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Ma H, Qu J, Pang Z, Luo J, Yan M, Xu W, Zhuang H, Liu L, Qu Q. Super-enhancer omics in stem cell. Mol Cancer 2024; 23:153. [PMID: 39090713 PMCID: PMC11293198 DOI: 10.1186/s12943-024-02066-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 07/12/2024] [Indexed: 08/04/2024] Open
Abstract
The hallmarks of stem cells, such as proliferation, self-renewal, development, differentiation, and regeneration, are critical to maintain stem cell identity which is sustained by genetic and epigenetic factors. Super-enhancers (SEs), which consist of clusters of active enhancers, play a central role in maintaining stemness hallmarks by specifically transcriptional model. The SE-navigated transcriptional complex, including SEs, non-coding RNAs, master transcriptional factors, Mediators and other co-activators, forms phase-separated condensates, which offers a toggle for directing diverse stem cell fate. With the burgeoning technologies of multiple-omics applied to examine different aspects of SE, we firstly raise the concept of "super-enhancer omics", inextricably linking to Pan-omics. In the review, we discuss the spatiotemporal organization and concepts of SEs, and describe links between SE-navigated transcriptional complex and stem cell features, such as stem cell identity, self-renewal, pluripotency, differentiation and development. We also elucidate the mechanism of stemness and oncogenic SEs modulating cancer stem cells via genomic and epigenetic alterations hijack in cancer stem cell. Additionally, we discuss the potential of targeting components of the SE complex using small molecule compounds, genome editing, and antisense oligonucleotides to treat SE-associated organ dysfunction and diseases, including cancer. This review also provides insights into the future of stem cell research through the paradigm of SEs.
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Affiliation(s)
- Hongying Ma
- Department of Pharmacy, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, People's Republic of China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
| | - Jian Qu
- Department of Pharmacy, the Second Xiangya Hospital, Institute of Clinical Pharmacy, Central South University, Changsha, 410011, People's Republic of China
- Hunan key laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, 410219, China
| | - Zicheng Pang
- Department of Pharmacy, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, People's Republic of China
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Jian Luo
- Department of Pharmacy, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, People's Republic of China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
| | - Min Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, People's Republic of China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
| | - Weixin Xu
- Department of Pharmacy, the Second Xiangya Hospital, Institute of Clinical Pharmacy, Central South University, Changsha, 410011, People's Republic of China
| | - Haihui Zhuang
- Department of Pharmacy, the Second Xiangya Hospital, Institute of Clinical Pharmacy, Central South University, Changsha, 410011, People's Republic of China
| | - Linxin Liu
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, People's Republic of China.
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China.
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Thakuri BKC, Zhang J, Zhao J, Nguyen LN, Nguyen LNT, Schank M, Khanal S, Dang X, Cao D, Lu Z, Wu XY, Jiang Y, El Gazzar M, Ning S, Wang L, Moorman JP, Yao ZQ. HCV-Associated Exosomes Upregulate RUNXOR and RUNX1 Expressions to Promote MDSC Expansion and Suppressive Functions through STAT3-miR124 Axis. Cells 2020; 9:cells9122715. [PMID: 33353065 PMCID: PMC7766103 DOI: 10.3390/cells9122715] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/09/2020] [Accepted: 12/17/2020] [Indexed: 12/17/2022] Open
Abstract
RUNX1 overlapping RNA (RUNXOR) is a long non-coding RNA and plays a pivotal role in the differentiation of myeloid cells via targeting runt-related transcription factor 1 (RUNX1). We and others have previously reported that myeloid-derived suppressor cells (MDSCs) expand and inhibit host immune responses during chronic viral infections; however, the mechanisms responsible for MDSC differentiation and suppressive functions, in particular the role of RUNXOR–RUNX1, remain unclear. Here, we demonstrated that RUNXOR and RUNX1 expressions are significantly upregulated and associated with elevated levels of immunosuppressive molecules, such as arginase 1 (Arg1), inducible nitric oxide synthase (iNOS), signal transducer and activator of transcription 3 (STAT3), and reactive oxygen species (ROS) in MDSCs during chronic hepatitis C virus (HCV) infection. Mechanistically, we discovered that HCV-associated exosomes (HCV-Exo) can induce the expressions of RUNXOR and RUNX1, which in turn regulates miR-124 expression via STAT3 signaling, thereby promoting MDSC differentiation and suppressive functions. Importantly, overexpression of RUNXOR in healthy CD33+ myeloid cells promoted differentiation and suppressive functions of MDSCs. Conversely, silencing RUNXOR or RUNX1 expression in HCV-derived CD33+ myeloid cells significantly inhibited their differentiation and expressions of suppressive molecules and improved the function of co-cultured autologous CD4 T cells. Taken together, these results indicate that the RUNXOR–RUNX1–STAT3–miR124 axis enhances the differentiation and suppressive functions of MDSCs and could be a potential target for immunomodulation in conjunction with antiviral therapy during chronic HCV infection.
