a mainstay of functional genomics, but it relies on manually curated databases of gene functions that are incomplete and unaware of biological context. Here we evaluate the ability of OpenAI's GPT-4, a Large Language Model (LLM), to develop hypotheses about common gene functions from its embedded biomedical knowledge. We created a GPT-4 pipeline to label gene sets with names that summarize their consensus functions, substantiated by analysis text and citations. Benchmarking against named gene sets in the Gene Ontology, GPT-4 generated very similar names in 50% of cases, while in most remaining cases it recovered the name of a more general concept. In gene sets discovered in 'omics data, GPT-4 names were more informative than gene set enrichment, with supporting statements and citations that largely verified in human review. The ability to rapidly synthesize common gene functions positions LLMs as valuable functional genomics assistants.
Collapse
Affiliation(s)
- Mengzhou Hu
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Sahar Alkhairy
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Ingoo Lee
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Rudolf T. Pillich
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Robin Bachelder
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Dexter Pratt
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| |
Collapse
|
5
|
Che Q, Wang Q, Lu H, Li C, Zeng K. Enhancement of the cytotoxic effect of dihydroartemisinin in high-risk human papillomavirus-infected cells by aminolevulinic acid via the Bax/Bcl-2-caspase pathway. Photodiagnosis Photodyn Ther 2022; 40:103053. [PMID: 35932961 DOI: 10.1016/j.pdpdt.2022.103053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/27/2022] [Accepted: 08/02/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Traditional treatments for human papillomavirus-related cutaneous diseases include 5-aminolevulinic acid photodynamic therapy, cryotherapy, microwave ablation, and surgical resection. These treatment methods involvevarious adverse reactions; therefore, it remains necessary to explore new treatment methods. Dihydroartemisinin shows cytotoxic effects against several malignancies by producing reactive oxygen species, and heme environments reportedly enhance its activity. However, the underlying mechanismsare still unclear. Therefore, we investigated the mechanism of dihydroartemisininin inhuman papillomavirus-infected cells. METHODS HeLa cells were treated with dihydroartemisinin, 5-aminolevulinic acid, and succinylacetone. The cell viability, apoptosis, mitochondrial membrane potential, and reactive oxygen species levels were investigated, and via western blotting analysis and polymerase chain reaction, dihydroartemisinin activity-related pathways were also determined. RESULTS Dihydroartemisinin inhibited HeLa cell proliferation and promoted cell apoptosis via the Bax/Bcl-2-Caspase pathway in a concentration-dependent manner. The specific cytotoxicity toward HeLa cells was enhanced by the addition of 5-aminolevulinic acid, a clinically used heme-synthesis precursor, owing to an increase in heme levels. Conversely, following the addition of succinylacetone, a heme synthesis blocker, heme levels decreased. Furthermore, dihydroartemisinin significantly increased reactive oxygen species levels as intracellular heme synthesis increased. Moreover, photodynamic therapy following dihydroartemisinin and 5-aminolevulinic acid treatment further enhanced the cytotoxic effect of dihydroartemisinin on high-risk human papillomavirus-infected cells. CONCLUSIONS Dihydroartemisinin exerts acytotoxic effect on high-risk human papillomavirus-infected cells by modulating heme levels via the Bax/Bcl-2-Caspase pathway, and the dihydroartemisinin, 5-aminolevulinic acid, photodynamic therapy combination treatment significantly enhanced its cytotoxic effect on human papillomavirus-infected cells.
Collapse
Affiliation(s)
- Qilei Che
- Department of Dermatology and Venereology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China; Department of Medical Cosmetology, Chengdu Second People's Hospital, Chengdu 610031,China
| | - Qi Wang
- Department of Dermatology and Venereology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Hongyan Lu
- Department of Dermatology and Venereology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Changxing Li
- Department of Dermatology and Venereology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.
| | - Kang Zeng
- Department of Dermatology and Venereology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.
| |
Collapse
|
6
|
Hunter GA, Ferreira GC. An Extended C-Terminus, the Possible Culprit for Differential Regulation of 5-Aminolevulinate Synthase Isoforms. Front Mol Biosci 2022; 9:920668. [PMID: 35911972 PMCID: PMC9329541 DOI: 10.3389/fmolb.2022.920668] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/30/2022] [Indexed: 12/05/2022] Open
Abstract
5-Aminolevulinate synthase (ALAS; E.C. 2.3.1.37) is a pyridoxal 5′-phosphate (PLP)-dependent enzyme that catalyzes the key regulatory step of porphyrin biosynthesis in metazoa, fungi, and α-proteobacteria. ALAS is evolutionarily related to transaminases and is therefore classified as a fold type I PLP-dependent enzyme. As an enzyme controlling the key committed and rate-determining step of a crucial biochemical pathway ALAS is ideally positioned to be subject to allosteric feedback inhibition. Extensive kinetic and mutational studies demonstrated that the overall enzyme reaction is limited by subtle conformational changes of a hairpin loop gating the active site. These findings, coupled with structural information, facilitated early prediction of allosteric regulation of activity via an extended C-terminal tail unique to eukaryotic forms of the enzyme. This prediction was subsequently supported by the discoveries that mutations in the extended C-terminus of the erythroid ALAS isoform (ALAS2) cause a metabolic disorder known as X-linked protoporphyria not by diminishing activity, but by enhancing it. Furthermore, kinetic, structural, and molecular modeling studies demonstrated that the extended C-terminal tail controls the catalytic rate by modulating conformational flexibility of the active site loop. However, the precise identity of any such molecule remains to be defined. Here we discuss the most plausible allosteric regulators of ALAS activity based on divergences in AlphaFold-predicted ALAS structures and suggest how the mystery of the mechanism whereby the extended C-terminus of mammalian ALASs allosterically controls the rate of porphyrin biosynthesis might be unraveled.
Collapse
Affiliation(s)
- Gregory A. Hunter
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
- *Correspondence: Gregory A. Hunter, ; Gloria C. Ferreira,
| | - Gloria C. Ferreira
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
- Department of Chemistry, College of Arts and Sciences, University of South Florida, Tampa, FL, United States
- Global and Planetary Health, College of Public Health, University of South Florida, Tampa, FL, United States
- *Correspondence: Gregory A. Hunter, ; Gloria C. Ferreira,
| |
Collapse
|
7
|
Abstract
The hematopoietic transcription factor GATA1 induces heme accumulation during erythropoiesis by directly activating genes mediating heme biosynthesis. In addition to its canonical functions as a hemoglobin prosthetic group and enzyme cofactor, heme regulates gene expression in erythroid cells both transcriptionally and post-transcriptionally. Heme binding to the transcriptional repressor BACH1 triggers its proteolytic degradation. In heme-deficient cells, BACH1 accumulates and represses transcription of target genes, including α- and β-like globin genes, preventing the accumulation of cytotoxic free globin chains. A recently described BACH1-independent mechanism of heme-dependent transcriptional regulation is associated with a DNA motif termed heme-regulated motif (HERM), which resides at the majority of loci harboring heme-regulated chromatin accessibility sites. Progress on these problems has led to a paradigm in which cell type-specific transcriptional mechanisms determine the expression of enzymes mediating the synthesis of small molecules, which generate feedback loops, converging upon the transcription factor itself and the genome. This marriage between transcription factors and the small molecules that they control is predicted to be a canonical attribute of regulatory networks governing cell state transitions such as differentiation in the hematopoietic system and more broadly.
