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Wang Z, Tan W, Li B, Chen J, Zhu J, Xu F, Tang F, Yoshida S, Zhou Y. LncRNA-MM2P regulates retinal neovascularization through M2 macrophage polarization. Exp Eye Res 2024; 248:110072. [PMID: 39241859 DOI: 10.1016/j.exer.2024.110072] [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: 04/13/2024] [Revised: 07/19/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
The study aims to investigate the effects and potential mechanisms of lncRNA-MM2P on retinal neovascularization in a mouse model of oxygen-induced retinopathy (OIR). The OIR model was established in C57BL/6J mice. RAW264.7 cell line and bone marrow-derived macrophages (BMDMs) from mice were used for in vitro studies. RT-qPCR was used to analyze the expressions of lncRNA and mRNAs. The protein expression levels were determined by western blotting. The size of avascular areas and neovascular tufts were assessed based on isolectin B4 immunofluorescence staining images. The human retinal endothelial cells (HRECs) were used to evaluate the proliferation, migration, and tube formation of endothelial cells. The expression of lncRNA-MM2P was significantly upregulated from P17 to P25 in OIR retinas. Knockdown of lncRNA-MM2P levels in vivo led to a significant reduction in the neovascular tufts and avascular areas in the retinas of OIR mice. Knockdown of lncRNA-MM2P levels in vitro suppressed the expression of M2 markers in macrophages. Moreover, we found a significant inhibition of avascular areas and neovascular tufts in OIR mice injected intravitreally with M2 macrophages treated by shRNA-MM2P. The cellular functions of proliferation, migration, and tube formation were significantly attenuated in HRECs cultured with a supernatant of shRNA-MM2P-treated M2 macrophages. Our results indicate that lncRNA-MM2P regulates retinal neovascularization by inducing M2 polarization of macrophages in OIR mice. Therefore, lncRNA-MM2P may be a potential molecular target for immunoregulation of retinal neovascularization.
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Affiliation(s)
- Zicong Wang
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Hunan Clinical Research Center of Ophthalmic Diseases, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Wei Tan
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Hunan Clinical Research Center of Ophthalmic Diseases, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Bingyan Li
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Hunan Clinical Research Center of Ophthalmic Diseases, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Junyu Chen
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Hunan Clinical Research Center of Ophthalmic Diseases, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Junye Zhu
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Hunan Clinical Research Center of Ophthalmic Diseases, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Fan Xu
- Department of Ophthalmology, The People's Hospital of Guangxi Zhuang Autonomous Region & Guangxi Key Laboratory of Eye Health, Nanning, Guangxi, 530021, China
| | - Fen Tang
- Department of Ophthalmology, The People's Hospital of Guangxi Zhuang Autonomous Region & Guangxi Key Laboratory of Eye Health, Nanning, Guangxi, 530021, China
| | - Shigeo Yoshida
- Department of Ophthalmology, Kurume University School of Medicine, Fukuoka, 830-0011, Japan
| | - Yedi Zhou
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China; Hunan Clinical Research Center of Ophthalmic Diseases, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China.
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Pietrogrande G, Shaker MR, Stednitz SJ, Soheilmoghaddam F, Aguado J, Morrison SD, Zambrano S, Tabassum T, Javed I, Cooper-White J, Davis TP, O'Brien TJ, Scott EK, Wolvetang EJ. Valproic acid-induced teratogenicity is driven by senescence and prevented by Rapamycin in human spinal cord and animal models. Mol Psychiatry 2024:10.1038/s41380-024-02732-0. [PMID: 39227432 DOI: 10.1038/s41380-024-02732-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 08/21/2024] [Accepted: 08/27/2024] [Indexed: 09/05/2024]
Abstract
Valproic acid (VPA) is an effective and widely used anti-seizure medication but is teratogenic when used during pregnancy, affecting brain and spinal cord development for reasons that remain largely unclear. Here we designed a genetic recombinase-based SOX10 reporter system in human pluripotent stem cells that enables tracking and lineage tracing of Neural Crest cells (NCCs) in a human organoid model of the developing neural tube. We found that VPA induces extensive cellular senescence and promotes mesenchymal differentiation of human NCCs. We next show that the clinically approved drug Rapamycin inhibits senescence and restores aberrant NCC differentiation trajectory after VPA exposure in human organoids and in developing zebrafish, highlighting the therapeutic promise of this approach. Finally, we identify the pioneer factor AP1 as a key element of this process. Collectively our data reveal cellular senescence as a central driver of VPA-associated neurodevelopmental teratogenicity and identifies a new pharmacological strategy for prevention. These results exemplify the power of genetically modified human stem cell-derived organoid models for drug discovery.
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Affiliation(s)
- Giovanni Pietrogrande
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia.
| | - Mohammed R Shaker
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Sarah J Stednitz
- Department of Anatomy & Physiology, University of Melbourne, Parkville, VIC, Australia
| | - Farhad Soheilmoghaddam
- School of Chemical Engineering, University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Julio Aguado
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Sean D Morrison
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Samuel Zambrano
- School of Medicine, Vita-Salute San Raffaele University, Milan, 20132, Italy
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Tahmina Tabassum
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Ibrahim Javed
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Justin Cooper-White
- School of Chemical Engineering, University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Thomas P Davis
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Terence J O'Brien
- Department of Neuroscience, The Central Clinical School, Alfred Health, Monash University, Melbourne, VIC, Australia
- The Departments of Medicine and Neurology, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
| | - Ethan K Scott
- Department of Anatomy & Physiology, University of Melbourne, Parkville, VIC, Australia
- Queensland Brain Institute, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Ernst J Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
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Li R, Wei R, Liu C, Zhang K, He S, Liu Z, Huang J, Tang Y, An Q, Lin L, Gan L, Zhao L, Zou X, Wang F, Ping Y, Ma Q. Heme oxygenase 1-mediated ferroptosis in Kupffer cells initiates liver injury during heat stroke. Acta Pharm Sin B 2024; 14:3983-4000. [PMID: 39309491 PMCID: PMC11413699 DOI: 10.1016/j.apsb.2024.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 03/05/2024] [Accepted: 03/15/2024] [Indexed: 09/25/2024] Open
Abstract
With the escalating prevalence of global heat waves, heat stroke has become a prominent health concern, leading to substantial liver damage. Unlike other forms of liver injury, heat stroke-induced damage is characterized by heat cytotoxicity and heightened inflammation, directly contributing to elevated mortality rates. While clinical assessments have identified elevated bilirubin levels as indicative of Kupffer cell dysfunction, their specific correlation with heat stroke liver injury remains unclear. Our hypothesis proposes the involvement of Kupffer cell ferroptosis during heat stroke, initiating IL-1β-mediated inflammation. Using single-cell RNA sequencing of murine macrophages, a distinct and highly susceptible Kupffer cell subtype, Clec4F+/CD206+, emerged, with heme oxygenase 1 (HMOX-1) playing a pivotal role. Mechanistically, heat-induced HMOX-1, regulated by early growth response factor 1, mediated ferroptosis in Kupffer cells, specifically in the Clec4F+/CD206+ subtype (KC2), activating phosphatidylinositol 4-kinase beta and promoting PI4P production. This cascade triggered NLRP3 inflammasome activation and maturation of IL-1β. These findings underscore the critical role of targeted therapy against HMOX-1 in ferroptosis within Kupffer cells, particularly in Clec4F+/CD206+ KCs. Such an approach has the potential to mitigate inflammation and alleviate acute liver injury in the context of heat stroke, offering a promising avenue for future therapeutic interventions.
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Affiliation(s)
- Ru Li
- The Seventh Affiliated Hospital, Southern Medical University, Foshan 528244, China
- Department of Biopharmaceutics, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510000, China
| | - Riqing Wei
- Department of Biopharmaceutics, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510000, China
| | - Chenxin Liu
- Department of Biopharmaceutics, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510000, China
| | - Keying Zhang
- Department of Biopharmaceutics, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510000, China
| | - Sixiao He
- Department of Biopharmaceutics, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510000, China
| | - Zhifeng Liu
- Medical Critical Care Medicine, General Hospital of Southern Theatre Command of PLA, Guangzhou 510000, China
- Guangdong Branch Center, National Clinical Research Center for Geriatric Diseases (Chinese PLA General Hospital), Guangzhou 510000, China
| | - Junhao Huang
- Department of Biopharmaceutics, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510000, China
| | - Youyong Tang
- Department of Biopharmaceutics, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510000, China
| | - Qiyuan An
- Department of Biopharmaceutics, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510000, China
| | - Ligen Lin
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macao 999078, China
| | - Lishe Gan
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, China
| | - Liying Zhao
- Department of General Surgery, Nanfang Hospital, the First School of Clinical Medicine, Southern Medical University, Guangzhou 510000, China
| | - Xiaoming Zou
- The Seventh Affiliated Hospital, Southern Medical University, Foshan 528244, China
| | - Fudi Wang
- The Fourth Affiliated Hospital, the First Affiliated Hospital, School of Public Health, Institute of Translational Medicine, Cancer Center, State Key Laboratory of Experimental Hematology, Zhejiang University School of Medicine, Hangzhou 310000, China
- The First Affiliated Hospital, the Second Affiliated Hospital, Basic Medical Sciences, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421200, China
| | - Yuan Ping
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310000, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 310000, China
| | - Qiang Ma
- Department of Biopharmaceutics, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510000, China
- Guangdong Provincial Key Laboratory of Immune Regulation and Immunotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510000, China
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4
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Lahnsteiner A, Ellmer V, Oberlercher A, Liutkeviciute Z, Schönauer E, Paulweber B, Aigner E, Risch A. G-quadruplex forming regions in GCK and TM6SF2 are targets for differential DNA methylation in metabolic disease and hepatocellular carcinoma patients. Sci Rep 2024; 14:20215. [PMID: 39215018 PMCID: PMC11364803 DOI: 10.1038/s41598-024-70749-0] [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: 03/16/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
The alarming increase in global rates of metabolic diseases (MetDs) and their association with cancer risk renders them a considerable burden on our society. The interplay of environmental and genetic factors in causing MetDs may be reflected in DNA methylation patterns, particularly at non-canonical (non-B) DNA structures, such as G-quadruplexes (G4s) or R-loops. To gain insight into the mechanisms of MetD progression, we focused on DNA methylation and functional analyses on intragenic regions of two MetD risk genes, the glucokinase (GCK) exon 7 and the transmembrane 6 superfamily 2 (TM6SF2) intron 2-exon 3 boundary, which harbor non-B DNA motifs for G4s and R-loops.Pyrosequencing of 148 blood samples from a nested cohort study revealed significant differential methylation in GCK and TM6SF2 in MetD patients versus healthy controls. Furthermore, these regions harbor hypervariable and differentially methylated CpGs also in hepatocellular carcinoma versus normal tissue samples from The Cancer Genome Atlas (TCGA). Permanganate/S1 nuclease footprinting with direct adapter ligation (PDAL-Seq), native polyacrylamide DNA gel electrophoresis and circular dichroism (CD) spectroscopy revealed the formation of G4 structures in these regions and demonstrated that their topology and stability is affected by DNA methylation. Detailed analyses including histone marks, chromatin conformation capture data, and luciferase reporter assays, highlighted the cell-type specific regulatory function of the target regions. Based on our analyses, we hypothesize that changes in DNA methylation lead to topological changes, especially in GCK exon 7, and cause the activation of alternative regulatory elements or potentially play a role in alternative splicing.Our analyses provide a new view on the mechanisms underlying the progression of MetDs and their link to hepatocellular carcinomas, unveiling non-B DNA structures as important key players already in early disease stages.
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Affiliation(s)
- Angelika Lahnsteiner
- Division of Cancer (Epi-)Genetics, Department of Biosciences and Medical Biology, Center for Tumor Biology and Immunology (CTBI), Paris Lodron University Salzburg, Hellbrunnerstraße 34, 5020, Salzburg, Austria.
- Cancer Cluster Salzburg, Salzburg, Austria.
| | - Victoria Ellmer
- Division of Cancer (Epi-)Genetics, Department of Biosciences and Medical Biology, Center for Tumor Biology and Immunology (CTBI), Paris Lodron University Salzburg, Hellbrunnerstraße 34, 5020, Salzburg, Austria
| | - Anna Oberlercher
- Division of Cancer (Epi-)Genetics, Department of Biosciences and Medical Biology, Center for Tumor Biology and Immunology (CTBI), Paris Lodron University Salzburg, Hellbrunnerstraße 34, 5020, Salzburg, Austria
| | - Zita Liutkeviciute
- Division of Cancer (Epi-)Genetics, Department of Biosciences and Medical Biology, Center for Tumor Biology and Immunology (CTBI), Paris Lodron University Salzburg, Hellbrunnerstraße 34, 5020, Salzburg, Austria
| | - Esther Schönauer
- Division of Structural Biology, Department of Biosciences and Medical Biology, Center for Tumor Biology and Immunology (CTBI), Paris Lodron University Salzburg, Salzburg, Austria
| | - Bernhard Paulweber
- First Department of Medicine, University Clinic Salzburg, Salzburg, Austria
| | - Elmar Aigner
- First Department of Medicine, University Clinic Salzburg, Salzburg, Austria
- Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Angela Risch
- Division of Cancer (Epi-)Genetics, Department of Biosciences and Medical Biology, Center for Tumor Biology and Immunology (CTBI), Paris Lodron University Salzburg, Hellbrunnerstraße 34, 5020, Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
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5
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Yeo H, Ahn SS, Ou S, Yun SJ, Lim Y, Koh D, Lee YH, Shin SY. The EGR1-Artemin Axis in Keratinocytes Enhances the Innervation of Epidermal Sensory Neurons during Skin Inflammation Induced by House Dust Mite Extract from Dermatophagoidesfarinae. J Invest Dermatol 2024; 144:1817-1828.e17. [PMID: 38302010 DOI: 10.1016/j.jid.2024.01.017] [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: 06/27/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 02/03/2024]
Abstract
Epidermal hyperinnervation is a critical feature of pruritus during skin inflammation. However, the mechanisms underlying epidermal hyperinnervation are unclear. This study investigates the role of the transcription factor EGR1 in epidermal innervation by utilizing wild-type (Egr1+/+) and Egr1-null (Egr1‒/‒) mice topically applied Dermatophagoides farinae extract from dust mite. Our findings revealed that Egr1‒/‒ mice exhibited reduced scratching behaviors and decreased density of epidermal innervation compared with Egr1+/+ mice. Furthermore, we identified artemin, a neurotrophic factor, as an EGR1 target responsible for Dermatophagoides farinae extract-induced hyperinnervation. It has been demonstrated that Dermatophagoides farinae extract stimulates toll-like receptors in keratinocytes. To elucidate the cellular mechanism, we stimulated keratinocytes with Pam3CSK4, a toll-like receptor 1/2 ligand. Pam3CSK4 triggered a toll-like receptor 1/2-mediated signaling cascade involving IRAK4, IκB kinase, MAPKs, ELK1, EGR1, and artemin, leading to increased neurite outgrowth and neuronal migration. In addition, increased expression of EGR1 and artemin was observed in the skin tissues of patients with atopic dermatitis. These findings highlight the significance of the EGR1-artemin axis in keratinocytes, promoting the process of epidermal innervation and suggesting it as a potential therapeutic target for alleviating itch and pain associated with house dust mite-induced skin inflammation.
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Affiliation(s)
- Hyunjin Yeo
- Department of Biological Sciences, Sang-huh College of Life Science, Konkuk University, Seoul, Republic of Korea
| | - Sung Shin Ahn
- Department of Biological Sciences, Sang-huh College of Life Science, Konkuk University, Seoul, Republic of Korea
| | - Sukjin Ou
- Department of Biological Sciences, Sang-huh College of Life Science, Konkuk University, Seoul, Republic of Korea
| | - Sook Jung Yun
- Department of Dermatology, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Yoongho Lim
- Division of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Dongsoo Koh
- Department of Applied Chemistry, Dongduk Women's University, Seoul, Republic of Korea
| | - Young Han Lee
- Department of Biological Sciences, Sang-huh College of Life Science, Konkuk University, Seoul, Republic of Korea; Cancer and Metabolism Institute, Konkuk University, Seoul, Republic of Korea
| | - Soon Young Shin
- Department of Biological Sciences, Sang-huh College of Life Science, Konkuk University, Seoul, Republic of Korea; Cancer and Metabolism Institute, Konkuk University, Seoul, Republic of Korea.