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Affiliation(s)
- Bal Krishna Chand Thakuri
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Jinyu Zhang
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Juan Zhao
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Lam N. Nguyen
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Lam N. T. Nguyen
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Madison Schank
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Sushant Khanal
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Xindi Dang
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Dechao Cao
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Zeyuan Lu
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Xiao Y. Wu
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Yong Jiang
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
| | - Mohamed El Gazzar
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
| | - Shunbin Ning
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Ling Wang
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
| | - Jonathan P. Moorman
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
- Hepatitis (HCV/HBV/HIV) Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, TN 37614, USA
| | - Zhi Q. Yao
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA; (B.K.C.T.); (J.Z.); (J.Z.); (L.N.N.); (L.N.T.N.); (M.S.); (S.K.); (X.D.); (D.C.); (Z.L.); (X.Y.W.); (Y.J.); (M.E.G.); (S.N.); (L.W.); (J.P.M.)
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614, USA
- Hepatitis (HCV/HBV/HIV) Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, TN 37614, USA
- Correspondence: ; Tel.: +1-423-439-8029; Fax: +1-423-439-7010
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Thakuri BKC, Zhang J, Zhao J, Nguyen LN, Nguyen LNT, Khanal S, Cao D, Dang X, Schank M, Wu XY, Morrison ZD, Gazzar ME, Li Z, Jiang Y, Ning S, Wang L, Moorman JP, Yao ZQ. LncRNA HOTAIRM1 promotes MDSC expansion and suppressive functions through the HOXA1-miR124 axis during HCV infection. Sci Rep 2020; 10:22033. [PMID: 33328510 PMCID: PMC7745042 DOI: 10.1038/s41598-020-78786-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/27/2020] [Indexed: 02/07/2023] Open
Abstract
HOXA transcript antisense RNA myeloid-specific 1 (HOTAIRM1) is a long non-coding RNA (lncRNA) that plays a pivotal role in regulating myeloid cell development via targeting HOXA1 gene expression. We and others have previously shown that myeloid-derived suppressor cells (MDSCs), a heterogeneous population of immature myeloid cells, expand during chronic viral (HCV, HIV) infections. However, the role of HOTAIRM1 in the development and suppression of MDSCs during viral infection remains unknown. In this study, we demonstrate that the expressions of HOTAIRM1 and its target HOXA1 are substantially upregulated to promote the expressions of immunosuppressive molecules, including arginase 1, inducible nitric oxide synthase, signal transducer and activator of transcription 3, and reactive oxygen species, in CD33+ myeloid cells derived from hepatitis C virus (HCV)-infected patients. We show that HCV-associated exosomes (HCV-Exo) can modulate HOTAIRM1, HOXA1, and miR124 expressions to regulate MDSC development. Importantly, overexpression of HOTAIRM1 or HOXA1 in healthy CD33+ myeloid cells promoted the MDSC differentiation and suppressive functions; conversely, silencing of HOTAIRM1 or HOXA1 expression in MDSCs from HCV patients significantly reduced the MDSC frequency and their suppressive functions. In essence, these results indicate that the HOTAIRM1-HOXA1-miR124 axis enhances the differentiation and suppressive functions of MDSCs and may be a potential target for immunomodulation in conjunction with antiviral therapy during chronic viral infection.
