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Chen X, Pacis A, Aracena KA, Gona S, Kwan T, Groza C, Lin YL, Sindeaux R, Yotova V, Pramatarova A, Simon MM, Pastinen T, Barreiro LB, Bourque G. Transposable elements are associated with the variable response to influenza infection. CELL GENOMICS 2023; 3:100292. [PMID: 37228757 PMCID: PMC10203045 DOI: 10.1016/j.xgen.2023.100292] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 11/15/2022] [Accepted: 03/06/2023] [Indexed: 05/27/2023]
Abstract
Influenza A virus (IAV) infections are frequent every year and result in a range of disease severity. Here, we wanted to explore the potential contribution of transposable elements (TEs) to the variable human immune response. Transcriptome profiling in monocyte-derived macrophages from 39 individuals following IAV infection revealed significant inter-individual variation in viral load post-infection. Using transposase-accessible chromatin using sequencing (ATAC-seq), we identified a set of TE families with either enhanced or reduced accessibility upon infection. Of the enhanced families, 15 showed high variability between individuals and had distinct epigenetic profiles. Motif analysis showed an association with known immune regulators (e.g., BATFs, FOSs/JUNs, IRFs, STATs, NFkBs, NFYs, and RELs) in stably enriched families and with other factors in variable families, including KRAB-ZNFs. We showed that TEs and host factors regulating TEs were predictive of viral load post-infection. Our findings shed light on the role TEs and KRAB-ZNFs may play in inter-individual variation in immunity.
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Affiliation(s)
- Xun Chen
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
| | - Alain Pacis
- Canadian Center for Computational Genomics, McGill University, Montréal, QC H3A 0G1, Canada
| | | | - Saideep Gona
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Tony Kwan
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC H3A 0G1, Canada
| | - Cristian Groza
- Quantitative Life Science, McGill University, Montréal, QC H3A 1E3, Canada
| | - Yen Lung Lin
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Renata Sindeaux
- Centre de Recherche, CHU Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Vania Yotova
- Centre de Recherche, CHU Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Albena Pramatarova
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC H3A 0G1, Canada
| | - Marie-Michelle Simon
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC H3A 0G1, Canada
| | - Tomi Pastinen
- Genomic Medicine Center, Children’s Mercy Hospital and Research Institute, Kansas City, MO 64108, USA
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Luis B. Barreiro
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Guillaume Bourque
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan
- Canadian Center for Computational Genomics, McGill University, Montréal, QC H3A 0G1, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC H3A 0G1, Canada
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
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Reimann TM, Müdsam C, Schachtler C, Ince S, Sticht H, Herrmann C, Stürzl M, Kost B. The large GTPase AtGBPL3 links nuclear envelope formation and morphogenesis to transcriptional repression. NATURE PLANTS 2023; 9:766-784. [PMID: 37095224 DOI: 10.1038/s41477-023-01400-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
Guanylate binding proteins (GBPs) are prominent regulators of immunity not known to be required for nuclear envelope formation and morphogenesis. Here we identify the Arabidopsis GBP orthologue AtGBPL3 as a lamina component with essential functions in mitotic nuclear envelope reformation, nuclear morphogenesis and transcriptional repression during interphase. AtGBPL3 is preferentially expressed in mitotically active root tips, accumulates at the nuclear envelope and interacts with centromeric chromatin as well as with lamina components transcriptionally repressing pericentromeric chromatin. Reduced expression of AtGBPL3 or associated lamina components similarly altered nuclear morphology and caused overlapping transcriptional deregulation. Investigating the dynamics of AtGBPL3-GFP and other nuclear markers during mitosis (1) revealed that AtGBPL3 accumulation on the surface of daughter nuclei precedes nuclear envelope reformation and (2) uncovered defects in this process in roots of AtGBPL3 mutants, which cause programmed cell death and impair growth. AtGBPL3 functions established by these observations are unique among dynamin-family large GTPases.
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Affiliation(s)
- Theresa Maria Reimann
- Cell Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Christina Müdsam
- Cell Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Christina Schachtler
- Cell Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Semra Ince
- Physical and Biophysical Chemistry, Department of Physical Chemistry 1, Ruhr-Universität Bochum (RUB), Bochum, Germany
| | - Heinrich Sticht
- Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Christian Herrmann
- Physical and Biophysical Chemistry, Department of Physical Chemistry 1, Ruhr-Universität Bochum (RUB), Bochum, Germany
| | - Michael Stürzl
- Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Benedikt Kost
- Cell Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
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53
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Tran VL, Liu P, Katsumura KR, Kim E, Schoff BM, Johnson KD, Bresnick EH. Restricting genomic actions of innate immune mediators on fetal hematopoietic progenitor cells. iScience 2023; 26:106297. [PMID: 36950124 PMCID: PMC10025987 DOI: 10.1016/j.isci.2023.106297] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/03/2023] [Accepted: 02/24/2023] [Indexed: 03/15/2023] Open
Abstract
Innate immune signaling protects against pathogens, controls hematopoietic development, and functions in oncogenesis, yet the relationship between these mechanisms is undefined. Downregulating the GATA2 transcription factor in fetal hematopoietic progenitor cells upregulates genes encoding innate immune regulators, increases Interferon-γ (IFNγ) signaling, and disrupts differentiation. We demonstrate that deletion of an enhancer that confers GATA2 expression in fetal progenitors elevated Toll-like receptor (TLR) TLR1/2 and TLR2/6 expression and signaling. Rescue by expressing GATA2 downregulated elevated TLR signaling. IFNγ amplified TLR1/2 and TLR2/6 signaling in GATA2-deficient progenitors, synergistically activating cytokine/chemokine genes and elevating cytokine/chemokine production in myeloid cell progeny. Genomic analysis of how innate immune signaling remodels the GATA2-deficient progenitor transcriptome revealed hypersensitive responses at innate immune genes harboring motifs for signal-dependent transcription factors and factors not linked to these mechanisms. As GATA2 establishes a transcriptome that constrains innate immune signaling, insufficient GATA2 renders fetal progenitor cells hypersensitive to innate immune signaling.
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Affiliation(s)
- Vu L. Tran
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Peng Liu
- Department of Biostatistics and Biomedical Informatics, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Koichi R. Katsumura
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Erin Kim
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Bjorn M. Schoff
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Kirby D. Johnson
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Emery H. Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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Meng K, Li YY, Liu DY, Hu LL, Pan YL, Zhang CZ, He QY. A five-protein prognostic signature with GBP2 functioning in immune cell infiltration of clear cell renal cell carcinoma. Comput Struct Biotechnol J 2023; 21:2621-2630. [PMID: 38213893 PMCID: PMC10781714 DOI: 10.1016/j.csbj.2023.04.015] [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: 11/30/2022] [Revised: 04/16/2023] [Accepted: 04/16/2023] [Indexed: 01/13/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is of poor clinical outcomes, and currently lacks reliable prognostic biomarkers. By analyzing the datasets of the Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC), we established a five-protein prognostic signature containing GBP2, HLA-DRA, ISG15, ISG20 and ITGAX. Our data indicate that this signature was closely correlated with advanced stage, higher pathological grade, and unfavorable survivals in patients with ccRCC. We further functionally characterized GBP2. Overexpression of GBP2 enhanced the phosphorylation of STAT2 and STAT3 to trigger JAK-STAT signaling and promote cell migration and invasion in ccRCC. Treatment of Ruxolitinib, a specific inhibitor of JAK/STAT, attenuated the GBP2-mediated phenotypes. Patients with high GBP2 expression were accompanied with more infiltration of immune cells positively stained with CD3, CD8, CD68, and immune checkpoint markers PD-1 and CTLA4, which was validated by Opal multiplex immunohistochemistry in ccRCC tissues. More CD8 + T cells and CD68 + macrophages were observed in patients expressing high GBP2. Taken together, a five-protein prognostic signature was constructed in our study. GBP2 has an oncogenic role via modulating JAK-STAT signaling and tumor immune infiltration, and thus may serve as a potential therapeutic target in ccRCC.
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Affiliation(s)
- Kun Meng
- The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yu-Ying Li
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Dan-Ya Liu
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Li-Ling Hu
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yun-Long Pan
- The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
| | - Chris Zhiyi Zhang
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Qing-Yu He
- The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510632, China
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
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55
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Kurhade C, Kang S, Biering SB, Hwang S, Randall G. CAPRIN1 Is Required for Control of Viral Replication Complexes by Interferon Gamma. mBio 2023:e0017223. [PMID: 37052473 DOI: 10.1128/mbio.00172-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Replication complexes (RCs), formed by positive-strand (+) RNA viruses through rearrangements of host endomembranes, protect their replicating RNA from host innate immune defenses. We have shown that two evolutionarily conserved defense systems, autophagy and interferon (IFN), target viral RCs and inhibit viral replication collaboratively. However, the mechanism by which autophagy proteins target viral RCs and the role of IFN-inducible GTPases in the disruption of RCs remains poorly understood. Here, using murine norovirus (MNV) as a model (+) RNA virus, we show that the guanylate binding protein 1 (GBP1) is the human GTPase responsible for inhibiting RCs. Furthermore, we found that ATG16L1 mediates the LC3 targeting of MNV RC by binding to WIPI2B and CAPRIN1, and that IFN gamma-mediated control of MNV replication was dependent on CAPRIN1. Collectively, this study identifies a novel mechanism for the autophagy machinery-mediated recognition and inhibition of viral RCs, a hallmark of (+) RNA virus replication. IMPORTANCE Replication complexes provide a microenvironment important for (+) RNA virus replication and shield it from host immune response. Previously we have shown that interferon gamma (IFNG) disrupts the RC of MNV via evolutionarily conserved autophagy proteins and IFN-inducible GTPases. Elucidating the mechanism of targeting of viral RC by ATG16L1 and IFN-induced GTPase will pave the way for development of therapeutics targeting the viral replication complexes. Here, we have identified GBP1 as the sole GBP targeting viral RC and uncovered the novel role of CAPRIN1 in recruiting ATG16L1 to the viral RC.
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Affiliation(s)
- Chaitanya Kurhade
- Department of Microbiology, The University of Chicago, Chicago, Illinois, USA
| | - Soowon Kang
- Department of Microbiology, The University of Chicago, Chicago, Illinois, USA
| | - Scott B Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Seungmin Hwang
- Department of Pathology, The University of Chicago, Chicago, Illinois, USA
| | - Glenn Randall
- Department of Microbiology, The University of Chicago, Chicago, Illinois, USA
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Ma H, Hu T, Tao W, Tong J, Han Z, Herndler-Brandstetter D, Wei Z, Liu R, Zhou T, Liu Q, Xu X, Zhang K, Zhou R, Cho JH, Li HB, Huang H, Flavell RA, Zhu S. A lncRNA from an inflammatory bowel disease risk locus maintains intestinal host-commensal homeostasis. Cell Res 2023; 33:372-388. [PMID: 37055591 PMCID: PMC10156687 DOI: 10.1038/s41422-023-00790-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 02/10/2023] [Indexed: 04/15/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are known to have complex, genetically influenced etiologies, involving dysfunctional interactions between the intestinal immune system and the microbiome. Here, we characterized how the RNA transcript from an IBD-associated long non-coding RNA locus ("CARINH-Colitis Associated IRF1 antisense Regulator of Intestinal Homeostasis") protects against IBD. We show that CARINH and its neighboring gene coding for the transcription factor IRF1 together form a feedforward loop in host myeloid cells. The loop activation is sustained by microbial factors, and functions to maintain the intestinal host-commensal homeostasis via the induction of the anti-inflammatory factor IL-18BP and anti-microbial factors called guanylate-binding proteins (GBPs). Extending these mechanistic insights back to humans, we demonstrate that the function of the CARINH/IRF1 loop is conserved between mice and humans. Genetically, the T allele of rs2188962, the most probable causal variant of IBD within the CARINH locus from the human genetics study, impairs the inducible expression of the CARINH/IRF1 loop and thus increases genetic predisposition to IBD. Our study thus illustrates how an IBD-associated lncRNA maintains intestinal homeostasis and protects the host against colitis.
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Affiliation(s)
- Hongdi Ma
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Taidou Hu
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Wanyin Tao
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Jiyu Tong
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Zili Han
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | | | - Zheng Wei
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Ruize Liu
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tingyue Zhou
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Qiuyuan Liu
- The Key Laboratory of Digestive Diseases of Anhui Province, Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xuemei Xu
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Kaiguang Zhang
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Rongbin Zhou
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Judy H Cho
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Hua-Bing Li
- Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China.