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Li Y, Xu C, Qian X, Wang G, Han C, Hua H, Dong M, Chen J, Yu H, Zhang R, Feng X, Yang Z, Pan Y. Myeloid PTEN loss affects the therapeutic response by promoting stress granule assembly and impairing phagocytosis by macrophages in breast cancer. Cell Death Discov 2024; 10:344. [PMID: 39080255 PMCID: PMC11289284 DOI: 10.1038/s41420-024-02094-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 06/25/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024] Open
Abstract
Breast cancer (BRCA) has become the most common type of cancer in women. Improving the therapeutic response remains a challenge. Phosphatase and tensin homologue deleted on chromosome 10 (PTEN) is a classic tumour suppressor with emerging new functions discovered in recent years, and myeloid PTEN loss has been reported to impair antitumour immunity. In this study, we revealed a novel mechanism by which myeloid PTEN potentially affects antitumour immunity in BRCA. We detected accelerated stress granule (SG) assembly under oxidative stress in PTEN-deficient bone marrow-derived macrophages (BMDMs) through the EGR1-promoted upregulation of TIAL1 transcription. PI3K/AKT/mTOR (PAM) pathway activation also promoted SG formation. ATP consumption during SG assembly in BMDMs impaired the phagocytic ability of 4T1 cells, potentially contributing to the disruption of antitumour immunity. In a BRCA neoadjuvant cohort, we observed a poorer response in myeloid PTENlow patients with G3BP1 aggregating as SGs in CD68+ cells, a finding that was consistent with the observation in our study that PTEN-deficient macrophages tended to more readily assemble SGs with impaired phagocytosis. Our results revealed the unconventional impact of SGs on BMDMs and might provide new perspectives on drug resistance and therapeutic strategies for the treatment of BRCA patients.
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Affiliation(s)
- Yan Li
- Department of Clinical Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Chao Xu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Xiaojun Qian
- Department of Clinical Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Gang Wang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Chaoqiang Han
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Hui Hua
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Menghao Dong
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Jian Chen
- Department of Clinical Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Haiyang Yu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Rutong Zhang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Xiaoxi Feng
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Zhenye Yang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.
| | - Yueyin Pan
- Department of Clinical Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.
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7
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Hyder U, Challa A, Thornton M, Nandu T, Kraus WL, D'Orso I. KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription. Nat Commun 2024; 15:5859. [PMID: 38997286 PMCID: PMC11245487 DOI: 10.1038/s41467-024-49905-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
Signal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction remain poorly understood. By combining an acute depletion system with several genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. Acute KAP1 loss triggers an increase in RNA polymerase II elongation kinetics during early stimulation time points. This elongation defect derails the normal progression through the transcriptional cycle during late stimulation time points, ultimately leading to decreased recruitment of the transcription apparatus for re-initiation thereby dampening IEGs transcriptional output. Collectively, KAP1 plays a counterintuitive role by negatively regulating transcription elongation to support full activation across multiple transcription cycles of genes critical for cell physiology and organismal functions.
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Affiliation(s)
- Usman Hyder
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ashwini Challa
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Micah Thornton
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Iván D'Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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8
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Moghe M, Kim SS, Guan M, Rait A, Pirollo KF, Harford JB, Chang EH. scL-2PAM: A Novel Countermeasure That Ameliorates Neuroinflammation and Neuronal Losses in Mice Exposed to an Anticholinesterase Organophosphate. Int J Mol Sci 2024; 25:7539. [PMID: 39062781 PMCID: PMC11276659 DOI: 10.3390/ijms25147539] [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: 05/26/2024] [Revised: 07/01/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
Due to their inhibition of acetylcholinesterase, organophosphates are among the most toxic of chemicals. Pralidoxime (a.k.a 2-PAM) is the only acetylcholinesterase reactivator approved in the U.S., but 2-PAM only poorly traverses the blood-brain barrier. Previously, we have demonstrated that scL-2PAM, a nanoformulation designed to enter the brain via receptor-mediated transcytosis, is superior to unencapsulated 2-PAM for reactivating brain acetylcholinesterase, ameliorating cholinergic crisis, and improving survival rates for paraoxon-exposed mice. Here, we employ histology and transcriptome analyses to assess the ability of scL-2PAM to prevent neurological sequelae including microglial activation, expression of inflammatory cytokines, and ultimately loss of neurons in mice surviving paraoxon exposures. Levels of the mRNA encoding chemokine ligand 2 (CCL2) were significantly upregulated after paraoxon exposures, with CCL2 mRNA levels in the brain correlating well with the intensity and duration of cholinergic symptoms. Our nanoformulation of 2-PAM was found to be superior to unencapsulated 2-PAM in reducing the levels of the CCL2 transcript. Moreover, brain histology revealed that scL-2PAM was more effective than unencapsulated 2-PAM in preventing microglial activation and the subsequent loss of neurons. Thus, scL-2PAM appears to be a new and improved countermeasure for reducing neuroinflammation and mitigating brain damage in survivors of organophosphate exposures.
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Affiliation(s)
- Manish Moghe
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA; (M.M.); (A.R.); (K.F.P.)
| | - Sang-Soo Kim
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA; (M.M.); (A.R.); (K.F.P.)
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC 20057, USA
- SynerGene Therapeutics, Inc., Potomac, MD 20854, USA;
| | - Miaoyin Guan
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA; (M.M.); (A.R.); (K.F.P.)
| | - Antonina Rait
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA; (M.M.); (A.R.); (K.F.P.)
| | - Kathleen F. Pirollo
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA; (M.M.); (A.R.); (K.F.P.)
| | | | - Esther H. Chang
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA; (M.M.); (A.R.); (K.F.P.)
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC 20057, USA
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9
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Wang Y, Shen Z, Mo S, Zhang H, Chen J, Zhu C, Lv S, Zhang D, Huang X, Gu Y, Yu X, Ding X, Zhang X. Crosstalk among proximal tubular cells, macrophages, and fibroblasts in acute kidney injury: single-cell profiling from the perspective of ferroptosis. Hum Cell 2024; 37:1039-1055. [PMID: 38753279 PMCID: PMC11194220 DOI: 10.1007/s13577-024-01072-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: 10/20/2023] [Accepted: 04/27/2024] [Indexed: 06/24/2024]
Abstract
The link between ferroptosis, a form of cell death mediated by iron and acute kidney injury (AKI) is recently gaining widespread attention. However, the mechanism of the crosstalk between cells in the pathogenesis and progression of acute kidney injury remains unexplored. In our research, we performed a non-negative matrix decomposition (NMF) algorithm on acute kidney injury single-cell RNA sequencing data based specifically focusing in ferroptosis-associated genes. Through a combination with pseudo-time analysis, cell-cell interaction analysis and SCENIC analysis, we discovered that proximal tubular cells, macrophages, and fibroblasts all showed associations with ferroptosis in different pathways and at various time. This involvement influenced cellular functions, enhancing cellular communication and activating multiple transcription factors. In addition, analyzing bulk expression profiles and marker genes of newly defined ferroptosis subtypes of cells, we have identified crucial cell subtypes, including Egr1 + PTC-C1, Jun + PTC-C3, Cxcl2 + Mac-C1 and Egr1 + Fib-C1. All these subtypes which were found in AKI mice kidneys and played significantly distinct roles from those of normal mice. Moreover, we verified the differential expression of Egr1, Jun, and Cxcl2 in the IRI mouse model and acute kidney injury human samples. Finally, our research presented a novel analysis of the crosstalk of proximal tubular cells, macrophages and fibroblasts in acute kidney injury targeting ferroptosis, therefore, contributing to better understanding the acute kidney injury pathogenesis, self-repairment and acute kidney injury-chronic kidney disease (AKI-CKD) progression.
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Affiliation(s)
- Yulin Wang
- Department of Nephrology, Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Medical Center of Kidney Disease, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Kidney and Blood Purification, No. 180 Fenglin Road, Shanghai, 200032, China
| | - Ziyan Shen
- Department of Nephrology, Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Medical Center of Kidney Disease, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Institute of Kidney and Dialysis, No. 180 Fenglin Road, Shanghai, 200032, China
| | - Shaocong Mo
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Han Zhang
- Department of Nephrology, Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Medical Center of Kidney Disease, No. 180 Fenglin Road, Shanghai, 200032, China
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Jing Chen
- Department of Nephrology, Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Medical Center of Kidney Disease, No. 180 Fenglin Road, Shanghai, 200032, China
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Cheng Zhu
- Department of Nephrology, Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Medical Center of Kidney Disease, No. 180 Fenglin Road, Shanghai, 200032, China
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Shiqi Lv
- Department of Nephrology, Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Medical Center of Kidney Disease, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Kidney and Blood Purification, No. 180 Fenglin Road, Shanghai, 200032, China
| | - Di Zhang
- Department of Nephrology, Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Medical Center of Kidney Disease, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Kidney and Blood Purification, No. 180 Fenglin Road, Shanghai, 200032, China
| | - Xinhui Huang
- Department of Nephrology, Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Medical Center of Kidney Disease, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Kidney and Blood Purification, No. 180 Fenglin Road, Shanghai, 200032, China
| | - Yulu Gu
- Division of Nephrology, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, 213100, Jiangsu, China
| | - Xixi Yu
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xiaoqiang Ding
- Department of Nephrology, Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Shanghai, 200032, China.
- Shanghai Medical Center of Kidney Disease, No. 180 Fenglin Road, Shanghai, 200032, China.
- Shanghai Key Laboratory of Kidney and Blood Purification, No. 180 Fenglin Road, Shanghai, 200032, China.
- Shanghai Institute of Kidney and Dialysis, No. 180 Fenglin Road, Shanghai, 200032, China.
| | - Xiaoyan Zhang
- Department of Nephrology, Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Shanghai, 200032, China.
- Shanghai Medical Center of Kidney Disease, No. 180 Fenglin Road, Shanghai, 200032, China.
- Shanghai Key Laboratory of Kidney and Blood Purification, No. 180 Fenglin Road, Shanghai, 200032, China.
- Shanghai Institute of Kidney and Dialysis, No. 180 Fenglin Road, Shanghai, 200032, China.
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10
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Edalat SG, Gerber R, Houtman M, Lückgen J, Teixeira RL, Palacios Cisneros MDP, Pfanner T, Kuret T, Ižanc N, Micheroli R, Polido-Pereira J, Saraiva F, Lingam S, Burki K, Burja B, Pauli C, Rotar Ž, Tomšič M, Čučnik S, Fonseca JE, Distler O, Calado Â, Romão VC, Ospelt C, Sodin-Semrl S, Robinson MD, Frank Bertoncelj M. Molecular maps of synovial cells in inflammatory arthritis using an optimized synovial tissue dissociation protocol. iScience 2024; 27:109707. [PMID: 38832018 PMCID: PMC11144743 DOI: 10.1016/j.isci.2024.109707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 02/25/2024] [Accepted: 04/06/2024] [Indexed: 06/05/2024] Open
Abstract
In this study, we optimized the dissociation of synovial tissue biopsies for single-cell omics studies and created a single-cell atlas of human synovium in inflammatory arthritis. The optimized protocol allowed consistent isolation of highly viable cells from tiny fresh synovial biopsies, minimizing the synovial biopsy drop-out rate. The synovium scRNA-seq atlas contained over 100,000 unsorted synovial cells from 25 synovial tissues affected by inflammatory arthritis, including 16 structural, 11 lymphoid, and 15 myeloid cell clusters. This synovial cell map expanded the diversity of synovial cell types/states, detected synovial neutrophils, and broadened synovial endothelial cell classification. We revealed tissue-resident macrophage subsets with proposed matrix-sensing (FOLR2+COLEC12high) and iron-recycling (LYVE1+SLC40A1+) activities and identified fibroblast subsets with proposed functions in cartilage breakdown (SOD2highSAA1+SAA2+SDC4+) and extracellular matrix remodeling (SERPINE1+COL5A3+LOXL2+). Our study offers an efficient synovium dissociation method and a reference scRNA-seq resource, that advances the current understanding of synovial cell heterogeneity in inflammatory arthritis.
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Affiliation(s)
- Sam G. Edalat
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich and University of Zurich, 8952 Schlieren, Switzerland
| | - Reto Gerber
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich and University of Zurich, 8952 Schlieren, Switzerland
- Department of Molecular Life Sciences and SIB, Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Miranda Houtman
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich and University of Zurich, 8952 Schlieren, Switzerland
| | | | - Rui Lourenço Teixeira
- Instituto de Medicina Molecular (iMM) João Lobo Antunes, Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
- Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
- Rheumatology Department, Hospital de Santa Maria, Lisbon Academic Medical Center, 1649-028 Lisbon, Portugal
| | | | | | - Tadeja Kuret
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich and University of Zurich, 8952 Schlieren, Switzerland
- Department of Rheumatology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Nadja Ižanc
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich and University of Zurich, 8952 Schlieren, Switzerland
- Department of Rheumatology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Raphael Micheroli
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich and University of Zurich, 8952 Schlieren, Switzerland
| | - Joaquim Polido-Pereira
- Instituto de Medicina Molecular (iMM) João Lobo Antunes, Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
- Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
- Rheumatology Department, Hospital de Santa Maria, Lisbon Academic Medical Center, 1649-028 Lisbon, Portugal
| | - Fernando Saraiva
- Instituto de Medicina Molecular (iMM) João Lobo Antunes, Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
- Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
- Rheumatology Department, Hospital de Santa Maria, Lisbon Academic Medical Center, 1649-028 Lisbon, Portugal
| | - Swathi Lingam
- Team PTA, BioMed X Institute, 69120 Heidelberg, Germany
| | - Kristina Burki
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich and University of Zurich, 8952 Schlieren, Switzerland
| | - Blaž Burja
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich and University of Zurich, 8952 Schlieren, Switzerland
- Department of Rheumatology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Chantal Pauli
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Žiga Rotar
- Department of Rheumatology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Matija Tomšič
- Department of Rheumatology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Saša Čučnik
- Department of Rheumatology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - João Eurico Fonseca
- Instituto de Medicina Molecular (iMM) João Lobo Antunes, Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
- Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
- Rheumatology Department, Hospital de Santa Maria, Lisbon Academic Medical Center, 1649-028 Lisbon, Portugal
| | - Oliver Distler
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich and University of Zurich, 8952 Schlieren, Switzerland
| | - Ângelo Calado
- Instituto de Medicina Molecular (iMM) João Lobo Antunes, Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
| | - Vasco C. Romão
- Instituto de Medicina Molecular (iMM) João Lobo Antunes, Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
- Faculdade de Medicina, University of Lisbon, 1649-028 Lisbon, Portugal
- Rheumatology Department, Hospital de Santa Maria, Lisbon Academic Medical Center, 1649-028 Lisbon, Portugal
| | - Caroline Ospelt
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich and University of Zurich, 8952 Schlieren, Switzerland
| | - Snežna Sodin-Semrl
- Department of Rheumatology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, 6000 Koper, Slovenia
| | - Mark D. Robinson
- Department of Molecular Life Sciences and SIB, Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Mojca Frank Bertoncelj
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich and University of Zurich, 8952 Schlieren, Switzerland
- Department of Molecular Life Sciences and SIB, Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
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11
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Ferreté-Bonastre AG, Martínez-Gallo M, Morante-Palacios O, Calvillo CL, Calafell-Segura J, Rodríguez-Ubreva J, Esteller M, Cortés-Hernández J, Ballestar E. Disease activity drives divergent epigenetic and transcriptomic reprogramming of monocyte subpopulations in systemic lupus erythematosus. Ann Rheum Dis 2024; 83:865-878. [PMID: 38413168 DOI: 10.1136/ard-2023-225433] [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: 12/17/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024]
Abstract
OBJECTIVES Systemic lupus erythematosus (SLE) is characterised by systemic inflammation involving various immune cell types. Monocytes, pivotal in promoting and regulating inflammation in SLE, differentiate from classic monocytes into intermediate and non-classic monocytes, assuming diverse roles and changing their proportions in inflammation. In this study, we investigated the epigenetic and transcriptomic profiles of these and novel monocyte subsets in SLE in relation to activity and progression. METHODS We obtained the DNA methylomes and transcriptomes of classic, intermediate, non-classic monocytes in patients with SLE (at first and follow-up visits) and healthy donors. We integrated these data with single-cell transcriptomics of SLE and healthy donors and interrogated their relationships with activity and progression. RESULTS In addition to shared DNA methylation and transcriptomic alterations associated with a strong interferon signature, we identified monocyte subset-specific alterations, especially in DNA methylation, which reflect an impact of SLE on monocyte differentiation. SLE classic monocytes exhibited a proinflammatory profile and were primed for macrophage differentiation. SLE non-classic monocytes displayed a T cell differentiation-related phenotype, with Th17-regulating features. Changes in monocyte proportions, DNA methylation and expression occurred in relation to disease activity and involved the STAT pathway. Integration of bulk with single-cell RNA sequencing datasets revealed disease activity-dependent expansion of SLE-specific monocyte subsets, further supported the interferon signature for classic monocytes, and associated intermediate and non-classic populations with exacerbated complement activation. CONCLUSIONS Disease activity in SLE drives a subversion of the epigenome and transcriptome programme in monocyte differentiation, impacting the function of different subsets and allowing to generate predictive methods for activity and progression.