Collapse
Affiliation(s)
- Ruiqi Liao
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI, 53705, USA
| | - Emery H Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI, 53705, USA.
| |
Collapse
|
8
|
Wang L, Piao Y, Zhang D, Feng W, Wang C, Cui X, Ren Q, Zhu X, Zheng G. Fbxw11 impairs the repopulation capacity of hematopoietic stem/progenitor cells. Stem Cell Res Ther 2022; 13:245. [PMID: 35690796 PMCID: PMC9188144 DOI: 10.1186/s13287-022-02926-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The ubiquitin-proteasome system plays important roles in maintaining the self-renewal and differentiation of stem and progenitor cells through highly ordered degradation of cellular proteins. Fbxw11, an E3 ligase, participates in many important biological processes by targeting a broad range of proteins. However, its roles in hematopoietic stem/progenitor cells (HSPCs) have not been established. METHODS In this study, the effects of Fbxw11 on HSPCs were studied in vitro and in vivo by an overexpression strategy. Real-time PCR was performed to detect the expression of Fbxw11 in hematopoietic subpopulations. Colony-forming assays were performed to evaluate the in vitro function of Fbxw11 on HSPCs. Hoechst 33342 and Ki67 staining was performed to determine the cell-cycle distribution of HSPCs. Competitive transplantation experiments were used to evaluate the effect of Fbxw11 on the reconstitution potential of HSPCs. Single-cell RNA sequencing (scRNA-seq) was employed to reveal the transcriptomic alterations in HSPCs. RESULTS The expression of Fbxw11 was higher in Lin-c-Kit+Sca-1+ (LSK) cells and myeloid progenitors than in lymphoid progenitors. Fbxw11 played negative roles in colony-forming and quiescence maintenance of HSPCs in vitro. Furthermore, serial competitive transplantation experiments revealed that Fbxw11 impaired the repopulation capacity of HSPCs. The proportion of granulocytes (Gr-1+CD11b+) in the differentiated mature cells was significantly higher than that in the control group, T cells and B cells were lower. Moreover, scRNA-seq revealed seven cell clusters in HSPCs. In addition, Fbxw11 downregulated the expression of Cebpa, Myc and Arid5b, which are significant regulators of HSPC activity, in most cell clusters. CONCLUSION Our data demonstrate that Fbxw11 plays a negative role in the maintenance of HSPCs in vitro and repopulation capacity in vivo. Our data also provide valuable transcriptome references for HSPCs in homeostasis.
Collapse
Affiliation(s)
- Lina Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China.
| | - Yongjun Piao
- School of Medicine, Nankai University, Tianjin, China
| | - Dongyue Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
| | - Wenli Feng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
| | - Chenchen Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
| | - Xiaoxi Cui
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
| | - Qian Ren
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
| | - Guoguang Zheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China.
| |
Collapse
|
9
|
Ono K, Fujiwara T, Saito K, Nishizawa H, Takahashi N, Suzuki C, Ochi T, Kato H, Ishii Y, Onodera K, Ichikawa S, Fukuhara N, Onishi Y, Yokoyama H, Yamada R, Nakamura Y, Igarashi K, Harigae H. Congenital sideroblastic anemia model due to ALAS2 mutation is susceptible to ferroptosis. Sci Rep 2022; 12. [PMID: 35637209 PMCID: PMC9151922 DOI: 10.1038/s41598-022-12940-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 05/18/2022] [Indexed: 11/20/2022] Open
Abstract
X-linked sideroblastic anemia (XLSA), the most common form of congenital sideroblastic anemia, is caused by a germline mutation in the erythroid-specific 5-aminolevulinate synthase (ALAS2) gene. In XLSA, defective heme biosynthesis leads to ring sideroblast formation because of excess mitochondrial iron accumulation. In this study, we introduced ALAS2 missense mutations on human umbilical cord blood-derived erythroblasts; hereafter, we refer to them as XLSA clones. XLSA clones that differentiated into mature erythroblasts showed an increased frequency of ring sideroblast formation with impaired hemoglobin biosynthesis. The expression profiling revealed significant enrichment of genes involved in ferroptosis, which is a form of regulated cell death induced by iron accumulation and lipid peroxidation. Notably, treatment with erastin, a ferroptosis inducer, caused a higher proportion of cell death in XLSA clones. XLSA clones exhibited significantly higher levels of intracellular lipid peroxides and enhanced expression of BACH1, a regulator of iron metabolism and potential accelerator of ferroptosis. In XLSA clones, BACH1 repressed genes involved in iron metabolism and glutathione synthesis. Collectively, defective heme biosynthesis in XLSA clones could confer enhanced BACH1 expression, leading to increased susceptibility to ferroptosis. The results of our study provide important information for the development of novel therapeutic targets for XLSA.
Collapse
|
10
|
Taylor JL, Brown BL. Structural basis for dysregulation of aminolevulinic acid synthase in human disease. J Biol Chem 2022; 298:101643. [PMID: 35093382 PMCID: PMC8892079 DOI: 10.1016/j.jbc.2022.101643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/19/2023] Open
Abstract
Heme is a critical biomolecule that is synthesized in vivo by several organisms such as plants, animals, and bacteria. Reflecting the importance of this molecule, defects in heme biosynthesis underlie several blood disorders in humans. Aminolevulinic acid synthase (ALAS) initiates heme biosynthesis in α-proteobacteria and nonplant eukaryotes. Debilitating and painful diseases such as X-linked sideroblastic anemia and X-linked protoporphyria can result from one of more than 91 genetic mutations in the human erythroid-specific enzyme ALAS2. This review will focus on recent structure-based insights into human ALAS2 function in health and how it dysfunctions in disease. We will also discuss how certain genetic mutations potentially result in disease-causing structural perturbations. Furthermore, we use thermodynamic and structural information to hypothesize how the mutations affect the human ALAS2 structure and categorize some of the unique human ALAS2 mutations that do not respond to typical treatments, that have paradoxical in vitro activity, or that are highly intolerable to changes. Finally, we will examine where future structure-based insights into the family of ALA synthases are needed to develop additional enzyme therapeutics.
