1
|
Guak H, Weiland M, Ark AV, Zhai L, Lau K, Corrado M, Davidson P, Asiedu E, Mabvakure B, Compton S, DeCamp L, Scullion CA, Jones RG, Nowinski SM, Krawczyk CM. Transcriptional programming mediated by the histone demethylase KDM5C regulates dendritic cell population heterogeneity and function. Cell Rep 2024; 43:114506. [PMID: 39052479 DOI: 10.1016/j.celrep.2024.114506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/30/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024] Open
Abstract
Functional and phenotypic heterogeneity of dendritic cells (DCs) play crucial roles in facilitating the development of diverse immune responses essential for host protection. Here, we report that KDM5C, a histone lysine demethylase, regulates conventional or classical DC (cDC) and plasmacytoid DC (pDC) population heterogeneity and function. Mice deficient in KDM5C in DCs have increased proportions of cDC2Bs and cDC1s, which is partly dependent on type I interferon (IFN) and pDCs. Loss of KDM5C results in an increase in Ly6C- pDCs, which, compared to Ly6C+ pDCs, have limited ability to produce type I IFN and more efficiently stimulate antigen-specific CD8 T cells. KDM5C-deficient DCs have increased expression of inflammatory genes, altered expression of lineage-specific genes, and decreased function. In response to Listeria infection, KDM5C-deficient mice mount reduced CD8 T cell responses due to decreased antigen presentation by cDC1s. Thus, KDM5C is a key regulator of DC heterogeneity and critical driver of the functional properties of DCs.
Collapse
Affiliation(s)
- Hannah Guak
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA; Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew Weiland
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Alexandra Vander Ark
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Lukai Zhai
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Kin Lau
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Mario Corrado
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA; Department of Internal Medicine, University of Toronto, Toronto, ON M5S 3H2, Canada
| | - Paula Davidson
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ebenezer Asiedu
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Batsirai Mabvakure
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA; Department of Oncology, Georgetown University School of Medicine, Washington, DC 20057, USA; Georgetown Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Shelby Compton
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Lisa DeCamp
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Catherine A Scullion
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA; Department of Experimental Medicine, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Russell G Jones
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Sara M Nowinski
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Connie M Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA.
| |
Collapse
|
2
|
Caldwell BA, Li L. Epigenetic regulation of innate immune dynamics during inflammation. J Leukoc Biol 2024; 115:589-606. [PMID: 38301269 PMCID: PMC10980576 DOI: 10.1093/jleuko/qiae026] [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: 12/11/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/03/2024] Open
Abstract
Innate immune cells play essential roles in modulating both immune defense and inflammation by expressing a diverse array of cytokines and inflammatory mediators, phagocytizing pathogens to promote immune clearance, and assisting with the adaptive immune processes through antigen presentation. Rudimentary innate immune "memory" states such as training, tolerance, and exhaustion develop based on the nature, strength, and duration of immune challenge, thereby enabling dynamic transcriptional reprogramming to alter present and future cell behavior. Underlying transcriptional reprogramming are broad changes to the epigenome, or chromatin alterations above the level of DNA sequence. These changes include direct modification of DNA through cytosine methylation as well as indirect modifications through alterations to histones that comprise the protein core of nucleosomes. In this review, we will discuss recent advances in our understanding of how these epigenetic changes influence the dynamic behavior of the innate immune system during both acute and chronic inflammation, as well as how stable changes to the epigenome result in long-term alterations of innate cell behavior related to pathophysiology.
Collapse
Affiliation(s)
- Blake A. Caldwell
- Department of Biological Sciences, Virginia Tech, 970 Washington St. SW, Blacksburg, VA 24061-0910, USA
| | - Liwu Li
- Department of Biological Sciences, Virginia Tech, 970 Washington St. SW, Blacksburg, VA 24061-0910, USA
| |
Collapse
|
3
|
Guo X, Bai Y, Jia X, Wu P, Luo L, Wang J, Li H, Guo H, Li J, Guo Z, Yun K, Gao C, Yan J. DNA methylation profiling reveals potential biomarkers of β-lactams induced fatal anaphylactic shock. Forensic Sci Int 2024; 356:111943. [PMID: 38290418 DOI: 10.1016/j.forsciint.2024.111943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 10/30/2023] [Accepted: 01/14/2024] [Indexed: 02/01/2024]
Abstract
Anaphylaxis is a serious reaction of systemic hypersensitivity with that rapid onset and sudden death. Drug hypersensitivity, particularly induced by β-lactams, is one of the most frequent causes of anaphylaxis in adults. But identification of anaphylactic shock, in forensic sciences recently, is difficult, because it mainly depends on nonspecific characteristic morphological changes, as well as exclusion and circumstantial evidence. Here, we detected DNA methylation signatures of β-lactams-induced fatal anaphylactic shock with the Illumina Infinium Human Methylation EPIC BeadChip, to screen potential forensic biomarkers and reveal the molecular mechanisms of drug-induced anaphylaxis with fatal shock and sudden death. Our results indicated that DNA methylation was associated with β-lactams-induced fatal anaphylactic shock, in which the hypomethylation played a vital role. We found that 1459 differentially methylated positions (DMPs) were mainly involved in β-lactams-induced fatal anaphylactic shock by regulating MAPK and other signaling pathways. 18 DNA methylation signatures that could separate β-lactams-induced anaphylactic shock from healthy individuals were identified. The altered methylation of DMPs can affect the transcription of corresponding genes and promote β-lactams-induced fatal anaphylactic shock. The results suggest that DNA methylation can detect forensic identification markers of drug-induced anaphylaxis with fatal shock and sudden death, and it is an effective method for the forensic diagnosis.
Collapse
Affiliation(s)
- Xiangjie Guo
- Department of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi, China; Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China; Shanxi Key Laboratory of Drug Toxicology and Drug for Radiation Injury, China Institute for Radiation Protection, Taiyuan, ShanXi, China.
| | - Yaqin Bai
- Department of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiao Jia
- College of Pharmacy, Nankai University, Tianjin, China
| | - Peng Wu
- Department of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Li Luo
- Department of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jiaqi Wang
- Department of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Hao Li
- Institute of Forensic Science of China, Beijing, China
| | - Hualin Guo
- China Astronaut Research and Training Center, Beijing, China
| | - Jianguo Li
- Shanxi Key Laboratory of Drug Toxicology and Drug for Radiation Injury, China Institute for Radiation Protection, Taiyuan, ShanXi, China
| | - Zhongyuan Guo
- Department of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Keming Yun
- Department of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Cairong Gao
- Department of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi, China.
| | - Jiangwei Yan
- Department of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi, China.
| |
Collapse
|
4
|
Fazazi MR, Ruda GF, Brennan PE, Rangachari M. The X-linked histone demethylases KDM5C and KDM6A as regulators of T cell-driven autoimmunity in the central nervous system. Brain Res Bull 2023; 202:110748. [PMID: 37657612 DOI: 10.1016/j.brainresbull.2023.110748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/03/2023]
Abstract
T cell-driven autoimmune responses are subject to striking sex-dependent effects. While the contributions of sex hormones are well-understood, those of sex chromosomes are meeting with increased appreciation. Here, we outline what is known about the contribution of sex chromosome-linked factors to experimental autoimmune encephalomyelitis (EAE), a mouse model that recapitulates many of the T cell-driven mechanisms of multiple sclerosis (MS) pathology. Particular attention is paid to the KDM family of histone demethylases, several of which - KDM5C, KDM5D and KDM6A - are sex chromosome encoded. Finally, we provide evidence that functional inhibition of KDM5 molecules can suppress interferon (IFN)γ production from murine male effector T cells, and that an increased ratio of inflammatory Kdm6a to immunomodulatory Kdm5c transcript is observed in T helper 17 (Th17) cells from women with the autoimmune disorder ankylosing spondylitis (AS). Histone lysine demethlyases thus represent intriguing targets for the treatment of T cell-driven autoimmune disorders.