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Affiliation(s)
| | - Mónica Martínez-Gallo
- Immunology Division, Vall d'Hebron University Hospital and Diagnostic Immunology Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | | | - Celia Lourdes Calvillo
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Josep Calafell-Segura
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
- Centro de Investigación Biomédica en Red Cancer (CIBERONC), Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain
| | - Josefina Cortés-Hernández
- Rheumatology Department, Hospital Vall d'Hebron and Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
- Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center (HSC), East China Normal University (ECNU), Shanghai, China
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12
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Hyder U, Challa A, Thornton M, Nandu T, Kraus WL, D’Orso I. KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.05.592422. [PMID: 38746145 PMCID: PMC11092767 DOI: 10.1101/2024.05.05.592422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Signal-induced transcriptional programs regulate critical biological processes through the precise spatiotemporal activation of Immediate Early Genes (IEGs); however, the mechanisms of transcription induction remain poorly understood. By combining an acute depletion system with high resolution genomics approaches to interrogate synchronized, temporal transcription, we reveal that KAP1/TRIM28 is a first responder that fulfills the temporal and heightened transcriptional demand of IEGs. Unexpectedly, acute KAP1 loss triggers an increase in RNA polymerase II elongation kinetics during early stimulation time points. This elongation defect derails the normal progression through the transcriptional cycle during late stimulation time points, ultimately leading to decreased recruitment of the transcription apparatus for re-initiation thereby dampening IEGs transcriptional output. Collectively, KAP1 plays a counterintuitive role by negatively regulating transcription elongation to support full activation across multiple transcription cycles of genes critical for cell physiology and organismal functions.
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Affiliation(s)
- Usman Hyder
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ashwini Challa
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Micah Thornton
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W. Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Iván D’Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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13
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Hashoul D, Saliba W, Broza YY, Haick H. Non-contact immunological signaling for highly-efficient regulation of the transcriptional map of human monocytes. Bioeng Transl Med 2024; 9:e10519. [PMID: 38818125 PMCID: PMC11135151 DOI: 10.1002/btm2.10519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/18/2023] [Accepted: 03/29/2023] [Indexed: 06/01/2024] Open
Abstract
The different immune system cells communicate and coordinate a response using a complex and evolved language of cytokines and chemokines. These cellular interactions carry out multiple functions in distinct cell types with numerous developmental outcomes. Despite the plethora of different cytokines and their cognate receptors, there is a restricted number of signal transducers and activators to control immune responses. Herein, we report on a new class of immunomodulatory signaling molecules based on volatile molecules (VMs, namely, volatile organic compounds [VOCs]), by which they can affect and/or control immune cell behavior and transcriptomic profile without any physical contact with other cells. The study demonstrates the role of VMs by analyzing non-contact cell communication between normal and cancerous lung cells and U937 monocytes, which are key players in the tumor microenvironment. Integrated transcriptome and proteome analyses showed the suggested regulatory role of VMs released from normal and cancer cells on neighboring monocytes in several molecular pathways, including PI3K/AKT, PPAR, and HIF-1. Presented data provide an initial platform for a new class of immunomodulatory molecules that can potentially mirror the genomic and proteomic profile of cells, thereby paving the way toward non-invasive immunomonitoring.
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Affiliation(s)
- Dina Hashoul
- Department of Chemical Engineering and Russell Berrie Nanotechnology InstituteTechnion ‐ Israel Institute of TechnologyHaifaIsrael
| | - Walaa Saliba
- Department of Chemical Engineering and Russell Berrie Nanotechnology InstituteTechnion ‐ Israel Institute of TechnologyHaifaIsrael
| | - Yoav Y. Broza
- Department of Chemical Engineering and Russell Berrie Nanotechnology InstituteTechnion ‐ Israel Institute of TechnologyHaifaIsrael
| | - Hossam Haick
- Department of Chemical Engineering and Russell Berrie Nanotechnology InstituteTechnion ‐ Israel Institute of TechnologyHaifaIsrael
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14
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Jiang S, Lu H, Pan Y, Yang A, Aikemu A, Li H, Hao R, Huang Q, Qi X, Tao Z, Wu Y, Quan C, Zhou G, Lu Y. Characterization of the distinct immune microenvironments between hepatocellular carcinoma and intrahepatic cholangiocarcinoma. Cancer Lett 2024; 588:216799. [PMID: 38479553 DOI: 10.1016/j.canlet.2024.216799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/06/2024] [Accepted: 03/05/2024] [Indexed: 03/18/2024]
Abstract
As two major types of primary liver cancers, the tumor immune microenvironment (TIME) of hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC) have been well studied separately. However, a systemic assessment of the similarities and differences between the TIME of HCC and ICC is still lacking. In this study, we pictured a landscape of combined TIME of HCC and ICC by sequencing and integrating 41 single-cell RNA-seq samples from four different tissue types of both malignancies. We found that T cells in HCC tumors generally exhibit higher levels of immunosuppression and exhaustion than those in ICC tumors. Myeloid cells in HCC and ICC tumors also exhibit distinct phenotypes and may serve as a key factor driving the differences between their TIMEs. Besides, we identified a cluster of EGR1+ macrophages specifically enriched in HCC tumors. Together, our study provides new insights into cellular composition, states and interactions in the TIMEs of HCC and ICC, which could pave the way for the development of future therapeutic targets for liver cancers.
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Affiliation(s)
- Siao Jiang
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, PR China; School of Life Science, University of Hebei, Baoding City, Hebei Province, PR China
| | - Hao Lu
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, PR China
| | - Yingwei Pan
- Department of Hepatobiliary Surgery, The First Medical Center of Chinese PLA General Hospital, Beijing, PR China
| | - Aiqing Yang
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, PR China
| | - Ainiwaer Aikemu
- College of Xinjiang Uyghur Medicine, Hetian City, Xinjiang Province, PR China
| | - Hao Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, PR China
| | - Rongjiao Hao
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, PR China; School of Life Science, University of Hebei, Baoding City, Hebei Province, PR China
| | - Qilin Huang
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, PR China; Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing City, Jiangsu Province, PR China
| | - Xin Qi
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, PR China; Medical College, Guizhou University, Guiyang City, Guizhou Province, PR China
| | - Zongjian Tao
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, PR China
| | - Yinglong Wu
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, PR China
| | - Cheng Quan
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, PR China.
| | - Gangqiao Zhou
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, PR China; School of Life Science, University of Hebei, Baoding City, Hebei Province, PR China; Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing City, Jiangsu Province, PR China; Medical College, Guizhou University, Guiyang City, Guizhou Province, PR China.
| | - Yiming Lu
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, PR China; School of Life Science, University of Hebei, Baoding City, Hebei Province, PR China.
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15
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Challagundla N, Shah D, Dalai SK, Agrawal-Rajput R. IFNγ insufficiency during mouse intra-vaginal Chlamydia trachomatis infection exacerbates alternative activation in macrophages with compromised CD40 functions. Int Immunopharmacol 2024; 131:111821. [PMID: 38484664 DOI: 10.1016/j.intimp.2024.111821] [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: 11/04/2023] [Revised: 03/03/2024] [Accepted: 03/05/2024] [Indexed: 04/10/2024]
Abstract
Chlamydia trachomatis (C.tr), an obligate intracellular pathogen, causes asymptomatic genital infections in women and is a leading cause of preventable blindness. We have developed in vivo mouse models of acute and chronic C. trachomatis genital infection to explore the significance of macrophage-directed response in mediating immune activation/suppression. Our findings reveal that during chronic and repeated C. trachomatis infections, Th1 response is abated while Treg response is enhanced. Additionally, an increase in exhaustion (PD1, CTLA4) and anergic (Klrg3, Tim3) T cell markers is observed during chronic infection. We have also observed that M2 macrophages with low CD40 expression promote Th2 and Treg differentiation leading to sustained C. trachomatis genital infection. Macrophages infected with C. trachomatis or treated with supernatant of infected epithelial cells drive them to an M2 phenotype. C. trachomatis infection prevents the increase in CD40 expression as observed in western blots and flow cytometric analysis. Insufficient IFNγ, as observed during chronic infection, leads to incomplete clearance of bacteria and poor immune activation. C. trachomatis decapacitates IFNγ responsiveness in macrophages via hampering IFNγRI and IFNγRII expression which can be correlated with poor expression of MHC-II, CD40, iNOS and NO release even following IFNγ supplementation. M2 macrophages during C. trachomatis infection express low CD40 rendering immunosuppressive, Th2 and Treg differentiation which could not be reverted even by IFNγ supplementation. The alternative macrophages also harbour high bacterial load and are poor responders to IFNγ, thus promoting immunosuppression. In summary, C. trachomatis modulates the innate immune cells, attenuating the anti-chlamydial functions of T cells in a manner that involves decreased CD40 expression on macrophages.
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Affiliation(s)
- Naveen Challagundla
- Immunology Lab, Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Gandhinagar, Gujarat, India.
| | - Dhruvi Shah
- Immunology Lab, Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Gandhinagar, Gujarat, India.
| | - Sarat K Dalai
- Institute of Science, Nirma University, S.G. Highway, Ahmedabad, Gujarat, India.
| | - Reena Agrawal-Rajput
- Immunology Lab, Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Gandhinagar, Gujarat, India.
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16
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Wang H, Tian Q, Zhang R, Du Q, Hu J, Gao T, Gao S, Fan K, Cheng X, Yan S, Zheng G, Dong H. Nobiletin alleviates atherosclerosis by inhibiting lipid uptake via the PPARG/CD36 pathway. Lipids Health Dis 2024; 23:76. [PMID: 38468335 PMCID: PMC10926578 DOI: 10.1186/s12944-024-02049-5] [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: 12/01/2023] [Accepted: 02/18/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND Atherosclerosis (AS) is a persistent inflammatory condition triggered and exacerbated by several factors including lipid accumulation, endothelial dysfunction and macrophages infiltration. Nobiletin (NOB) has been reported to alleviate atherosclerosis; however, the underlying mechanism remains incompletely understood. METHODS This study involved comprehensive bioinformatic analysis, including multidatabase target prediction; GO and KEGG enrichment analyses for function and pathway exploration; DeepSite and AutoDock for drug binding site prediction; and CIBERSORT for immune cell involvement. In addition, target intervention was verified via cell scratch assays, oil red O staining, ELISA, flow cytometry, qRT‒PCR and Western blotting. In addition, by establishing a mouse model of AS, it was demonstrated that NOB attenuated lipid accumulation and the extent of atherosclerotic lesions. RESULTS (1) Altogether, 141 potentially targetable genes were identified through which NOB could intervene in atherosclerosis. (2) Lipid and atherosclerosis, fluid shear stress and atherosclerosis may be the dominant pathways and potential mechanisms. (3) ALB, AKT1, CASP3 and 7 other genes were identified as the top 10 target genes. (4) Six genes, including PPARG, MMP9, SRC and 3 other genes, were related to the M0 fraction. (5) CD36 and PPARG were upregulated in atherosclerosis samples compared to the normal control. (6) By inhibiting lipid uptake in RAW264.7 cells, NOB prevents the formation of foam cell. (7) In RAW264.7 cells, the inhibitory effect of oxidized low-density lipoprotein on foam cells formation and lipid accumulation was closely associated with the PPARG signaling pathway. (8) In vivo validation showed that NOB significantly attenuated intra-arterial lipid accumulation and macrophage infiltration and reduced CD36 expression. CONCLUSIONS Nobiletin alleviates atherosclerosis by inhibiting lipid uptake via the PPARG/CD36 pathway.
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Affiliation(s)
- Heng Wang
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Qinqin Tian
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ruijing Zhang
- Department of Nephrology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Qiujing Du
- Jiangyin People's Hospital, Wuxi, Jiangsu, China
- Shanxi Bethune Hospital, Third Hospital of Shanxi Medical University, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, Shanxi, China
| | - Jie Hu
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Tingting Gao
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Siqi Gao
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Keyi Fan
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xing Cheng
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Sheng Yan
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Guoping Zheng
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China.
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia.
| | - Honglin Dong
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China.
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17
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Wang W, Jiang J, Yang C, Meng X, Gao L, Yuan Y, Lei T, Ding P, Yin R, Li Q. A critical time window for leukapheresis product transportation to manufacture clinical-grade dendritic cells with optimal anti-tumor activities. Cytotherapy 2024; 26:210-220. [PMID: 38127032 DOI: 10.1016/j.jcyt.2023.12.003] [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: 05/15/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND AIMS Dendritic cell (DC)-based immunotherapy is a promising approach to treat cancer. However, key aspects governing the reproducible manufacturing of high-quality DC remain incompletely defined. Here, we show that the time window between leukapheresis and DC manufacturing is critical. METHODS Transcriptomic profiling by RNA-seq was used to unbiasedly characterize cellular states during each step of DC manufacturing process, and functional assays were used to determine the anti-tumor activities of DC. RESULTS During preclinical development of a DC-based cytotherapy platform, CUD-002 (NCT05270720), we found that DC quality varied among different batches, even though commonly used DC maturation markers CD80, CD83 and CD86 were indistinguishable. Multivariate analysis indicated that DC quality was negatively associated with the shipping time from the leukapheresis site to the manufacturing center. To investigate the potential effect of shipping time, we stored leukapheresis materials from three donors for 0, 1, 2 or 3 days before DC manufacturing. For each step, we carried out RNA-seq analysis to unbiasedly characterize cellular states. Integrated bioinformatic analyses indicated that longer storage time reduced the expression of several transcription factors to attenuate interferon pathways. CONCLUSIONS Consistently, we found that 3-day storage of leukapheresis materials significantly lowered the efficiency to generate DC but also impaired DC responses to inflammatory signals, resulting in inferior antigen-presentation and cytotoxic T-cell activities. Thus, we recommend using leukapheresis materials within 48 h to manufacture therapeutic DCs.
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Affiliation(s)
- Wenxiang Wang
- Departments of Obstetrics & Gynecology and Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Center of Growth, Metabolism and Aging, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, Sichuan, China; Xinxiang Central Hospital, The Fourth Clinical College of Xinxiang Medical University, Xinxiang, Henan, China
| | - Jinfeng Jiang
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, China
| | - Chao Yang
- Departments of Obstetrics & Gynecology and Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Center of Growth, Metabolism and Aging, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, Sichuan, China
| | - Xiangjun Meng
- Division of Cell Manufacturing, Sichuan Cunde Therapeutics, Chengdu, Sichuan, China
| | - Li Gao
- Division of Cell Manufacturing, Sichuan Cunde Therapeutics, Chengdu, Sichuan, China
| | - Yuan Yuan
- Division of Cell Manufacturing, Sichuan Cunde Therapeutics, Chengdu, Sichuan, China
| | - Tingjun Lei
- Division of Cell Manufacturing, Sichuan Cunde Therapeutics, Chengdu, Sichuan, China
| | - Ping Ding
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, China.
| | - Rutie Yin
- Departments of Obstetrics & Gynecology and Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Center of Growth, Metabolism and Aging, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, Sichuan, China.
| | - Qintong Li
- Departments of Obstetrics & Gynecology and Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Center of Growth, Metabolism and Aging, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, Sichuan, China.