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA.
| | - Shu Zhu
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
- School of Data Science, University of Science and Technology of China, Hefei, Anhui, China.
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, Anhui, China.
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Zhou L, Zhao H, Zhao H, Meng X, Zhao Z, Xie H, Li J, Tang Y, Zhang Y. GBP5 exacerbates rosacea-like skin inflammation by skewing macrophage polarization towards M1 phenotype through the NF-κB signalling pathway. J Eur Acad Dermatol Venereol 2023; 37:796-809. [PMID: 36367676 DOI: 10.1111/jdv.18725] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND Rosacea is a chronic inflammatory skin disease with increased macrophage infiltration. However, the molecular mechanism remains unclear. OBJECTIVES To determine the significance of macrophage infiltration, and the correlation between Guanylate-binding protein 5 (GBP5) and polarization of macrophages in rosacea-like inflammation. METHODS Here we tested the hypothesis that Guanylate-binding protein 5 (GBP5) aggravates rosacea-like skin inflammation by promoting the polarization of the M1 macrophages through the NF-κB signalling pathway. We depleted macrophage by injecting clodronate-containing liposomes. We next explored the association between GBP5 and macrophage in rosacea tissue through transcriptome analysis and immunofluorescence analysis. We evaluated the severity of rosacea-like skin inflammation when BALB/c mice were injected with GBP5 siRNA intradermally daily for three consecutive days. At last, to study the causality of knocking down GBP5-blunted M1 macrophage polarization, THP-1 cell was treated with GBP5 siRNA. RESULTS Macrophage depletion ameliorated rosacea-like skin inflammation in mice, implying the important role of macrophages in rosacea. Based on the transcriptome analysis, Guanylate-binding protein 5 (GBP5) was identified as hub gene that was associated with macrophage infiltration in rosacea. Next, we found that GBP5 expression was significantly upregulated in rosacea tissues and positively correlated with macrophage infiltration, the immunofluorescence analysis revealed the co-localization between GBP5 and macrophages. In vivo, silencing of GBP5 attenuated rosacea-like skin inflammation in the LL-37-induced mouse model and suppressed the expression of M1 signature genes such as IL-6, iNOS and TNF-a. In vitro, knocking down GBP5 significantly blunted the polarization of the M1 macrophages partly by repressing the activation of the NF-κB signalling pathways. CONCLUSIONS Together, our study revealed the important role of macrophages in rosacea and identified GBP5 as a key regulator of rosacea by inducing M1 macrophage polarization via NF-κB signalling pathways.
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Affiliation(s)
- Lei Zhou
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Han Zhao
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - He Zhao
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Xin Meng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zhixiang Zhao
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Hongfu Xie
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Ji Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yan Tang
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yiya Zhang
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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Jiang T, Jin P, Huang G, Li SC. The function of guanylate binding protein 3 (GBP3) in human cancers by pan-cancer bioinformatics. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:9511-9529. [PMID: 37161254 DOI: 10.3934/mbe.2023418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
As a guanylate binding protein (GBPs) member, GBP3 is immune-associated and may participate in oncogenesis and cancer therapy. Since little has been reported on GBP3 in this field, we provide pan-cancer bioinformatics to investigate the role of GBP3 in human cancers. The GBP3 expression, related clinical outcomes, immune infiltrates, potential mechanisms and mutations were conducted using tools including TIMER2.0, GEPIA2.0, SRING, DAVID and cBioPortal. Results showed an increased risk of high GBP3 in Brain Lower Grade Glioma (LGG) and Lung Squamous Cell Carcinoma (LUSC) and a decreased risk of GBP3 in Sarcoma (SARC) and Skin Cutaneous Melanoma (SKCM) (p ≤ 0.05). GBP3 was negatively correlated with CAFs in Esophageal Adenocarcinoma (ESCA) and positively correlated with CAFs in LGG, LUSC and TGCG (p ≤ 0.05). In addition, GBP3 was positively correlated with CD8+ T cells in Bladder Urothelial Carcinoma (BLCA), Cervical Squamous Cell Carcinoma (CESC), Kidney Renal Clear Cell Carcinoma (KIRC), SARC, SKCM, SKCM-Metastasis and Uveal Melanoma (UVM) (p ≤ 0.05). Potentially, GBP3 may participate in the homeostasis between immune and adaptive immunity in cancers. Moreover, the most frequent mutation sites of GBP3 in cancers are R151Q/* and K380N. This study would provide new insight into cancer prognosis and therapy.
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Affiliation(s)
- Tongmeng Jiang
- Key Laboratory of Hainan Trauma and Disaster Rescue, The First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou 571199, China
- Engineering Research Center for Hainan Bio-Smart Materials and Bio-Medical Devices, Key Laboratory of Hainan Functional Materials and Molecular Imaging, Key Laboratory of Emergency and Trauma, Ministry of Education, College of Emergency and Trauma, Hainan Medical University, Haikou 571199, China
| | - Pan Jin
- Health Science Center, Yangtze University, Jingzhou 434023, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning 530021, China
| | - Guoxiu Huang
- Health Management Center, The People's Hospital of Guangxi Zhuang Autonomous Region; Guangxi Health Examination Center, Nanning 530021, China
| | - Shi-Cheng Li
- Department of Cardiology, The People's Hospital of Guangxi Zhuang Autonomous Region; Institute of Cardiovascular Sciences, Guangxi Academy of Medical Sciences, Nanning 530021, China
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59
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Zhang X, Du Q, Chen G, Jiang Y, Huang K, Li L, Tong D, Huang Y. Guanylate-binding protein 1 inhibits nuclear delivery of pseudorabies virus by disrupting structure of actin filaments. Vet Res 2023; 54:21. [PMID: 36918936 PMCID: PMC10015811 DOI: 10.1186/s13567-023-01154-0] [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: 09/20/2022] [Accepted: 12/23/2022] [Indexed: 03/16/2023] Open
Abstract
The alphaherpesvirus pseudorabies virus (PRV) is the causative agent of pseudorabies, responsible for severe economic losses to the swine industry worldwide. The interferon-inducible GTPase guanylate-binding protein 1 (GBP1) exhibits antiviral immunity. Our findings show that there is a robust upregulation in the expression of porcine GBP1 during PRV infection. GBP1 knockout promotes PRV infection, while GBP1 overexpression restricts it. Importantly, we found that GBP1 impeded the normal structure of actin filaments in a GTPase-dependent manner, preventing PRV virions from reaching the nucleus. We also discovered that viral US3 protein bound GBP1 to interfere with its GTPase activity. Finally, the interaction between US3 and GBP1 requires US3 serine/threonine kinase activity sites and the GTPase domain (aa 1 to 308) of GBP1. Taken together, this study offers fresh perspectives on how PRV manipulates the host's antiviral immune system.
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Affiliation(s)
- Xiaohua Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Qian Du
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Guiyuan Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yiyuan Jiang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Kai Huang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Linghao Li
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Dewen Tong
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.
| | - Yong Huang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.
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60
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Ma P, Gu K, Wen R, Li C, Zhou C, Zhao Y, Li H, Lei C, Yang X, Wang H. Guanylate-binding protein 1 restricts avian coronavirus infectious bronchitis virus-infected HD11 cells. Poult Sci 2023; 102:102398. [PMID: 36580763 PMCID: PMC9731647 DOI: 10.1016/j.psj.2022.102398] [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: 08/17/2022] [Revised: 10/23/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
The Infectious Bronchitis Virus (IBV), a coronavirus, is a key avian pathogen that causes acute and highly infectious viral respiratory diseases. IBV is an enveloped, positive-sense RNA virus, and the host factors that restrict infection and replication of the virus remain poorly understood. Guanylate-binding protein 1 (GBP1), an interferon-gamma (IFN-γ)-inducible guanosine triphosphatase (GTPase), is a major player in host immunity and provides defense against viral replication. However, the role of chicken GBP1 (chGBP1) in the IBV-life cycle is not well understood. Therefore, this study aimed to reveal the potential role of IFN-γ-induced chGBP1 in mediating host anti-IBV infection responses. We identified the host restriction factor, chGBP1, in IBV-infected chicken macrophages HD11 cell lines. We showed that chGBP1 was upregulated by treatment with both IFN-γ and IBV in HD11 cells. chGBP1 inhibited IBV replication in a dose-dependent manner and enhanced IFN-γ anti-IBV activity. Importantly, the GTPase domain of chGBP1 played a pivotal role in its anti-IBV activity. Furthermore, chGBP1 interacts with IBV Nucleocapsids protein to degrade IBV-N protein through the autophagy pathway. Taken together, our results demonstrate a critical role of chGBP1 in anti-IBV in macrophages HD11 cells.
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Affiliation(s)
- Peng Ma
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Kui Gu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Renqiao Wen
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Chao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Changyu Zhou
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Yu Zhao
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Hao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Changwei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Xin Yang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China.
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61
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Lacrimal Gland Epithelial Cells Shape Immune Responses through the Modulation of Inflammasomes and Lipid Metabolism. Int J Mol Sci 2023; 24:ijms24054309. [PMID: 36901740 PMCID: PMC10001612 DOI: 10.3390/ijms24054309] [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: 12/28/2022] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Lacrimal gland inflammation triggers dry eye disease through impaired tear secretion by the epithelium. As aberrant inflammasome activation occurs in autoimmune disorders including Sjögren's syndrome, we analyzed the inflammasome pathway during acute and chronic inflammation and investigated its potential regulators. Bacterial infection was mimicked by the intraglandular injection of lipopolysaccharide (LPS) and nigericin, known to activate the NLRP3 inflammasome. Acute injury of the lacrimal gland was induced by interleukin (IL)-1α injection. Chronic inflammation was studied using two Sjögren's syndrome models: diseased NOD.H2b compared to healthy BALBc mice and Thrombospondin-1-null (TSP-1-/-) compared to TSP-1WTC57BL/6J mice. Inflammasome activation was investigated by immunostaining using the R26ASC-citrine reporter mouse, by Western blotting, and by RNAseq. LPS/Nigericin, IL-1α and chronic inflammation induced inflammasomes in lacrimal gland epithelial cells. Acute and chronic inflammation of the lacrimal gland upregulated multiple inflammasome sensors, caspases 1/4, and interleukins Il1b and Il18. We also found increased IL-1β maturation in Sjögren's syndrome models compared with healthy control lacrimal glands. Using RNA-seq data of regenerating lacrimal glands, we found that lipogenic genes were upregulated during the resolution of inflammation following acute injury. In chronically inflamed NOD.H2b lacrimal glands, an altered lipid metabolism was associated with disease progression: genes for cholesterol metabolism were upregulated, while genes involved in mitochondrial metabolism and fatty acid synthesis were downregulated, including peroxisome proliferator-activated receptor alpha (PPARα)/sterol regulatory element-binding 1 (SREBP-1)-dependent signaling. We conclude that epithelial cells can promote immune responses by forming inflammasomes, and that sustained inflammasome activation, together with an altered lipid metabolism, are key players of Sjögren's syndrome-like pathogenesis in the NOD.H2b mouse lacrimal gland by promoting epithelial dysfunction and inflammation.
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62
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Olive AJ, Smith CM, Baer CE, Coers J, Sassetti CM. Mycobacterium tuberculosis Evasion of Guanylate Binding Protein-Mediated Host Defense in Mice Requires the ESX1 Secretion System. Int J Mol Sci 2023; 24:2861. [PMID: 36769182 PMCID: PMC9917499 DOI: 10.3390/ijms24032861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/24/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Cell-intrinsic immune mechanisms control intracellular pathogens that infect eukaryotes. The intracellular pathogen Mycobacterium tuberculosis (Mtb) evolved to withstand cell-autonomous immunity to cause persistent infections and disease. A potent inducer of cell-autonomous immunity is the lymphocyte-derived cytokine IFNγ. While the production of IFNγ by T cells is essential to protect against Mtb, it is not capable of fully eradicating Mtb infection. This suggests that Mtb evades a subset of IFNγ-mediated antimicrobial responses, yet what mechanisms Mtb resists remains unclear. The IFNγ-inducible Guanylate binding proteins (GBPs) are key host defense proteins able to control infections with intracellular pathogens. GBPs were previously shown to directly restrict Mycobacterium bovis BCG yet their role during Mtb infection has remained unknown. Here, we examine the importance of a cluster of five GBPs on mouse chromosome 3 in controlling Mycobacterial infection. While M. bovis BCG is directly restricted by GBPs, we find that the GBPs on chromosome 3 do not contribute to the control of Mtb replication or the associated host response to infection. The differential effects of GBPs during Mtb versus M. bovis BCG infection is at least partially explained by the absence of the ESX1 secretion system from M. bovis BCG, since Mtb mutants lacking the ESX1 secretion system become similarly susceptible to GBP-mediated immune defense. Therefore, this specific genetic interaction between the murine host and Mycobacteria reveals a novel function for the ESX1 virulence system in the evasion of GBP-mediated immunity.