Collapse
Affiliation(s)
- Mohamed Reda Fazazi
- axe Neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Gian Filippo Ruda
- Centre for Medicines Discovery and NIHR, Oxford Biomedical Research Centre, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Paul E Brennan
- Centre for Medicines Discovery and NIHR, Oxford Biomedical Research Centre, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Alzheimer's Research UK, Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Manu Rangachari
- axe Neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada; Département de médecine moléculaire, Faculté de médecine, Université Laval, Québec, QC, Canada.
| |
Collapse
|
5
|
Gupta N, Yakhou L, Albert JR, Azogui A, Ferry L, Kirsh O, Miura F, Battault S, Yamaguchi K, Laisné M, Domrane C, Bonhomme F, Sarkar A, Delagrange M, Ducos B, Cristofari G, Ito T, Greenberg MVC, Defossez PA. A genome-wide screen reveals new regulators of the 2-cell-like cell state. Nat Struct Mol Biol 2023; 30:1105-1118. [PMID: 37488355 DOI: 10.1038/s41594-023-01038-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/19/2023] [Indexed: 07/26/2023]
Abstract
In mammals, only the zygote and blastomeres of the early embryo are totipotent. This totipotency is mirrored in vitro by mouse '2-cell-like cells' (2CLCs), which appear at low frequency in cultures of embryonic stem cells (ESCs). Because totipotency is not completely understood, we carried out a genome-wide CRISPR knockout screen in mouse ESCs, searching for mutants that reactivate the expression of Dazl, a gene expressed in 2CLCs. Here we report the identification of four mutants that reactivate Dazl and a broader 2-cell-like signature: the E3 ubiquitin ligase adaptor SPOP, the Zinc-Finger transcription factor ZBTB14, MCM3AP, a component of the RNA processing complex TREX-2, and the lysine demethylase KDM5C. All four factors function upstream of DPPA2 and DUX, but not via p53. In addition, SPOP binds DPPA2, and KDM5C interacts with ncPRC1.6 and inhibits 2CLC gene expression in a catalytic-independent manner. These results extend our knowledge of totipotency, a key phase of organismal life.
Collapse
Affiliation(s)
- Nikhil Gupta
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France.
- Joint AZ CRUK Functional Genomics Centre, The Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
| | - Lounis Yakhou
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | | | - Anaelle Azogui
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Laure Ferry
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Olivier Kirsh
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Fukuoka, Japan
| | - Sarah Battault
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Kosuke Yamaguchi
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Marthe Laisné
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Cécilia Domrane
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Frédéric Bonhomme
- Epigenetic Chemical Biology, UMR3523, Institut Pasteur, Université Paris Cité, CNRS, Paris, France
| | - Arpita Sarkar
- IRCAN, Université Côte d'Azur, Inserm, CNRS, Nice, France
| | - Marine Delagrange
- High Throughput qPCR Facility, Institut de Biologie de l'École Normale Supérieure (IBENS), Laboratoire de Physique de l'ENS CNRS UMR8023, PSL Research University, Paris, France
| | - Bertrand Ducos
- High Throughput qPCR Facility, Institut de Biologie de l'École Normale Supérieure (IBENS), Laboratoire de Physique de l'ENS CNRS UMR8023, PSL Research University, Paris, France
| | | | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Fukuoka, Japan
| | | | | |
Collapse
|
6
|
Qu L, Yin T, Zhao Y, Lv W, Liu Z, Chen C, Liu K, Shan S, Zhou R, Li X, Dong H. Histone demethylases in the regulation of immunity and inflammation. Cell Death Discov 2023; 9:188. [PMID: 37353521 DOI: 10.1038/s41420-023-01489-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/22/2023] [Accepted: 06/15/2023] [Indexed: 06/25/2023] Open
Abstract
Pathogens or danger signals trigger the immune response. Moderate immune response activation removes pathogens and avoids excessive inflammation and tissue damage. Histone demethylases (KDMs) regulate gene expression and play essential roles in numerous physiological processes by removing methyl groups from lysine residues on target proteins. Abnormal expression of KDMs is closely associated with the pathogenesis of various inflammatory diseases such as liver fibrosis, lung injury, and autoimmune diseases. Despite becoming exciting targets for diagnosing and treating these diseases, the role of these enzymes in the regulation of immune and inflammatory response is still unclear. Here, we review the underlying mechanisms through which KDMs regulate immune-related pathways and inflammatory responses. In addition, we also discuss the future applications of KDMs inhibitors in immune and inflammatory diseases.
Collapse
Affiliation(s)
- Lihua Qu
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, China
| | - Tong Yin
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Yijin Zhao
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Wenting Lv
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Ziqi Liu
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Chao Chen
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Kejun Liu
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Shigang Shan
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, China
| | - Rui Zhou
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Xiaoqing Li
- Biological Targeted Therapy Key Laboratory in Hubei, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Center for Stem Cell Research and Application, Union Hospital, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Huifen Dong
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China.
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China.
| |
Collapse
|
7
|
Liu H, Zhai L, Liu Y, Lu D, Vander Ark A, Yang T, Krawczyk CM. The histone demethylase KDM5C controls female bone mass by promoting energy metabolism in osteoclasts. SCIENCE ADVANCES 2023; 9:eadg0731. [PMID: 37018401 PMCID: PMC10075994 DOI: 10.1126/sciadv.adg0731] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/06/2023] [Indexed: 05/28/2023]
Abstract
Women experience osteoporosis at higher rates than men. Aside from hormones, the mechanisms driving sex-dependent bone mass regulation are not well understood. Here, we demonstrate that the X-linked H3K4me2/3 demethylase KDM5C regulates sex-specific bone mass. Loss of KDM5C in hematopoietic stem cells or bone marrow monocytes increases bone mass in female but not male mice. Mechanistically, loss of KDM5C impairs the bioenergetic metabolism, resulting in impaired osteoclastogenesis. Treatment with the KDM5 inhibitor reduces osteoclastogenesis and energy metabolism of both female mice and human monocytes. Our report details a sex-dependent mechanism for bone homeostasis, connecting epigenetic regulation to osteoclast metabolism and positions KDM5C as a potential target for future treatment of osteoporosis in women.
Collapse
Affiliation(s)
- Huadie Liu
- Laboratory of Skeletal Biology, Department of Cell Biology, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
| | - Lukai Zhai
- Department of Metabolism and Nutritional Programming, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Ye Liu
- Laboratory of Skeletal Biology, Department of Cell Biology, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
| | - Di Lu
- Laboratory of Skeletal Biology, Department of Cell Biology, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
| | - Alexandra Vander Ark
- Department of Metabolism and Nutritional Programming, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Tao Yang
- Laboratory of Skeletal Biology, Department of Cell Biology, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
| | - Connie M. Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| |
Collapse
|
8
|
The histone demethylase KDM5C controls female bone mass by promoting energy metabolism in osteoclasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.23.529728. [PMID: 36865269 PMCID: PMC9980061 DOI: 10.1101/2023.02.23.529728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Women experience osteoporosis at higher rates than men. Aside from hormones, the mechanisms driving sex-dependent bone mass regulation are not well-understood. Here, we demonstrate that the X-linked H3K4me2/3 demethylase KDM5C regulates sex-specific bone mass. Loss of KDM5C in hematopoietic stem cells or bone marrow monocytes (BMM) increases bone mass in female but not male mice. Mechanistically, loss of KDM5C impairs the bioenergetic metabolism resulting in impaired osteoclastogenesis. Treatment with the KDM5 inhibitor reduces osteoclastogenesis and energy metabolism of both female mice and human monocytes. Our report details a novel sex-dependent mechanism for bone homeostasis, connecting epigenetic regulation to osteoclast metabolism, and positions KDM5C as a target for future treatment of osteoporosis in women. One-Sentence Summary KDM5C, an X-linked epigenetic regulator, controls female bone homeostasis by promoting energy metabolism in osteoclasts.