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18
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Yang R, Wang X, Liu H, Chen J, Tan C, Chen H, Wang X. Egr-1 is a key regulator of the blood-brain barrier damage induced by meningitic Escherichia coli. Cell Commun Signal 2024; 22:44. [PMID: 38233877 PMCID: PMC10795328 DOI: 10.1186/s12964-024-01488-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/11/2024] [Indexed: 01/19/2024] Open
Abstract
Bacterial meningitis remains a leading cause of infection-related mortality worldwide. Although Escherichia coli (E. coli) is the most common etiology of neonatal meningitis, the underlying mechanisms governing bacterial blood-brain barrier (BBB) disruption during infection remain elusive. We observed that infection of human brain microvascular endothelial cells with meningitic E. coli triggers the activation of early growth response 1 (Egr-1), a host transcriptional activator. Through integrated chromatin immunoprecipitation sequencing and transcriptome analysis, we identified Egr-1 as a crucial regulator for maintaining BBB integrity. Mechanistically, Egr-1 induced cytoskeletal changes and downregulated tight junction protein expression by directly targeting VEGFA, PDGFB, and ANGPTL4, resulting in increased BBB permeability. Meanwhile, Egr-1 also served as a master regulator in the initiation of neuroinflammatory response during meningitic E. coli infection. Our findings support an Egr-1-dependent mechanism of BBB disruption by meningitic E. coli, highlighting a promising therapeutic target for bacterial meningitis.
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Affiliation(s)
- Ruicheng Yang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Xinyi Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Hulin Liu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Jiaqi Chen
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Chen Tan
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology of the People's Republic of China, Wuhan, 430070, China
| | - Huanchun Chen
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, 430070, China
- International Research Center for Animal Disease, Ministry of Science and Technology of the People's Republic of China, Wuhan, 430070, China
| | - Xiangru Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China.
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, 430070, China.
- International Research Center for Animal Disease, Ministry of Science and Technology of the People's Republic of China, Wuhan, 430070, China.
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19
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Rocks D, Purisic E, Gallo EF, Greally JM, Suzuki M, Kundakovic M. Egr1 is a sex-specific regulator of neuronal chromatin, synaptic plasticity, and behaviour. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572697. [PMID: 38187614 PMCID: PMC10769422 DOI: 10.1101/2023.12.20.572697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Sex differences are found in brain structure and function across species, and across brain disorders in humans1-3. The major source of brain sex differences is differential secretion of steroid hormones from the gonads across the lifespan4. Specifically, ovarian hormones oestrogens and progesterone are known to dynamically change structure and function of the adult female brain, having a major impact on psychiatric risk5-7. However, due to limited molecular studies in female rodents8, very little is still known about molecular drivers of female-specific brain and behavioural plasticity. Here we show that overexpressing Egr1, a candidate oestrous cycle-dependent transcription factor9, induces sex-specific changes in ventral hippocampal neuronal chromatin, gene expression, and synaptic plasticity, along with hippocampus-dependent behaviours. Importantly, Egr1 overexpression mimics the high-oestrogenic phase of the oestrous cycle, and affects behaviours in ovarian hormone-depleted females but not in males. We demonstrate that Egr1 opens neuronal chromatin directly across the sexes, although with limited genomic overlap. Our study not only reveals the first sex-specific chromatin regulator in the brain, but also provides functional evidence that this sex-specific gene regulation drives neuronal gene expression, synaptic plasticity, and anxiety- and depression-related behaviour. Our study exemplifies an innovative sex-based approach to studying neuronal gene regulation1 in order to understand sex-specific synaptic and behavioural plasticity and inform novel brain disease treatments.
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Affiliation(s)
- Devin Rocks
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - Eric Purisic
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - Eduardo F. Gallo
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - John M. Greally
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Masako Suzuki
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Nutrition, Texas A&M University, College Station, TX, USA
| | - Marija Kundakovic
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
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20
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Leary JR, Bacher R. Interpretable trajectory inference with single-cell Linear Adaptive Negative-binomial Expression (scLANE) testing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572477. [PMID: 38187622 PMCID: PMC10769309 DOI: 10.1101/2023.12.19.572477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The rapid proliferation of trajectory inference methods for single-cell RNA-seq data has allowed researchers to investigate complex biological processes by examining underlying gene expression dynamics. After estimating a latent cell ordering, statistical models are used to determine which genes exhibit changes in expression that are significantly associated with progression through the biological trajectory. While a few techniques for performing trajectory differential expression exist, most rely on the flexibility of generalized additive models in order to account for the inherent nonlinearity of changes in gene expression. As such, the results can be difficult to interpret, and biological conclusions often rest on subjective visual inspections of the most dynamic genes. To address this challenge, we propose scLANE testing, which is built around an interpretable generalized linear model and handles nonlinearity with basis splines chosen empirically for each gene. In addition, extensions to estimating equations and mixed models allow for reliable trajectory testing under complex experimental designs. After validating the accuracy of scLANE under several different simulation scenarios, we apply it to a set of diverse biological datasets and display its ability to provide novel biological information when used downstream of both pseudotime and RNA velocity estimation methods.
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Affiliation(s)
- Jack R. Leary
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32610, USA
| | - Rhonda Bacher
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32610, USA
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21
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Cantu A, Gutierrez MC, Dong X, Leek C, Anguera M, Lingappan K. Modulation of recovery from neonatal hyperoxic lung injury by sex as a biological variable. Redox Biol 2023; 68:102933. [PMID: 38661305 PMCID: PMC10628633 DOI: 10.1016/j.redox.2023.102933] [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: 08/09/2023] [Revised: 10/07/2023] [Accepted: 10/11/2023] [Indexed: 04/26/2024] Open
Abstract
Recovery from lung injury during the neonatal period requires the orchestration of many biological pathways. The modulation of such pathways can drive the developing lung towards proper repair or persistent maldevelopment that can lead to a disease phenotype. Sex as a biological variable can regulate these pathways differently in the male and female lung exposed to neonatal hyperoxia. In this study, we assessed the contribution of cellular diversity in the male and female neonatal lung following injury. Our objective was to investigate sex and cell-type specific transcriptional changes that drive repair or persistent injury in the neonatal lung and delineate the alterations in the immune-endothelial cell communication networks using single cell RNA sequencing (sc-RNAseq) in a murine model of hyperoxic injury. We generated transcriptional profiles of >55,000 cells isolated from the lungs of postnatal day 1 (PND 1; pre-exposure), PND 7, and PND 21neonatal male and female C57BL/6 mice exposed to 95 % FiO2 between PND 1-5 (saccular stage of lung development). We show the presence of sex-based differences in the transcriptional states of lung endothelial and immune cells at PND 1 and PND 21. Furthermore, we demonstrate that biological sex significantly influences the response to injury, with a greater number of differentially expressed genes showing sex-specific patterns than those shared between male and female lungs. Pseudotime trajectory analysis highlighted genes needed for lung development that were altered by hyperoxia. Finally, we show intercellular communication between endothelial and immune cells at saccular and alveolar stages of lung development with sex-based biases in the crosstalk and identify novel ligand-receptor pairs. Our findings provide valuable insights into the cell diversity, transcriptional state, developmental trajectory, and cell-cell communication underlying neonatal lung injury, with implications for understanding lung development and possible therapeutic interventions while highlighting the crucial role of sex as a biological variable.
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Affiliation(s)
- Abiud Cantu
- Department of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Xiaoyu Dong
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Connor Leek
- Department of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Montserrat Anguera
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Krithika Lingappan
- Department of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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22
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Zhang M, Lv L, Luo H, Cai H, Yu L, Jiang Y, Gao F, Tong W, Li L, Li G, Zhou Y, Tong G, Liu C. The CD2v protein of African swine fever virus inhibits macrophage migration and inflammatory cytokines expression by downregulating EGR1 expression through dampening ERK1/2 activity. Vet Res 2023; 54:106. [PMID: 37968713 PMCID: PMC10648359 DOI: 10.1186/s13567-023-01239-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/12/2023] [Indexed: 11/17/2023] Open
Abstract
African swine fever virus (ASFV) is a highly contagious and deadly virus that leads to high mortality rates in domestic swine populations. Although the envelope protein CD2v of ASFV has been implicated in immunomodulation, the molecular mechanisms underlying CD2v-mediated immunoregulation remain unclear. In this study, we generated a stable CD2v-expressing porcine macrophage (PAM-CD2v) line and investigated the CD2v-dependent transcriptomic landscape using RNA-seq. GO terms enrichment analysis and gene set enrichment analysis revealed that CD2v predominantly affected the organization and assembly process of the extracellular matrix. Wound healing and Transwell assays showed that CD2v inhibited swine macrophage migration. Further investigation revealed a significant decrease in the expression of transcription factor early growth response 1 (EGR1) through inhibiting the activity of extracellular signal-regulated kinase 1 and 2 (ERK1/2). Notably, EGR1 knockout in swine macrophages restricted cell migration, whereas EGR1 overexpression in PAM-CD2v restored the ability of macrophage migration, suggesting that CD2v inhibits swine macrophage motility by downregulating EGR1 expression. Furthermore, we performed chromatin immunoprecipitation and sequencing for EGR1 and the histone mark H3K27 acetylation (H3K27ac), and we found that EGR1 co-localized with the activated histone modification H3K27ac neighboring the transcriptional start sites. Further analysis indicated that EGR1 and H3K27ac co-occupy the promoter regions of cell locomotion-related genes. Finally, by treating various derivatives of swine macrophages with lipopolysaccharides, we showed that depletion of EGR1 decreased the expression of inflammatory cytokines including TNFα, IL1α, IL1β, IL6, and IL8, which play essential roles in inflammation and host immune response. Collectively, our results provide new insights into the immunomodulatory mechanism of ASFV CD2v.
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Affiliation(s)
- Min Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Lilei Lv
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Huaye Luo
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Hongming Cai
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lingxue Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Yifeng Jiang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Fei Gao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Wu Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Liwei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Guoxin Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Yanjun Zhou
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China.
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China.
| | - Changlong Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, 225009, China.
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23
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Maria NI, Papoin J, Raparia C, Sun Z, Josselsohn R, Lu A, Katerji H, Syeda MM, Polsky D, Paulson R, Kalfa T, Barnes BJ, Zhang W, Blanc L, Davidson A. Human TLR8 induces inflammatory bone marrow erythromyeloblastic islands and anemia in SLE-prone mice. Life Sci Alliance 2023; 6:e202302241. [PMID: 37495396 PMCID: PMC10372407 DOI: 10.26508/lsa.202302241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/28/2023] Open
Abstract
Anemia commonly occurs in systemic lupus erythematosus, a disease characterized by innate immune activation by nucleic acids. Overactivation of cytoplasmic sensors by self-DNA or RNA can cause erythroid cell death, while sparing other hematopoietic cell lineages. Whereas chronic inflammation is involved in this mechanism, less is known about the impact of systemic lupus erythematosus on the BM erythropoietic niche. We discovered that expression of the endosomal ssRNA sensor human TLR8 induces fatal anemia in Sle1.Yaa lupus mice. We observed that anemia was associated with a decrease in erythromyeloblastic islands and a block in differentiation at the CFU-E to proerythroblast transition in the BM. Single-cell RNAseq analyses of isolated BM erythromyeloblastic islands from human TLR8-expressing mice revealed that genes associated with essential central macrophage functions including adhesion and provision of nutrients were down-regulated. Although compensatory stress erythropoiesis occurred in the spleen, red blood cell half-life decreased because of hemophagocytosis. These data implicate the endosomal RNA sensor TLR8 as an additional innate receptor whose overactivation causes acquired failure of erythropoiesis via myeloid cell dysregulation.
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Affiliation(s)
- Naomi I Maria
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Donald and Barbara Zucker School of Medicine at Northwell Health, Hempstead, NY, USA
| | - Julien Papoin
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Donald and Barbara Zucker School of Medicine at Northwell Health, Hempstead, NY, USA
| | - Chirag Raparia
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Donald and Barbara Zucker School of Medicine at Northwell Health, Hempstead, NY, USA
| | - Zeguo Sun
- Department of Medicine, Mount Sinai Medical Center, New York, NY, USA
| | - Rachel Josselsohn
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - Ailing Lu
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - Hani Katerji
- Department of Pathology, University of Rochester, Rochester, NY, USA
| | - Mahrukh M Syeda
- The Ronald O. Perelman Department of Dermatology, New York University Grossman School of Medicine, New York, NY, USA
| | - David Polsky
- The Ronald O. Perelman Department of Dermatology, New York University Grossman School of Medicine, New York, NY, USA
| | - Robert Paulson
- Department of Veterinary and Biomedical Sciences, Penn State College of Agricultural Sciences, University Park, PA, USA
| | - Theodosia Kalfa
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Betsy J Barnes
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Donald and Barbara Zucker School of Medicine at Northwell Health, Hempstead, NY, USA
| | - Weijia Zhang
- Department of Medicine, Mount Sinai Medical Center, New York, NY, USA
| | - Lionel Blanc
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Donald and Barbara Zucker School of Medicine at Northwell Health, Hempstead, NY, USA
| | - Anne Davidson
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Donald and Barbara Zucker School of Medicine at Northwell Health, Hempstead, NY, USA
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Shin S, Choi EJ, Moon SW, Lee SB, Chung YJ, Lee SH. Leprosy-specific subsets of macrophages and Schwann cells identified by single-cell RNA-sequencing. Pathol Res Pract 2023; 250:154821. [PMID: 37757621 DOI: 10.1016/j.prp.2023.154821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/10/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023]
Abstract
In Mycobacterium leprae (M. leprae)-infection, inflammatory cells' subsets and dynamics as well as the interactions with Schwann cells have remained elusive. We investigated individual cells in M. leprae-inoculated nude mice by single-cell RNA-sequencing (scRNA-seq). For macrophages, we dissected two M1-like subsets and five M2-like subsets, where lipid-associated signatures were pervasive in both M1-like and M2-like subsets. There were four macrophage trajectories showing: (i) pro-inflammatory (M1), (ii) lipid metabolism-related (M2), (iii) anti-inflammatory (M2), and (iv) interferon-stimulated gene-related (M2) fates. They displayed early divergence without ever rejoining along the paths, suggesting simultaneous or continuous stimuli for macrophage activation in leprosy. The scRNA-seq predicted Schwann cell-macrophage interactions (Notch1-Jag1, Plxnb1-Sema4d interactions). An immature Schwann cell subset showing Tfap2a expression was identified, indicating Schwann cell dedifferentiation in leprosy tissues. Expressions of Notch1, Jag1, Plxnb1, Sema4d, and Tfap2a were validated in mouse or human leprosy tissues by immunohistochemistry. We identified both pro-inflammatory and inflammation-resolution signatures, where lipid-associated signatures were pervasive to the macrophages, representing leprosy-specific macrophage states for prolonged and repeated episodes of inflammation and resolution. Our study identified refined molecular states and interactions of macrophages and Schwann cells, suggesting novel insights into the pathogenesis of unhealed inflammation with neuropathy and potential therapeutic targets for leprosy.
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Affiliation(s)
- Sun Shin
- Departments of Microbiology, College of Medicine, The Catholic University of Korea, Republic of Korea; Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Eun Ji Choi
- Departments of Pathology, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Seong Won Moon
- Departments of Pathology, College of Medicine, The Catholic University of Korea, Republic of Korea; Departments of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Seong-Beom Lee
- Institute of Hansen's Disease, College of Medicine, The Catholic University of Korea, Republic of Korea; Departments of Pathology, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Yeun-Jun Chung
- Departments of Microbiology, College of Medicine, The Catholic University of Korea, Republic of Korea; Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Republic of Korea; Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Republic of Korea.
| | - Sug Hyung Lee
- Departments of Pathology, College of Medicine, The Catholic University of Korea, Republic of Korea; Departments of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Republic of Korea; Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Republic of Korea.
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Wang C, Zhang X, Chen R, Zhu X, Lian N. EGR1 mediates METTL3/m 6A/CHI3L1 to promote osteoclastogenesis in osteoporosis. Genomics 2023; 115:110696. [PMID: 37558013 DOI: 10.1016/j.ygeno.2023.110696] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/27/2023] [Accepted: 08/06/2023] [Indexed: 08/11/2023]
Abstract
OBJECTIVE To investigate EGR1-mediated METTL3/m6A/CHI3L1 axis in osteoporosis. METHODS Ovariectomy (OVX) was performed on mice to induce osteoporosis, followed by μ-CT scanning of femurs, histological staining, immunohistochemistry analysis of MMP9 and NFATc1, and ELISA of serum BGP, ALP, Ca, and CTXI. The isolated mouse bone marrow mononuclear macrophages (BMMs) were differentiated into osteoclasts under cytokine stimulation. TRAP staining was performed to quantify osteoclasts. The levels of Nfatc1, c-Fos, Acp5, and Ctsk in osteoclasts, m6A level, and the relationships among EGR1, METTL3, and CHI3L1 were analyzed. RESULTS The EGR1/METTL3/CHI3L1 levels and m6A level were upregulated in osteoporotic mice and the derived BMMs. EGR1 was a transcription factor of METTL3. METTL3 promoted the post-transcriptional regulation of CHI3L1 by increasing m6A methylation. EGR1 downregulation reduced BMMs-differentiated osteoclasts and alleviated OVX-induced osteoporosis by regulating the METTL3/m6A/CHI3L1 axis. CONCLUSION EGR1 promotes METTL3 transcription and increases m6A-modified CHI3L1 level, thereby stimulating osteoclast differentiation and osteoporosis development.