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Affiliation(s)
- Andrew J. Olive
- Department of Microbiology & Molecular Genetics, College of Osteopathic Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Clare M. Smith
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 22710, USA
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Christina E. Baer
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01650, USA
| | - Jörn Coers
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 22710, USA
- Department of Immunology, Duke University Medical Center, Durham, NC 22710, USA
| | - Christopher M. Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01650, USA
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63
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Cypryk W, Czernek L, Horodecka K, Chrzanowski J, Stańczak M, Nurmi K, Bilicka M, Gadzinowski M, Walczak-Drzewiecka A, Stensland M, Eklund K, Fendler W, Nyman TA, Matikainen S. Lipopolysaccharide Primes Human Macrophages for Noncanonical Inflammasome-Induced Extracellular Vesicle Secretion. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:322-334. [PMID: 36525001 DOI: 10.4049/jimmunol.2200444] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 11/18/2022] [Indexed: 01/04/2023]
Abstract
Human macrophages secrete extracellular vesicles (EVs) loaded with numerous immunoregulatory proteins. Vesicle-mediated protein secretion in macrophages is regulated by poorly characterized mechanisms; however, it is now known that inflammatory conditions significantly alter both the quantities and protein composition of secreted vesicles. In this study, we employed high-throughput quantitative proteomics to characterize the modulation of EV-mediated protein secretion during noncanonical caspase-4/5 inflammasome activation via LPS transfection. We show that human macrophages activate robust caspase-4-dependent EV secretion upon transfection of LPS, and this process is also partially dependent on NLRP3 and caspase-5. A similar effect occurs with delivery of the LPS with Escherichia coli-derived outer membrane vesicles. Moreover, sensitization of the macrophages through TLR4 by LPS priming prior to LPS transfection dramatically augments the EV-mediated protein secretion. Our data demonstrate that this process differs significantly from canonical inflammasome activator ATP-induced vesiculation, and it is dependent on the autocrine IFN signal associated with TLR4 activation. LPS priming preceding the noncanonical inflammasome activation significantly enhances vesicle-mediated secretion of inflammasome components caspase-1, ASC, and lytic cell death effectors GSDMD, MLKL, and NINJ1, suggesting that inflammatory EV transfer may exert paracrine effects in recipient cells. Moreover, using bioinformatics methods, we identify 15-deoxy-Δ12,14-PGJ2 and parthenolide as inhibitors of caspase-4-mediated inflammation and vesicle secretion, indicating new therapeutic potential of these anti-inflammatory drugs.
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Affiliation(s)
- Wojciech Cypryk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz, Poland
| | - Liliana Czernek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz, Poland
| | - Katarzyna Horodecka
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz, Poland
| | - Jędrzej Chrzanowski
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, Lodz, Poland
| | - Marcin Stańczak
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, Lodz, Poland
| | - Katariina Nurmi
- Department of Rheumatology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Marcelina Bilicka
- Department of Rheumatology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Mariusz Gadzinowski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz, Poland
| | | | - Maria Stensland
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway; and
| | - Kari Eklund
- Department of Rheumatology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Wojciech Fendler
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, Lodz, Poland.,Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Tuula A Nyman
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway; and
| | - Sampsa Matikainen
- Department of Rheumatology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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64
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Sullivan KM, Jiang X, Guha P, Lausted C, Carter JA, Hsu C, Labadie KP, Kohli K, Kenerson HL, Daniel SK, Yan X, Meng C, Abbasi A, Chan M, Seo YD, Park JO, Crispe IN, Yeung RS, Kim TS, Gujral TS, Tian Q, Katz SC, Pillarisetty VG. Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases. Gut 2023; 72:325-337. [PMID: 35705369 PMCID: PMC9872249 DOI: 10.1136/gutjnl-2021-325808] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 05/25/2022] [Indexed: 02/01/2023]
Abstract
OBJECTIVE Programmed cell death protein 1 (PD-1) checkpoint inhibition and adoptive cellular therapy have had limited success in patients with microsatellite stable colorectal cancer liver metastases (CRLM). We sought to evaluate the effect of interleukin 10 (IL-10) blockade on endogenous T cell and chimeric antigen receptor T (CAR-T) cell antitumour function in CRLM slice cultures. DESIGN We created organotypic slice cultures from human CRLM (n=38 patients' tumours) and tested the antitumour effects of a neutralising antibody against IL-10 (αIL-10) both alone as treatment and in combination with exogenously administered carcinoembryonic antigen (CEA)-specific CAR-T cells. We evaluated slice cultures with single and multiplex immunohistochemistry, in situ hybridisation, single-cell RNA sequencing, reverse-phase protein arrays and time-lapse fluorescent microscopy. RESULTS αIL-10 generated a 1.8-fold increase in T cell-mediated carcinoma cell death in human CRLM slice cultures. αIL-10 significantly increased proportions of CD8+ T cells without exhaustion transcription changes, and increased human leukocyte antigen - DR isotype (HLA-DR) expression of macrophages. The antitumour effects of αIL-10 were reversed by major histocompatibility complex class I or II (MHC-I or MHC-II) blockade, confirming the essential role of antigen presenting cells. Interrupting IL-10 signalling also rescued murine CAR-T cell proliferation and cytotoxicity from myeloid cell-mediated immunosuppression. In human CRLM slices, αIL-10 increased CEA-specific CAR-T cell activation and CAR-T cell-mediated cytotoxicity, with nearly 70% carcinoma cell apoptosis across multiple human tumours. Pretreatment with an IL-10 receptor blocking antibody also potentiated CAR-T function. CONCLUSION Neutralising the effects of IL-10 in human CRLM has therapeutic potential as a stand-alone treatment and to augment the function of adoptively transferred CAR-T cells.
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Affiliation(s)
- Kevin M Sullivan
- Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Xiuyun Jiang
- Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Prajna Guha
- Immuno-Oncology Institute and Department of Medicine, Roger Williams Medical Center, Providence, Rhode Island, USA,Department of Surgery, Boston University School of Medicine, Boston, Massachusetts, USA
| | | | - Jason A Carter
- Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Cynthia Hsu
- Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Kevin P Labadie
- Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Karan Kohli
- Department of Surgery, University of Washington, Seattle, Washington, USA,Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Heidi L Kenerson
- Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Sara K Daniel
- Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Xiaowei Yan
- Institute for Systems Biology, Seattle, Washington, USA
| | | | - Arezou Abbasi
- Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Marina Chan
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Y David Seo
- Department of Surgery, University of Washington, Seattle, Washington, USA
| | - James O Park
- Department of Surgery, University of Washington, Seattle, Washington, USA
| | | | - Raymond S Yeung
- Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Teresa S Kim
- Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Taranjit S Gujral
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Qiang Tian
- Institute for Systems Biology, Seattle, Washington, USA .,National Research Center for Translational Medicine, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Steven C Katz
- Immuno-Oncology Institute and Department of Medicine, Roger Williams Medical Center, Providence, Rhode Island, USA,Department of Surgery, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Venu G Pillarisetty
- Department of Surgery, University of Washington, Seattle, Washington, USA .,Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
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65
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Ye S, Li S, Qin L, Zheng W, Liu B, Li X, Ren Z, Zhao H, Hu X, Ye N, Li G. GBP2 promotes clear cell renal cell carcinoma progression through immune infiltration and regulation of PD‑L1 expression via STAT1 signaling. Oncol Rep 2023; 49:49. [PMID: 36660930 PMCID: PMC9887463 DOI: 10.3892/or.2023.8486] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/05/2023] [Indexed: 01/21/2023] Open
Abstract
Guanylate‑binding protein 2 (GBP2) has been widely studied in cancer, however, its potential role in clear cell renal cell carcinoma (ccRCC) is not fully elucidated. The present study aimed to explore the effect of GBP2 on tumor progression and its possible underlying molecular mechanisms in ccRCC. The Cancer Genome Atlas, Gene Expression Omnibus, Cancer Cell Line Encyclopedia databases, and several bioinformatics analysis tools, such as Gene Expression Profiling Interactive Analysis 2, Kaplan‑Meier plotter, UALCAN, LinkedOmics, Metascape, GeneMANIA and Tumor Immune Estimation Resource, were used to characterize the functional relationship between GBP2 and ccRCC. Focusing on the association between GBP2 and programmed death ligand 1 (PD‑L1) in vitro, the regulatory mechanism was investigated by knockdown and overexpression of GBP2 in Caki‑1 and 786‑O cells using reverse transcription‑quantitative PCR, western blotting and co‑immunoprecipitation techniques. The results indicated that GBP2 was commonly upregulated in ccRCC, correlating with worse prognosis. In addition, GBP2 expression levels were positively associated with different patterns of immune cell infiltration, suggesting that the GBP2 gene regulates PD‑L1 expression via the signal transducer and activator of transcription 1 (STAT1) pathway. The present study suggested that GBP2 regulates tumor immune infiltration and promotes tumor immune escape through PD‑L1 expression, revealing a potential immunotherapeutic target for ccRCC.
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Affiliation(s)
- Shujiang Ye
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230012, P.R. China,Anhui Public Health Clinical Center, Hefei, Anhui 230012, P.R. China
| | - Siyu Li
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230012, P.R. China,Anhui Public Health Clinical Center, Hefei, Anhui 230012, P.R. China
| | - Lei Qin
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230012, P.R. China,Anhui Public Health Clinical Center, Hefei, Anhui 230012, P.R. China
| | - Wei Zheng
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230012, P.R. China,Anhui Public Health Clinical Center, Hefei, Anhui 230012, P.R. China
| | - Bin Liu
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230012, P.R. China,Anhui Public Health Clinical Center, Hefei, Anhui 230012, P.R. China
| | - Xiaohui Li
- Department of Anatomy, School of Basic Medicine, Anhui Medical University, Hefei, Anhui 230032, P.R. China
| | - Zhenhua Ren
- Department of Anatomy, School of Basic Medicine, Anhui Medical University, Hefei, Anhui 230032, P.R. China
| | - Huaiming Zhao
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230012, P.R. China,Anhui Public Health Clinical Center, Hefei, Anhui 230012, P.R. China
| | - Xudong Hu
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230012, P.R. China,Anhui Public Health Clinical Center, Hefei, Anhui 230012, P.R. China
| | - Nan Ye
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230012, P.R. China,Anhui Public Health Clinical Center, Hefei, Anhui 230012, P.R. China
| | - Guangyuan Li
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230012, P.R. China,Anhui Public Health Clinical Center, Hefei, Anhui 230012, P.R. China,The Lu'an Hospital Affiliated to Anhui Medical University, Lu'an, Anhui 237005, P.R. China,The Lu'an People's Hospital, Lu'an, Anhui 237005, P.R. China,Correspondence to: Dr Guangyuan Li, Department of Urology, The First Affiliated Hospital of Anhui Medical University, 100 Huaihai Avenue, Hefei, Anhui 230012, P.R. China, E-mail:
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66
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Korcari A, Nichols AEC, Buckley MR, Loiselle AE. Scleraxis-lineage cells are required for tendon homeostasis and their depletion induces an accelerated extracellular matrix aging phenotype. eLife 2023; 12:e84194. [PMID: 36656751 PMCID: PMC9908079 DOI: 10.7554/elife.84194] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/18/2023] [Indexed: 01/20/2023] Open
Abstract
Aged tendons have disrupted homeostasis, increased injury risk, and impaired healing capacity. Understanding mechanisms of homeostatic disruption is crucial for developing therapeutics to retain tendon health through the lifespan. Here, we developed a novel model of accelerated tendon extracellular matrix (ECM) aging via depletion of Scleraxis-lineage cells in young mice (Scx-DTR). Scx-DTR recapitulates many aspects of tendon aging including comparable declines in cellularity, alterations in ECM structure, organization, and composition. Single-cell RNA sequencing demonstrated a conserved decline in tenocytes associated with ECM biosynthesis in aged and Scx-DTR tendons, identifying the requirement for Scleraxis-lineage cells during homeostasis. However, the remaining cells in aged and Scx-DTR tendons demonstrate functional divergence. Aged tenocytes become pro-inflammatory and lose proteostasis. In contrast, tenocytes from Scx-DTR tendons demonstrate enhanced remodeling capacity. Collectively, this study defines Scx-DTR as a novel model of accelerated tendon ECM aging and identifies novel biological intervention points to maintain tendon function through the lifespan.