Collapse
Affiliation(s)
- Jessica L Taylor
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Breann L Brown
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
| |
Collapse
|
11
|
Saultier P, Cabantous S, Puceat M, Peiretti F, Bigot T, Saut N, Bordet JC, Canault M, van Agthoven J, Loosveld M, Payet-Bornet D, Potier D, Falaise C, Bernot D, Morange PE, Alessi MC, Poggi M. GATA1 pathogenic variants disrupt MYH10 silencing during megakaryopoiesis. J Thromb Haemost 2021; 19:2287-2301. [PMID: 34060193 DOI: 10.1111/jth.15412] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/24/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND GATA1 is an essential transcription factor for both polyploidization and megakaryocyte (MK) differentiation. The polyploidization defect observed in GATA1 variant carriers is not well understood. OBJECTIVE To extensively phenotype two pedigrees displaying different variants in the GATA1 gene and determine if GATA1 controls MYH10 expression levels, a key modulator of MK polyploidization. METHOD A total of 146 unrelated propositi with constitutional thrombocytopenia were screened on a multigene panel. We described the genotype-phenotype correlation in GATA1 variant carriers and investigated the effect of these novel variants on MYH10 transcription using luciferase constructs. RESULTS The clinical profile associated with the p.L268M variant localized in the C terminal zinc finger was unusual in that the patient displayed bleeding and severe platelet aggregation defects without early-onset thrombocytopenia. p.N206I localized in the N terminal zinc finger was associated, on the other hand, with severe thrombocytopenia (15G/L) in early life. High MYH10 levels were evidenced in platelets of GATA1 variant carriers. Analysis of MKs anti-GATA1 chromatin immunoprecipitation-sequencing data revealed two GATA1 binding sites, located in the 3' untranslated region and in intron 8 of the MYH10 gene. Luciferase reporter assays showed their respective role in the regulation of MYH10 gene expression. Both GATA1 variants significantly alter intron 8 driven MYH10 transcription. CONCLUSION The discovery of an association between MYH10 and GATA1 is a novel one. Overall, this study suggests that impaired MYH10 silencing via an intronic regulatory element is the most likely cause of GATA1-related polyploidization defect.
Collapse
Affiliation(s)
- Paul Saultier
- Aix Marseille Univ, INSERM, INRAe, C2VN, Marseille, France
- Department of Pediatric Hematology, Immunology and Oncology, APHM, La Timone Children's Hospital, Marseille, France
| | | | | | | | - Timothée Bigot
- Aix Marseille Univ, INSERM, INRAe, C2VN, Marseille, France
| | - Noémie Saut
- Aix Marseille Univ, INSERM, INRAe, C2VN, Marseille, France
- APHM, CHU Timone, French Reference Center on Inherited Platelet Disorders, Marseille, France
| | | | | | - Johannes van Agthoven
- Structural Biology Program, Division of Nephrology/Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Marie Loosveld
- APHM, CHU Timone, French Reference Center on Inherited Platelet Disorders, Marseille, France
- Aix-Marseille Univ, CNRS, INSERM, CIML, Marseille, France
| | | | | | - Céline Falaise
- Department of Pediatric Hematology, Immunology and Oncology, APHM, La Timone Children's Hospital, Marseille, France
- APHM, CHU Timone, French Reference Center on Inherited Platelet Disorders, Marseille, France
| | - Denis Bernot
- Aix Marseille Univ, INSERM, INRAe, C2VN, Marseille, France
| | - Pierre-Emmanuel Morange
- Aix Marseille Univ, INSERM, INRAe, C2VN, Marseille, France
- APHM, CHU Timone, French Reference Center on Inherited Platelet Disorders, Marseille, France
| | - Marie-Christine Alessi
- Aix Marseille Univ, INSERM, INRAe, C2VN, Marseille, France
- APHM, CHU Timone, French Reference Center on Inherited Platelet Disorders, Marseille, France
| | - Marjorie Poggi
- Aix Marseille Univ, INSERM, INRAe, C2VN, Marseille, France
| |
Collapse
|
12
|
Gupta R, Srivastava D, Sahu M, Tiwari S, Ambasta RK, Kumar P. Artificial intelligence to deep learning: machine intelligence approach for drug discovery. Mol Divers 2021; 25:1315-1360. [PMID: 33844136 PMCID: PMC8040371 DOI: 10.1007/s11030-021-10217-3] [Citation(s) in RCA: 228] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/22/2021] [Indexed: 02/06/2023]
Abstract
Drug designing and development is an important area of research for pharmaceutical companies and chemical scientists. However, low efficacy, off-target delivery, time consumption, and high cost impose a hurdle and challenges that impact drug design and discovery. Further, complex and big data from genomics, proteomics, microarray data, and clinical trials also impose an obstacle in the drug discovery pipeline. Artificial intelligence and machine learning technology play a crucial role in drug discovery and development. In other words, artificial neural networks and deep learning algorithms have modernized the area. Machine learning and deep learning algorithms have been implemented in several drug discovery processes such as peptide synthesis, structure-based virtual screening, ligand-based virtual screening, toxicity prediction, drug monitoring and release, pharmacophore modeling, quantitative structure-activity relationship, drug repositioning, polypharmacology, and physiochemical activity. Evidence from the past strengthens the implementation of artificial intelligence and deep learning in this field. Moreover, novel data mining, curation, and management techniques provided critical support to recently developed modeling algorithms. In summary, artificial intelligence and deep learning advancements provide an excellent opportunity for rational drug design and discovery process, which will eventually impact mankind. The primary concern associated with drug design and development is time consumption and production cost. Further, inefficiency, inaccurate target delivery, and inappropriate dosage are other hurdles that inhibit the process of drug delivery and development. With advancements in technology, computer-aided drug design integrating artificial intelligence algorithms can eliminate the challenges and hurdles of traditional drug design and development. Artificial intelligence is referred to as superset comprising machine learning, whereas machine learning comprises supervised learning, unsupervised learning, and reinforcement learning. Further, deep learning, a subset of machine learning, has been extensively implemented in drug design and development. The artificial neural network, deep neural network, support vector machines, classification and regression, generative adversarial networks, symbolic learning, and meta-learning are examples of the algorithms applied to the drug design and discovery process. Artificial intelligence has been applied to different areas of drug design and development process, such as from peptide synthesis to molecule design, virtual screening to molecular docking, quantitative structure-activity relationship to drug repositioning, protein misfolding to protein-protein interactions, and molecular pathway identification to polypharmacology. Artificial intelligence principles have been applied to the classification of active and inactive, monitoring drug release, pre-clinical and clinical development, primary and secondary drug screening, biomarker development, pharmaceutical manufacturing, bioactivity identification and physiochemical properties, prediction of toxicity, and identification of mode of action.