Collapse
|
9
|
Tang WW, Bauer KM, Barba C, Ekiz HA, O’Connell RM. miR-aculous new avenues for cancer immunotherapy. Front Immunol 2022; 13:929677. [PMID: 36248881 PMCID: PMC9554277 DOI: 10.3389/fimmu.2022.929677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/18/2022] [Indexed: 01/25/2023] Open
Abstract
The rising toll of cancer globally necessitates ingenuity in early detection and therapy. In the last decade, the utilization of immune signatures and immune-based therapies has made significant progress in the clinic; however, clinical standards leave many current and future patients without options. Non-coding RNAs, specifically microRNAs, have been explored in pre-clinical contexts with tremendous success. MicroRNAs play indispensable roles in programming the interactions between immune and cancer cells, many of which are current or potential immunotherapy targets. MicroRNAs mechanistically control a network of target genes that can alter immune and cancer cell biology. These insights provide us with opportunities and tools that may complement and improve immunotherapies. In this review, we discuss immune and cancer cell-derived miRNAs that regulate cancer immunity and examine miRNAs as an integral part of cancer diagnosis, classification, and therapy.
Collapse
Affiliation(s)
- William W. Tang
- Divison of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, United States
- Hunstman Cancer Institute, University of Utah, Salt Lake City, UT, United States
| | - Kaylyn M. Bauer
- Divison of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, United States
- Hunstman Cancer Institute, University of Utah, Salt Lake City, UT, United States
| | - Cindy Barba
- Divison of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, United States
- Hunstman Cancer Institute, University of Utah, Salt Lake City, UT, United States
| | - Huseyin Atakan Ekiz
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, İzmir, Turkey
| | - Ryan M. O’Connell
- Divison of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT, United States
- Hunstman Cancer Institute, University of Utah, Salt Lake City, UT, United States
| |
Collapse
|
10
|
Lan X, Ding S, Zhang T, Yi Y, Li C, Jin W, Chen J, Liang K, Wang H, Jiang W. PCGF6 controls neuroectoderm specification of human pluripotent stem cells by activating SOX2 expression. Nat Commun 2022; 13:4601. [PMID: 35933409 PMCID: PMC9357003 DOI: 10.1038/s41467-022-32295-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 07/25/2022] [Indexed: 11/28/2022] Open
Abstract
Polycomb group (PcG) proteins are known to repress developmental genes during embryonic development and tissue homeostasis. Here, we report that PCGF6 controls neuroectoderm specification of human pluripotent stem cells (PSCs) by activating SOX2 gene. Human PSCs with PCGF6 depletion display impaired neuroectoderm differentiation coupled with increased mesendoderm outcomes. Transcriptome analysis reveals that de-repression of the WNT/β-catenin signaling pathway is responsible for the differentiation of PSC toward the mesendodermal lineage. Interestingly, PCGF6 and MYC directly interact and co-occupy a distal regulatory element of SOX2 to activate SOX2 expression, which likely accounts for the regulation in neuroectoderm differentiation. Supporting this notion, genomic deletion of the SOX2-regulatory element phenocopies the impaired neuroectoderm differentiation, while overexpressing SOX2 rescues the neuroectoderm phenotype caused by PCGF6-depletion. Together, our study reveals that PCGF6 can function as lineage switcher between mesendoderm and neuroectoderm in human PSCs by both suppression and activation mechanisms. Variant Polycomb complexes can have tissue-specific roles during development. Here they show that PCGF6 controls lineage-specification in human PSCs by promoting neuroectoderm differentiation and repressing mesendoderm differentiation via distinct downstream targets.
Collapse
Affiliation(s)
- Xianchun Lan
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Song Ding
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Tianzhe Zhang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Ying Yi
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Conghui Li
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Wenwen Jin
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Jian Chen
- Chinese Institute for Brain Research (Beijing), Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, 102206, Beijing, China
| | - Kaiwei Liang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Hengbin Wang
- Department of Internal Medicine, Division of Hematology, Oncology, and Palliative Care, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Wei Jiang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China. .,Human Genetics Resource Preservation Center of Wuhan University, Wuhan, China. .,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, China.
| |
Collapse
|
11
|
Umair M, Fazazi MR, Rangachari M. Biological Sex As a Critical Variable in CD4 + Effector T Cell Function in Preclinical Models of Multiple Sclerosis. Antioxid Redox Signal 2022; 37:135-149. [PMID: 34538129 PMCID: PMC9293683 DOI: 10.1089/ars.2021.0202] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Significance: T cells play a pivotal role in maintaining adaptive immune responses against pathogens. However, misdirected T cell responses against self-tissues may lead to autoimmune disease. Biological sex has profound effects on T cell function and is an important determinant of disease incidence and severity in autoimmune diseases such as multiple sclerosis (MS). Recent Advances: Many autoimmune diseases skew toward higher female incidence, including MS; however, it is has become increasingly more accepted that men living with MS are more prone to developing a progressive disease course and to having worsened disease outcomes. Critical Issues: In this review, we discuss what is known about the role of biological sex on T cell development and differentiation, examining evidence that male sex can augment T helper 17 (Th17) responses. Next, we outline what is known about sex differences in animal models of MS, and about the distinct roles played by sex hormones versus sex chromosomes in pathogenesis in these models. Finally, we discuss recent advances that examine the molecular basis for worsened disease outcomes in males, with a particular focus on the role played by Th17 cells in these models. Future Directions: Better understanding the role of biological sex in T cell function may pave the way to effective personalized treatment strategies in MS and other autoimmune diseases. Antioxid. Redox Signal. 37, 135-149.
Collapse
Affiliation(s)
- Muhammad Umair
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, Quebec, Canada
| | - Mohamed Reda Fazazi
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, Quebec, Canada
| | - Manu Rangachari
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, Quebec, Canada.,Faculty of Medicine, Université Laval, Quebec, Canada
| |
Collapse
|
12
|
Tanaskovic N, Dalsass M, Filipuzzi M, Ceccotti G, Verrecchia A, Nicoli P, Doni M, Olivero D, Pasini D, Koseki H, Sabò A, Bisso A, Amati B. Polycomb group ring finger protein 6 suppresses Myc-induced lymphomagenesis. Life Sci Alliance 2022; 5:5/8/e202101344. [PMID: 35422437 PMCID: PMC9012912 DOI: 10.26508/lsa.202101344] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 12/15/2022] Open
Abstract
Max dimerizes with Mga to form the repressive complex PRC1.6; another PRC1.6 subunit, Pcgf6, suppresses Myc-induced lymphomagenesis but, unexpectedly, does so in a Mga- and PRC1.6-independent manner. Max is an obligate dimerization partner for the Myc transcription factors and for several repressors, such as Mnt, Mxd1-4, and Mga, collectively thought to antagonize Myc function in transcription and oncogenesis. Mga, in particular, is part of the variant Polycomb group repressive complex PRC1.6. Here, we show that ablation of the distinct PRC1.6 subunit Pcgf6–but not Mga–accelerates Myc-induced lymphomagenesis in Eµ-myc transgenic mice. Unexpectedly, however, Pcgf6 loss shows no significant impact on transcriptional profiles, in neither pre-tumoral B-cells, nor lymphomas. Altogether, these data unravel an unforeseen, Mga- and PRC1.6-independent tumor suppressor activity of Pcgf6.