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Affiliation(s)
- Changsheng Wang
- Department of Spinal Surgery, First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, PR China.
| | - Xiaobo Zhang
- Department of Spinal Surgery, First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, PR China
| | - Rongsheng Chen
- Department of Spinal Surgery, First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, PR China
| | - Xitian Zhu
- Department of Spinal Surgery, First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, PR China
| | - Nancheng Lian
- Department of Spinal Surgery, First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, PR China
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Shen L, Yin H, Sun L, Zhang Z, Jin Y, Cao S, Fu Q, Fan C, Bao C, Lu L, Zhan Y, Xu X, Chen X, Yan Q. Iguratimod attenuated fibrosis in systemic sclerosis via targeting early growth response 1 expression. Arthritis Res Ther 2023; 25:151. [PMID: 37596660 PMCID: PMC10439582 DOI: 10.1186/s13075-023-03135-2] [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: 02/01/2023] [Accepted: 08/02/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND The early growth response 1 (EGR1) is a central transcription factor involved in systemic sclerosis (SSc) pathogenesis. Iguratimod is a synthesized anti-rheumatic disease-modifying drug, which shows drastic inhibition to EGR1 expression in B cells. This study is aiming to investigate the anti-fibrotic effect of iguratimod in SSc. METHODS EGR1 was detected by immunofluorescence staining real-time PCR or western blot. Iguratimod was applied in EGR1 overexpressed or knockdown human dermal fibroblast, bleomycin pre-treated mice, tight skin 1 mice, and SSc skin xenografts. RNA sequencing was performed in cultured fibroblast and xenografts to identify the iguratimod regulated genes. RESULTS EGR1 overexpressed predominantly in non-immune cells of SSc patients. Iguratimod reduced EGR1 expression in fibroblasts and neutralized changes of EGR1 response genes regulated by TGFβ. The extracellular matrix (ECM) production and activation of fibroblasts were attenuated by iguratimod while EGR1 overexpression reversed this effect of iguratimod. Iguratimod ameliorated the skin fibrosis induced by bleomycin and hypodermal fibrosis in TSK-1 mice. Decreasing in the collagen content as well as the density of EGR1 or TGFβ positive fibroblasts of skin xenografts from naïve SSc patients was observed after local treatment of iguratimod. CONCLUSION Targeting EGR1 expression is a probable underlying mechanism for the anti-fibrotic effect of iguratimod.
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Affiliation(s)
- Lichong Shen
- Department of Rheumatology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200001, China
| | - Hanlin Yin
- Department of Rheumatology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200001, China
| | - Li Sun
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Zhiliang Zhang
- Department of Plastic Surgery, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200001, China
| | - Yuyang Jin
- Department of Rheumatology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200001, China
| | - Shan Cao
- Department of Rheumatology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200001, China
| | - Qiong Fu
- Department of Rheumatology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200001, China
| | - Chaofan Fan
- Department of Rheumatology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200001, China
| | - Chunde Bao
- Department of Rheumatology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200001, China
| | - Liangjing Lu
- Department of Rheumatology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200001, China
| | - Yifan Zhan
- Department of Drug Discovery, Shanghai Huaota Biopharm, Shanghai, 201203, China
| | - Xiaojiang Xu
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, USA.
| | - Xiaoxiang Chen
- Department of Rheumatology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200001, China.
- Department of Rheumatology, Nantong First People's Hospital, Affiliated Hospital 2 of Nantong Universuty, Nantong Hospital of Renji Hospital Affiliated to Shanghai Jiao Tong Universuty School of Medicine, Nantong, 226006, China.
| | - Qingran Yan
- Department of Rheumatology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200001, China.
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Cantu A, Gutierrez MC, Dong X, Leek C, Anguera M, Lingappan K. Modulation of Recovery from Neonatal Hyperoxic Lung Injury by Sex as a Biological Variable. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.09.552532. [PMID: 37609288 PMCID: PMC10441379 DOI: 10.1101/2023.08.09.552532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Recovery from lung injury during the neonatal period requires the orchestration of many biological pathways. The modulation of such pathways can drive the developing lung towards proper repair or persistent maldevelopment that can lead to a disease phenotype. Sex as a biological variable can regulate these pathways differently in the male and female lung exposed to neonatal hyperoxia. In this study, we assessed the contribution of cellular diversity in the male and female neonatal lung following injury. Our objective was to investigate sex and cell-type specific transcriptional changes that drive repair or persistent injury in the neonatal lung and delineate the alterations in the immune-endothelial cell communication networks using single cell RNA sequencing (sc-RNAseq) in a murine model of hyperoxic injury. We generated transcriptional profiles of >55,000 cells isolated from the lungs of postnatal day 1 (PND 1) and postnatal day 21 (PND 21) neonatal male and female C57BL/6 mice exposed to 95% FiO 2 between PND 1-5 (saccular stage of lung development). We show the presence of sex-based differences in the transcriptional states of lung endothelial and immune cells at PND 1 and PND 21. Furthermore, we demonstrate that biological sex significantly influences the response to injury, with a greater number of differentially expressed genes showing sex-specific patterns than those shared between male and female lungs. Pseudotime trajectory analysis highlighted genes needed for lung development that were altered by hyperoxia. Finally, we show intercellular communication between endothelial and immune cells at saccular and alveolar stages of lung development with sex-based biases in the crosstalk and identify novel ligand-receptor pairs. Our findings provide valuable insights into the cell diversity, transcriptional state, developmental trajectory, and cell-cell communication underlying neonatal lung injury, with implications for understanding lung development and possible therapeutic interventions while highlighting the crucial role of sex as a biological variable.
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Zou K, Zeng Z. Role of early growth response 1 in inflammation-associated lung diseases. Am J Physiol Lung Cell Mol Physiol 2023; 325:L143-L154. [PMID: 37401387 PMCID: PMC10511164 DOI: 10.1152/ajplung.00413.2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/03/2023] [Accepted: 06/27/2023] [Indexed: 07/05/2023] Open
Abstract
Early growth response 1 (EGR1), which is involved in cell proliferation, differentiation, apoptosis, adhesion, migration, and immune and inflammatory responses, is a zinc finger transcription factor. EGR1 is a member of the EGR family of early response genes and can be activated by external stimuli such as neurotransmitters, cytokines, hormones, endotoxins, hypoxia, and oxidative stress. EGR1 expression is upregulated during several common respiratory diseases, such as acute lung injury/acute respiratory distress syndrome, chronic obstructive pulmonary disease, asthma, pneumonia, and novel coronavirus disease 2019. Inflammatory response is the common pathophysiological basis of these common respiratory diseases. EGR1 is highly expressed early in the disease, amplifying pathological signals from the extracellular environment and driving disease progression. Thus, EGR1 may be a target for early and effective intervention in these inflammation-associated lung diseases.
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Affiliation(s)
- Kang Zou
- Department of Critical Care Medicine, The First Affiliated Hospital of Gannan Medical College, Ganzhou, People's Republic of China
- Department of Critical Care Medicine, Medical Center of Anesthesiology and Pain, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Zhenguo Zeng
- Department of Critical Care Medicine, Medical Center of Anesthesiology and Pain, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
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Chowdary AR, Maerz T, Henn D, Hankenson KD, Pagani CA, Marini S, Gallagher K, Aguilar CA, Tower RJ, Levi B. Macrophage-mediated PDGF Activation Correlates With Regenerative Outcomes Following Musculoskeletal Trauma. Ann Surg 2023; 278:e349-e359. [PMID: 36111847 PMCID: PMC10014496 DOI: 10.1097/sla.0000000000005704] [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] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Our objective was to identify macrophage subpopulations and gene signatures associated with regenerative or fibrotic healing across different musculoskeletal injury types. BACKGROUND Subpopulations of macrophages are hypothesized to fine tune the immune response after damage, promoting either normal regenerative, or aberrant fibrotic healing. METHODS Mouse single-cell RNA sequencing data before and after injury were assembled from models of musculoskeletal injury, including regenerative and fibrotic mouse volumetric muscle loss (VML), regenerative digit tip amputation, and fibrotic heterotopic ossification. R packages Harmony , MacSpectrum , and Seurat were used for data integration, analysis, and visualizations. RESULTS There was a substantial overlap between macrophages from the regenerative VML (2 mm injury) and regenerative bone models, as well as a separate overlap between the fibrotic VML (3 mm injury) and fibrotic bone (heterotopic ossification) models. We identified 2 fibrotic-like (FL 1 and FL 2) along with 3 regenerative-like (RL 1, RL 2, and RL 3) subpopulations of macrophages, each of which was transcriptionally distinct. We found that regenerative and fibrotic conditions had similar compositions of proinflammatory and anti-inflammatory macrophages, suggesting that macrophage polarization state did not correlate with healing outcomes. Receptor/ligand analysis of macrophage-to-mesenchymal progenitor cell crosstalk showed enhanced transforming growth factor β in fibrotic conditions and enhanced platelet-derived growth factor signaling in regenerative conditions. CONCLUSION Characterization of macrophage subtypes could be used to predict fibrotic responses following injury and provide a therapeutic target to tune the healing microenvironment towards more regenerative conditions.
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Affiliation(s)
- Ashish R. Chowdary
- Center for Organogenesis and Trauma, Department of Surgery, University of Texas Southwestern, Dallas, TX, 75235
| | - Tristan Maerz
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dominic Henn
- Department of Plastic Surgery, University of Texas Southwestern, Dallas, TX, 75235
| | - Kurt D. Hankenson
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chase A. Pagani
- Center for Organogenesis and Trauma, Department of Surgery, University of Texas Southwestern, Dallas, TX, 75235
| | - Simone Marini
- Department of Epidemiology, University of Florida, Gainesville, FL 32611, USA
| | - Katherine Gallagher
- Section of Vascular Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carlos A. Aguilar
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robert J. Tower
- Center for Organogenesis and Trauma, Department of Surgery, University of Texas Southwestern, Dallas, TX, 75235
| | - Benjamin Levi
- Center for Organogenesis and Trauma, Department of Surgery, University of Texas Southwestern, Dallas, TX, 75235
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Lu H, Ma J, Li Y, Zhang J, An Y, Du W, Cai X. Bioinformatic and systems biology approach revealing the shared genes and molecular mechanisms between COVID-19 and non-alcoholic hepatitis. Front Mol Biosci 2023; 10:1164220. [PMID: 37405258 PMCID: PMC10315682 DOI: 10.3389/fmolb.2023.1164220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/01/2023] [Indexed: 07/06/2023] Open
Abstract
Introduction: Coronavirus disease 2019 (COVID-19) has become a global pandemic and poses a serious threat to human health. Many studies have shown that pre-existing nonalcoholic steatohepatitis (NASH) can worsen the clinical symptoms in patients suffering from COVID-19. However, the potential molecular mechanisms between NASH and COVID-19 remain unclear. To this end, key molecules and pathways between COVID-19 and NASH were herein explored by bioinformatic analysis. Methods: The common differentially expressed genes (DEGs) between NASH and COVID-19 were obtained by differential gene analysis. Enrichment analysis and protein-protein interaction (PPI) network analysis were carried out using the obtained common DEGs. The key modules and hub genes in PPI network were obtained by using the plug-in of Cytoscape software. Subsequently, the hub genes were verified using datasets of NASH (GSE180882) and COVID-19 (GSE150316), and further evaluated by principal component analysis (PCA) and receiver operating characteristic (ROC). Finally, the verified hub genes were analyzed by single-sample gene set enrichment analysis (ssGSEA) and NetworkAnalyst was used for the analysis of transcription factor (TF)-gene interactions, TF-microRNAs (miRNA) coregulatory network, and Protein-chemical Interactions. Results: A total of 120 DEGs between NASH and COVID-19 datasets were obtained, and the PPI network was constructed. Two key modules were obtained via the PPI network, and enrichment analysis of the key modules revealed the common association between NASH and COVID-19. In total, 16 hub genes were obtained by five algorithms, and six of them, namely, Kruppel-like factor 6 (KLF6), early growth response 1 (EGR1), growth arrest and DNA-damage-inducible 45 beta (GADD45B), JUNB, FOS, and FOS-like antigen 1 (FOSL1) were confirmed to be closely related to NASH and COVID-19. Finally, the relationship between hub genes and related pathways was analyzed, and the interaction network of six hub genes was constructed with TFs, miRNAs, and compounds. Conclusion: This study identified six hub genes related to COVID-19 and NASH, providing a new perspective for disease diagnosis and drug development.
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Guo Y, Miao X, Sun X, Li L, Zhou A, Zhu X, Xu Y, Wang Q, Li Z, Fan Z. Zinc finger transcription factor Egf1 promotes non-alcoholic fatty liver disease. JHEP Rep 2023; 5:100724. [PMID: 37234276 PMCID: PMC10206499 DOI: 10.1016/j.jhepr.2023.100724] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/19/2023] [Accepted: 02/22/2023] [Indexed: 05/27/2023] Open
Abstract
Background & Aims Non-alcoholic fatty liver disease (NAFLD) contributes to the global epidemic of metabolic syndrome and is considered a prelude to end-stage liver diseases such as cirrhosis and hepatocellular carcinoma. During NAFLD pathogenesis, hepatic parenchymal cells (hepatocytes) undergo both morphological and functional changes owing to a rewired transcriptome. The underlying mechanism is not entirely clear. In the present study, we investigated the involvement of early growth response 1 (Egr1) in NAFLD. Methods Quantitative PCR, Western blotting, and histochemical staining were used to assess gene expression levels. Chromatin immunoprecipitation was used to evaluate protein binding to DNA. NAFLD was evaluated in leptin receptor-deficient (db/db) mice. Results We report here that Egr1 was upregulated by pro-NAFLD stimuli in vitro and in vivo. Further analysis revealed that serum response factor (SRF) was recruited to the Egr1 promoter and mediated Egr1 transactivation. Importantly, Egr1 depletion markedly mitigated NAFLD in db/db mice. RNA sequencing revealed that Egr1 knockdown in hepatocytes, on the one hand, boosted fatty acid oxidation (FAO) and, on the other hand, suppressed the synthesis of chemoattractants. Mechanistically, Egr1 interacted with peroxisome proliferator-activated receptor α (PPARα) to repress PPARα-dependent transcription of FAO genes by recruiting its co-repressor NGFI-A binding protein 1 (Nab1), which potentially led to promoter deacetylation of FAO genes. Conclusions Our data identify Egr1 as a novel modulator of NAFLD and a potential target for NAFLD intervention. Impact and Implications Non-alcoholic fatty liver disease (NAFLD) precedes cirrhosis and hepatocellular carcinoma. In this paper, we describe a novel mechanism whereby early growth response 1 (Egr1), a transcription factor, contributes to NAFLD pathogenesis by regulating fatty acid oxidation. Our data provide novel insights and translational potential for NAFLD intervention.