Collapse
Affiliation(s)
- Rohan Gupta
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Devesh Srivastava
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Mehar Sahu
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Swati Tiwari
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Rashmi K Ambasta
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Shahbad Daulatpur, Bawana Road, Delhi, 110042, India.
| |
Collapse
|
13
|
Fang R, Zhang J, Yang H, Shi J, Zeng H, Zhu X, Wei D, Yuan P, Cheng T, Zhang Y. Highly efficient gene editing and single cell analysis of hematopoietic stem/progenitor cells from X-linked sideroblastic anemia patients. Signal Transduct Target Ther 2021; 6:248. [PMID: 34210953 PMCID: PMC8249499 DOI: 10.1038/s41392-021-00622-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/08/2021] [Accepted: 04/26/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- Riguo Fang
- EdiGene Inc., Beijing, China.,EdiGene (Guangzhou) Inc., Guangzhou, China
| | - Jingliao Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Huihui Yang
- EdiGene Inc., Beijing, China.,EdiGene (Guangzhou) Inc., Guangzhou, China
| | - Jia Shi
- EdiGene Inc., Beijing, China.,EdiGene (Guangzhou) Inc., Guangzhou, China
| | - Huimin Zeng
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Dong Wei
- EdiGene Inc., Beijing, China.,EdiGene (Guangzhou) Inc., Guangzhou, China
| | - Pengfei Yuan
- EdiGene Inc., Beijing, China. .,EdiGene (Guangzhou) Inc., Guangzhou, China.
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.
| | - Yingchi Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.
| |
Collapse
|
14
|
Ershova AS, Eliseeva IA, Nikonov OS, Fedorova AD, Vorontsov IE, Papatsenko D, Kulakovskiy IV. Enhanced C/EBP binding to G·T mismatches facilitates fixation of CpG mutations in cancer and adult stem cells. Cell Rep 2021; 35:109221. [PMID: 34107262 DOI: 10.1016/j.celrep.2021.109221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 03/21/2021] [Accepted: 05/13/2021] [Indexed: 10/21/2022] Open
Abstract
Somatic mutations in regulatory sites of human stem cells affect cell identity or cause malignant transformation. By mining the human genome for co-occurrence of mutations and transcription factor binding sites, we show that C/EBP binding sites are strongly enriched with [C > T]G mutations in cancer and adult stem cells, which is of special interest because C/EBPs regulate cell fate and differentiation. In vitro protein-DNA binding assay and structural modeling of the CEBPB-DNA complex show that the G·T mismatch in the core CG dinucleotide strongly enhances affinity of the binding site. We conclude that enhanced binding of C/EBPs shields CpG·TpG mismatches from DNA repair, leading to selective accumulation of [C > T]G mutations and consequent deterioration of the binding sites. This mechanism of targeted mutagenesis highlights the effect of a mutational process on certain regulatory sites and reveals the molecular basis of putative regulatory alterations in stem cells.
Collapse
Affiliation(s)
- Anna S Ershova
- Belozersky Institute of Physical and Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.
| | - Irina A Eliseeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Oleg S Nikonov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Alla D Fedorova
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland
| | - Ilya E Vorontsov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia; Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Dmitry Papatsenko
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143026, Russia
| | - Ivan V Kulakovskiy
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia; Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.
| |
Collapse
|
15
|
Shahbaz S, Xu L, Osman M, Sligl W, Shields J, Joyce M, Tyrrell DL, Oyegbami O, Elahi S. Erythroid precursors and progenitors suppress adaptive immunity and get invaded by SARS-CoV-2. Stem Cell Reports 2021; 16:1165-1181. [PMID: 33979601 PMCID: PMC8111797 DOI: 10.1016/j.stemcr.2021.04.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2 infection is associated with lower blood oxygen levels, even in patients without hypoxia requiring hospitalization. This discordance illustrates the need for a more unifying explanation as to whether SARS-CoV-2 directly or indirectly affects erythropoiesis. Here, we show significantly enriched CD71+ erythroid precursors/progenitors in the blood circulation of COVID-19 patients. We found that these cells have distinctive immunosuppressive properties. In agreement, we observed a strong negative correlation between the frequency of these cells with T and B cell proportions in COVID-19 patients. The expansion of these CD71+ erythroid precursors/progenitors was negatively correlated with the hemoglobin levels. A subpopulation of abundant erythroid cells, CD45+ CD71+ cells, co-express ACE2, TMPRSS2, CD147, and CD26, and these can be infected with SARS-CoV-2. In turn, pre-treatment of erythroid cells with dexamethasone significantly diminished ACE2/TMPRSS2 expression and subsequently reduced their infectivity with SARS-CoV-2. This provides a novel insight into the impact of SARS-CoV-2 on erythropoiesis and hypoxia seen in COVID-19 patients.
Collapse
Affiliation(s)
- Shima Shahbaz
- School of Dentistry, Division of Foundational Sciences, University of Alberta, Edmonton, T6G2E1, AB, Canada
| | - Lai Xu
- School of Dentistry, Division of Foundational Sciences, University of Alberta, Edmonton, T6G2E1, AB, Canada
| | - Mohammed Osman
- Department of Medicine, University of Alberta, Edmonton, T6G2E1, AB, Canada
| | - Wendy Sligl
- Department of Medicine, University of Alberta, Edmonton, T6G2E1, AB, Canada; Department of Critical Care Medicine, University of Alberta, Edmonton, T6G2E1, AB, Canada; Division of Infectious Diseases, University of Alberta, Edmonton, T6G2E1, AB, Canada
| | - Justin Shields
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, T6G2E1, AB, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, T6G2E1, AB, Canada
| | - Michael Joyce
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, T6G2E1, AB, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, T6G2E1, AB, Canada
| | - D Lorne Tyrrell
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, T6G2E1, AB, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, T6G2E1, AB, Canada
| | - Olaide Oyegbami
- School of Dentistry, Division of Foundational Sciences, University of Alberta, Edmonton, T6G2E1, AB, Canada
| | - Shokrollah Elahi
- School of Dentistry, Division of Foundational Sciences, University of Alberta, Edmonton, T6G2E1, AB, Canada; Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, T6G2E1, AB, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, T6G2E1, AB, Canada; Department of Medical Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, T6G2E1, AB, Canada.
| |
Collapse
|
16
|
Liao R, Zheng Y, Liu X, Zhang Y, Seim G, Tanimura N, Wilson GM, Hematti P, Coon JJ, Fan J, Xu J, Keles S, Bresnick EH. Discovering How Heme Controls Genome Function Through Heme-omics. Cell Rep 2021; 31:107832. [PMID: 32610133 DOI: 10.1016/j.celrep.2020.107832] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/03/2020] [Accepted: 06/08/2020] [Indexed: 12/15/2022] Open
Abstract
Protein ensembles control genome function by establishing, maintaining, and deconstructing cell-type-specific chromosomal landscapes. A plethora of small molecules orchestrate cellular functions and therefore may link physiological processes with genome biology. The metabolic enzyme and hemoglobin cofactor heme induces proteolysis of a transcriptional repressor, Bach1, and regulates gene expression post-transcriptionally. However, whether heme controls genome function broadly or through prescriptive actions is unclear. Using assay for transposase-accessible chromatin sequencing (ATAC-seq), we establish a heme-dependent chromatin atlas in wild-type and mutant erythroblasts lacking enhancers that confer normal heme synthesis. Amalgamating chromatin landscapes and transcriptomes in cells with sub-physiological heme and post-heme rescue reveals parallel Bach1-dependent and Bach1-independent mechanisms that target heme-sensing chromosomal hotspots. The hotspots harbor a DNA motif demarcating heme-regulated chromatin and genes encoding proteins not known to be heme regulated, including metabolic enzymes. The heme-omics analysis establishes how an essential biochemical cofactor controls genome function and cellular physiology.