Collapse
Affiliation(s)
| | - Mattia Dalsass
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | | | | | | | - Paola Nicoli
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | - Mirko Doni
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | - Daniela Olivero
- Laboratorio Analisi Veterinarie BiEsseA, A Company of Scil Animal Care Company Srl, Milan, Italy
| | - Diego Pasini
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
- Department of Health Sciences, University of Milan, Milan, Italy
| | - Haruhiko Koseki
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Cellular and Molecular Medicine, Advanced Research Departments, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Arianna Sabò
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | - Andrea Bisso
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | - Bruno Amati
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| |
Collapse
|
13
|
Godoy-Tena G, Ballestar E. Epigenetics of Dendritic Cells in Tumor Immunology. Cancers (Basel) 2022; 14:cancers14051179. [PMID: 35267487 PMCID: PMC8909611 DOI: 10.3390/cancers14051179] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 12/14/2022] Open
Abstract
Dendritic cells (DCs) are professional antigen-presenting cells with the distinctive property of inducing the priming and differentiation of naïve CD4+ and CD8+ T cells into helper and cytotoxic effector T cells to develop efficient tumor-immune responses. DCs display pathogenic and tumorigenic antigens on their surface through major histocompatibility complexes to directly influence the differentiation of T cells. Cells in the tumor microenvironment (TME), including cancer cells and other immune-infiltrated cells, can lead DCs to acquire an immune-tolerogenic phenotype that facilitates tumor progression. Epigenetic alterations contribute to cancer development, not only by directly affecting cancer cells, but also by their fundamental role in the differentiation of DCs that acquire a tolerogenic phenotype that, in turn, suppresses T cell-mediated responses. In this review, we focus on the epigenetic regulation of DCs that have infiltrated the TME and discuss how knowledge of the epigenetic control of DCs can be used to improve DC-based vaccines for cancer immunotherapy.
Collapse
Affiliation(s)
- Gerard Godoy-Tena
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Barcelona, Spain;
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Barcelona, Spain;
- Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center (HSC), East China Normal University (ECNU), Shanghai 200241, China
- Correspondence:
| |
Collapse
|
14
|
Cho S, Dong J, Lu LF. Cell-intrinsic and -extrinsic roles of miRNAs in regulating T cell immunity. Immunol Rev 2021; 304:126-140. [PMID: 34549446 DOI: 10.1111/imr.13029] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 12/14/2022]
Abstract
T cells are crucial to generate an effective response against numerous invading microbial pathogens and play a pivotal role in tumor surveillance and elimination. However, unwanted T cell activation can also lead to deleterious immune-mediated inflammation and tissue damage. To ensure that an optimal T cell response can be established, each step, beginning from T cell development in the thymus to their activation and function in the periphery, is tightly regulated by many transcription factors and epigenetic regulators including microRNAs (miRNAs). Here, we first summarize recent progress in identifying major immune regulatory miRNAs in controlling the differentiation and function of distinct T cell subsets. Moreover, as emerging evidence has demonstrated that miRNAs can impact T cell immunity through targeting both immune- and non-immune cell populations that T cells closely interact with, the T cell-extrinsic role of miRNAs in regulating different aspects of T cell biology is also addressed. Finally, we discuss the complex nature of miRNA-mediated control of T cell immunity and highlight important questions that remain to be further investigated.
Collapse
Affiliation(s)
- Sunglim Cho
- Division of Biological Sciences, University of California, La Jolla, California, USA
| | - Jiayi Dong
- Division of Biological Sciences, University of California, La Jolla, California, USA
| | - Li-Fan Lu
- Division of Biological Sciences, University of California, La Jolla, California, USA.,Moores Cancer Center, University of California, La Jolla, California, USA.,Center for Microbiome Innovation, University of California, La Jolla, California, USA
| |
Collapse
|
15
|
Comparison of Histone H3K4me3 between IVF and ICSI Technologies and between Boy and Girl Offspring. Int J Mol Sci 2021; 22:ijms22168574. [PMID: 34445278 PMCID: PMC8395251 DOI: 10.3390/ijms22168574] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 01/04/2023] Open
Abstract
Epigenetics play a vital role in early embryo development. Offspring conceived via assisted reproductive technologies (ARTs) have a three times higher risk of epigenetic diseases than naturally conceived children. However, investigations into ART-associated placental histone modifications or sex-stratified analyses of ART-associated histone modifications remain limited. In the current study, we carried out immunohistochemistry, chip-sequence analysis, and a series of in vitro experiments. Our results demonstrated that placentas from intra-cytoplasmic sperm injection (ICSI), but not in vitro fertilization (IVF), showed global tri-methylated-histone-H3-lysine-4 (H3K4me3) alteration compared to those from natural conception. However, for acetylated-histone-H3-lysine-9 (H3K9ac) and acetylated-histone-H3-lysine-27 (H3K27ac), no significant differences between groups could be found. Further, sex -stratified analysis found that, compared with the same-gender newborn cord blood mononuclear cell (CBMC) from natural conceptions, CBMC from ICSI-boys presented more genes with differentially enriched H3K4me3 (n = 198) than those from ICSI-girls (n = 79), IVF-girls (n = 5), and IVF-boys (n = 2). We also found that varying oxygen conditions, RNA polymerase II subunit A (Polr2A), and lysine demethylase 5A (KDM5A) regulated H3K4me3. These findings revealed a difference between IVF and ICSI and a difference between boys and girls in H3K4me3 modification, providing greater insight into ART-associated epigenetic alteration.
Collapse
|
16
|
Doss PMIA, Umair M, Baillargeon J, Fazazi R, Fudge N, Akbar I, Yeola AP, Williams JB, Leclercq M, Joly-Beauparlant C, Beauchemin P, Ruda GF, Alpaugh M, Anderson AC, Brennan PE, Droit A, Lassmann H, Moore CS, Rangachari M. Male sex chromosomal complement exacerbates the pathogenicity of Th17 cells in a chronic model of central nervous system autoimmunity. Cell Rep 2021; 34:108833. [PMID: 33691111 DOI: 10.1016/j.celrep.2021.108833] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 12/13/2020] [Accepted: 02/16/2021] [Indexed: 12/13/2022] Open
Abstract
Sex differences in multiple sclerosis (MS) incidence and severity have long been recognized. However, the underlying cellular and molecular mechanisms for why male sex is associated with more aggressive disease remain poorly defined. Using a T cell adoptive transfer model of chronic experimental autoimmune encephalomyelitis (EAE), we find that male Th17 cells induce disease of increased severity relative to female Th17 cells, irrespective of whether transferred to male or female recipients. Throughout the disease course, a greater frequency of male Th17 cells produce IFNγ, a hallmark of pathogenic Th17 responses. Intriguingly, XY chromosomal complement increases the pathogenicity of male Th17 cells. An X-linked immune regulator, Jarid1c, is downregulated in pathogenic male murine Th17 cells, and functional experiments reveal that it represses the severity of Th17-mediated EAE. Furthermore, Jarid1c expression is downregulated in CD4+ T cells from MS-affected individuals. Our data indicate that male sex chromosomal complement critically regulates Th17 cell pathogenicity.