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Affiliation(s)
- Yan Guo
- Institute of Biomedical Research and College of Life Sciences, Liaocheng University, Liaocheng, China
| | - Xiulian Miao
- Institute of Biomedical Research and College of Life Sciences, Liaocheng University, Liaocheng, China
| | - Xinyue Sun
- State Key Laboratory of Natural Medicines, Department of Pharmacology, China Pharmaceutical University, Nanjing, China
| | - Luyang Li
- Department of Oral Medicine, Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
| | - Anqi Zhou
- Institute of Biomedical Research and College of Life Sciences, Liaocheng University, Liaocheng, China
| | - Xi Zhu
- Department of Infectious Diseases, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, China
| | - Yong Xu
- Institute of Biomedical Research and College of Life Sciences, Liaocheng University, Liaocheng, China
- State Key Laboratory of Natural Medicines, Department of Pharmacology, China Pharmaceutical University, Nanjing, China
| | - Qinghua Wang
- Department of Gastroenterology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, China
| | - Zilong Li
- State Key Laboratory of Natural Medicines, Department of Pharmacology, China Pharmaceutical University, Nanjing, China
| | - Zhiwen Fan
- Department of Pathology, Affiliated Nanjing Drum Tower Hospital, Nanjing University School of Medicine, Nanjing, China
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Wang Y, He Y, Dong W, Jia M, Yang C, Wang J. DDIT3 aggravates pulpitis by modulating M1 polarization through EGR1 in macrophages. Int Immunopharmacol 2023; 120:110328. [PMID: 37235961 DOI: 10.1016/j.intimp.2023.110328] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 05/06/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023]
Abstract
DNA damage-inducible transcript 3 (DDIT3), a stress response gene, engages in the physiological and pathological processes of organisms, whereas its impact on pulpitis has not been defined yet. It has been demonstrated that macrophage polarization has a significant impact on inflammation. This research intends to investigate the effect of DDIT3 on the inflammation of pulpitis and macrophage polarization. C57BL/6J mice were used to model experimental pulpitis at 6, 12, 24, and 72 h after pulp exposure, with untreated mice as the control. The progression of pulpitis was visible histologically, and DDIT3 showed a trend of initially upward and downward later. Compared with wild-type mice, inflammatory cytokines and M1 macrophages were reduced, while M2 macrophages were increased in DDIT3 knockout mice. In RAW264.7 cells and bone borrow-derived macrophages, DDIT3 was found to enhance M1 polarization while impair M2 polarization. Targeted knockdown of early growth response 1 (EGR1) could rescue the blocking effect of DDIT3 deletion on M1 polarization. In conclusion, our results indicated that DDIT3 could exacerbate inflammation of pulpitis through the regulation of macrophage polarization, and DDIT3 could promote M1 polarization by inhibiting EGR1. It provides a new target for pulpitis treatment and tissue regeneration in the future.
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Affiliation(s)
- Yan Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China
| | - Ying He
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China
| | - Wei Dong
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China
| | - Meie Jia
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China
| | - Chang Yang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China
| | - Jiawei Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, Hubei 430079, China.
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Arzate-Mejia RG, Mansuy IM. Remembering through the genome: the role of chromatin states in brain functions and diseases. Transl Psychiatry 2023; 13:122. [PMID: 37041131 PMCID: PMC10090084 DOI: 10.1038/s41398-023-02415-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/19/2023] [Accepted: 03/24/2023] [Indexed: 04/13/2023] Open
Abstract
Chromatin is the physical substrate of the genome that carries the DNA sequence and ensures its proper functions and regulation in the cell nucleus. While a lot is known about the dynamics of chromatin during programmed cellular processes such as development, the role of chromatin in experience-dependent functions remains not well defined. Accumulating evidence suggests that in brain cells, environmental stimuli can trigger long-lasting changes in chromatin structure and tri-dimensional (3D) organization that can influence future transcriptional programs. This review describes recent findings suggesting that chromatin plays an important role in cellular memory, particularly in the maintenance of traces of prior activity in the brain. Inspired by findings in immune and epithelial cells, we discuss the underlying mechanisms and the implications for experience-dependent transcriptional regulation in health and disease. We conclude by presenting a holistic view of chromatin as potential molecular substrate for the integration and assimilation of environmental information that may constitute a conceptual basis for future research.
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Affiliation(s)
- Rodrigo G Arzate-Mejia
- Laboratory of Neuroepigenetics, Brain Research Institute, Medical Faculty, University of Zurich, Zurich, Switzerland
- Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology Zürich (ETHZ), Zurich, Switzerland
- Center for Neuroscience Zürich, University Zürich and ETHZ, Zürich, Switzerland
| | - Isabelle M Mansuy
- Laboratory of Neuroepigenetics, Brain Research Institute, Medical Faculty, University of Zurich, Zurich, Switzerland.
- Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology Zürich (ETHZ), Zurich, Switzerland.
- Center for Neuroscience Zürich, University Zürich and ETHZ, Zürich, Switzerland.
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Liu J, Zhang B, Zhu G, Liu C, Wang S, Zhao Z. Discovering genetic linkage between periodontitis and type 1 diabetes: A bioinformatics study. Front Genet 2023; 14:1147819. [PMID: 37051594 PMCID: PMC10083320 DOI: 10.3389/fgene.2023.1147819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
Background: Relationship between periodontitis (PD) and type 1 diabetes (T1D) has been reported, but the detailed pathogenesis requires further elucidation. This study aimed to reveal the genetic linkage between PD and T1D through bioinformatics analysis, thereby providing novel insights into scientific research and clinical treatment of the two diseases.Methods: PD-related datasets (GSE10334, GSE16134, GSE23586) and T1D-related datasets(GSE162689)were downloaded from NCBI Gene Expression Omnibus (GEO). Following batch correction and merging of PD-related datasets as one cohort, differential expression analysis was performed (adjusted p-value <0.05 and ∣log2 fold change| > 0.5), and common differentially expressed genes (DEGs) between PD and T1D were extracted. Functional enrichment analysis was conducted via Metascape website. The protein-protein interaction (PPI) network of common DEGs was generated in The Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database. Hub genes were selected by Cytoscape software and validated by receiver operating characteristic (ROC) curve analysis.Results: 59 common DEGs of PD and T1D were identified. Among these DEGs, 23 genes were commonly upregulated, and 36 genes were commonly downregulated in both PD- and T1D-related cohorts. Functional enrichment analysis indicated that common DEGs were mainly enriched in tube morphogenesis, supramolecular fiber organization, 9 + 0 non-motile cilium, plasma membrane bounded cell projection assembly, glomerulus development, enzyme-linked receptor protein signaling pathway, endochondral bone morphogenesis, positive regulation of kinase activity, cell projection membrane and regulation of lipid metabolic process. After PPI construction and modules selection, 6 hub genes (CD34, EGR1, BBS7, FMOD, IGF2, TXN) were screened out and expected to be critical in linking PD and T1D. ROC analysis showed that the AUC values of hub genes were all greater than 70% in PD-related cohort and greater than 60% in T1D-related datasets.Conclusion: Shared molecular mechanisms between PD and T1D were revealed in this study, and 6 hub genes were identified as potential targets in treating PD and T1D.
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Affiliation(s)
- Junqi Liu
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Bo Zhang
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Guanyin Zhu
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Chenlu Liu
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Shuangcheng Wang
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhihe Zhao
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- *Correspondence: Zhihe Zhao,
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Servaas NH, Hiddingh S, Chouri E, Wichers CGK, Affandi AJ, Ottria A, Bekker CPJ, Cossu M, Silva-Cardoso SC, van der Kroef M, Hinrichs AC, Carvalheiro T, Vazirpanah N, Beretta L, Rossato M, Bonte-Mineur F, Radstake TRDJ, Kuiper JJW, Boes M, Pandit A. Nuclear Receptor Subfamily 4A Signaling as a Key Disease Pathway of CD1c+ Dendritic Cell Dysregulation in Systemic Sclerosis. Arthritis Rheumatol 2023; 75:279-292. [PMID: 36482877 PMCID: PMC10108054 DOI: 10.1002/art.42319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 06/28/2022] [Accepted: 07/26/2022] [Indexed: 02/02/2023]
Abstract
OBJECTIVE This study was undertaken to identify key disease pathways driving conventional dendritic cell (cDC) alterations in systemic sclerosis (SSc). METHODS Transcriptomic profiling was performed on peripheral blood CD1c+ cDCs (cDC2s) isolated from 12 healthy donors and 48 patients with SSc, including all major disease subtypes. We performed differential expression analysis for the different SSc subtypes and healthy donors to uncover genes dysregulated in SSc. To identify biologically relevant pathways, we built a gene coexpression network using weighted gene correlation network analysis. We validated the role of key transcriptional regulators using chromatin immunoprecipitation (ChIP) sequencing and in vitro functional assays. RESULTS We identified 17 modules of coexpressed genes in cDCs that correlated with SSc subtypes and key clinical traits, including autoantibodies, skin score, and occurrence of interstitial lung disease. A module of immunoregulatory genes was markedly down-regulated in patients with the diffuse SSc subtype characterized by severe fibrosis. Transcriptional regulatory network analysis performed on this module predicted nuclear receptor 4A (NR4A) subfamily genes (NR4A1, NR4A2, NR4A3) as the key transcriptional regulators of inflammation. Indeed, ChIP-sequencing analysis indicated that these NR4A members target numerous differentially expressed genes in SSc cDC2s. Inclusion of NR4A receptor agonists in culture-based experiments provided functional proof that dysregulation of NR4As affects cytokine production by cDC2s and modulates downstream T cell activation. CONCLUSION NR4A1, NR4A2, and NR4A3 are important regulators of immunosuppressive and fibrosis-associated pathways in SSc cDCs. Thus, the NR4A family represents novel potential targets to restore cDC homeostasis in SSc.
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Affiliation(s)
- Nila H Servaas
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Sanne Hiddingh
- Center for Translational Immunology and Ophthalmo-Immunology Unit, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Eleni Chouri
- Center for Translational Immunology and Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Catharina G K Wichers
- Center for Translational Immunology and Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Alsya J Affandi
- Center for Translational Immunology and Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Andrea Ottria
- Center for Translational Immunology and Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Cornelis P J Bekker
- Center for Translational Immunology and Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marta Cossu
- Center for Translational Immunology and Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Sandra C Silva-Cardoso
- Center for Translational Immunology and Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Maarten van der Kroef
- Center for Translational Immunology and Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Anneline C Hinrichs
- Center for Translational Immunology and Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Tiago Carvalheiro
- Center for Translational Immunology and Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Nadia Vazirpanah
- Center for Translational Immunology and Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Lorenzo Beretta
- Scleroderma Unit, Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Marzia Rossato
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Femke Bonte-Mineur
- Department of Rheumatology and Clinical Immunology, Maasstad Hospital, Rotterdam, The Netherlands
| | - Timothy R D J Radstake
- Center for Translational Immunology and Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jonas J W Kuiper
- Center for Translational Immunology and Ophthalmo-Immunology Unit, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marianne Boes
- Department of Pediatrics, University Medical Center Utrecht, Utrecht University, The Netherlands
| | - Aridaman Pandit
- Center for Translational Immunology and Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
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Qiu L, Sheng P, Wang X. Identification of Metabolic Syndrome-Related miRNA-mRNA Regulatory Networks and Key Genes Based on Bioinformatics Analysis. Biochem Genet 2023; 61:428-447. [PMID: 35877019 DOI: 10.1007/s10528-022-10257-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/18/2022] [Indexed: 01/24/2023]
Abstract
Metabolic syndrome, which affects approximately one-quarter of the world's population, is a combination of multiple traits and is associated with high all-cause mortality, increased cancer risk, and other hazards. It has been shown that the epigenetic functions of miRNAs are closely related to metabolic syndrome, but epigenetic studies have not yet fully elucidated the regulatory network and key genes associated with metabolic syndrome. To perform data analysis and screening of potential differentially expressed target miRNAs, mRNAs and genes based on a bioinformatics approach using a metabolic syndrome mRNA and miRNA gene microarray, leading to further analysis and identification of metabolic syndrome-related miRNA-mRNA regulatory networks and key genes. The miRNA gene set (GSE98896) and mRNA gene set (GSE98895) of peripheral blood samples from patients with metabolic syndrome from the GEO database were screened, and set|logFC|> 1 and adjusted P < 0.05 were used to identify the differentially expressed miRNAs and mRNAs. Differentially expressed miRNA transcription factors were predicted using FunRich software and subjected to GO and KEGG enrichment analysis. Next, biological process enrichment analysis of differentially expressed mRNAs was performed with Metascape. Differentially expressed miRNAs and mRNAs were identified and visualized as miRNA-mRNA regulatory networks based on the complementary pairing principle. Data analysis of genome-wide metabolic syndrome-related mRNAs was performed using the gene set enrichment analysis (GSEA) database. Finally, further WGCNA of the set of genes most closely associated with metabolic syndrome was performed to validate the findings. A total of 217 differentially expressed mRNAs and 158 differentially expressed miRNAs were identified by screening the metabolic syndrome miRNA and mRNA gene sets, and these molecules mainly included transcription factors, such as SP1, SP4, and EGR1, that function in the IL-17 signalling pathway; cytokine-cytokine receptor interaction; proteoglycan syndecan-mediated signalling events; and the glypican pathway, which is involved in the inflammatory response and glucose and lipid metabolism. miR-34C-5P, which was identified by constructing a miRNA-mRNA regulatory network, could regulate DPYSL4 expression to influence insulin β-cells, the inflammatory response and glucose oxidative catabolism. Based on GSEA, metabolic syndrome is known to be closely related to oxidative phosphorylation, DNA repair, neuronal damage, and glycolysis. Finally, RStudio and DAVID were used to perform WGCNA of the gene sets most closely associated with metabolic syndrome, and the results further validated the conclusions. Metabolic syndrome is a common metabolic disease worldwide, and its mechanism of action is closely related to the inflammatory response, glycolipid metabolism, and impaired mitochondrial function. miR-34C-5P can regulate DPYSL4 expression and can be a potential research target. In addition, UQCRQ and NDUFA8 are core genes of oxidative phosphorylation and have also been identified as potential targets for the future treatment of metabolic syndrome.
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Affiliation(s)
- Lingyan Qiu
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210029, China.,The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Pei Sheng
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210029, China.,The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China
| | - Xu Wang
- The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210029, China. .,The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, China.
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37
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Chemotherapy suppresses SHH gene expression via a specific enhancer. J Genet Genomics 2023; 50:27-37. [PMID: 35998878 DOI: 10.1016/j.jgg.2022.08.002] [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: 12/06/2021] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 02/06/2023]
Abstract
Sonic hedgehog (SHH) signaling is a key regulator of embryonic development and tissue homeostasis that is involved in gastrointestinal (GI) cancer progression. Regulation of SHH gene expression is a paradigm of long-range enhancer function. Using the classical chemotherapy drug 5-fluorouracil (5FU) as an example, here we show that SHH gene expression is suppressed by chemotherapy. SHH is downstream of immediate early genes (IEGs), including Early growth response 1 (Egr1). A specific 139 kb upstream enhancer is responsible for its down-regulation. Knocking down EGR1 expression or blocking its binding to this enhancer renders SHH unresponsive to chemotherapy. We further demonstrate that down-regulation of SHH expression does not depend on 5FU's impact on nucleotide metabolism or DNA damage; rather, a sustained oxidative stress response mediates this rapid suppression. This enhancer is present in a wide range of tumors and normal tissues, thus providing a target for cancer chemotherapy and its adverse effects on normal tissues. We propose that SHH is a stress-responsive gene downstream of IEGs, and that traditional chemotherapy targets a specific enhancer to suppress its expression.
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38
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Shi X, Tang L, Ni H, Li M, Wu Y, Xu Y. Identification of Ferroptosis-Related Biomarkers for Diagnosis and Molecular Classification of Staphylococcus aureus-Induced Osteomyelitis. J Inflamm Res 2023; 16:1805-1823. [PMID: 37131411 PMCID: PMC10149083 DOI: 10.2147/jir.s406562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/21/2023] [Indexed: 05/04/2023] Open
Abstract
Objective Staphylococcus aureus (SA)-induced osteomyelitis (OM) is one of the most common refractory diseases in orthopedics. Early diagnosis is beneficial to improve the prognosis of patients. Ferroptosis plays a key role in inflammation and immune response, while the mechanism of ferroptosis-related genes (FRGs) in SA-induced OM is still unclear. The purpose of this study was to determine the role of ferroptosis-related genes in the diagnosis, molecular classification and immune infiltration of SA-induced OM by bioinformatics. Methods Datasets related to SA-induced OM and ferroptosis were collected from the Gene Expression Omnibus (GEO) and ferroptosis databases, respectively. The least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE) algorithms were combined to screen out differentially expressed-FRGs (DE-FRGs) with diagnostic characteristics, and gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) were used to explore specific biological functions and pathways. Based on these key DE-FRGs, a diagnostic model was established, and molecular subtypes were divided to explore the changes in the immune microenvironment between molecular subtypes. Results A total of 41 DE-FRGs were identified. After screening and intersecting with LASSO and SVM-RFE algorithms, 8 key DE-FRGs with diagnostic characteristics were obtained, which may regulate the pathogenesis of OM through the immune response and amino acid metabolism. The ROC curve indicated that the 8 DE-FRGs had excellent diagnostic ability for SA-induced OM (AUC=0.993). Two different molecular subtypes (subtype 1 and subtype 2) were identified by unsupervised cluster analysis. The CIBERSORT analysis revealed that the subtype 1 OM had higher immune cell infiltration rates, mainly in T cells CD4 memory resting, macrophages M0, macrophages M2, dendritic cells resting, and dendritic cells activated. Conclusion We developed a diagnostic model related to ferroptosis and molecular subtypes significantly related to immune infiltration, which may provide a novel insight for exploring the pathogenesis and immunotherapy of SA-induced OM.