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Affiliation(s)
- Antonion Korcari
- Center for Musculoskeletal Research, Department of Orthopaedics & Rehabilitation, University of Rochester Medical CenterRochesterUnited States
- Department of Biomedical Engineering, University of RochesterRochesterUnited States
| | - Anne EC Nichols
- Center for Musculoskeletal Research, Department of Orthopaedics & Rehabilitation, University of Rochester Medical CenterRochesterUnited States
| | - Mark R Buckley
- Center for Musculoskeletal Research, Department of Orthopaedics & Rehabilitation, University of Rochester Medical CenterRochesterUnited States
- Department of Biomedical Engineering, University of RochesterRochesterUnited States
| | - Alayna E Loiselle
- Center for Musculoskeletal Research, Department of Orthopaedics & Rehabilitation, University of Rochester Medical CenterRochesterUnited States
- Department of Biomedical Engineering, University of RochesterRochesterUnited States
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67
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Mariappan V, Adikari S, Shanmugam L, Easow JM, Balakrishna Pillai A. Differential expression of interferon inducible protein: Guanylate binding protein (GBP1 & GBP2) in severe dengue. Free Radic Biol Med 2023; 194:131-146. [PMID: 36460216 DOI: 10.1016/j.freeradbiomed.2022.11.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/17/2022] [Accepted: 11/27/2022] [Indexed: 12/02/2022]
Abstract
Dengue virus is reported to activate endothelial cells (EC), but the precise cause for severe dengue (SD) is not known. Guanylate binding proteins (GBPs) are IFN-inducible proteins secreted by ECs and are involved in the anti-oxidant and anti-viral response. The involvement of GBPs in the pathogenesis of dengue remains under explored. In the present study, we quantified the mRNA and protein levels of GBP1 and 2 during acute, defervescence and convalescent phase in SD-10, dengue without warning sign-15 and dengue with warning sign-25 compared to other febrile illnesses-10 and healthy controls-8 using RT-PCR and ELISA respectively. Lipid peroxidation in plasma samples were measured using the Kei Satoh method. Protein and DNA oxidation were determined by ELISA. The efficacy of the proteins in predicting disease severity was done by Support Vector Machine (SVM) model. A significant (P ≤ 0.01) decrease in the levels of mRNA and protein of both GBP1 and GBP2 was observed during defervescence in both SD and DWW cases. The levels were significantly (P ≤ 0.05) tapered off in SD cases from acute till critical phases compared to other study groups. DNA, protein and lipid oxidation markers showed an increasing trend in SD (P ≤ 0.01). Both GBP1 & 2 were found to be negatively associated plasma leakage and oxidative stress markers. EC's activated with SD serum showed a reduced expression of GBP 1 and 2. Nevertheless, the SVM model revealed that plasma levels of proteins along with clinical symptoms could predict the disease outcomes with higher precision. This is the first study reporting a downregulated expression of GBP1 & 2 and their association with oxidative stress and plasma leakage in dengue cases. This suggests the importance of GBPs in regulating disease manifestation. However, further investigations are required to ascertain its role as a biomarker or therapeutic target in dengue infection.
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Affiliation(s)
- Vignesh Mariappan
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI) (Formerly Central Inter-Disciplinary Research Facility-CIDRF), Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, 607 402, India
| | - Shalinda Adikari
- Department of Information System and Analytics, National University of Singapore (NUS), Singapore, 117 417, Republic of Singapore
| | - Lokesh Shanmugam
- ICMR-National Institute of Epidemiology (ICMR-NIE), Ayapakkam, Chennai, 600 070, India; Mahatma Gandhi Medical College and Research Institute (MGMCRI), Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, 607 402, India
| | - Joshy M Easow
- Mahatma Gandhi Medical College and Research Institute (MGMCRI), Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, 607 402, India
| | - Agieshkumar Balakrishna Pillai
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI) (Formerly Central Inter-Disciplinary Research Facility-CIDRF), Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, 607 402, India.
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68
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Giannos P, Prokopidis K, Isanejad M, Wright HL. Markers of immune dysregulation in response to the ageing gut: insights from aged murine gut microbiota transplants. BMC Gastroenterol 2022; 22:533. [PMID: 36544093 PMCID: PMC9773626 DOI: 10.1186/s12876-022-02613-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Perturbations in the composition and diversity of the gut microbiota are accompanied by a decline in immune homeostasis during ageing, characterized by chronic low-grade inflammation and enhanced innate immunity. Genetic insights into the interaction between age-related alterations in the gut microbiota and immune function remain largely unexplored. METHODS We investigated publicly available transcriptomic gut profiles of young germ-free mouse hosts transplanted with old donor gut microbiota to identify immune-associated differentially expressed genes (DEGs). Literature screening of the Gene Expression Omnibus and PubMed identified one murine (Mus musculus) gene expression dataset (GSE130026) that included small intestine tissues from young (5-6 weeks old) germ-free mice hosts that were compared following 8 weeks after transplantation with either old (~ 24-month old; n = 5) or young (5-6 weeks old; n = 4) mouse donor gut microbiota. RESULTS A total of 112 differentially expressed genes (DEGs) were identified and used to construct a gut network of encoded proteins, in which DEGs were functionally annotated as being involved in an immune process based on gene ontology. The association between the expression of immune-process DEGs and abundance of immune infiltrates from gene signatures in normal colorectal tissues was estimated from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) project. The analysis revealed a 25-gene signature of immune-associated DEGs and their expression profile was positively correlated with naïve T-cell, effector memory T-cell, central memory T-cell, resident memory T-cell, exhausted T-cell, resting Treg T-cell, effector Treg T-cell and Th1-like colorectal gene signatures. Conclusions These genes may have a potential role as candidate markers of immune dysregulation during gut microbiota ageing. Moreover, these DEGs may provide insights into the altered immune response to microbiota in the ageing gut, including reduced antigen presentation and alterations in cytokine and chemokine production.
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Affiliation(s)
- Panagiotis Giannos
- Society of Meta-Research and Biomedical Innovation, London, UK.,Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Konstantinos Prokopidis
- Society of Meta-Research and Biomedical Innovation, London, UK.,Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK
| | - Masoud Isanejad
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK
| | - Helen L Wright
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, William Henry Duncan Building, 6 West Derby Street, Liverpool, L7 8TX, UK.
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69
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Plaza-Jennings AL, Valada A, O'Shea C, Iskhakova M, Hu B, Javidfar B, Ben Hutta G, Lambert TY, Murray J, Kassim B, Chandrasekaran S, Chen BK, Morgello S, Won H, Akbarian S. HIV integration in the human brain is linked to microglial activation and 3D genome remodeling. Mol Cell 2022; 82:4647-4663.e8. [PMID: 36525955 PMCID: PMC9831062 DOI: 10.1016/j.molcel.2022.11.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 09/12/2022] [Accepted: 11/17/2022] [Indexed: 12/23/2022]
Abstract
To explore genome organization and function in the HIV-infected brain, we applied single-nuclei transcriptomics, cell-type-specific chromosomal conformation mapping, and viral integration site sequencing (IS-seq) to frontal cortex from individuals with encephalitis (HIVE) and without (HIV+). Derepressive changes in 3D genomic compartment structures in HIVE microglia were linked to the transcriptional activation of interferon (IFN) signaling and cell migratory pathways, while transcriptional downregulation and repressive compartmentalization of neuronal health and signaling genes occurred in both HIVE and HIV+ microglia. IS-seq recovered 1,221 brain integration sites showing distinct genomic patterns compared with peripheral lymphocytes, with enrichment for sequences newly mobilized into a permissive chromatin environment after infection. Viral transcription occurred in a subset of highly activated microglia comprising 0.33% of all nuclei in HIVE brain. Our findings point to disrupted microglia-neuronal interactions in HIV and link retroviral integration to remodeling of the microglial 3D genome during infection.
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Affiliation(s)
- Amara L Plaza-Jennings
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aditi Valada
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Callan O'Shea
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marina Iskhakova
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Benxia Hu
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Behnam Javidfar
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gabriella Ben Hutta
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tova Y Lambert
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jacinta Murray
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bibi Kassim
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sandhya Chandrasekaran
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Benjamin K Chen
- Division of Infectious Diseases, Department of Medicine, Immunology Institute, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Susan Morgello
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Hyejung Won
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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70
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Peng Z, Zhang R, Kuang X, Yu C, Niu S, Du Y, Lu D, Li S, Teng Z, Lu S. Single-cell RNA-seq reveals interferon-induced guanylate-binding proteins are linked with sarcopenia. J Cachexia Sarcopenia Muscle 2022; 13:2985-2998. [PMID: 36162807 PMCID: PMC9745549 DOI: 10.1002/jcsm.13091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/07/2021] [Accepted: 09/02/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Sarcopenia is defined as an age-related progressive loss of muscle mass and/or strength. Although different factors can contribute to this disease, the underlying mechanisms remain unclear. We assessed transcriptional heterogeneity in skeletal muscles from sarcopenic and control mice at single-cell resolution. METHODS A mouse model was established to study sarcopenic skeletal muscles. Single-cell RNA-seq was performed on tibialis anterior (TA) muscle cells collected from sarcopenic and control mice. A series of bioinformatic analyses were carried out to identify and compare different cell types under different conditions. Immunofluorescence staining and western blotting were used to validate the findings from single-cell experiments. Tube formation assays were conducted to further evaluate the effects of Gbp2 on endothelial cells during angiogenesis. RESULTS A murine sarcopenia model was successfully established using a senescence-accelerated mouse strain (SAMP6, n = 5). Sarcopenia phenotype was induced by administration of dexamethasone (20 mg/kg) and reduced physical activity. Senescence-resistant mice strain (SAMR1) and SAMP6 strain with similar activity but injected with PBS were recruited as two control groups. As signs of sarcopenia, body weight, muscle cell counts and cross-sectional fibre area were all significantly decreased in sarcopenic mice (P value = 0.004, 0.03 and 0.035, respectively). After quality control, 13 612 TA muscle single-cell transcriptomes were retained for analysis. Fourteen cell clusters were identified from the profiled cells. Among them, two distinct endothelial subtypes were found to be dominant in the sarcopenia group (42.2% cells) and in the two control groups (59.1% and 47.9% cells), respectively. 191 differentially expressed genes were detected between the two endothelial subtypes. Sarcopenia-specific endothelial cell subtype exhibited a dramatic increase in the interferon family genes and the interferon-inducible guanylate-binding protein (GBP) family gene expressions. For example, Igtp and Gbp2 in sarcopenic endothelial cells were 5.4 and 13.3 times higher than those in the control groups, respectively. We further validated our findings in muscle specimens of sarcopenia patients and observed that GBP2 levels were increased in endothelial cells of a subset of patients (11 of 40 patients, 27.5%), and we identified significantly higher CD31 and GBP2 co-localization (P value = 0.001128). Finally, we overexpressed Gbp2 in human umbilical vein endothelial cells in vitro. The endothelial cells with elevated Gbp2 expression displayed compromised tube formation. CONCLUSIONS Our single-cell-based results suggested that endothelial cells may play critical roles in sarcopenia development through interferon-GBP signalling pathways, highlighting new therapeutic directions to slow down or even reverse age-related sarcopenia.