Collapse
Affiliation(s)
- Prenitha Mercy Ignatius Arokia Doss
- axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada
| | - Muhammad Umair
- axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada
| | - Joanie Baillargeon
- axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada
| | - Reda Fazazi
- axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada
| | - Neva Fudge
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL A1B 3V6, Canada
| | - Irshad Akbar
- axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada
| | - Asmita Pradeep Yeola
- axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada
| | - John B Williams
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL A1B 3V6, Canada
| | - Mickael Leclercq
- axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada
| | - Charles Joly-Beauparlant
- axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada
| | - Philippe Beauchemin
- Department of Neurology, CHU de Québec-Université Laval, Quebec City, QC G1V 4G2, Canada; Faculty of Medicine, Université Laval, 1050 ave de la Médecine, Quebec City, QC, Canada
| | - Gian Filipo Ruda
- Target Discovery Institute and NIHR, Oxford Biomedical Research Centre, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Melanie Alpaugh
- axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada
| | - Ana C Anderson
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham & Women's Hospital, 60 Fenwood Road, Boston, MA 02115, USA
| | - Paul E Brennan
- Target Discovery Institute and NIHR, Oxford Biomedical Research Centre, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Alzheimer's Research UK, Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Arnaud Droit
- axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; Faculty of Medicine, Université Laval, 1050 ave de la Médecine, Quebec City, QC, Canada
| | - Hans Lassmann
- Division of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, Vienna 1090, Austria
| | - Craig S Moore
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL A1B 3V6, Canada; Department of Neurology, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL A1B 3V6, Canada
| | - Manu Rangachari
- axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; Faculty of Medicine, Université Laval, 1050 ave de la Médecine, Quebec City, QC, Canada.
| |
Collapse
|
17
|
Boukhaled GM, Harding S, Brooks DG. Opposing Roles of Type I Interferons in Cancer Immunity. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2021; 16:167-198. [PMID: 33264572 DOI: 10.1146/annurev-pathol-031920-093932] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The immune system is tasked with identifying malignant cells to eliminate or prevent cancer spread. This involves a complex orchestration of many immune cell types that together recognize different aspects of tumor transformation and growth. In response, tumors have developed mechanisms to circumvent immune attack. Type I interferons (IFN-Is) are a class of proinflammatory cytokines produced in response to viruses and other environmental stressors. IFN-Is are also emerging as essential drivers of antitumor immunity, potently stimulating the ability of immune cells to eliminate tumor cells. However, a more complicated role for IFN-Is has arisen, as prolonged stimulation can promote feedback inhibitory mechanisms that contribute to immune exhaustion and other deleterious effects that directly or indirectly permit cancer cells to escape immune clearance. We review the fundamental and opposing functions of IFN-Is that modulate tumor growth and impact immune function and ultimately how these functions can be harnessed for the design of new cancer therapies.
Collapse
Affiliation(s)
- Giselle M Boukhaled
- Princess Margaret Cancer Centre, University Health Network Toronto, Ontario M5G 2M9, Canada; .,Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Shane Harding
- Princess Margaret Cancer Centre, University Health Network Toronto, Ontario M5G 2M9, Canada; .,Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Departments of Medical Biophysics and Radiation Oncology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - David G Brooks
- Princess Margaret Cancer Centre, University Health Network Toronto, Ontario M5G 2M9, Canada; .,Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| |
Collapse
|
18
|
Cai Q, He B, Xie H, Zhang P, Peng X, Zhang Y, Zhao Z, Wang X. Identification of a novel prognostic DNA methylation signature for lung adenocarcinoma based on consensus clustering method. Cancer Med 2020; 9:7488-7502. [PMID: 32860318 PMCID: PMC7571836 DOI: 10.1002/cam4.3343] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 07/06/2020] [Accepted: 07/12/2020] [Indexed: 12/22/2022] Open
Abstract
Abnormal DNA methylation persists throughout carcinogenesis and cancer development. Hence, gene promoter methylation may act as a prognostic tool and provide new potential therapeutic targets for patients with lung adenocarcinoma (LUAD). In this study, to explore prognostic methylation signature, data regarding DNA methylation and RNA-seq, and clinical data of patients with LUAD from the Cancer Genome Atlas database (TCGA) were downloaded. After data preprocessing, the methylation data were divided into training (N = 405) and test sets (N = 62). Then, patients in the training set were assigned to five subgroups based on their different methylation levels using the consensus clustering method. We comprehensively analyzed the survival information, methylation levels, and clinical variables, including American Joint Committee on Cancer (AJCC) stage, tumor-node-metastasis (TNM) staging, age, smoking history, and gender of these five groups. Subsequently, we identified a 16-CpG prognostic signature and constructed a prognostic model, which was verified in the test set. Further analyses showed stable prognostic performance in the stratified cohorts. In conclusion, the new predictive DNA methylation signature proposed in this study may be used as an independent biomarker to assess the overall survival of LUAD patients and provide bioinformatics information for development of targeted therapy.
Collapse
Affiliation(s)
- Qidong Cai
- Department of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
- Hunan Key Laboratory of Early Diagnosis and Precision TherapyDepartment of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Boxue He
- Department of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
- Hunan Key Laboratory of Early Diagnosis and Precision TherapyDepartment of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Hui Xie
- Department of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
- Hunan Key Laboratory of Early Diagnosis and Precision TherapyDepartment of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Pengfei Zhang
- Department of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
- Hunan Key Laboratory of Early Diagnosis and Precision TherapyDepartment of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Xiong Peng
- Department of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
- Hunan Key Laboratory of Early Diagnosis and Precision TherapyDepartment of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Yuqian Zhang
- Department of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
- Hunan Key Laboratory of Early Diagnosis and Precision TherapyDepartment of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Zhenyu Zhao
- Department of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
- Hunan Key Laboratory of Early Diagnosis and Precision TherapyDepartment of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Xiang Wang
- Department of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
- Hunan Key Laboratory of Early Diagnosis and Precision TherapyDepartment of Thoracic SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| |
Collapse
|
19
|
Lieberman NAP, Peddu V, Xie H, Shrestha L, Huang ML, Mears MC, Cajimat MN, Bente DA, Shi PY, Bovier F, Roychoudhury P, Jerome KR, Moscona A, Porotto M, Greninger AL. In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age. PLoS Biol 2020; 18:e3000849. [PMID: 32898168 PMCID: PMC7478592 DOI: 10.1371/journal.pbio.3000849] [Citation(s) in RCA: 192] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/05/2020] [Indexed: 01/12/2023] Open
Abstract
Despite limited genomic diversity, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown a wide range of clinical manifestations in different patient populations. The mechanisms behind these host differences are still unclear. Here, we examined host response gene expression across infection status, viral load, age, and sex among shotgun RNA sequencing profiles of nasopharyngeal (NP) swabs from 430 individuals with PCR-confirmed SARS-CoV-2 and 54 negative controls. SARS-CoV-2 induced a strong antiviral response with up-regulation of antiviral factors such as OAS1-3 and IFIT1-3 and T helper type 1 (Th1) chemokines CXCL9/10/11, as well as a reduction in transcription of ribosomal proteins. SARS-CoV-2 culture in human airway epithelial (HAE) cultures replicated the in vivo antiviral host response 7 days post infection, with no induction of interferon-stimulated genes after 3 days. Patient-matched longitudinal specimens (mean elapsed time = 6.3 days) demonstrated reduction in interferon-induced transcription, recovery of transcription of ribosomal proteins, and initiation of wound healing and humoral immune responses. Expression of interferon-responsive genes, including ACE2, increased as a function of viral load, while transcripts for B cell-specific proteins and neutrophil chemokines were elevated in patients with lower viral load. Older individuals had reduced expression of the Th1 chemokines CXCL9/10/11 and their cognate receptor CXCR3, as well as CD8A and granzyme B, suggesting deficiencies in trafficking and/or function of cytotoxic T cells and natural killer (NK) cells. Relative to females, males had reduced B cell-specific and NK cell-specific transcripts and an increase in inhibitors of nuclear factor kappa-B (NF-κB) signaling, possibly inappropriately throttling antiviral responses. Collectively, our data demonstrate that host responses to SARS-CoV-2 are dependent on viral load and infection time course, with observed differences due to age and sex that may contribute to disease severity.