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Affiliation(s)
- Bal Krishna Chand Thakuri
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Jinyu Zhang
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Juan Zhao
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Lam N Nguyen
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Lam N T Nguyen
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Sushant Khanal
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Dechao Cao
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Xindi Dang
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Madison Schank
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Xiao Y Wu
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Zheng D Morrison
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Mohamed El Gazzar
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
| | - Zhengke Li
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
| | - Yong Jiang
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
| | - Shunbin Ning
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Ling Wang
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
| | - Jonathan P Moorman
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA
- Department of Veterans Affairs, Hepatitis (HCV/HBV/HIV) Program, James H. Quillen VA Medical Center, Johnson City, TN, 37614, USA
| | - Zhi Q Yao
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA.
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN, 37614, USA.
- Department of Veterans Affairs, Hepatitis (HCV/HBV/HIV) Program, James H. Quillen VA Medical Center, Johnson City, TN, 37614, USA.
- Center of Excellence for HIV/AIDS Care, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37614, USA.
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Long noncoding RNA HOTAIRM1 promotes myeloid-derived suppressor cell expansion and suppressive functions through up-regulating HOXA1 expression during latent HIV infection. AIDS 2020; 34:2211-2221. [PMID: 33048872 PMCID: PMC7674250 DOI: 10.1097/qad.0000000000002700] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
OBJECTIVE Myeloid-derived suppressor cells (MDSCs) contribute to HIV progression by impairing antiviral immunity; however, the mechanisms responsible for MDSC development during HIV infection are incompletely understood. HOX antisense intergenic RNA myeloid 1 (HOTAIRM1) is a long noncoding RNA (lncRNA) that plays a pivotal role in regulating myeloid cell development via targeting HOXA1. The role of HOTAIRM1--HOXA1 in the differentiation and functions of MDSCs during HIV infection remains unclear. METHODS In this study, we measured MDSC induction and suppressive functions by flow cytometry, RT-PCR, and co-culture experiments using CD33 myeloid cells derived from people living with HIV (PLHIV) on antiretroviral therapy (ART). We also manipulated the HOTAIRM1--HOXA1 axis in myeloid cells using knockdown and overexpression approaches. RESULTS We demonstrate that HOTAIRM1 and HOXA1 expressions are reciprocally upregulated and are responsible for increased levels of immunosuppressive molecules, such as arginase 1 (Arg1), inducible nitric oxide synthase (iNOS), signal transducer and activator of transcription 3 (STAT3), and reactive oxygen species (ROS), in CD33 myeloid cells derived from PLHIV on ART. We found that overexpression of HOTAIRM1 or HOXA1 in CD33 cells isolated from healthy individuals promoted the differentiation and suppressive functions of MDSCs, whereas silencing of HOTAIRM1 or HOXA1 expression in MDSCs derived from PLHIV significantly inhibited the frequency of MDSCs and expressions of the immunosuppressive molecules and reduced their immunosuppressive effects on T cells. CONCLUSION These results indicate that the HOTAIRM1--HOXA1 axis enhances differentiation and suppressive functions of MDSCs and could be a potential therapeutic target for immunomodulation during latent HIV infection.