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Affiliation(s)
- Zhi Peng
- Department of Orthopedic Surgery, the First People's Hospital of Yunnan Province, the Affiliated Hospital of Kunming University of Science and Technology, the Key Laboratory of Digital Orthopaedics of Yunnan Provincial, Kunming, Yunnan, China
| | - Ruoyu Zhang
- InnoVec Biotherapeutics Co., Ltd, Beijing, China
| | - Xiaolin Kuang
- the First Department of Hepatic Diseases, the Third People's Hospital of Kunming City, Kunming, Yunnan, China
| | - Chen Yu
- Graduate School of Kunming Medical University, Kunming, Yunnan, China
| | - Shiwei Niu
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Science and Technology Achievement Incubation Center, Kunming Medical University, Kunming, Yunnan, China
| | - Yongjun Du
- Department of Orthopedic Surgery, the First People's Hospital of Yunnan Province, the Affiliated Hospital of Kunming University of Science and Technology, the Key Laboratory of Digital Orthopaedics of Yunnan Provincial, Kunming, Yunnan, China
| | - Di Lu
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Science and Technology Achievement Incubation Center, Kunming Medical University, Kunming, Yunnan, China
| | - Shaobo Li
- Department of Spinal Surgery, the First Affiliated Hospital of Dali University (School of Clinical Medicine), Dali, Yunnan, China
| | - Zhaowei Teng
- Department of Orthopedic Surgery, the First People's Hospital of Yunnan Province, the Affiliated Hospital of Kunming University of Science and Technology, the Key Laboratory of Digital Orthopaedics of Yunnan Provincial, Kunming, Yunnan, China
| | - Sheng Lu
- Department of Orthopedic Surgery, the First People's Hospital of Yunnan Province, the Affiliated Hospital of Kunming University of Science and Technology, the Key Laboratory of Digital Orthopaedics of Yunnan Provincial, Kunming, Yunnan, China
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Melo-Silva CR, Roman MI, Knudson CJ, Tang L, Xu RH, Tassetto M, Dolan P, Andino R, Sigal LJ. Interferon partly dictates a divergent transcriptional response in poxvirus-infected and bystander inflammatory monocytes. Cell Rep 2022; 41:111676. [PMID: 36417857 PMCID: PMC9798443 DOI: 10.1016/j.celrep.2022.111676] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/07/2022] [Accepted: 10/25/2022] [Indexed: 11/23/2022] Open
Abstract
Inflammatory monocytes (iMOs) and B cells are the main targets of the poxvirus ectromelia virus (ECTV) in the lymph nodes of mice and play distinct roles in surviving the infection. Infected and bystander iMOs control ECTV's systemic spread, preventing early death, while B cells make antibodies that eliminate ECTV. Our work demonstrates that within an infected animal that survives ECTV infection, intrinsic and bystander infection of iMOs and B cells differentially control the transcription of genes important for immune cell function and, perhaps, cell identity. Bystander cells upregulate metabolism, antigen presentation, and interferon-stimulated genes. Infected cells downregulate many cell-type-specific genes and upregulate transcripts typical of non-immune cells. Bystander (Bys) and infected (Inf) iMOs non-redundantly contribute to the cytokine milieu and the interferon response. Furthermore, we uncover how type I interferon (IFN-I) or IFN-γ signaling differentially regulates immune pathways in Inf and Bys iMOs and that, at steady state, IFN-I primes iMOs for rapid IFN-I production and antigen presentation.
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Affiliation(s)
- Carolina R. Melo-Silva
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Marisa I. Roman
- Department of Physics, St. Joseph University, Philadelphia PA 19131, USA
| | - Cory J. Knudson
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA,GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, PA 19426, USA
| | - Lingjuan Tang
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Ren-Huan Xu
- Advanced RNA Vaccine Technologies, Inc., 12358 Parklawn Dr, North Bethesda, MD 20852, USA
| | - Michel Tassetto
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Patrick Dolan
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94158, USA,Laboratory of Viral Diseases, NIAID, NIH, Bethesda, MD 20892-3210, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Luis J. Sigal
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107, USA,Lead contact,Correspondence:
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Coexpression Network Analysis-Based Identification of Critical Genes Differentiating between Latent and Active Tuberculosis. DISEASE MARKERS 2022; 2022:2090560. [PMID: 36411825 PMCID: PMC9674975 DOI: 10.1155/2022/2090560] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 10/25/2022] [Indexed: 11/13/2022]
Abstract
Methods Three Gene Expression Omnibus (GEO) microarray datasets (GSE19491, GSE98461, and GSE152532) were downloaded, with GSE19491 and GSE98461 then being merged to form a training dataset. Hub genes capable of differentiating between ATB and LTBI were then identified through differential expression analyses and a WGCNA analysis of this training dataset. Receiver operating characteristic (ROC) curves were then used to gauge to the diagnostic accuracy of these hub genes in the test dataset (GSE152532). Gene expression-based immune cell infiltration and the relationship between such infiltration and hub gene expression were further assessed via a single-sample gene set enrichment analysis (ssGSEA). Results In total, 485 differentially expressed genes were analyzed, with the WGCNA approach yielding 8 coexpression models. Of these, the black module was the most closely correlated with ATB. In total, five hub genes (FBXO6, ATF3, GBP1, GBP4, and GBP5) were identified as potential biomarkers associated with LTBI progression to ATB based on a combination of differential expression and LASSO analyses. The area under the ROC curve values for these five genes ranged from 0.8 to 0.9 in the test dataset, and ssGSEA revealed the expression of these genes to be negatively correlated with lymphocyte activity but positively correlated with myeloid and inflammatory cell activity. Conclusion The five hub genes identified in this study may play a novel role in tuberculosis-related immunopathology and offer value as novel biomarkers differentiating LTBI from ATB.
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73
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Varzari A, Deyneko IV, Bruun GH, Dembic M, Hofmann W, Cebotari VM, Ginda SS, Andresen BS, Illig T. Candidate genes and sequence variants for susceptibility to mycobacterial infection identified by whole-exome sequencing. Front Genet 2022; 13:969895. [PMID: 36338958 PMCID: PMC9632272 DOI: 10.3389/fgene.2022.969895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/04/2022] [Indexed: 11/13/2022] Open
Abstract
Inborn errors of immunity are known to influence susceptibility to mycobacterial infections. The aim of this study was to characterize the genetic profile of nine patients with mycobacterial infections (eight with BCGitis and one with disseminated tuberculosis) from the Republic of Moldova using whole-exome sequencing. In total, 12 variants in eight genes known to be associated with Mendelian Susceptibility to Mycobacterial Disease (MSMD) were detected in six out of nine patients examined. In particular, a novel splice site mutation c.373–2A>C in STAT1 gene was found and functionally confirmed in a patient with disseminated tuberculosis. Trio analysis was possible for seven out of nine patients, and resulted in 23 candidate variants in 15 novel genes. Four of these genes - GBP2, HEATR3, PPP1R9B and KDM6A were further prioritized, considering their elevated expression in immune-related tissues. Compound heterozygosity was found in GBP2 in a single patient, comprising a maternally inherited missense variant c.412G>A/p.(Ala138Thr) predicted to be deleterious and a paternally inherited intronic mutation c.1149+14T>C. Functional studies demonstrated that the intronic mutation affects splicing and the level of transcript. Finally, we analyzed pathogenicity of variant combinations in gene pairs and identified five patients with putative oligogenic inheritance. In summary, our study expands the spectrum of genetic variation contributing to susceptibility to mycobacterial infections in children and provides insight into the complex/oligogenic disease-causing mode.
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Affiliation(s)
- Alexander Varzari
- Laboratory of Human Genetics, Chiril Draganiuc Institute of Phthisiopneumology, Kishinev, Moldova
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
- *Correspondence: Alexander Varzari,
| | - Igor V. Deyneko
- Laboratory of Functional Genomics, Timiryazev Institute of Plant Physiology Russian Academy of Sciences, Moscow, Russia
| | - Gitte Hoffmann Bruun
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
- The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Maja Dembic
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
- The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Winfried Hofmann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Victor M. Cebotari
- Municipal Hospital of Phthisiopneumology, Department of Pediatrics, Kishinev, Moldova
| | - Sergei S. Ginda
- Laboratory of Immunology and Allergology, Chiril Draganiuc Institute of Phthisiopneumology, Kishinev, Moldova
| | - Brage S. Andresen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
- The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Thomas Illig
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
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Tian Y, Wang H, Guan W, Zhang X, Sun Y, Qian C, Song X, Peng B, Cui X. GBP2 serves as a novel prognostic biomarker and potential immune microenvironment indicator in renal cell carcinoma. Mol Carcinog 2022; 61:1082-1098. [PMID: 36222186 DOI: 10.1002/mc.23447] [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: 03/14/2022] [Revised: 05/18/2022] [Accepted: 06/29/2022] [Indexed: 11/11/2022]
Abstract
Since the application of immune checkpoint therapy (ICT) has gradually become a new strategy for clear cell renal cell carcinoma (ccRCC) treatment, biomarkers that predict the individual response to ICT is needed. This study aimed to identify a new clinical indicator for postoperative surveillance of ccRCC and prediction of ICT response. We investigated the GBP2 expression and its relation with immune cell infiltration in tumor microenvironment using public databases, clinical specimens and ccRCC cell lines. Bioinformatic analysis using public database revealed that GBP2 expression is higher in cancer tissues than in adherent normal tissues among different cancer types including ccRCC, and the same results were acquired from clinical tissue samples tested by Western Blot and PCR. In ccRCC cell lines, CCk-8 proliferation assay and apoptosis assessment suggested GBP2 facilitates the malignancy of ccRCC. 286 ccRCC patients were randomly divided into a training or validation cohort, and immunohistochemistry (IHC) and Kaplan-Meier analysis revealed that higher GBP2 expression is related to worse prognosis. C-index analysis implied that integrating GBP2 expression with TNM stage improved the accuracy in predicting prognosis of ccRCC patients compared to the solitary use of either. Bioinformatic analysis implied a relation between GBP2 and immunity, and GBP2 expression is positively related with suppressive immune markers in ccRCC microenvironment. Taken together, our study demonstrated the potential of GBP2 to sever as a prognostic predictor of ccRCC, and an association between GBP2 and tumor-infiltrating lymphocytes in ccRCC was observed, making it a promising indicator of ICT response.
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Affiliation(s)
- Yijun Tian
- Department of Urinary Surgery, The Third Affiliated Hospital of Naval Medical University (Eastern Hepatobiliary Surgery Hospital), Shanghai, China
| | - Hongru Wang
- Department of Urinary Surgery, The Third Affiliated Hospital of Naval Medical University (Eastern Hepatobiliary Surgery Hospital), Shanghai, China
| | - Wenbin Guan
- Department of Pathology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Xiangmin Zhang
- Department of Urinary Surgery, Luodian Hospital, Shanghai, China
| | - Ye Sun
- Department of Urinary Surgery, Postgraduate Training Base in Shanghai Gongli Hospital, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Cheng Qian
- Department of Urinary Surgery, Postgraduate Training Base in Shanghai Gongli Hospital, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Xu Song
- Department of Urology, Shanghai Seventh People's Hospital, Shanghai, China
| | - Bo Peng
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xingang Cui
- Department of Urinary Surgery, The Third Affiliated Hospital of Naval Medical University (Eastern Hepatobiliary Surgery Hospital), Shanghai, China.,Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
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Rinsky M, Weizman E, Ben-Asher HW, Eyal G, Zhu B, Levy O. Temporal gene expression patterns in the coral Euphyllia paradivisa reveal the complexity of biological clocks in the cnidarian-algal symbiosis. SCIENCE ADVANCES 2022; 8:eabo6467. [PMID: 36112690 PMCID: PMC9481131 DOI: 10.1126/sciadv.abo6467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/02/2022] [Indexed: 05/25/2023]
Abstract
Studying chronobiology in reef-building corals is challenging due to the tightly coupled symbiosis with their photosynthetic algae, Symbiodiniaceae. Although symbiosis requires metabolic synchronization and coordination of cellular processes in the holobiont, the cross-talk between the host and symbiont's clocks is still puzzling. Here, we use the mesophotic coral Euphyllia paradivisa to examine temporal gene expression patterns in symbiotic and aposymbiotic morphs exposed to natural light/dark cycles and constant darkness. Our comparative transcriptomic analyses revealed circadian and circatidal cycles of gene expression with a predominant diel pattern in both coral morphs. We found a substantial number of transcripts consistently rhythmic under both light conditions, including genes likely involved in the cnidarians' circadian clock, thus indicating that an endogenous clock, which can oscillate independently from the Symbiodiniaceae clock, exists in E. paradivisa. The analysis further manifests the remarkable impacts of symbiosis on transcriptional rhythms and implies that the algae's presence influences the host's biorhythm.