Collapse
Affiliation(s)
- Nicole A. P. Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Vikas Peddu
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Lasata Shrestha
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Megan C. Mears
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Experimental Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Maria N. Cajimat
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Experimental Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Dennis A. Bente
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Pei-Yong Shi
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Francesca Bovier
- Center for Host–Pathogen Interaction, Columbia University Medical Center, New York, New York, United States of America
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Keith R. Jerome
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Anne Moscona
- Center for Host–Pathogen Interaction, Columbia University Medical Center, New York, New York, United States of America
- Department of Pediatrics, Columbia University Medical Center, New York, New York, United States of America
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, New York, United States of America
- Department of Physiology & Cellular Biophysics, Columbia University Medical Center, New York, New York, United States of America
| | - Matteo Porotto
- Center for Host–Pathogen Interaction, Columbia University Medical Center, New York, New York, United States of America
- Department of Pediatrics, Columbia University Medical Center, New York, New York, United States of America
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli,” Caserta, Italy
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| |
Collapse
|
20
|
Lieberman NAP, Peddu V, Xie H, Shrestha L, Huang ML, Mears MC, Cajimat MN, Bente DA, Shi PY, Bovier F, Roychoudhury P, Jerome KR, Moscona A, Porotto M, Greninger AL. In vivo antiviral host response to SARS-CoV-2 by viral load, sex, and age. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.22.165225. [PMID: 32607510 PMCID: PMC7325176 DOI: 10.1101/2020.06.22.165225] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Despite limited genomic diversity, SARS-CoV-2 has shown a wide range of clinical manifestations in different patient populations. The mechanisms behind these host differences are still unclear. Here, we examined host response gene expression across infection status, viral load, age, and sex among shotgun RNA-sequencing profiles of nasopharyngeal swabs from 430 individuals with PCR-confirmed SARS-CoV-2 and 54 negative controls. SARS-CoV-2 induced a strong antiviral response with upregulation of antiviral factors such as OAS1-3 and IFIT1-3 , and Th1 chemokines CXCL9/10/11 , as well as a reduction in transcription of ribosomal proteins. SARS-CoV-2 culture in human airway epithelial cultures replicated the in vivo antiviral host response. Patient-matched longitudinal specimens (mean elapsed time = 6.3 days) demonstrated reduction in interferon-induced transcription, recovery of transcription of ribosomal proteins, and initiation of wound healing and humoral immune responses. Expression of interferon-responsive genes, including ACE2 , increased as a function of viral load, while transcripts for B cell-specific proteins and neutrophil chemokines were elevated in patients with lower viral load. Older individuals had reduced expression of Th1 chemokines CXCL9/10/11 and their cognate receptor, CXCR3 , as well as CD8A and granzyme B, suggesting deficiencies in trafficking and/or function of cytotoxic T cells and natural killer (NK) cells. Relative to females, males had reduced B and NK cell-specific transcripts and an increase in inhibitors of NF-κB signaling, possibly inappropriately throttling antiviral responses. Collectively, our data demonstrate that host responses to SARS-CoV-2 are dependent on viral load and infection time course, with observed differences due to age and sex that may contribute to disease severity.
Collapse
|
21
|
Cordeiro B, Jeon P, Boukhaled GM, Corrado M, Lapohos O, Roy DG, Williams K, Jones RG, Gruenheid S, Sagan SM, Krawczyk CM. MicroRNA-9 Fine-Tunes Dendritic Cell Function by Suppressing Negative Regulators in a Cell-Type-Specific Manner. Cell Rep 2020; 31:107585. [PMID: 32375032 DOI: 10.1016/j.celrep.2020.107585] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 08/08/2019] [Accepted: 04/07/2020] [Indexed: 12/12/2022] Open
Abstract
Dendritic cells, cells of the innate immune system, are found in a steady state poised to respond to activating stimuli. Once stimulated, they rapidly undergo dynamic changes in gene expression to adopt an activated phenotype capable of stimulating immune responses. We find that the microRNA miR-9 is upregulated in both bone marrow-derived DCs and conventional DC1s but not in conventional DC2s following stimulation. miR-9 expression in BMDCs and conventional DC1s promotes enhanced DC activation and function, including the ability to stimulate T cell activation and control tumor growth. We find that miR-9 regulated the expression of several negative regulators of transcription, including the transcriptional repressor Polycomb group factor 6 (Pcgf6). These findings demonstrate that miR-9 facilitates the transition of DCs from steady state to mature state by regulating the expression of several negative regulators of DC function in a cell-type-specific manner.
Collapse
Affiliation(s)
- Brendan Cordeiro
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Peter Jeon
- Goodman Cancer Research Center, Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Giselle M Boukhaled
- Goodman Cancer Research Center, Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Mario Corrado
- Goodman Cancer Research Center, Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Orsolya Lapohos
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Dominic G Roy
- Goodman Cancer Research Center, Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Kelsey Williams
- Metabolic and Nutritional Programming Group, Van Andel Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA
| | - Russell G Jones
- Goodman Cancer Research Center, Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada; Metabolic and Nutritional Programming Group, Van Andel Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA
| | - Samantha Gruenheid
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Selena M Sagan
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Connie M Krawczyk
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3G 1Y6, Canada; Goodman Cancer Research Center, Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada; Metabolic and Nutritional Programming Group, Van Andel Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA.
| |
Collapse
|
22
|
Llabata P, Mitsuishi Y, Choi PS, Cai D, Francis JM, Torres-Diz M, Udeshi ND, Golomb L, Wu Z, Zhou J, Svinkina T, Aguilera-Jimenez E, Liu Y, Carr SA, Sanchez-Cespedes M, Meyerson M, Zhang X. Multi-Omics Analysis Identifies MGA as a Negative Regulator of the MYC Pathway in Lung Adenocarcinoma. Mol Cancer Res 2020; 18:574-584. [PMID: 31862696 PMCID: PMC7219472 DOI: 10.1158/1541-7786.mcr-19-0657] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/25/2019] [Accepted: 12/18/2019] [Indexed: 01/24/2023]
Abstract
Genomic analysis of lung adenocarcinomas has revealed that the MGA gene, which encodes a heterodimeric partner of the MYC-interacting protein MAX, is significantly mutated or deleted in lung adenocarcinomas. Most of the mutations are loss of function for MGA, suggesting that MGA may act as a tumor suppressor. Here, we characterize both the molecular and cellular role of MGA in lung adenocarcinomas and illustrate its functional relevance in the MYC pathway. Although MGA and MYC interact with the same binding partner, MAX, and recognize the same E-box DNA motif, we show that the molecular function of MGA appears to be antagonistic to that of MYC. Using mass spectrometry-based affinity proteomics, we demonstrate that MGA interacts with a noncanonical PCGF6-PRC1 complex containing MAX and E2F6 that is involved in gene repression, while MYC is not part of this MGA complex, in agreement with previous studies describing the interactomes of E2F6 and PCGF6. Chromatin immunoprecipitation-sequencing and RNA sequencing assays show that MGA binds to and represses genes that are bound and activated by MYC. In addition, we show that, as opposed to the MYC oncoprotein, MGA acts as a negative regulator for cancer cell proliferation. Our study defines a novel MYC/MAX/MGA pathway, in which MYC and MGA play opposite roles in protein interaction, transcriptional regulation, and cellular proliferation. IMPLICATIONS: This study expands the range of key cancer-associated genes whose dysregulation is functionally equivalent to MYC activation and places MYC within a linear pathway analogous to cell-cycle or receptor tyrosine kinase/RAS/RAF pathways in lung adenocarcinomas.