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Affiliation(s)
- Xiangwen Shi
- Kunming Medical University, Kunming, People’s Republic of China
- Laboratory of Yunnan Traumatology and Orthopedics Clinical Medical Center, Yunnan Orthopedics and Sports Rehabilitation Clinical Medical Research Center, Department of Orthopedic Surgery, 920th Hospital of Joint Logistics Support Force of PLA, Kunming, People’s Republic of China
| | - Linmeng Tang
- Bone and Joint Imaging Center, Department of Medical Imaging, the First Affiliated Hospital of Hebei North University, Zhangjiakou, People’s Republic of China
| | - Haonan Ni
- Kunming Medical University, Kunming, People’s Republic of China
| | - Mingjun Li
- Kunming Medical University, Kunming, People’s Republic of China
| | - Yipeng Wu
- Kunming Medical University, Kunming, People’s Republic of China
- Laboratory of Yunnan Traumatology and Orthopedics Clinical Medical Center, Yunnan Orthopedics and Sports Rehabilitation Clinical Medical Research Center, Department of Orthopedic Surgery, 920th Hospital of Joint Logistics Support Force of PLA, Kunming, People’s Republic of China
| | - Yongqing Xu
- Laboratory of Yunnan Traumatology and Orthopedics Clinical Medical Center, Yunnan Orthopedics and Sports Rehabilitation Clinical Medical Research Center, Department of Orthopedic Surgery, 920th Hospital of Joint Logistics Support Force of PLA, Kunming, People’s Republic of China
- Correspondence: Yongqing Xu; Yipeng Wu, Department of Orthopedic Surgery, 920th Hospital of Joint Logistics Support Force, 212 Daguan Road, Xi Shan District, Kunming, Yunnan, 650100, People’s Republic of China, Email ;
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Tiemeijer BM, Heester S, Sturtewagen AYW, Smits AIPM, Tel J. Single-cell analysis reveals TLR-induced macrophage heterogeneity and quorum sensing dictate population wide anti-inflammatory feedback in response to LPS. Front Immunol 2023; 14:1135223. [PMID: 36911668 PMCID: PMC9998924 DOI: 10.3389/fimmu.2023.1135223] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 02/13/2023] [Indexed: 03/14/2023] Open
Abstract
The role of macrophages in controlling tissue inflammation is indispensable to ensure a context-appropriate response to pathogens whilst preventing excessive tissue damage. Their initial response is largely characterized by high production of tumor necrosis factor alpha (TNFα) which primes and attracts other immune cells, thereafter, followed by production of interleukin 10 (IL-10) which inhibits cell activation and steers towards resolving of inflammation. This delicate balance is understood at a population level but how it is initiated at a single-cell level remains elusive. Here, we utilize our previously developed droplet approach to probe single-cell macrophage activation in response to toll-like receptor 4 (TLR4) stimulation, and how single-cell heterogeneity and cellular communication affect macrophage-mediated inflammatory homeostasis. We show that only a fraction of macrophages can produce IL-10 in addition to TNFα upon LPS-induced activation, and that these cells are not phenotypically different from IL-10 non-producers nor exhibit a distinct transcriptional pathway. Finally, we demonstrate that the dynamics of TNFα and IL-10 are heavily controlled by macrophage density as evidenced by 3D hydrogel cultures suggesting a potential role for quorum sensing. These exploratory results emphasize the relevance of understanding the complex communication between macrophages and other immune cells and how these amount to population-wide responses.
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Affiliation(s)
- Bart M Tiemeijer
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Sebastiaan Heester
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Ashley Y W Sturtewagen
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Anthal I P M Smits
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands.,Laboratory of Soft Tissue Engineering and Mechanobiology, Department Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Jurjen Tel
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
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40
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Genomics, Origin and Selection Signals of Loudi Cattle in Central Hunan. BIOLOGY 2022; 11:biology11121775. [PMID: 36552284 PMCID: PMC9775101 DOI: 10.3390/biology11121775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/23/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022]
Abstract
Due to the geographical, cultural and environmental variability in Xiangxi, China, distinctive indigenous cattle populations have formed. Among them, Loudi cattle and Xiangxi cattle are the local cattle in Hunan, and the environment in Loudi is relatively more enclosed and humid than that in Xiangxi. To study the genome and origin of Loudi cattle in hot and humid environments, 29 individuals were collected and sequenced by whole-genome resequencing. In addition, genomic data were obtained from public databases for 96 individuals representing different cattle breeds worldwide, including 23 Xiangxi cattle from western Hunan. Genetic analysis indicated that the genetic diversity of Loudi cattle was close to that of Chinese cattle and higher than that of other breeds. Population structure and ancestral origin analysis indicated the relationship between Loudi cattle and other breeds. Loudi has four distinctive seasons, with a stereoscopic climate and extremely rich water resources. Selective sweep analysis revealed candidate genes and pathways associated with environmental adaptation and homeostasis. Our findings provide a valuable source of information on the genetic diversity of Loudi cattle and ideas for population conservation and genome-associated breeding of local cattle in today's extreme climate environment.
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41
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Hernandez-Beeftink T, Guillen-Guio B, Lorenzo-Salazar JM, Corrales A, Suarez-Pajes E, Feng R, Rubio-Rodríguez LA, Paynton ML, Cruz R, García-Laorden MI, Prieto-González M, Rodríguez-Pérez A, Carriedo D, Blanco J, Ambrós A, González-Higueras E, Espinosa E, Muriel A, Tamayo E, Martin MM, Lorente L, Domínguez D, de Lorenzo AG, Giannini HM, Reilly JP, Jones TK, Añón JM, Soro M, Carracedo Á, Wain LV, Meyer NJ, Villar J, Flores C. A genome-wide association study of survival in patients with sepsis. Crit Care 2022; 26:341. [PMID: 36335405 PMCID: PMC9637317 DOI: 10.1186/s13054-022-04208-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Sepsis is a severe systemic inflammatory response to infections that is accompanied by organ dysfunction and has a high mortality rate in adult intensive care units. Most genetic studies have identified gene variants associated with development and outcomes of sepsis focusing on biological candidates. We conducted the first genome-wide association study (GWAS) of 28-day survival in adult patients with sepsis. METHODS This study was conducted in two stages. The first stage was performed on 687 European sepsis patients from the GEN-SEP network and 7.5 million imputed variants. Association testing was conducted with Cox regression models, adjusting by sex, age, and the main principal components of genetic variation. A second stage focusing on the prioritized genetic variants was performed on 2,063 ICU sepsis patients (1362 European Americans and 701 African-Americans) from the MESSI study. A meta-analysis of results from the two stages was conducted and significance was established at p < 5.0 × 10-8. Whole-blood transcriptomic, functional annotations, and sensitivity analyses were evaluated on the identified genes and variants. FINDINGS We identified three independent low-frequency variants associated with reduced 28-day sepsis survival, including a missense variant in SAMD9 (hazard ratio [95% confidence interval] = 1.64 [1.37-6.78], p = 4.92 × 10-8). SAMD9 encodes a possible mediator of the inflammatory response to tissue injury. INTERPRETATION We performed the first GWAS of 28-day sepsis survival and identified novel variants associated with reduced survival. Larger sample size studies are needed to better assess the genetic effects in sepsis survival and to validate the findings.
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Affiliation(s)
- Tamara Hernandez-Beeftink
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Carretera del Rosario S/N, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Beatriz Guillen-Guio
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Carretera del Rosario S/N, Santa Cruz de Tenerife, Spain
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Jose M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Almudena Corrales
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Carretera del Rosario S/N, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Eva Suarez-Pajes
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Carretera del Rosario S/N, Santa Cruz de Tenerife, Spain
| | - Rui Feng
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Luis A Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Megan L Paynton
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Raquel Cruz
- Genomic Medicine Group, Biomedical Research Center of Rare Diseases (CIBERER), University of Santiago de Compostela, Santiago de Compostela, Spain
| | - M Isabel García-Laorden
- Research Unit, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Aurelio Rodríguez-Pérez
- Department of Anesthesiology, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain
- Department of Medical and Surgical Sciences, University of Las Palmas de Gran Canaria, Gran Canaria, Spain
| | - Demetrio Carriedo
- Intensive Care Unit, Complejo Hospitalario Universitario de León, León, Spain
| | - Jesús Blanco
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Intensive Care Unit, Hospital Universitario Rio Hortega, Valladolid, Spain
| | - Alfonso Ambrós
- Intensive Care Unit, Hospital General de Ciudad Real, Ciudad Real, Spain
| | | | - Elena Espinosa
- Department of Anesthesiology, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Arturo Muriel
- Intensive Care Unit, Hospital Universitario Rio Hortega, Valladolid, Spain
| | - Eduardo Tamayo
- CIBER de Enfermedades Infecciosas, Department of Anesthesiology and Resuscitation, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
- Departamento de Cirugía, Facultad de Medicina, Universidad de Valladolid, Valladolid, Spain
| | - María M Martin
- Intensive Care Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Leonardo Lorente
- Intensive Care Unit, Hospital Universitario de Canarias, La Laguna, Tenerife, Spain
| | - David Domínguez
- Department of Anesthesiology, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | | | - Heather M Giannini
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - John P Reilly
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Tiffanie K Jones
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - José M Añón
- Intensive Care Unit, Hospital Universitario La Paz, IdiPAZ, Madrid, Spain
| | - Marina Soro
- Department of Anesthesiology, Hospital Clinico Universitario de Valencia, Valencia, Spain
| | - Ángel Carracedo
- Genomic Medicine Group, Biomedical Research Center of Rare Diseases (CIBERER), University of Santiago de Compostela, Santiago de Compostela, Spain
- Genomic Medicine Group, CIMUS, University of Santiago de Compostela, Santiago de Compostela, Spain
- Galician Foundation of Genomic Medicine, Foundation of Health Research Institute of Santiago de Compostela (FIDIS), SERGAS, Santiago de Compostela, Spain
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
- Leicester Respiratory Biomedical Research, Centre, National Institute for Health Research, Glenfield Hospital, Leicester, UK
| | - Nuala J Meyer
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Jesús Villar
- Research Unit, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Carretera del Rosario S/N, Santa Cruz de Tenerife, Spain.
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain.
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Stoddart A, Fernald AA, Davis EM, McNerney ME, Le Beau MM. EGR1 Haploinsufficiency Confers a Fitness Advantage to Hematopoietic Stem Cells Following Chemotherapy. Exp Hematol 2022; 115:54-67. [PMID: 35995095 PMCID: PMC10617250 DOI: 10.1016/j.exphem.2022.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022]
Abstract
Therapy-related myeloid neoplasms (t-MNs) share many clinical and molecular characteristics with AML de novo in the elderly. One common factor is that they arise in the setting of chronic inflammation, likely because of advanced age or chemotherapy-induced senescence. Here, we examined the effect of haploinsufficient loss of the del(5q) tumor suppressor gene, EGR1, commonly deleted in high-risk MNs. In mice, under the exogenous stress of either serial transplant or successive doses of the alkylating agent N-ethyl-nitrosourea (ENU), Egr1-haploinsufficient hematopoietic stem cells (HSCs) exhibit a clonal advantage. Complete loss of EGR1 function is incompatible with transformation; mutations of EGR1 are rare and are not observed in the remaining allele in del(5q) patients, and complete knockout of Egr1 in mice leads to HSC exhaustion. Using chromatin immunoprecipitation sequencing (ChIP-seq), we identified EGR1 binding sites in human CD34+ cord blood-derived stem and progenitor cells (HSPCs) and found that EGR1 binds genes critical for stem cell differentiation, inflammatory signaling, and the DNA damage response. Notably, in the chromosome 5 sequences frequently deleted in patients, there is a significant enrichment of innate and inflammatory genes, which may confer a fitness advantage in an inflammatory environment. Short hairpin RNA (shRNA)-mediated silencing of EGR1 biases HSPCs toward a self-renewal transcriptional signature. In the absence of EGR1, HSPCs are characterized by upregulated MYC-driven proliferative signals, downregulated CDKN1A (p21), disrupted DNA damage response, and downregulated inflammation-adaptations anticipated to confer a relative fitness advantage for stem cells especially in an environment of chronic inflammation.
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Affiliation(s)
| | | | | | - Megan E McNerney
- Department of Pathology, University of Chicago, Chicago, IL; University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL; Department of Pediatrics, University of Chicago, Chicago IL
| | - Michelle M Le Beau
- Department of Medicine, University of Chicago, Chicago, IL; University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL
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Tung YC, Wu LS, Hsiao FC, Hsu LA, Yeh YH, Chang CH, Chen YC, Chang CJ. Upregulation of Myocardial Neutrophil Gelatinase-Associated Lipocalin during Development of Heart Failure Caused by Volume-Overload and the Effect in Regulating Activity of Matrix Metalloproteinase-9. ACTA CARDIOLOGICA SINICA 2022; 38:765-777. [PMID: 36440239 PMCID: PMC9692222 DOI: 10.6515/acs.202211_38(6).20220814a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 08/14/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND In patients with heart failure (HF), circulating neutrophil gelatinase-associated lipocalin (NGAL) level is increased, which is considered to be a predictor of mortality or renal outcomes. The expression of NGAL in the heart and kidney and its role in HF remain unclear. METHODS Aortocaval fistula was created in rats as a model of volume overload (VO)-induced HF. RESULTS During the development of HF, NGAL expression was upregulated in the heart but not in the kidney at both transcriptional and translational levels in the compensatory and HF phases, with a similar level in both phases. Cardiomyocytes were identified as the cell type responsible for NGAL expression. Consistent with the myocardial NGAL expression pattern, the plasma NGAL level was increased in both phases, and the level was not significantly different between both phases. We demonstrated the presence of a matrix metalloproteinase (MMP)-9/NGAL complex in cultured medium of cardiomyocytes isolated from volume-overloaded hearts by gelatin zymography. Formation of MMP-9/NGAL complex was shown to enhance the enzymatic activity of MMP-9. We found that early growth response (Egr)-1 was upregulated in the heart in both compensatory and HF phases. In neonatal cardiomyocytes, Egr-1 overexpression induced the gene expression of NGAL, which was dose-dependently suppressed by an interleukin-1 receptor antagonist. CONCLUSIONS During the development of HF due to VO, NGAL was upregulated in the heart but not in the kidney in both compensatory and HF phases, with a similar expression level. Myocardial NGAL upregulation enhanced MMP-9 activity through formation of the MMP-9/NGAL complex. The expression of myocardial NGAL was regulated by Egr-1.
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Affiliation(s)
| | | | | | | | | | - Chih-Hsiang Chang
- Division of Nephrology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Yung-Chang Chen
- Division of Nephrology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
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Woodson CM, Kehn-Hall K. Examining the role of EGR1 during viral infections. Front Microbiol 2022; 13:1020220. [PMID: 36338037 PMCID: PMC9634628 DOI: 10.3389/fmicb.2022.1020220] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/26/2022] [Indexed: 09/06/2023] Open
Abstract
Early growth response 1 (EGR1) is a multifunctional mammalian transcription factor capable of both enhancing and/or inhibiting gene expression. EGR1 can be activated by a wide array of stimuli such as exposure to growth factors, cytokines, apoptosis, and various cellular stress states including viral infections by both DNA and RNA viruses. Following induction, EGR1 functions as a convergence point for numerous specialized signaling cascades and couples short-term extracellular signals to influence transcriptional regulation of genes required to initiate the appropriate biological response. The role of EGR1 has been extensively studied in both physiological and pathological conditions of the adult nervous system where it is readily expressed in various regions of the brain and is critical for neuronal plasticity and the formation of memories. In addition to its involvement in neuropsychiatric disorders, EGR1 has also been widely examined in the field of cancer where it plays paradoxical roles as a tumor suppressor gene or oncogene. EGR1 is also associated with multiple viral infections such as Venezuelan equine encephalitis virus (VEEV), Kaposi's sarcoma-associated herpesvirus (KSHV), herpes simplex virus 1 (HSV-1), human polyomavirus JC virus (JCV), human immunodeficiency virus (HIV), and Epstein-Barr virus (EBV). In this review, we examine EGR1 and its role(s) during viral infections. First, we provide an overview of EGR1 in terms of its structure, other family members, and a brief overview of its roles in non-viral disease states. We also review upstream regulators of EGR1 and downstream factors impacted by EGR1. Then, we extensively examine EGR1 and its roles, both direct and indirect, in regulating replication of DNA and RNA viruses.