Collapse
Affiliation(s)
- Ruiqi Liao
- 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
| | - Ye Zheng
- Department of Statistics, Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Xin Liu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yuannyu Zhang
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gretchen Seim
- Department of Nutritional Sciences, Morgridge Institute for Research, University of Wisconsin-Madison, 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
| | - Gary M Wilson
- Department of Chemistry, Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Peiman Hematti
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Joshua J Coon
- Department of Chemistry, Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Jing Fan
- Department of Nutritional Sciences, Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, USA
| | - Jian Xu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sunduz Keles
- Department of Statistics, Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI, 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.
| |
Collapse
|
17
|
Tong J, Sun T, Ma S, Zhao Y, Ju M, Gao Y, Zhu P, Tan P, Fu R, Zhang A, Wang D, Wang D, Xiao Z, Zhou J, Yang R, Loughran SJ, Li J, Green AR, Bresnick EH, Wang D, Cheng T, Zhang L, Shi L. Hematopoietic stem cell heterogeneity is linked to the initiation and therapeutic response of myeloproliferative neoplasms. Cell Stem Cell 2021; 28:780. [PMID: 33798424 PMCID: PMC7613297 DOI: 10.1016/j.stem.2021.02.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The implications of stem cell heterogeneity for disease pathogenesis and therapy are poorly defined. JAK2V617F+ myeloproliferative neoplasms (MPNs), harboring the same mutation in hematopoietic stem cells (HSCs), display diverse phenotypes, including polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). These chronic malignant disorders are ideal models to analyze the pathological consequences of stem cell heterogeneity. Single-cell gene expression profiling with parallel mutation detection demonstrated that the megakaryocyte (Mk)-primed HSC subpopulation expanded significantly with enhanced potential in untreated individuals with JAK2V617F+ ET, driven primarily by the JAK2 mutation and elevated interferon signaling. During treatment, mutant HSCs were targeted preferentially in the Mk-primed HSC subpopulation. Interestingly, homozygous mutant HSCs were forced to re-enter quiescence, whereas their heterozygous counterparts underwent apoptosis. This study provides important evidence for the association of stem cell heterogeneity with the pathogenesis and therapeutic response of a malignant disease.
Collapse
Affiliation(s)
- Jingyuan Tong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China
- Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China
| | - Ting Sun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- CAMS Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China
- Tianjin Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China
| | - Shihui Ma
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China
- Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China
| | - Yanhong Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Mankai Ju
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- CAMS Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China
- Tianjin Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China
| | - Yuchen Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- CAMS Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China
- Tianjin Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China
| | - Ping Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China
- Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China
| | - Puwen Tan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Rongfeng Fu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- CAMS Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China
- Tianjin Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China
| | - Anqi Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China
- Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China
- CAMS Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China
| | - Ding Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Di Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Zhijian Xiao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Jiaxi Zhou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China
- Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China
| | - Renchi Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- CAMS Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China
- Tianjin Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China
| | - Stephen J. Loughran
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge CB2 0AW, UK
| | - Juan Li
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge CB2 0AW, UK
| | - Anthony R. Green
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge CB2 0AW, UK
| | - Emery H. Bresnick
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53562, USA
| | - Dong Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Correspondence: (D.W.), (T.C.), (L.Z.), (L.S.)
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China
- Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China
- Correspondence: (D.W.), (T.C.), (L.Z.), (L.S.)
| | - Lei Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China
- Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China
- CAMS Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China
- Tianjin Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China
- Correspondence: (D.W.), (T.C.), (L.Z.), (L.S.)
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China
- Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China
- Correspondence: (D.W.), (T.C.), (L.Z.), (L.S.)
| |
Collapse
|
18
|
Tong J, Sun T, Ma S, Zhao Y, Ju M, Gao Y, Zhu P, Tan P, Fu R, Zhang A, Wang D, Wang D, Xiao Z, Zhou J, Yang R, Loughran SJ, Li J, Green AR, Bresnick EH, Wang D, Cheng T, Zhang L, Shi L. Hematopoietic Stem Cell Heterogeneity Is Linked to the Initiation and Therapeutic Response of Myeloproliferative Neoplasms. Cell Stem Cell 2021; 28:502-513.e6. [PMID: 33621485 DOI: 10.1016/j.stem.2021.01.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 11/23/2020] [Accepted: 01/27/2021] [Indexed: 12/19/2022]
Abstract
The implications of stem cell heterogeneity for disease pathogenesis and therapy are poorly defined. JAK2V617F+ myeloproliferative neoplasms (MPNs), harboring the same mutation in hematopoietic stem cells (HSCs), display diverse phenotypes, including polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). These chronic malignant disorders are ideal models to analyze the pathological consequences of stem cell heterogeneity. Single-cell gene expression profiling with parallel mutation detection demonstrated that the megakaryocyte (Mk)-primed HSC subpopulation expanded significantly with enhanced potential in untreated individuals with JAK2V617F+ ET, driven primarily by the JAK2 mutation and elevated interferon signaling. During treatment, mutant HSCs were targeted preferentially in the Mk-primed HSC subpopulation. Interestingly, homozygous mutant HSCs were forced to re-enter quiescence, whereas their heterozygous counterparts underwent apoptosis. This study provides important evidence for the association of stem cell heterogeneity with the pathogenesis and therapeutic response of a malignant disease.
Collapse
Affiliation(s)
- Jingyuan Tong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China; Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China
| | - Ting Sun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China; Tianjin Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China
| | - Shihui Ma
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China; Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China
| | - Yanhong Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Mankai Ju
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China; Tianjin Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China
| | - Yuchen Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China; Tianjin Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China
| | - Ping Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China; Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China
| | - Puwen Tan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Rongfeng Fu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China; Tianjin Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China
| | - Anqi Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China; Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China; CAMS Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China
| | - Ding Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Di Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Zhijian Xiao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Jiaxi Zhou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China; Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China
| | - Renchi Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China; Tianjin Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China
| | - Stephen J Loughran
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge CB2 0AW, UK
| | - Juan Li
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge CB2 0AW, UK
| | - Anthony R Green
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge CB2 0AW, UK
| | - Emery H Bresnick
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53562, USA
| | - Dong Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China; Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China.
| | - Lei Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China; Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China; CAMS Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China; Tianjin Key Laboratory of Gene Therapy for Blood Diseases, Tianjin 300020, China.