Collapse
Affiliation(s)
- Paula Llabata
- Cancer Epigenetics and Biology Program-PEBC (IDIBELL), Barcelona, Spain
| | - Yoichiro Mitsuishi
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Peter S Choi
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Diana Cai
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Joshua M Francis
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Manuel Torres-Diz
- Cancer Epigenetics and Biology Program-PEBC (IDIBELL), Barcelona, Spain
| | - Namrata D Udeshi
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Lior Golomb
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Zhong Wu
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Jin Zhou
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Tanya Svinkina
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Estrella Aguilera-Jimenez
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Yanli Liu
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Steven A Carr
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Matthew Meyerson
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts.
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Xiaoyang Zhang
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.
| |
Collapse
|
23
|
Chen Z, Li M, Ma K, Shang G, Liang J, Yin J, Luo J, Zhan C, Shi Y, Wang Q. Analysis of the clinicopathological characteristics, genetic phenotypes, and prognostic of pure mucinous adenocarcinoma. Cancer Med 2019; 9:517-529. [PMID: 31769218 PMCID: PMC6970056 DOI: 10.1002/cam4.2726] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 10/15/2019] [Accepted: 11/09/2019] [Indexed: 12/25/2022] Open
Abstract
Background Primary pure mucinous adenocarcinoma of the lung (PMA) is a rare subtype. However, correlations between clinicopathological features and genetic phenotypes with survival have not been described comprehensively. Methods Pure mucinous adenocarcinoma patient information collected from the Surveillance, Epidemiology, and End Results (SEER) database, the Department of Thoracic Surgery, Zhongshan Hospital, Fudan University (FDZSH), and the Cancer Genome Atlas (TCGA) were extracted, evaluated, and compared with other lung adenocarcinomas (LUAD) patient data. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to explore the functional importance of underlying molecular changes. Overall survival (OS) was evaluated with the Kaplan‐Meier method. Univariate and multivariate analysis through Cox proportional hazard regression identified risk factors that predicted OS, and the results were used to construct a nomogram to predict OS for PMA patients. Results Overall, 3622 patients, 41 patients, and 15 patients with PMA were identified from the SEER, FDZSH, and TCGA databases, respectively. There were 345 differentially expressed genes, 30 differentially mutated genes and 72 differentially methylated genes were identified between PMA and other LUAD samples. In the SEER database, PMA had a better prognosis compared to other LUAD. Compared with patients with other LUAD, patients with PMA exhibited unique clinicopathological features, including fewer grade III/IV tumors, less pleural invasion, more early‐stage cancer, and more lower lobe carcinomas. Multivariate analyses showed that age, race, T stage, N stage, surgery, and chemotherapy were independent risk factors. The nomogram had a calibration index of 0.724. Conclusions Our research identified unique clinicopathological characteristics and genetic phenotypes for PMA and other LUAD. The nomogram accurately predicted OS.
Collapse
Affiliation(s)
- Zhencong Chen
- Department of Thoracic of Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ming Li
- Department of Thoracic of Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ke Ma
- Department of Thoracic of Zhongshan Hospital, Fudan University, Shanghai, China
| | - Guoguo Shang
- Department of Pathology of Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiaqi Liang
- Department of Thoracic of Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiacheng Yin
- Department of Thoracic of Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jizhuang Luo
- Department of Thoracic of Zhongshan Hospital, Fudan University, Shanghai, China
| | - Cheng Zhan
- Department of Thoracic of Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yu Shi
- Department of Thoracic of Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qun Wang
- Department of Thoracic of Zhongshan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
24
|
Evolving Role of RING1 and YY1 Binding Protein in the Regulation of Germ-Cell-Specific Transcription. Genes (Basel) 2019; 10:genes10110941. [PMID: 31752312 PMCID: PMC6895862 DOI: 10.3390/genes10110941] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/07/2019] [Accepted: 11/14/2019] [Indexed: 12/11/2022] Open
Abstract
Separation of germline cells from somatic lineages is one of the earliest decisions of embryogenesis. Genes expressed in germline cells include apoptotic and meiotic factors, which are not transcribed in the soma normally, but a number of testis-specific genes are active in numerous cancer types. During germ cell development, germ-cell-specific genes can be regulated by specific transcription factors, retinoic acid signaling and multimeric protein complexes. Non-canonical polycomb repressive complexes, like ncPRC1.6, play a critical role in the regulation of the activity of germ-cell-specific genes. RING1 and YY1 binding protein (RYBP) is one of the core members of the ncPRC1.6. Surprisingly, the role of Rybp in germ cell differentiation has not been defined yet. This review is focusing on the possible role of Rybp in this process. By analyzing whole-genome transcriptome alterations of the Rybp-/- embryonic stem (ES) cells and correlating this data with experimentally identified binding sites of ncPRC1.6 subunits and retinoic acid receptors in ES cells, we propose a model how germ-cell-specific transcription can be governed by an RYBP centered regulatory network, underlining the possible role of RYBP in germ cell differentiation and tumorigenesis.
Collapse
|
25
|
Divide and conquer: two stem cell populations in squamous epithelia, reserves and the active duty forces. Int J Oral Sci 2019; 11:26. [PMID: 31451683 PMCID: PMC6802623 DOI: 10.1038/s41368-019-0061-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/09/2019] [Accepted: 07/22/2019] [Indexed: 12/22/2022] Open
Abstract
Stem cells are of great interest to the scientific community due to their potential role in regenerative and rejuvenative medicine. However, their role in the aging process and carcinogenesis remains unclear. Because DNA replication in stem cells may contribute to the background mutation rate and thereby to cancer, reducing proliferation and establishing a relatively quiescent stem cell compartment has been hypothesized to limit DNA replication-associated mutagenesis. On the other hand, as the main function of stem cells is to provide daughter cells to build and maintain tissues, the idea of a quiescent stem cell compartment appears counterintuitive. Intriguing observations in mice have led to the idea of separated stem cell compartments that consist of cells with different proliferative activity. Some epithelia of short-lived rodents appear to lack quiescent stem cells. Comparing stem cells of different species and different organs (comparative stem cell biology) may allow us to elucidate the evolutionary pressures such as the balance between cancer and longevity that govern stem cell biology (evolutionary stem cell biology). The oral mucosa and its stem cells are an exciting model system to explore the characteristics of quiescent stem cells that have eluded biologists for decades.