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Affiliation(s)
- Mieka Rinsky
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Eviatar Weizman
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Hiba Waldman Ben-Asher
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Gal Eyal
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
- ARC Centre of Excellence for Coral Reef Studies, School of Biological Sciences, University of Queensland St. Lucia, Queensland 4072, Australia
| | - Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Oren Levy
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
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76
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Li R, Wang YY, Wang SL, Li XP, Chen Y, Li ZA, He JH, Zhou ZH, Li JY, Guo XL, Wang XG, Wu YQ, Ren YQ, Zhang WJ, Wang XM, Guo G. GBP2 as a potential prognostic predictor with immune-related characteristics in glioma. Front Genet 2022; 13:956632. [PMID: 36186425 PMCID: PMC9523311 DOI: 10.3389/fgene.2022.956632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/05/2022] [Indexed: 11/20/2022] Open
Abstract
Guanylate binding protein 2 (GBP2) is a member of the guanine binding protein family, and its relationship with prognostic outcomes and tumor immune microenvironments in glioma remains elusive. We found GBP2 were increased in glioma tissues at both mRNA and protein levels. Kaplan-Meier curves revealed that high GBP2 expression was linked with worse survival of glioma patients, and multivariate Cox regression analysis indicated that high GBP2 expression was an independent prognostic factor for glioma. Combined analysis in immune database revealed that the expression of GBP2 was significantly related to the level of immune infiltration and immunomodulators. Single-cell analysis illustrated the high expression of GBP2 in malignant glioma cells showed the high antigen presentation capability, which were confirmed by real-time polymerase chain reaction (qRT-PCR) data. Additionally, the hsa-mir-26b-5p and hsa-mir-335-5p were predicted as GBP2 regulators and were validated in U87 and U251 cells. Our results first decipher immune-related characteristics and noncoding regulators of GBP2 in glioma, which may provide insights into associated immunotherapies and prognostic predictor.
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Affiliation(s)
- Ren Li
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yuan-Yuan Wang
- Department of Radiology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shu-Le Wang
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xue-Peng Li
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yang Chen
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Zi-Ao Li
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jian-Hang He
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Zi-Han Zhou
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jia-Yu Li
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiao-Long Guo
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiao-Gang Wang
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Yong-Qiang Wu
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ye-Qing Ren
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Wen-Ju Zhang
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiao-Man Wang
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Geng Guo
- Department of Neurosurgery, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- *Correspondence: Geng Guo,
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77
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Wang Z, He Y, Cun Y, Li Q, Zhao Y, Luo Z. Identification of potential key genes for immune infiltration in childhood asthma by data mining and biological validation. Front Genet 2022; 13:957030. [PMID: 36118895 PMCID: PMC9479007 DOI: 10.3389/fgene.2022.957030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/08/2022] [Indexed: 11/26/2022] Open
Abstract
Asthma is the most common chronic condition among children; however, the underlying molecular mechanism remains unclear. Dysregulated immune response and different infiltration states of immune cells are critical for asthma pathogenesis. Here, three childhood asthma gene expression datasets were used to detect key genes, immune cells, and pathways involved in childhood asthma. From these datasets, 33 common differentially expressed genes (DEGs) were identified, which showed enrichment in the T helper 1 (Th1) and T helper 2 (Th2) cell differentiation pathway and the T helper 17 (Th17) cell differentiation pathway. Using the weighted gene co-expression network analysis (WGCNA), CD3D and CD3G were identified as key genes closely correlated with childhood asthma. Upregulation of CD3D and CD3G was further validated in bronchoalveolar lavage cells from childhood asthmatics with control individuals by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The immune cell infiltration analysis indicated that CD3D and CD3G were negatively correlated with increased resting mast cells and eosinophils, and highly correlated with several cell markers of Th1, Th2, and Th17 cells. In addition, we found that CD3D and CD3G were closely related to the Th1 and Th2 cell differentiation pathway and the Th17 cell differentiation pathway. Our results reveal the important roles of two key genes and immune infiltration in the pathogenesis of childhood asthma. Thus, this study provides a new perspective for exploring potential molecular targets for childhood asthma treatment.
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Affiliation(s)
- Zhili Wang
- Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, Department of Respiratory Medicine, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Yu He
- Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, Department of Respiratory Medicine, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Yupeng Cun
- Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, Department of Respiratory Medicine, Children’s Hospital of Chongqing Medical University, Chongqing, China
- China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Qinyuan Li
- Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, Department of Respiratory Medicine, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Yan Zhao
- Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, Department of Respiratory Medicine, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Zhengxiu Luo
- Department of Respiratory Medicine, Children’s Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Zhengxiu Luo,
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78
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Sintov E, Nikolskiy I, Barrera V, Hyoje-Ryu Kenty J, Atkin AS, Gerace D, Ho Sui SJ, Boulanger K, Melton DA. Whole-genome CRISPR screening identifies genetic manipulations to reduce immune rejection of stem cell-derived islets. Stem Cell Reports 2022; 17:1976-1990. [PMID: 36055241 PMCID: PMC9481918 DOI: 10.1016/j.stemcr.2022.08.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/05/2022] [Accepted: 08/06/2022] [Indexed: 11/11/2022] Open
Abstract
Human embryonic stem cells (hESCs) provide opportunities for cell replacement therapy of insulin-dependent diabetes. Therapeutic quantities of human stem cell-derived islets (SC-islets) can be produced by directed differentiation. However, preventing allo-rejection and recurring autoimmunity, without the use of encapsulation or systemic immunosuppressants, remains a challenge. An attractive approach is to transplant SC-islets, genetically modified to reduce the impact of immune rejection. To determine the underlying forces that drive immunogenicity of SC-islets in inflammatory environments, we performed single-cell RNA sequencing (scRNA-seq) and whole-genome CRISPR screen of SC-islets under immune interaction with allogeneic peripheral blood mononuclear cells (PBMCs). Data analysis points to “alarmed” populations of SC-islets that upregulate genes in the interferon (IFN) pathway. The CRISPR screen in vivo confirms that targeting IFNγ-induced mediators has beneficial effects on SC-islet survival under immune attack. Manipulating the IFN response by depleting chemokine ligand 10 (CXCL10) in SC-islet grafts confers improved survival against allo-rejection compared with wild-type grafts in humanized mice. These results offer insights into the nature of immune destruction of SC-islets during allogeneic responses and provide targets for gene editing. IFN pathway induction sets the fate of SC-islets under allogeneic immune challenge “Alarm” genes drive immunogenicity of SC-islets Genetically modified SC-islets were generated and evaluated for hypo-immunogenicity CXCL10 depletion can reduce immune activation and SC-islet graft rejection
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Affiliation(s)
- Elad Sintov
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
| | - Igor Nikolskiy
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Victor Barrera
- Bioinformatics Core, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jennifer Hyoje-Ryu Kenty
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Alexander S Atkin
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Dario Gerace
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Shannan J Ho Sui
- Bioinformatics Core, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kyle Boulanger
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Douglas A Melton
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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79
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Geng X, Wu X, Yang Q, Xin H, Zhang B, Wang D, Liu L, Liu S, Chen Q, Liu Z, Zhang M, Pan S, Zhang X, Gao L, Jin Q. Whole transcriptome sequencing reveals neutrophils’ transcriptional landscape associated with active tuberculosis. Front Immunol 2022; 13:954221. [PMID: 36059536 PMCID: PMC9436479 DOI: 10.3389/fimmu.2022.954221] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Neutrophils have been recognized to play an important role in the pathogenesis of tuberculosis in recent years. Interferon-induced blood transcriptional signatures in ATB are predominantly driven by neutrophils. In this study, we performed global RNA-seq on peripheral blood neutrophils from active tuberculosis patients (ATB, n=15); latent tuberculosis infections (LTBI, n=22); and healthy controls (HC, n=21). The results showed that greater perturbations of gene expression patterns happened in neutrophils from ATB individuals than HC or those with LTBI, and a total of 344 differentially expressed genes (DEGs) were observed. Functional enrichment analysis showed that besides the interferon signaling pathway, multiple pattern recognition receptor pathways were significantly activated in ATB, such as NOD-like receptors and Toll-like receptors. Meanwhile, we also observed that the expression of genes related to endocytosis, secretory granules, and neutrophils degranulation were downregulated. Our data also showed that the NF-κB signaling pathway might be inhibited in patients with ATB, which could increase Mycobacterium tuberculosis survival and lead to active tuberculosis status. Furthermore, we validated the accuracy of some differentially expressed genes in an independent cohort using quantitative PCR, and obtained three novel genes (RBM3, CSRNP1, SRSF5) with the ability to discriminate active tuberculosis from LTBI and HC.
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Affiliation(s)
- Xingzhu Geng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaolin Wu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qianting Yang
- Guangdong Key Laboratory for Emerging Infectious Diseases, Shenzhen Key Laboratory of Infection & Immunity, Shenzhen Third People’s Hospital, Shenzhen, China
| | - Henan Xin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bin Zhang
- Center for Diseases Control and Prevention of Zhongmu, Zhengzhou, China
| | - Dakuan Wang
- Center for Diseases Control and Prevention of Zhongmu, Zhengzhou, China
| | - Liguo Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Song Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qi Chen
- Guangdong Key Laboratory for Emerging Infectious Diseases, Shenzhen Key Laboratory of Infection & Immunity, Shenzhen Third People’s Hospital, Shenzhen, China
| | - Zisen Liu
- Center for Diseases Control and Prevention of Zhongmu, Zhengzhou, China
| | - Mingxia Zhang
- Guangdong Key Laboratory for Emerging Infectious Diseases, Shenzhen Key Laboratory of Infection & Immunity, Shenzhen Third People’s Hospital, Shenzhen, China
| | - Shouguo Pan
- Center for Diseases Control and Prevention of Zhongmu, Zhengzhou, China
| | - Xiaobing Zhang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Qi Jin, ; Xiaobing Zhang, ; Lei Gao,
| | - Lei Gao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Qi Jin, ; Xiaobing Zhang, ; Lei Gao,
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Qi Jin, ; Xiaobing Zhang, ; Lei Gao,
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80
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Liu L, Chen F, Jiang S, Zhong B, Li W, Xu K, Wang Q, Wang Y, Cao J. Analysis of gene expression profile of peripheral blood in alveolar and cystic echinococcosis. Front Cell Infect Microbiol 2022; 12:913393. [PMID: 36034715 PMCID: PMC9405190 DOI: 10.3389/fcimb.2022.913393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
RNA-sequencing (RNA-seq) is a versatile, high-throughput technology that is being widely employed for screening differentially expressed genes (DEGs) in various diseases. Echinococcosis, a globally distributed zoonosis, has been reported to impose a heavy disease burden in pastoral areas of China. Herein we aimed to explore the molecular mechanisms underlying echinococcosis. In this study, peripheral blood samples were collected from six patients with alveolar echinococcosis (AE), six patients with cystic echinococcosis (CE), and six healthy controls. RNA-Seq (mRNA) was performed to detect gene transcript and expression levels, and DEGs were subjected to bioinformatic analyses. In comparison with healthy controls, 492 DEGs (270 upregulated, 222 downregulated) were found in the AE group and 424 DEGs (170 upregulated, 254 downregulated) were found in the CE group (|log2 (fold change)| > 1 and P < 0.05). Further, 60 genes were upregulated and 39 were downregulated in both the AE and CE groups. Gene ontology enrichment analysis indicated that DEGs were mainly involved in molecular functions, including extracellular space, extracellular region, organ and system development, and anatomical structure development. Protein–protein interaction (PPI) networks were constructed to depict the complex relationship between DEGs and interacting proteins.