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China; Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China.
| |
Collapse
|
19
|
Bao B, An W, Lu Q, Wang Y, Lu Z, Tu J, Zhang H, Duan Y, Yuan W, Zhu X, Jia H. Sfxn1 is essential for erythrocyte maturation via facilitating hemoglobin production in zebrafish. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166096. [PMID: 33524530 DOI: 10.1016/j.bbadis.2021.166096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 12/19/2020] [Accepted: 01/26/2021] [Indexed: 12/31/2022]
Abstract
Previous reports revealed that mutation of mitochondrial inner-membrane located protein SFXN1 led to pleiotropic hematological and skeletal defects in mice, associated with the presence of hypochromic erythroid cell, iron overload in mitochondrion of erythroblast and the development of sideroblastic anemia (SA). However, the potential role of sfxn1 during erythrocyte differentiation and the development of anemia, especially the pathological molecular mechanism still remains elusive. In this study, the correlation between sfxn1 and erythroid cell development is explored through zebrafish in vivo coupled with human hematopoietic cells assay ex vivo. Both knockdown and knockout of sfxn1 result in hypochromic anemia phenotype in zebrafish. Further analyses demonstrate that the development of anemia attributes to the biosynthetic deficiency of hemoglobin, which is caused by the biosynthetic disorder of heme that associates with one‑carbon (1C) metabolism process of mitochondrial branch in erythrocyte. Sfxn1 is also involved in the differentiation and maturation of erythrocyte in inducible human umbilical cord blood stem cells. In addition, we found that functional disruption of sfxn1 causes hypochromic anemia that is distinct from SA. These findings reveal that sfxn1 is genetically conserved and essential for the maturation of erythrocyte via facilitating the production of hemoglobin, which may provide a possible guidance for the future clinical treatment of sfxn1 mutation associated hematological disorders.
Collapse
Affiliation(s)
- Binghao Bao
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Wenbin An
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, ,China
| | - Qunwei Lu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Yaqin Wang
- Department of Pediatrics, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Zhichao Lu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Jiayi Tu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Heng Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Yongjuan Duan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, ,China
| | - Weiping Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, ,China.
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, ,China.
| | - Haibo Jia
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China.
| |
Collapse
|
20
|
Hasenauer FC, Rossi UA, Caffaro ME, Raschia MA, Maurizio E, Poli MA, Rossetti CA. Association of TNF rs668920841 and INRA111 polymorphisms with caprine brucellosis: A case-control study of candidate genes involved in innate immunity. Genomics 2020; 112:3925-3932. [PMID: 32629097 DOI: 10.1016/j.ygeno.2020.06.050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/25/2020] [Accepted: 06/28/2020] [Indexed: 01/24/2023]
Abstract
Caprine brucellosis is an infectious, contagious zoonotic disease caused by Brucella melitensis. Multiple factors, including host genetics, can influence the outcome of the exposure to Brucella; and it is expected that genetic variants that affect the host innate immune response could have a key role in Brucella infection and pathogenesis. In this study, we evaluated if polymorphisms in innate immunity-related genes are associated with results of Brucella infection in goats. Nine polymorphisms within interferon gamma (IFNG), tumor necrosis factor (TNF), MyD88 innate immune signal transduction adaptor (MYD88), interleukin 10 (IL10) and IL-10 receptor subunit alpha (IL10RA) genes and two molecular markers (BMS2753 and INRA111) were resolved by PCR-capillary electrophoresis in samples from 81 seronegative and 61 seropositive goats for brucellosis. A heterozygous genotype at INRA111, a microsatellite near the VRK serine/threonine kinase 2 (VRK2) gene, was associated with absence of Brucella-specific antibodies in goats naturally exposed to the pathogen (P = .004). Conversely, variants in the TNF gene (rs668920841) and near the IFN gamma receptor 1 (IFNGR1) gene (microsatellite BMS2753) were significantly associated with presence of Brucella-specific antibodies at allelic (P = .042 and P = .046) and genotypic level (P = .012 and P = .041, respectively). Moreover, an in silico analysis predicted a functional role of the insertion-deletion polymorphism rs668920841 on the transcriptional regulation of the caprine TNF gene. Altogether, these results contribute to the identification of genetic factors that have a putative effect on the resistance / susceptibility phenotype of goats to Brucella infection.
Collapse
Affiliation(s)
- F C Hasenauer
- Instituto de Patobiología, CICVyA, INTA, Nicolás Repetto y de Los Reseros s/n, Hurlingham, B1686, Buenos Aires, Argentina; CONICET, Godoy Cruz 2290, C1425 CABA, Argentina
| | - U A Rossi
- Instituto de Patobiología, CICVyA, INTA, Nicolás Repetto y de Los Reseros s/n, Hurlingham, B1686, Buenos Aires, Argentina; CONICET, Godoy Cruz 2290, C1425 CABA, Argentina
| | - M E Caffaro
- Instituto de Genética "Ewald A. Favret", CICVyA, INTA, Nicolás Repetto y de Los Reseros s/n, Hurlingham, B1686, Buenos Aires, Argentina
| | - M A Raschia
- Instituto de Genética "Ewald A. Favret", CICVyA, INTA, Nicolás Repetto y de Los Reseros s/n, Hurlingham, B1686, Buenos Aires, Argentina
| | - E Maurizio
- Instituto de Patobiología, CICVyA, INTA, Nicolás Repetto y de Los Reseros s/n, Hurlingham, B1686, Buenos Aires, Argentina; CONICET, Godoy Cruz 2290, C1425 CABA, Argentina
| | - M A Poli
- Instituto de Genética "Ewald A. Favret", CICVyA, INTA, Nicolás Repetto y de Los Reseros s/n, Hurlingham, B1686, Buenos Aires, Argentina
| | - C A Rossetti
- Instituto de Patobiología, CICVyA, INTA, Nicolás Repetto y de Los Reseros s/n, Hurlingham, B1686, Buenos Aires, Argentina.
| |
Collapse
|
21
|
Abstract
Coronary artery disease is a complex cardiovascular disease involving an interplay of genetic and environmental influences over a lifetime. Although considerable progress has been made in understanding lifestyle risk factors, genetic factors identified from genome-wide association studies may capture additional hidden risk undetected by traditional clinical tests. These genetic discoveries have highlighted many candidate genes and pathways dysregulated in the vessel wall, including those involving smooth muscle cell phenotypic modulation and injury responses. Here, we summarize experimental evidence for a few genome-wide significant loci supporting their roles in smooth muscle cell biology and disease. We also discuss molecular quantitative trait locus mapping as a powerful discovery and fine-mapping approach applied to smooth muscle cell and coronary artery disease-relevant tissues. We emphasize the critical need for alternative genetic strategies, including cis/trans-regulatory network analysis, genome editing, and perturbations, as well as single-cell sequencing in smooth muscle cell tissues and model organisms, under both normal and disease states. By integrating multiple experimental and analytical modalities, these multidimensional datasets should improve the interpretation of coronary artery disease genome-wide association studies and molecular quantitative trait locus signals and inform candidate targets for therapeutic intervention or risk prediction.