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Affiliation(s)
- Caitlin M. Woodson
- Department of Biomedical Science and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Kylene Kehn-Hall
- Department of Biomedical Science and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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45
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Wen P, Ma T, Zhang B, Hao L, Wang Y, Guo J, Song W, Wang J, Zhang Y. Identifying hub circadian rhythm biomarkers and immune cell infiltration in rheumatoid arthritis. Front Immunol 2022; 13:1004883. [PMID: 36238290 PMCID: PMC9550876 DOI: 10.3389/fimmu.2022.1004883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundRheumatoid arthritis (RA) is a chronic systemic autoimmune disease with symptoms characterized by typical circadian rhythmic changes. This study aimed to identify the hub circadian rhythm genes (CRGs) in RA and explore their association with immune cell infiltration and pathogenesis of RA.MethodsThe differentially expressed CRGs (DECRGs) between RA and normal control samples were screened from Datasets GSE12021 and GSE55235. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Gene Set Enrichment Analysis were used to explore the potential functional mechanisms of DECRGs in RA. Weighted Gene Co-expression Network Analysis and Least Absolute Shrinkage and Selection Operator regression analysis were performed to identify hub CRGs of RA. CIBERSORT was conducted to compare the infiltration level of immune cells in RA and control synovial tissue and their relationship with hub genes. In addition, the diagnostic value of hub biomarkers was evaluated by the area under the receiver operator characteristic curve. Further, a nomogram prediction model was constructed and its significance for clinical decision-making was evaluated.ResultsThe green module was identified as the hub module associated with RA. Four hub CRGs (EGR1, FOSL2, GADD45B, and NFIL3) were identified and showed that they had the highest specificity and sensitivity for RA diagnosis, respectively. The expression levels and diagnostic values of these genes were externally validated in the dataset GSE55457. A nomogram prediction model based on the four hub CRGs was constructed and proved to have a certain clinical decision value. Additionally, the correlation analysis of immune cells with hub genes showed that all hub genes were significantly positively correlated with activated mast cells, resting memory CD4+ T cells, and monocytes. Whereas, all hub genes were negatively correlated with plasma cells, CD8+ T cells, and activated memory CD4+ T cells. Meanwhile, FOSL2 and GADD45B were negatively correlated with Tfh cells.ConclusionFour hub CRGs were identified and showed excellent diagnostic value for RA. These genes may be involved in the pathological process of RA by disrupting the rhythmic oscillations of cytokines through immune-related pathways and could be considered molecular targets for future chronotherapy against RA.
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Affiliation(s)
| | | | | | | | | | | | | | - Jun Wang
- *Correspondence: Yumin Zhang, ; Jun Wang,
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Zhang Y, Xu L, Li X, Chen Z, Chen J, Zhang T, Gu X, Yang J. Deciphering the dynamic niches and regeneration-associated transcriptional program of motoneurons following peripheral nerve injury. iScience 2022; 25:104917. [PMID: 36051182 PMCID: PMC9424597 DOI: 10.1016/j.isci.2022.104917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/10/2022] [Accepted: 08/08/2022] [Indexed: 11/25/2022] Open
Abstract
Robust axon regeneration of motoneurons (MNs) occurs in rodent models upon peripheral nerve injury (PNI). However, genome-wide dynamic molecules and permissive microenvironment following insult in MNs remain largely unknown. Here, we firstly tackled by high-coverage and massive sequencing of laser-dissected individual ChAT+ cells to uncover molecules and pro-regenerative programs of MNs from injury to the regenerating phase after PNI. "Injured" populations at 1d∼7d were well distinguished and three response phases were well defined by elucidating with several clues (Gap43, etc). We found remarkable changes of genes expressed by injured motoneurons to activate and enhance intrinsic axon regrowth or crosstalk with other cellular or non-cellular counterpart in the activated regenerative microenvironment, specifically microglia/macrophage. We also identified an injury and regeneration-associated module and critical regulators including core transcription factors (Atf3, Arid5a, Klf6, Klf7, Jun, Stat3, and Myc). This study provides a vital resource and critical molecules for studying neural repair of axotomized motoneurons.
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Affiliation(s)
- Yu Zhang
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210000, China
| | - Lian Xu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong 226001, China
| | - Xiaodi Li
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210000, China
| | - Zhifeng Chen
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong 226001, China
| | - Jing Chen
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong 226001, China
| | - Tao Zhang
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210000, China
| | - Xiaosong Gu
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210000, China.,Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong 226001, China
| | - Jian Yang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong 226001, China
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Lesseur C, Jessel RH, Ohrn S, Ma Y, Li Q, Dekio F, Brody RI, Wetmur JG, Gigase FA, Lieber M, Lieb W, Lynch J, Afzal O, Ibroci E, Rommel AS, Janevic T, Stone J, Howell EA, Galang RR, Dolan SM, Bergink V, De Witte LD, Chen J. Gestational SARS-CoV-2 infection is associated with placental expression of immune and trophoblast genes. Placenta 2022; 126:125-132. [PMID: 35797939 PMCID: PMC9242701 DOI: 10.1016/j.placenta.2022.06.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/13/2022] [Accepted: 06/26/2022] [Indexed: 11/28/2022]
Abstract
INTRODUCTION Maternal SARS-CoV-2 infection during pregnancy is associated with adverse pregnancy outcomes and can have effects on the placenta, even in the absence of severe disease or vertical transmission to the fetus. This study aimed to evaluate histopathologic and molecular effects in the placenta after SARS-CoV-2 infection during pregnancy. METHODS We performed a study of 45 pregnant participants from the Generation C prospective cohort study at the Mount Sinai Health System in New York City. We compared histologic features and the expression of 48 immune and trophoblast genes in placentas delivered from 15 SARS-CoV-2 IgG antibody positive and 30 IgG SARS-CoV-2 antibody negative mothers. Statistical analyses were performed using Fisher's exact tests, Spearman correlations and linear regression models. RESULTS The median gestational age at the time of SARS-CoV-2 IgG serology test was 35 weeks. Two of the IgG positive participants also had a positive RT-PCR nasal swab at delivery. 82.2% of the infants were delivered at term (≥37 weeks), and gestational age at delivery did not differ between the SARS-CoV-2 antibody positive and negative groups. No significant differences were detected between the groups in placental histopathology features. Differential expression analyses revealed decreased expression of two trophoblast genes (PSG3 and CGB3) and increased expression of three immune genes (CXCL10, TLR3 and DDX58) in placentas delivered from SARS-CoV-2 IgG positive participants. DISCUSSION SARS-CoV-2 infection during pregnancy is associated with gene expression changes of immune and trophoblast genes in the placenta at birth which could potentially contribute to long-term health effects in the offspring.
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Affiliation(s)
- Corina Lesseur
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Rebecca H. Jessel
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Sophie Ohrn
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Yula Ma
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Qian Li
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Fumiko Dekio
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Rachel I. Brody
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - James G. Wetmur
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, Box 1054, 1 Gustave Levy Place, New York, NY, USA
| | - Frederieke A.J. Gigase
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Molly Lieber
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Whitney Lieb
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA,Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York City, NY, USA,Blavatnik Family Women's Health Research Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Jezelle Lynch
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Omara Afzal
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Erona Ibroci
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Anna-Sophie Rommel
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Teresa Janevic
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA,Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York City, NY, USA,Blavatnik Family Women's Health Research Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Joanne Stone
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Elizabeth A. Howell
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York City, NY, USA,Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Romeo R. Galang
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Siobhan M. Dolan
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Veerle Bergink
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York City, NY, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA,Blavatnik Family Women's Health Research Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Lotje D. De Witte
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Jia Chen
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York City, NY, USA,Corresponding author. Department of Environmental Medicine and Public Heath, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, Box 1057, New York, NY, 10029, USA
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Single-Cell Transcriptome Analysis of Radiation Pneumonitis Mice. Antioxidants (Basel) 2022; 11:antiox11081457. [PMID: 35892659 PMCID: PMC9331247 DOI: 10.3390/antiox11081457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/14/2022] [Accepted: 07/22/2022] [Indexed: 12/10/2022] Open
Abstract
Radiation-induced lung injury (RILI), especially radiation pneumonitis (RP), is a common clinical complication associated with thoracic radiotherapy for malignant tumors. However, the specific contributions of each cell subtype to this process are unknown. Here, we provide the single-cell pathology landscape of the RP in a mouse model by unbiased single-cell RNA-seq (scRNA-seq). We found a decline of type 2 alveolar cells in the RP lung tissue, with an expansion of macrophages, especially the Fabp4low and Spp1high subgroup, while Fabp4high macrophages were almost depleted. We observed an elevated expression of multiple mitochondrial genes in the RP group, indicating a type 2 alveolar cell (AT2) response to oxidative stress. We also calculated the enrichment of a cGAS-STING signaling pathway, which may be involved in regulating inflammatory responses and cancer progression in AT2 cells of PR mice. We delineate markers and transcriptional states, identify a type 2 alveolar cell, and uncover fundamental determinants of lung fibrosis and inflammatory response in RP lung tissue of mice.
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Vurusaner B, Thevkar-Nages P, Kaur R, Giannarelli C, Garabedian MJ, Fisher EA. Loss of PRMT2 in myeloid cells in normoglycemic mice phenocopies impaired regression of atherosclerosis in diabetic mice. Sci Rep 2022; 12:12031. [PMID: 35835907 PMCID: PMC9283439 DOI: 10.1038/s41598-022-15349-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/22/2022] [Indexed: 12/24/2022] Open
Abstract
The regression, or resolution, of inflammation in atherosclerotic plaques is impaired in diabetes. However, the factors mediating this effect remain incomplete. We identified protein arginine methyltransferase 2 (PRMT2) as a protein whose expression in macrophages is reduced in hyperglycemia and diabetes. PRMT2 catalyzes arginine methylation to target proteins to modulate gene expression. Because PRMT2 expression is reduced in cells in hyperglycemia, we wanted to determine whether PRMT2 plays a causal role in the impairment of atherosclerosis regression in diabetes. We, therefore, examined the consequence of deleting PRMT2 in myeloid cells during the regression of atherosclerosis in normal and diabetic mice. Remarkably, we found significant impairment of atherosclerosis regression under normoglycemic conditions in mice lacking PRMT2 (Prmt2-/-) in myeloid cells that mimic the decrease in regression of atherosclerosis in WT mice under diabetic conditions. This was associated with increased plaque macrophage retention, as well as increased apoptosis and necrosis. PRMT2-deficient plaque CD68+ cells under normoglycemic conditions showed increased expression of genes involved in cytokine signaling and inflammation compared to WT cells. Consistently, Prmt2-/- bone marrow-derived macrophages (BMDMs) showed an increased response of proinflammatory genes to LPS and a decreased response of inflammation resolving genes to IL-4. This increased response to LPS in Prmt2-/- BMDMs occurs via enhanced NF-kappa B activity. Thus, the loss of PRMT2 is causally linked to impaired atherosclerosis regression via a heightened inflammatory response in macrophages. That PRMT2 expression was lower in myeloid cells in plaques from human subjects with diabetes supports the relevance of our findings to human atherosclerosis.
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Affiliation(s)
- Beyza Vurusaner
- Division of Cardiology, Department of Medicine, Cardiovascular Research Center, New York University Grossman School of Medicine, 435 E. 30th Street, Room 705, New York, NY, 10016, USA
| | - Prashanth Thevkar-Nages
- Division of Cardiology, Department of Medicine, Cardiovascular Research Center, New York University Grossman School of Medicine, 435 E. 30th Street, Room 705, New York, NY, 10016, USA.,Department of Microbiology, New York University Grossman School of Medicine, 450 E. 29th Street, Room 321, New York, NY, 10016, USA
| | - Ravneet Kaur
- Division of Cardiology, Department of Medicine, Cardiovascular Research Center, New York University Grossman School of Medicine, 435 E. 30th Street, Room 705, New York, NY, 10016, USA
| | - Chiara Giannarelli
- Division of Cardiology, Department of Medicine, Cardiovascular Research Center, New York University Grossman School of Medicine, 435 E. 30th Street, Room 705, New York, NY, 10016, USA
| | - Michael J Garabedian
- Department of Microbiology, New York University Grossman School of Medicine, 450 E. 29th Street, Room 321, New York, NY, 10016, USA.
| | - Edward A Fisher
- Division of Cardiology, Department of Medicine, Cardiovascular Research Center, New York University Grossman School of Medicine, 435 E. 30th Street, Room 705, New York, NY, 10016, USA. .,Department of Microbiology, New York University Grossman School of Medicine, 450 E. 29th Street, Room 321, New York, NY, 10016, USA. .,Marc and Ruti Bell Vascular Biology Program, New York University Grossman School of Medicine, New York, NY, 10016, USA.
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Brito V, Montalban E, Sancho-Balsells A, Pupak A, Flotta F, Masana M, Ginés S, Alberch J, Martin C, Girault JA, Giralt A. Hippocampal Egr1-Dependent Neuronal Ensembles Negatively Regulate Motor Learning. J Neurosci 2022; 42:5346-5360. [PMID: 35610044 PMCID: PMC9270920 DOI: 10.1523/jneurosci.2258-21.2022] [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: 11/11/2021] [Revised: 04/09/2022] [Accepted: 05/17/2022] [Indexed: 01/09/2023] Open
Abstract
Motor skills learning is classically associated with brain regions including cerebral and cerebellar cortices and basal ganglia nuclei. Less is known about the role of the hippocampus in the acquisition and storage of motor skills. Here, we show that mice receiving a long-term training in the accelerating rotarod display marked hippocampal transcriptional changes and reduced pyramidal neurons activity in the CA1 region when compared with naive mice. Then, we use mice in which neural ensembles are permanently labeled in an Egr1 activity-dependent fashion. Using these mice, we identify a subpopulation of Egr1-expressing pyramidal neurons in CA1 activated in short-term (STT) and long-term (LTT) trained mice in the rotarod task. When Egr1 is downregulated in the CA1 or these neuronal ensembles are depleted, motor learning is improved whereas their chemogenetic stimulation impairs motor learning performance. Thus, Egr1 organizes specific CA1 neuronal ensembles during the accelerating rotarod task that limit motor learning. These evidences highlight the role of the hippocampus in the control of this type of learning and we provide a possible underlying mechanism.SIGNIFICANCE STATEMENT It is a major topic in neurosciences the deciphering of the specific circuits underlying memory systems during the encoding of new information. However, the potential role of the hippocampus in the control of motor learning and the underlying mechanisms has been poorly addressed. In the present work we show how the hippocampus responds to motor learning and how the Egr1 molecule is one of the major responsible for such phenomenon controlling the rate of motor coordination performances.
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Affiliation(s)
- Verónica Brito
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurociències, Universitat de Barcelona, Barcelona 08036, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain, 28029 Madrid
| | - Enrica Montalban
- Biologie Fonctionnelle et Adaptative, Unité Mixte de Recherche 8251, Centre National de la Recherche Scientifique, Université de Paris, Paris F-75014, France
| | - Anna Sancho-Balsells
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurociències, Universitat de Barcelona, Barcelona 08036, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain, 28029 Madrid
| | - Anika Pupak
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurociències, Universitat de Barcelona, Barcelona 08036, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain, 28029 Madrid
| | - Francesca Flotta
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurociències, Universitat de Barcelona, Barcelona 08036, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain, 28029 Madrid
| | - Mercè Masana
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurociències, Universitat de Barcelona, Barcelona 08036, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain, 28029 Madrid
| | - Silvia Ginés
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurociències, Universitat de Barcelona, Barcelona 08036, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain, 28029 Madrid
| | - Jordi Alberch
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurociències, Universitat de Barcelona, Barcelona 08036, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain, 28029 Madrid
- Production and Validation Center of Advanced Therapies (Creatio), Faculty of Medicine and Health Science, University of Barcelona, Barcelona 08036, Spain
| | - Claire Martin
- Biologie Fonctionnelle et Adaptative, Unité Mixte de Recherche 8251, Centre National de la Recherche Scientifique, Université de Paris, Paris F-75014, France
| | - Jean-Antoine Girault
- Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche -S 1270, Paris 75005, France
- Science and Engineering Faculty, Sorbonne Université, Paris 75005, France
- Institut du Fer a Moulin, Paris 75005, France
| | - Albert Giralt
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurociències, Universitat de Barcelona, Barcelona 08036, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain, 28029 Madrid
- Production and Validation Center of Advanced Therapies (Creatio), Faculty of Medicine and Health Science, University of Barcelona, Barcelona 08036, Spain
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