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Ng M, Heckl D, Klusmann JH. The Regulatory Roles of Long Noncoding RNAs in Acute Myeloid Leukemia. Front Oncol 2019; 9:570. [PMID: 31338324 PMCID: PMC6629768 DOI: 10.3389/fonc.2019.00570] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/12/2019] [Indexed: 01/23/2023] Open
Abstract
In this post-genomic era, long noncoding RNAs (lncRNAs) are rapidly gaining recognition for their crucial roles across diverse biological processes and contexts. The human blood system is no exception, where dozens of lncRNAs have been established as regulators of normal and/or malignant hematopoiesis, and where ongoing works continue to uncover novel lncRNA functions. Our review focuses on lncRNAs that are involved in the pathogenesis of acute myeloid leukemia (AML) and the mechanisms through which they control gene expression in this disease context. We also comment on genome-wide sequencing or profiling studies that have implicated large sets of lncRNAs in AML pathophysiology.
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Affiliation(s)
- Michelle Ng
- Department of Pediatrics I, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Dirk Heckl
- Department of Pediatrics I, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Jan-Henning Klusmann
- Department of Pediatrics I, Martin Luther University Halle-Wittenberg, Halle, Germany
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6
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Mao R, Wu Y, Ming Y, Xu Y, Wang S, Chen X, Wang X, Fan Y. Enhancer RNAs: a missing regulatory layer in gene transcription. SCIENCE CHINA-LIFE SCIENCES 2018; 62:905-912. [PMID: 30593613 DOI: 10.1007/s11427-017-9370-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/01/2018] [Indexed: 01/12/2023]
Abstract
Enhancers and super-enhancers exert indispensable roles in maintaining cell identity through spatiotemporally regulating gene transcription. Meanwhile, active enhancers and super-enhancers also produce transcripts termed enhancer RNAs (eRNAs) from their DNA elements. Although enhancers have been identified for more than 30 years, widespread transcription from enhancers are just discovered by genome-wide sequencing and considered as the key to understand longstanding questions in gene transcription. RNA-transcribed enhancers are marked by histone modifications such as H3K4m1/2 and H3K27Ac, and enriched with transcription regulatory factors such as LDTFs, P300, CBP, BRD4 and MED1. Those regulatory factors might constitute a Mega-Trans-like complex to potently activate enhancers. Compared to mRNAs, eRNAs are quite unstable and play roles at local. Functionally, it has been shown that eRNAs promote formation of enhancer-promoter loops. Several studies also demonstrated that eRNAs help the binding of RNA polymerase II (RNAPII) or transition of paused RNAPII by de-association of the negative elongation factor (NELF) complex. Nevertheless, these proposed mechanisms are not universally accepted and still under controversy. Here, we comprehensively summarize the reported findings and make perspectives for future exploration. We also believe that super-enhancer derived RNAs (seRNAs) might be informative to understand the nature of super-enhancers.
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Affiliation(s)
- Renfang Mao
- Department of Pathophysiology, School of Medicine, Nantong University, Nantong, 226019, China
| | - Yuanyuan Wu
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, 226019, China
| | - Yue Ming
- Department of Immunology, School of Medicine, Nantong University, Nantong, 226019, China
| | - Yuanpei Xu
- Department of Immunology, School of Medicine, Nantong University, Nantong, 226019, China
| | - Shouyan Wang
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, 226019, China
| | - Xia Chen
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, 226019, China
| | - Xiaoying Wang
- Department of Immunology, School of Medicine, Nantong University, Nantong, 226019, China
| | - Yihui Fan
- Basic Medical Research Center, School of Medicine, Nantong University, Nantong, 226019, China.
- Department of Immunology, School of Medicine, Nantong University, Nantong, 226019, China.