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Affiliation(s)
- Lei Liu
- Department of Hospital Infection Management, Sichuan Provincial Orthopedic Hospital, Chengdu, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, (Chinese Center for Tropical Diseases Research); Key Laboratory of Parasite and Vector Biology, National Health Commission of People’s Republic of China; National Center for International Research on Tropical Diseases, China; World Health Organization Collaborating Center for Tropical Diseases, Shanghai, China
| | - Fan Chen
- Department of Microbiological Laboratory, Xindu County Center for Disease Control and Prevention, Chengdu, China
| | - Shan Jiang
- Department of Department of Environmental and School Health, Chengdu Center for Disease Control and Prevention, Chengdu, China
| | - Bo Zhong
- Institute of Parasitic Diseases, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Wei Li
- Department of Parasitic Diseases, Garzê Center for Disease Control and Prevention, Kangding, China
| | - Kejun Xu
- Department of Parasitic Diseases, Garzê Center for Disease Control and Prevention, Kangding, China
| | - Qi Wang
- Institute of Parasitic Diseases, Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Ying Wang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, (Chinese Center for Tropical Diseases Research); Key Laboratory of Parasite and Vector Biology, National Health Commission of People’s Republic of China; National Center for International Research on Tropical Diseases, China; World Health Organization Collaborating Center for Tropical Diseases, Shanghai, China
- *Correspondence: Ying Wang, ; Jianping Cao,
| | - Jianping Cao
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, (Chinese Center for Tropical Diseases Research); Key Laboratory of Parasite and Vector Biology, National Health Commission of People’s Republic of China; National Center for International Research on Tropical Diseases, China; World Health Organization Collaborating Center for Tropical Diseases, Shanghai, China
- The School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Ying Wang, ; Jianping Cao,
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81
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Pathogen-selective killing by guanylate-binding proteins as a molecular mechanism leading to inflammasome signaling. Nat Commun 2022; 13:4395. [PMID: 35906252 PMCID: PMC9338265 DOI: 10.1038/s41467-022-32127-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 07/18/2022] [Indexed: 11/08/2022] Open
Abstract
Inflammasomes are cytosolic signaling complexes capable of sensing microbial ligands to trigger inflammation and cell death responses. Here, we show that guanylate-binding proteins (GBPs) mediate pathogen-selective inflammasome activation. We show that mouse GBP1 and GBP3 are specifically required for inflammasome activation during infection with the cytosolic bacterium Francisella novicida. We show that the selectivity of mouse GBP1 and GBP3 derives from a region within the N-terminal domain containing charged and hydrophobic amino acids, which binds to and facilitates direct killing of F. novicida and Neisseria meningitidis, but not other bacteria or mammalian cells. This pathogen-selective recognition by this region of mouse GBP1 and GBP3 leads to pathogen membrane rupture and release of intracellular content for inflammasome sensing. Our results imply that GBPs discriminate between pathogens, confer activation of innate immunity, and provide a host-inspired roadmap for the design of synthetic antimicrobial peptides that may be of use against emerging and re-emerging pathogens. Guanylate-binding proteins (GBP) have a function in inflammasome formation and pathogen defence. Here the authors show that these GBP proteins are able to kill certain bacteria and promote selective inflammasome activation and that this is mediated by specific GBP protein regions.
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82
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Lara-Reyna S, Caseley EA, Topping J, Rodrigues F, Jimenez Macias J, Lawler SE, McDermott MF. Inflammasome activation: from molecular mechanisms to autoinflammation. Clin Transl Immunology 2022; 11:e1404. [PMID: 35832835 PMCID: PMC9262628 DOI: 10.1002/cti2.1404] [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: 04/27/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 11/09/2022] Open
Abstract
Inflammasomes are assembled by innate immune sensors that cells employ to detect a range of danger signals and respond with pro-inflammatory signalling. Inflammasomes activate inflammatory caspases, which trigger a cascade of molecular events with the potential to compromise cellular integrity and release the IL-1β and IL-18 pro-inflammatory cytokines. Several molecular mechanisms, working in concert, ensure that inflammasome activation is tightly regulated; these include NLRP3 post-translational modifications, ubiquitination and phosphorylation, as well as single-domain proteins that competitively bind to key inflammasome components, such as the CARD-only proteins (COPs) and PYD-only proteins (POPs). These diverse regulatory systems ensure that a suitable level of inflammation is initiated to counteract any cellular insult, while simultaneously preserving tissue architecture. When inflammasomes are aberrantly activated can drive excessive production of pro-inflammatory cytokines and cell death, leading to tissue damage. In several autoinflammatory conditions, inflammasomes are aberrantly activated with subsequent development of clinical features that reflect the degree of underlying tissue and organ damage. Several of the resulting disease complications may be successfully controlled by anti-inflammatory drugs and/or specific cytokine inhibitors, in addition to more recently developed small-molecule inhibitors. In this review, we will explore the molecular processes underlying the activation of several inflammasomes and highlight their role during health and disease. We also describe the detrimental effects of these inflammasome complexes, in some pathological conditions, and review current therapeutic approaches as well as future prospective treatments.
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Affiliation(s)
- Samuel Lara-Reyna
- Institute of Microbiology and Infection University of Birmingham Birmingham UK
| | - Emily A Caseley
- School of Biomedical Sciences, Faculty of Biological Sciences University of Leeds Leeds UK
| | - Joanne Topping
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, St James's University Hospital University of Leeds Leeds UK
| | - François Rodrigues
- AP-HP, Hôpital Tenon, Sorbonne Université, Service de Médecine interne Centre de Référence des Maladies Auto-inflammatoires et des Amyloses d'origine inflammatoire (CEREMAIA) Paris France
| | - Jorge Jimenez Macias
- Harvey Cushing Neuro-Oncology Laboratories, Department of Neurosurgery, Brigham and Women's Hospital Harvard Medical School Boston Massachusetts USA.,Brown Cancer Centre, Department of Pathology and Laboratory Medicine Brown University Providence Rhode Island USA
| | - Sean E Lawler
- Harvey Cushing Neuro-Oncology Laboratories, Department of Neurosurgery, Brigham and Women's Hospital Harvard Medical School Boston Massachusetts USA.,Brown Cancer Centre, Department of Pathology and Laboratory Medicine Brown University Providence Rhode Island USA
| | - Michael F McDermott
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, St James's University Hospital University of Leeds Leeds UK
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83
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Xu H, Jin J, Chen Y, Wu G, Zhu H, Wang Q, Wang J, Li S, Grigore FN, Ma J, Chen CC, Lan Q, Li M. GBP3 promotes glioblastoma resistance to temozolomide by enhancing DNA damage repair. Oncogene 2022; 41:3876-3885. [PMID: 35780181 DOI: 10.1038/s41388-022-02397-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 11/09/2022]
Abstract
Glioblastoma is the most common malignant brain cancer with dismal survival and prognosis. Temozolomide (TMZ) is a first-line chemotherapeutic agent for glioblastoma, but the emergence of drug resistance limits its anti-tumor activity. We previously discovered that the interferon inducible guanylate binding protein 3 (GBP3) is highly elevated and promotes tumorigenicity of glioblastoma. Here, we show that TMZ treatment significantly upregulates the expression of GBP3 and stimulator of interferon genes (STING), both of which increase TMZ-induced DNA damage repair and reduce cell apoptosis of glioblastoma cells. Mechanistically, relying on its N-terminal GTPase domain, GBP3 physically interacts with STING to stabilize STING protein levels, which in turn induces expression of p62 (Sequestosome 1), nuclear factor erythroid 2 like 2 (NFE2L2, NRF2), and O6-methlyguanine-DNA-methyltransferase (MGMT), leading to the resistance to TMZ treatment. Reducing GBP3 levels by RNA interference in glioblastoma cells markedly increases the sensitivity to TMZ treatment in vitro and in murine glioblastoma models. Clinically, GBP3 expression is high and positively correlated with STING, NRF2, p62, and MGMT expression in human glioblastoma tumors, and is associated with poor outcomes. These findings provide novel insight into TMZ resistance and suggest that GBP3 may represent a novel potential target for the treatment of glioblastoma.
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Affiliation(s)
- Hui Xu
- Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215004, Jiangsu, China.,Jiangsu Key Laboratory of Neuropsychiatric Disease, Institute of Neuroscience, Soochow University, Suzhou, 215004, Jiangsu, China
| | - Jing Jin
- Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215004, Jiangsu, China
| | - Ying Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215004, Jiangsu, China
| | - Guoqing Wu
- Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215004, Jiangsu, China
| | - Hua Zhu
- Department of Pediatrics, The First Hospital of China Medical University, Shenyang, 110122, Liaoning, China
| | - Qing Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215004, Jiangsu, China
| | - Ji Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215004, Jiangsu, China
| | - Shenggang Li
- Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215004, Jiangsu, China
| | | | - Jun Ma
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Clark C Chen
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Qing Lan
- Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Soochow University, Suzhou, 215004, Jiangsu, China. .,Jiangsu Key Laboratory of Neuropsychiatric Disease, Institute of Neuroscience, Soochow University, Suzhou, 215004, Jiangsu, China.
| | - Ming Li
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN, 55455, USA.
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84
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Correia CN, McHugo GP, Browne JA, McLoughlin KE, Nalpas NC, Magee DA, Whelan AO, Villarreal-Ramos B, Vordermeier HM, Gormley E, Gordon SV, MacHugh DE. High-resolution transcriptomics of bovine purified protein derivative-stimulated peripheral blood from cattle infected with Mycobacterium bovis across an experimental time course. Tuberculosis (Edinb) 2022; 136:102235. [DOI: 10.1016/j.tube.2022.102235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/08/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022]
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85
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Wei M, Qin Y, Qian K, Shang S, Zhao Y, Xie T, Xi J, Tang B. Class Ⅰ histone deacetylase inhibitor regulate of Mycobacteria-Driven guanylate-binding protein 1 gene expression. Microb Pathog 2022; 169:105655. [PMID: 35753598 DOI: 10.1016/j.micpath.2022.105655] [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: 01/25/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 11/27/2022]
Abstract
Guanylate-binding proteins (GBPs) are a class of interferon (IFN)-stimulated genes with well-established activity against viruses, intracellular bacteria, and parasites. The effect of epigenetic modification on GBP activity upon Mycobacterium tuberculosis (Mtb) infection is poorly understood. In this study, we found that Mtb infection can significantly increase the expression of GBPs. Class Ⅰ histone deacetylase inhibitor (HDACi) MS-275 can selectively inhibit GBP1 expression, ultimately affecting the release of inflammatory cytokines IL-1β and suppressing Mtb intracellular survival. Moreover, interfering with GBP1 expression could reduce the production of IL-1β and the level of cleaved-caspase-3 in response to Mtb infection. GBP1 silencing did not affect Mtb survival. Besides, using the bisulfite sequencing PCR, we showed that the CpG site of the GBP1 promoter was hypermethylated, and the methylation status of the GBP1 promoter did not change significantly upon Mtb infection. Overall, this study sheds light on the role of GBP in Mtb infection and provides a link between epigenetics and GBP1 activity.
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Affiliation(s)
- Meili Wei
- School of Life Science, Anhui Province Key Laboratory of Translational Cancer Research, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, Anhui, 233030, China; Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China.
| | - Yuexuan Qin
- School of Life Science, Anhui Province Key Laboratory of Translational Cancer Research, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, Anhui, 233030, China
| | - Kaiqiang Qian
- School of Life Science, Anhui Province Key Laboratory of Translational Cancer Research, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, Anhui, 233030, China
| | - Shengwen Shang
- School of Life Science, Anhui Province Key Laboratory of Translational Cancer Research, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, Anhui, 233030, China
| | - Yongjie Zhao
- School of Life Science, Anhui Province Key Laboratory of Translational Cancer Research, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, Anhui, 233030, China
| | - Tong Xie
- School of Life Science, Anhui Province Key Laboratory of Translational Cancer Research, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, Anhui, 233030, China
| | - Jun Xi
- School of Life Science, Anhui Province Key Laboratory of Translational Cancer Research, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, Anhui, 233030, China
| | - Bikui Tang
- School of Life Science, Anhui Province Key Laboratory of Translational Cancer Research, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, Anhui, 233030, China.
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86
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Akter S, Chauhan KS, Dunlap MD, Choreño-Parra JA, Lu L, Esaulova E, Zúñiga J, Artyomov MN, Kaushal D, Khader SA. Mycobacterium tuberculosis infection drives a type I IFN signature in lung lymphocytes. Cell Rep 2022; 39:110983. [PMID: 35732116 PMCID: PMC9616001 DOI: 10.1016/j.celrep.2022.110983] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 04/20/2022] [Accepted: 05/27/2022] [Indexed: 11/16/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) infects 25% of the world's population and causes tuberculosis (TB), which is a leading cause of death globally. A clear understanding of the dynamics of immune response at the cellular level is crucial to design better strategies to control TB. We use the single-cell RNA sequencing approach on lung lymphocytes derived from healthy and Mtb-infected mice. Our results show the enrichment of the type I IFN signature among the lymphoid cell clusters, as well as heat shock responses in natural killer (NK) cells from Mtb-infected mice lungs. We identify Ly6A as a lymphoid cell activation marker and validate its upregulation in activated lymphoid cells following infection. The cross-analysis of the type I IFN signature in human TB-infected peripheral blood samples further validates our results. These findings contribute toward understanding and characterizing the transcriptional parameters at a single-cell depth in a highly relevant and reproducible mouse model of TB.