Collapse
Affiliation(s)
- Doris Wong
- From the Center for Public Health Genomics (D.W., A.W.T., C.L.M.), University of Virginia, Charlottesville.,Department of Biochemistry and Molecular Genetics (D.W., C.L.M.), University of Virginia, Charlottesville
| | - Adam W Turner
- From the Center for Public Health Genomics (D.W., A.W.T., C.L.M.), University of Virginia, Charlottesville
| | - Clint L Miller
- From the Center for Public Health Genomics (D.W., A.W.T., C.L.M.), University of Virginia, Charlottesville.,Department of Biochemistry and Molecular Genetics (D.W., C.L.M.), University of Virginia, Charlottesville.,Department of Biomedical Engineering (C.L.M.), University of Virginia, Charlottesville.,Department of Public Health Sciences (C.L.M.), University of Virginia, Charlottesville
| |
Collapse
|
22
|
Zhang J, Hamza I. Zebrafish as a model system to delineate the role of heme and iron metabolism during erythropoiesis. Mol Genet Metab 2019; 128:204-212. [PMID: 30626549 PMCID: PMC6591114 DOI: 10.1016/j.ymgme.2018.12.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/14/2018] [Accepted: 12/14/2018] [Indexed: 11/17/2022]
Abstract
Coordination of iron acquisition and heme synthesis is required for effective erythropoiesis. The small teleost zebrafish (Danio rerio) is an ideal vertebrate animal model to replicate various aspects of human physiology and provides an efficient and cost-effective way to model human pathophysiology. Importantly, zebrafish erythropoiesis largely resembles mammalian erythropoiesis. Gene discovery by large-scale forward mutagenesis screening has identified key components in heme and iron metabolism. Reverse genetic screens, using morpholino-knockdown and CRISPR/Cas9, coupled with the genetic tractability of the developing embryo have further accelerated functional studies. Ultimately, the ex utero development of zebrafish embryos combined with their transparency and developmental plasticity could provide a deeper understanding of the role of iron and heme metabolism during early vertebrate embryonic development.
Collapse
Affiliation(s)
- Jianbing Zhang
- Department of Animal & Avian Sciences and Department of Cell Biology & Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Iqbal Hamza
- Department of Animal & Avian Sciences and Department of Cell Biology & Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
| |
Collapse
|
23
|
Abstract
GATA1 is an essential regulator of erythroid cell gene expression and maturation. In its absence, erythroid progenitors are arrested in differentiation and undergo apoptosis. Much has been learned about GATA1 function through animal models, which include genetic knockouts as well as ones with decreased levels of expression. However, even greater insights have come from the finding that a number of rare red cell disorders, including Diamond-Blackfan anemia, are associated with GATA1 mutations. These mutations affect the amino-terminal zinc finger (N-ZF) and the amino-terminus of the protein, and in both cases can alter the DNA-binding activity, which is primarily conferred by the third functional domain, the carboxyl-terminal zinc finger (C-ZF). Here we discuss the role of GATA1 in erythropoiesis with an emphasis on the mutations found in human patients with red cell disorders.
Collapse
Affiliation(s)
- Te Ling
- Division of Hematology/Oncology, Northwestern University, Chicago, Illinois
| | - John D Crispino
- Division of Hematology/Oncology, Northwestern University, Chicago, Illinois
| |
Collapse
|
24
|
Chen CP, Chen K, Feng Z, Wen X, Sun H. Synergistic antitumor activity of artesunate and HDAC inhibitors through elevating heme synthesis via synergistic upregulation of ALAS1 expression. Acta Pharm Sin B 2019; 9:937-51. [PMID: 31649844 DOI: 10.1016/j.apsb.2019.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/08/2019] [Accepted: 05/10/2019] [Indexed: 12/31/2022] Open
Abstract
Artemisinin and its derivatives (ARTs) were reported to display heme-dependent antitumor activity. On the other hand, histone deacetylase inhibitors (HDACi) were known to be able to promote heme synthesis in erythroid cells. Nevertheless, the effect of HDACi on heme homeostasis in non-erythrocytes remains unknown. We envisioned that the combination of HDACi and artesunate (ARS) might have synergistic antitumor activity through modulating heme synthesis. In vitro studies revealed that combination of ARS and HDACi exerted synergistic tumor inhibition by inducing cell death. Moreover, this combination exhibited more effective antitumor activity than either ARS or HDACi monotherapy in xenograft models without apparent toxicity. Importantly, mechanistic studies revealed that HDACi coordinated with ARS to increase 5-aminolevulinate synthase (ALAS1) expression, and subsequent heme production, leading to enhanced cytotoxicity of ARS. Notably, knocking down ALAS1 significantly blunted the synergistic effect of ARS and HDACi on tumor inhibition, indicating a critical role of ALAS1 upregulation in mediating ARS cytotoxicity. Collectively, our study revealed the mechanism of synergistic antitumor action of ARS and HDACi. This finding indicates that modulation of heme synthesis pathway by the combination based on ARTs and other heme synthesis modulators represents a promising therapeutic approach to solid tumors.
Collapse
Key Words
- ALA, 5-aminolevulinic acid
- ALAD, 5-aminolevulinate dehydratase
- ALAS, 5-aminolevulinate synthase
- ALAS1
- ARS, artesunate
- ART, artemisinin
- Antitumor
- Artesunate
- CCK-8, cell counting kit 8
- CI, combination index
- CMCNa, carboxymethyl cellulose
- DHA, dihydroartemisinin
- DMAB, (dimethylamino)benzaldehyde
- FECH, ferrochelatase
- GSDME, gasdermin E
- HDAC inhibitor
- HDAC, histone deacetylase
- HDACi, HDAC inhibitor
- HMBS, hydroxymethylbilane synthase
- Heme
- KD, knockdown
- KO, knockout
- LBH589, panobinostat
- PDT, photodynamic therapy
- PI, propidium iodide
- PpIX, protoporphyrin IX
- ROS, reactive oxygen species
- SA, succinyl acetone
- SAHA, vorinostat
- WT, wild-type
- sgRNA, single guide RNA
Collapse
|
25
|
Liu G, Dean A. Enhancer long-range contacts: The multi-adaptor protein LDB1 is the tie that binds. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 2019; 1862:625-33. [DOI: 10.1016/j.bbagrm.2019.04.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 11/20/2022]
|
26
|
Saito K, Fujiwara T, Hatta S, Morita M, Ono K, Suzuki C, Fukuhara N, Onishi Y, Nakamura Y, Kawamata S, Shimizu R, Yamamoto M, Harigae H. Generation and Molecular Characterization of Human Ring Sideroblasts: a Key Role of Ferrous Iron in Terminal Erythroid Differentiation and Ring Sideroblast Formation. Mol Cell Biol 2019; 39:e00387-18. [PMID: 30670569 DOI: 10.1128/MCB.00387-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/16/2019] [Indexed: 12/20/2022] Open
Abstract
Ring sideroblasts are a hallmark of sideroblastic anemia, although little is known about their characteristics. Here, we first generated mutant mice by disrupting the GATA-1 binding motif at the intron 1 enhancer of the ALAS2 gene, a gene responsible for X-linked sideroblastic anemia (XLSA). Although heterozygous female mice showed an anemic phenotype, ring sideroblasts were not observed in their bone marrow. We next established human induced pluripotent stem cell-derived proerythroblast clones harboring the same ALAS2 gene mutation. Through coculture with sodium ferrous citrate, mutant clones differentiated into mature erythroblasts and became ring sideroblasts with upregulation of metal transporters (MFRN1, ZIP8, and DMT1), suggesting a key role for ferrous iron in erythroid differentiation. Interestingly, holo-transferrin (holo-Tf) did not induce erythroid differentiation as well as ring sideroblast formation, and mutant cells underwent apoptosis. Despite massive iron granule content, ring sideroblasts were less apoptotic than holo-Tf-treated undifferentiated cells. Microarray analysis revealed upregulation of antiapoptotic genes in ring sideroblasts, a profile partly shared with erythroblasts from a patient with XLSA. These results suggest that ring sideroblasts exert a reaction to avoid cell death by activating antiapoptotic programs. Our model may become an important tool to clarify the pathophysiology of sideroblastic anemia.