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7
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Tian X, Ma J, Wang T, Tian J, Zhang Y, Mao L, Xu H, Wang S. Long Non-Coding RNA HOXA Transcript Antisense RNA Myeloid-Specific 1-HOXA1 Axis Downregulates the Immunosuppressive Activity of Myeloid-Derived Suppressor Cells in Lung Cancer. Front Immunol 2018; 9:473. [PMID: 29662483 PMCID: PMC5890118 DOI: 10.3389/fimmu.2018.00473] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/22/2018] [Indexed: 02/06/2023] Open
Abstract
HOXA transcript antisense RNA myeloid-specific 1 (HOTAIRM1) is a long non-coding RNA that has been shown to be a key regulator of myeloid cell development by targeting HOXA1. Myeloid-derived suppressor cells (MDSCs) are a heterogeneous population of immature myeloid cells that possess immunosuppressive function. However, the impact of HOTAIRM1 on the development of MDSCs remains unknown. In this study, we demonstrated that HOTAIRM1 was expressed in MDSCs and that overexpression of HOTAIRM1 could downregulate the expression of suppressive molecules in MDSCs. In addition, HOTAIRM1 levels were observed to be decreased in the peripheral blood cells of lung cancer patients compared with those of healthy controls. By analyzing HOTAIRM1 expression levels in different types of lung cancer, we found that HOTAIRM1 was mainly expressed in lung adenocarcinoma. Finally, it was confirmed that HOTAIRM1 could enhance the expression of HOXA1 in MDSCs and that high levels of HOXA1, the target gene of HOTAIRM1, could delay tumor progression and enhance the antitumor immune response by downregulating the immunosuppression of MDSCs. Taken together, this study illustrates that HOTAIRM1/HOXA1 downregulates the immunosuppressive function of MDSCs and may be a potential therapeutic target in lung cancer.
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Affiliation(s)
- Xinyu Tian
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China.,Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Jie Ma
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Ting Wang
- Department of Laboratory Medicine, Jiangsu Cancer Hospital, Nanjing, China
| | - Jie Tian
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yue Zhang
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Lingxiang Mao
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China
| | - Huaxi Xu
- Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Shengjun Wang
- Department of Laboratory Medicine, The Affiliated People's Hospital, Jiangsu University, Zhenjiang, China.,Department of Immunology, Jiangsu Key Laboratory of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
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8
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Kasper DM, Nicoli S. Epigenetic and Epitranscriptomic Factors Make a Mark on Hematopoietic Stem Cell Development. CURRENT STEM CELL REPORTS 2018. [DOI: 10.1007/s40778-018-0113-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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9
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Emerging mechanisms of long noncoding RNA function during normal and malignant hematopoiesis. Blood 2017; 130:1965-1975. [PMID: 28928124 DOI: 10.1182/blood-2017-06-788695] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/15/2017] [Indexed: 12/22/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are increasingly recognized as vital components of gene programs controlling cell differentiation and function. Central to their functions is an ability to act as scaffolds or as decoys that recruit or sequester effector proteins from their DNA, RNA, or protein targets. lncRNA-modulated effectors include regulators of transcription, chromatin organization, RNA processing, and translation, such that lncRNAs can influence gene expression at multiple levels. Here we review the current understanding of how lncRNAs help coordinate gene expression to modulate cell fate in the hematopoietic system. We focus on a growing number of mechanistic studies to synthesize emerging principles of lncRNA function, emphasizing how they facilitate diversification of gene programming during development. We also survey how disrupted lncRNA function can contribute to malignant transformation, highlighting opportunities for therapeutic intervention in specific myeloid and lymphoid cancers. Finally, we discuss challenges and prospects for further elucidation of lncRNA mechanisms.
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10
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Chromatin dynamics during the differentiation of long-term hematopoietic stem cells to multipotent progenitors. Blood Adv 2017; 1:887-898. [PMID: 29296732 DOI: 10.1182/bloodadvances.2016003384] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 05/01/2017] [Indexed: 12/31/2022] Open
Abstract
ATAC-seq provides genome-wide chromatin state in 3 cell types of hematopoietic stem/progenitor cells.Transcription factor cohorts are associated with dynamic changes of open chromatin during the differentiation of LT/ST-HSCs to MPPs.
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