Collapse
|
26
|
Boukhaled GM, Corrado M, Guak H, Krawczyk CM. Chromatin Architecture as an Essential Determinant of Dendritic Cell Function. Front Immunol 2019; 10:1119. [PMID: 31214161 PMCID: PMC6557980 DOI: 10.3389/fimmu.2019.01119] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 05/02/2019] [Indexed: 12/18/2022] Open
Abstract
Epigenetics has widespread implications in a variety of cellular processes ranging from cell identity and specification, to cellular adaptation to environmental stimuli. While typically associated with heritable changes in gene expression, epigenetic mechanisms are now appreciated to regulate dynamic changes in gene expression—even in post-mitotic cells. Cells of the innate immune system, including dendritic cells (DC), rapidly integrate signals from their microenvironment and respond accordingly, undergoing massive changes in transcriptional programming. This dynamic transcriptional reprogramming relies on epigenetic changes mediated by numerous enzymes and their substrates. This review highlights our current understanding of epigenetic regulation of DC function. Epigenetic mechanisms contribute to the maintenance of the steady state and are important for precise responses to proinflammatory stimuli. Interdependence between epigenetic modifications and the delicate balance of metabolites present another layer of complexity. In addition, dynamic regulation of the expression of proteins that modify chromatin architecture in DCs significantly impacts DC function. Environmental factors, including inflammation, aging, chemicals, nutrients, and lipid mediators, are increasingly appreciated to affect the epigenome in DCs, and, in doing so, regulate host immunity. Our understanding of how epigenetic mechanisms regulate DC function is in its infancy, and it must be expanded in order to discern the mechanisms underlying the balance between health and disease states.
Collapse
Affiliation(s)
- Giselle M Boukhaled
- Department of Physiology, Goodman Cancer Research Center, McGill University, Montreal, QC, Canada
| | - Mario Corrado
- Department of Physiology, Goodman Cancer Research Center, McGill University, Montreal, QC, Canada
| | - Hannah Guak
- Department of Physiology, Goodman Cancer Research Center, McGill University, Montreal, QC, Canada
| | - Connie M Krawczyk
- Department of Physiology, Goodman Cancer Research Center, McGill University, Montreal, QC, Canada.,Center for Cancer and Cell Biology, Program in Metabolic and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, United States
| |
Collapse
|
27
|
Abstract
RING1 is an E3-ubiquitin ligase that is involved in epigenetic control of transcription during development. It is a component of the polycomb repressive complex 1, and its role in that complex is to ubiquitylate histone H2A. In a 13-year-old girl with syndromic neurodevelopmental disabilities, we identified a de novo mutation, RING1 p.R95Q, which alters a conserved arginine residue in the catalytic RING domain. In vitro assays demonstrated that the mutant RING1 retains capacity to catalyze ubiquitin chain formation, but is defective in its ability to ubiquitylate histone H2A in nucleosomes. Consistent with this in vitro effect, cells of the patient showed decreased monoubiquitylation of histone H2A. We modeled the mutant RING1 in Caenorhabditis elegans by editing the comparable amino acid change into spat-3, the suggested RING1 ortholog. Animals with either the missense mutation or complete knockout of spat-3 were defective in monoubiquitylation of histone H2A and had defects in neuronal migration and axon guidance. Relevant to our patient, animals heterozygous for either the missense or knockout allele also showed neuronal defects. Our results support three conclusions: mutation of RING1 is the likely cause of a human neurodevelopmental syndrome, mutation of RING1 can disrupt histone H2A ubiquitylation without disrupting RING1 catalytic activity, and the comparable mutation in C. elegans spat-3 both recapitulates the effects on histone H2A ubiquitylation and leads to neurodevelopmental abnormalities. This role for RING1 adds to our understanding of the importance of aberrant epigenetic effects as causes of human neurodevelopmental disorders.
Collapse
|
28
|
Metabolic Plasticity in Dendritic Cell Responses: Implications in Allergic Asthma. J Immunol Res 2017; 2017:5134760. [PMID: 29387732 PMCID: PMC5745769 DOI: 10.1155/2017/5134760] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/07/2017] [Indexed: 12/25/2022] Open
Abstract
Dendritic cells (DCs) are highly specialized in antigen presentation and play a pivotal role in the initiation, progression, and perpetuation of adaptive immune responses. Emerging immune pathways are being recognized increasingly for DCs and their subsets that differentially regulate T lymphocyte function based on the type and interactions with the antigen. However, these interactions not only alter the signaling process and DC function but also render metabolic plasticity. The current review focuses on the metabolic cues of DCs that coordinate DC activation and differentiation and discuss whether targeting these fundamental cellular processes have implications to control airway inflammation and adaptive immunity. Therefore, strategies using metabolism-based therapeutic manipulation of DC functions could be developed into novel treatments for airway inflammation and asthma.
Collapse
|
29
|
Ma EH, Bantug G, Griss T, Condotta S, Johnson RM, Samborska B, Mainolfi N, Suri V, Guak H, Balmer ML, Verway MJ, Raissi TC, Tsui H, Boukhaled G, Henriques da Costa S, Frezza C, Krawczyk CM, Friedman A, Manfredi M, Richer MJ, Hess C, Jones RG. Serine Is an Essential Metabolite for Effector T Cell Expansion. Cell Metab 2017; 25:345-357. [PMID: 28111214 DOI: 10.1016/j.cmet.2016.12.011] [Citation(s) in RCA: 367] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 11/13/2016] [Accepted: 12/19/2016] [Indexed: 10/20/2022]
Abstract
During immune challenge, T lymphocytes engage pathways of anabolic metabolism to support clonal expansion and the development of effector functions. Here we report a critical role for the non-essential amino acid serine in effector T cell responses. Upon activation, T cells upregulate enzymes of the serine, glycine, one-carbon (SGOC) metabolic network, and rapidly increase processing of serine into one-carbon metabolism. We show that extracellular serine is required for optimal T cell expansion even in glucose concentrations sufficient to support T cell activation, bioenergetics, and effector function. Restricting dietary serine impairs pathogen-driven expansion of T cells in vivo, without affecting overall immune cell homeostasis. Mechanistically, serine supplies glycine and one-carbon units for de novo nucleotide biosynthesis in proliferating T cells, and one-carbon units from formate can rescue T cells from serine deprivation. Our data implicate serine as a key immunometabolite that directly modulates adaptive immunity by controlling T cell proliferative capacity.
Collapse
Affiliation(s)
- Eric H Ma
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Glenn Bantug
- Department of Biomedicine, Immunobiology, University of Basel, 4031 Basel, Switzerland
| | - Takla Griss
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Stephanie Condotta
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3G 1Y6, Canada; Microbiome and Disease Tolerance Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Radia M Johnson
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada
| | - Bozena Samborska
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Nello Mainolfi
- Raze Therapeutics, 400 Technology Square, 10th Floor, Cambridge, MA 02139, USA
| | - Vipin Suri
- Raze Therapeutics, 400 Technology Square, 10th Floor, Cambridge, MA 02139, USA
| | - Hannah Guak
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Maria L Balmer
- Department of Biomedicine, Immunobiology, University of Basel, 4031 Basel, Switzerland
| | - Mark J Verway
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Thomas C Raissi
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Harmony Tsui
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Giselle Boukhaled
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | | | | | - Connie M Krawczyk
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Adam Friedman
- Raze Therapeutics, 400 Technology Square, 10th Floor, Cambridge, MA 02139, USA
| | - Mark Manfredi
- Raze Therapeutics, 400 Technology Square, 10th Floor, Cambridge, MA 02139, USA
| | - Martin J Richer
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3G 1Y6, Canada; Microbiome and Disease Tolerance Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Christoph Hess
- Department of Biomedicine, Immunobiology, University of Basel, 4031 Basel, Switzerland
| | - Russell G Jones
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada.
| |
Collapse
|