Collapse
|
27
|
Fujiwara T, Harigae H. Molecular pathophysiology and genetic mutations in congenital sideroblastic anemia. Free Radic Biol Med 2019; 133:179-185. [PMID: 30098397 DOI: 10.1016/j.freeradbiomed.2018.08.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/02/2018] [Accepted: 08/04/2018] [Indexed: 01/19/2023]
Abstract
Sideroblastic anemia is a heterogeneous congenital and acquired disorder characterized by anemia and the presence of ring sideroblasts in the bone marrow. Congenital sideroblastic anemia (CSA) is a rare disease caused by mutations in genes involved in the heme biosynthesis, iron-sulfur [Fe-S] cluster biosynthesis, and mitochondrial protein synthesis. The most prevalent form of CSA is X-linked sideroblastic anemia, caused by mutations in the erythroid-specific δ-aminolevulinate synthase (ALAS2), which is the first enzyme of the heme biosynthesis pathway in erythroid cells. To date, a remarkable number of genetically undefined CSA cases remain, but a recent application of the next-generation sequencing technology has recognized novel causative genes for CSA. However, in most instances, the detailed molecular mechanisms of how defects of each gene result in the abnormal mitochondrial iron accumulation remain unclear. This review aims to cover the current understanding of the molecular pathophysiology of CSA.
Collapse
Affiliation(s)
- Tohru Fujiwara
- Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai 980-8575, Japan
| | - Hideo Harigae
- Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai 980-8575, Japan.
| |
Collapse
|
28
|
Abstract
Next generation sequencing has uncovered a trove of short noncoding RNAs (e.g., microRNAs) and long noncoding RNAs (lncRNAs) that act as molecular rheostats in the control of diverse homeostatic processes. Meanwhile, the tsunamic emergence of clustered regularly interspaced short palindromic repeats (CRISPR) editing has transformed our influence over all DNA-carrying entities, heralding global CRISPRization. This is evident in biomedical research where the ease and low-cost of CRISPR editing has made it the preferred method of manipulating the mouse genome, facilitating rapid discovery of genome function in an in vivo context. Here, CRISPR genome editing components are updated for elucidating lncRNA function in mice. Various strategies are highlighted for understanding the function of lncRNAs residing in intergenic sequence space, as host genes that harbor microRNAs or other genes, and as natural antisense, overlapping or intronic genes. Also discussed is CRISPR editing of mice carrying human lncRNAs as well as the editing of competing endogenous RNAs. The information described herein should assist labs in the rigorous design of experiments that interrogate lncRNA function in mice where complex disease processes can be modeled thus accelerating translational discovery.
Collapse
Affiliation(s)
- Joseph M Miano
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States of America.
| | - Xiaochun Long
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, United States of America
| | - Qing Lyu
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States of America
| |
Collapse
|
29
|
Liu J, Li Y, Tong J, Gao J, Guo Q, Zhang L, Wang B, Zhao H, Wang H, Jiang E, Kurita R, Nakamura Y, Tanabe O, Engel JD, Bresnick EH, Zhou J, Shi L. Long non-coding RNA-dependent mechanism to regulate heme biosynthesis and erythrocyte development. Nat Commun 2018; 9:4386. [PMID: 30349036 PMCID: PMC6197277 DOI: 10.1038/s41467-018-06883-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 10/02/2018] [Indexed: 01/19/2023] Open
Abstract
In addition to serving as a prosthetic group for enzymes and a hemoglobin structural component, heme is a crucial homeostatic regulator of erythroid cell development and function. While lncRNAs modulate diverse physiological and pathological cellular processes, their involvement in heme-dependent mechanisms is largely unexplored. In this study, we elucidated a lncRNA (UCA1)-mediated mechanism that regulates heme metabolism in human erythroid cells. We discovered that UCA1 expression is dynamically regulated during human erythroid maturation, with a maximal expression in proerythroblasts. UCA1 depletion predominantly impairs heme biosynthesis and arrests erythroid differentiation at the proerythroblast stage. Mechanistic analysis revealed that UCA1 physically interacts with the RNA-binding protein PTBP1, and UCA1 functions as an RNA scaffold to recruit PTBP1 to ALAS2 mRNA, which stabilizes ALAS2 mRNA. These results define a lncRNA-mediated posttranscriptional mechanism that provides a new dimension into how the fundamental heme biosynthetic process is regulated as a determinant of erythrocyte development. LncRNAs modulate diverse physiological cellular processes, however, their involvement in heme-dependent processes are not yet clear. Here the authors reveal the role of lncRNA UCA1 in erythroid cell development.
Collapse
Affiliation(s)
- Jinhua Liu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yapu Li
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Jingyuan Tong
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Jie Gao
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Qing Guo
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Lingling Zhang
- Tianjin Key Laboratory of Food and Biotechnology, School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, 300134, China
| | - Bingrui Wang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Hui Zhao
- Tianjin Key Laboratory of Food and Biotechnology, School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, 300134, China
| | - Hongtao Wang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Erlie Jiang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Ryo Kurita
- Japanese Red Cross Society, Department of Research and Development, Central Blood Institute, Tokyo, 105-8521, Japan
| | - Yukio Nakamura
- RIKEN BioResource Research Center, Cell Engineering Division, Ibaraki, 305-0074, Japan
| | - Osamu Tanabe
- Department of Integrative Genomics Tohoku Medical Megabank, Tohoku University, Sedai, 980-8573, Japan
| | - James Douglas Engel
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Emery H Bresnick
- Wisconsin Institutes for Medical Research, Paul Carbone Cancer Center, Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53562, USA
| | - Jiaxi Zhou
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China. .,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China. .,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| |
Collapse
|