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Affiliation(s)
- Sadia Akter
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA,These authors contributed equally
| | - Kuldeep S. Chauhan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA,These authors contributed equally
| | - Micah D. Dunlap
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - José Alberto Choreño-Parra
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA,Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas,” Mexico City 14080, Mexico,Laboratorio de Inmunoquímica I, Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 07320, Mexico
| | - Lan Lu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ekaterina Esaulova
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joaquin Zúñiga
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas,” Mexico City 14080, Mexico,Laboratorio de Inmunoquímica I, Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 07320, Mexico
| | - Maxim N. Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA.
| | - Shabaana A. Khader
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA,Lead contact,Correspondence: (D.K.), (S.A.K.) https://doi.org/10.1016/j.celrep.2022.110983
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87
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Ruhle M, Espinal-Enríquez J, Hernández-Lemus E. The Breast Cancer Protein Co-Expression Landscape. Cancers (Basel) 2022; 14:cancers14122957. [PMID: 35740621 PMCID: PMC9221059 DOI: 10.3390/cancers14122957] [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: 05/10/2022] [Revised: 06/03/2022] [Accepted: 06/11/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Proteins are among the most fundamental building blocks and molecular players behind the functions of cells and tissues. Their abundance and interaction patterns shape, to a large extent, what happens at the cellular and organ levels. This is also true regarding tumor tissues. In this work, we explored the patterns of abundance and co-occurrence of a large number of proteins in breast cancer cells and their healthy counterparts. We discovered the main differences and tried to see whether those differences may be associated with relevant aspects of the biology of these tumors. Our final goal is to provide information to empower cancer clinicians and pharmacologists to develop better diagnostic, prognostic, and therapeutic tools. Abstract Breast cancer is a complex phenotype (or better yet, several complex phenotypes) characterized by the interplay of a large number of cellular and biomolecular entities. Biological networks have been successfully used to capture some of the heterogeneity of intricate pathophenotypes, including cancer. Gene coexpression networks, in particular, have been used to study large-scale regulatory patterns. Ultimately, biological processes are carried out by proteins and their complexes. However, to date, most of the tumor profiling research has focused on the genomic and transcriptomic information. Here, we tried to expand this profiling through the analysis of open proteomic data via mutual information co-expression networks’ analysis. We could observe that there are distinctive biological processes associated with communities of these networks and how some transcriptional co-expression phenomena are lost at the protein level. These kinds of data and network analyses are a broad resource to explore cellular behavior and cancer research.
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Affiliation(s)
- Martín Ruhle
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico; (M.R.); (J.E.-E.)
| | - Jesús Espinal-Enríquez
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico; (M.R.); (J.E.-E.)
- Center for Complexity Sciences, Universidad Nacional Autonoma de Mexico, Mexico City 04510, Mexico
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City 14610, Mexico; (M.R.); (J.E.-E.)
- Center for Complexity Sciences, Universidad Nacional Autonoma de Mexico, Mexico City 04510, Mexico
- Correspondence: ; Tel.: +52-5555-5350-1970
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88
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Yao Y, Du Jiang P, Chao BN, Cagdas D, Kubo S, Balasubramaniyam A, Zhang Y, Shadur B, NaserEddin A, Folio LR, Schwarz B, Bohrnsen E, Zheng L, Lynberg M, Gottlieb S, Leney-Greene MA, Park AY, Tezcan I, Akdogan A, Gocmen R, Onder S, Rosenberg A, Soilleux EJ, Johnson E, Jackson PK, Demeter J, Chauvin SD, Paul F, Selbach M, Bulut H, Clatworthy MR, Tuong ZK, Zhang H, Stewart BJ, Bosio CM, Stepensky P, Clare S, Ganesan S, Pascall JC, Daumke O, Butcher GW, McMichael AJ, Simon AK, Lenardo MJ. GIMAP6 regulates autophagy, immune competence, and inflammation in mice and humans. J Exp Med 2022; 219:213217. [PMID: 35551368 PMCID: PMC9111091 DOI: 10.1084/jem.20201405] [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: 07/02/2020] [Revised: 01/18/2022] [Accepted: 03/16/2022] [Indexed: 11/26/2022] Open
Abstract
Inborn errors of immunity (IEIs) unveil regulatory pathways of human immunity. We describe a new IEI caused by mutations in the GTPase of the immune-associated protein 6 (GIMAP6) gene in patients with infections, lymphoproliferation, autoimmunity, and multiorgan vasculitis. Patients and Gimap6−/− mice show defects in autophagy, redox regulation, and polyunsaturated fatty acid (PUFA)–containing lipids. We find that GIMAP6 complexes with GABARAPL2 and GIMAP7 to regulate GTPase activity. Also, GIMAP6 is induced by IFN-γ and plays a critical role in antibacterial immunity. Finally, we observed that Gimap6−/− mice died prematurely from microangiopathic glomerulosclerosis most likely due to GIMAP6 deficiency in kidney endothelial cells.
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Affiliation(s)
- Yikun Yao
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Ping Du Jiang
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Brittany N Chao
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD.,Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Deniz Cagdas
- Division of Immunology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey.,Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey.,Ihsan Dogramaci Childrens Hospital, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Satoshi Kubo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Arasu Balasubramaniyam
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Yu Zhang
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Bella Shadur
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel.,The Garvan Institute of Medical Research, Immunology Division, Darlinghurst, Sydney, Australia.,St Vincent's Clinical School, University of New South Wales, Darlinghurst, Sydney, Australia
| | - Adeeb NaserEddin
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel
| | - Les R Folio
- Clinical Center, National Institutes of Health, Bethesda, MD
| | - Benjamin Schwarz
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Eric Bohrnsen
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Lixin Zheng
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Matthew Lynberg
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Simone Gottlieb
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Michael A Leney-Greene
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Ann Y Park
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Ilhan Tezcan
- Division of Immunology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey.,Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey.,Ihsan Dogramaci Childrens Hospital, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Ali Akdogan
- Division of Rheumatology, Department of Internal Medicine, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Rahsan Gocmen
- Department of Radiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Sevgen Onder
- Department of Pathology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Avi Rosenberg
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD.,Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
| | | | - Errin Johnson
- The Dunn School of Pathology, South Parks Road, Oxford, UK
| | - Peter K Jackson
- Baxter Laboratory, Departments of Microbiology & Immunology and Pathology Stanford University School of Medicine, Stanford, CA
| | - Janos Demeter
- Baxter Laboratory, Departments of Microbiology & Immunology and Pathology Stanford University School of Medicine, Stanford, CA
| | - Samuel D Chauvin
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Florian Paul
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Matthias Selbach
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Haydar Bulut
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Menna R Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Zewen K Tuong
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Hanlin Zhang
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Catharine M Bosio
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Polina Stepensky
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel
| | - Simon Clare
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Sundar Ganesan
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - John C Pascall
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Oliver Daumke
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Geoffrey W Butcher
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Andrew J McMichael
- Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anna Katharina Simon
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Michael J Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
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89
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Guanylate-Binding Protein 1 Regulates Infection-Induced Autophagy through TBK1 Phosphorylation. Cell Microbiol 2022. [DOI: 10.1155/2022/8612113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Invading bacteria can be degraded by selective autophagy, known as xenophagy. Recent studies have shown that the recruitment of autophagy adaptor proteins such as p62 to bacteria and its regulation by activated TANK-binding kinase 1 (TBK1) are required to overcome bacterial infection. However, the detailed molecular mechanisms behind this are not yet fully understood. Here, we show that the human guanylate-binding protein (GBP) family, especially GBP1, directs xenophagy against invading Group A Streptococcus (GAS) by promoting TBK1 phosphorylation. GBP1 exhibits a GAS-surrounding localization response to bacterially caused membrane damage mediated by the membrane damage sensor galectin-3. We found that GBP1 knockout attenuated TBK1 activation, followed by reduced p62 recruitment and lower bactericidal activity by xenophagy. Furthermore, GBP1-TBK1 interaction was detected by immunoprecipitation. Our findings collectively indicate that GBP1 contributes to GAS-targeted autophagy initiated by membrane damage detection by galectin-3 via TBK1 phosphorylation.
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90
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Chhabra S, Sharma KB, Kalia M. Human Guanylate-Binding Protein 1 Positively Regulates Japanese Encephalitis Virus Replication in an Interferon Gamma Primed Environment. Front Cell Infect Microbiol 2022; 12:832057. [PMID: 35663470 PMCID: PMC9160567 DOI: 10.3389/fcimb.2022.832057] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/19/2022] [Indexed: 12/03/2022] Open
Abstract
RNA virus infection triggers interferon (IFN) receptor signaling, leading to the activation of hundreds of interferon-stimulated genes (ISGs). Guanylate-binding proteins (GBPs) belong to one such IFN inducible subfamily of guanosine triphosphatases (GTPases) that have been reported to exert broad anti-microbial activity and regulate host defenses against several intracellular pathogens. Here, we investigated the role of human GBP1 (hGBP1) in Japanese encephalitis virus (JEV) infection of HeLa cells in both an IFNγ unprimed and primed environment. We observed enhanced expression of GBP1 both at transcript and protein levels upon JEV infection, and GBP1 association with the virus replication membranes. Depletion of hGBP1 through siRNA had no effect on JEV replication or virus induced cell death in the IFNγ unprimed environment. IFNγ stimulation provided robust protection against JEV infection. Knockdown of GBP1 in the primed environment upregulated expression and phosphorylation of signal transducer and activator of transcription 1 (STAT1) and significantly reduced JEV replication. Depletion of GBP1 in an IFNγ primed environment also inhibited virus replication in human neuroblastoma SH-SH5Y cells. Our data suggests that in the presence of IFNγ, GBP1 displays a proviral role by inhibiting innate immune responses to JEV infection.
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91
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Rowland RRR, Doerksen T, Lu A, Sheahan M, Lunney J, Dekkers J, Palinski RM. Effect of the host genotype at a Porcine Reproductive and Respiratory Syndrome (PRRS) resistance marker on evolution of the modified-live PRRS vaccine virus in pigs. Virus Res 2022; 316:198809. [PMID: 35568091 DOI: 10.1016/j.virusres.2022.198809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 10/18/2022]
Abstract
Porcine Reproductive and Respiratory Syndrome, Porcine Reproductive and Respiratory Syndrome Virus, PRRS, Whole genome sequencing, quasispecies, WUR allele.
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Affiliation(s)
- Raymond R R Rowland
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois, Champaign-Urbana, IL
| | - Tyler Doerksen
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS
| | - Andrea Lu
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS
| | - Maureen Sheahan
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS
| | - Joan Lunney
- USDA, ARS, BARC, Animal Parasitic Diseases Laboratory, Beltsville, MD
| | - Jack Dekkers
- Department of Animal Science, Iowa State University, Ames, IA
| | - Rachel M Palinski
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS; Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS.
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92
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Skariah S, Sultan AA, Mordue DG. IFN-induced cell-autonomous immune mechanisms in the control of intracellular protozoa. Parasitol Res 2022; 121:1559-1571. [DOI: 10.1007/s00436-022-07514-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 04/04/2022] [Indexed: 10/18/2022]
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93
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Schelle L, Côrte-Real JV, Esteves PJ, Abrantes J, Baldauf HM. Functional cross-species conservation of guanylate-binding proteins in innate immunity. Med Microbiol Immunol 2022; 212:141-152. [PMID: 35416510 PMCID: PMC9005921 DOI: 10.1007/s00430-022-00736-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/25/2022] [Indexed: 11/29/2022]
Abstract
Guanylate binding proteins (GBPs) represent an evolutionary ancient protein family widely distributed among eukaryotes. They are interferon (IFN)-inducible guanosine triphosphatases that belong to the dynamin superfamily. GBPs are known to have a major role in the cell-autonomous innate immune response against bacterial, parasitic and viral infections and are also involved in inflammasome activation. Evolutionary studies depicted that GBPs present a pattern of gain and loss of genes in each family with several genes pseudogenized and some genes more divergent, indicative for the birth-and-death evolution process. Most species harbor large GBP gene clusters encoding multiple paralogs. Previous functional studies mainly focused on mouse and human GBPs, but more data are becoming available, broadening the understanding of this multifunctional protein family. In this review, we will provide new insights and give a broad overview about GBP evolution, conservation and their roles in all studied species, including plants, invertebrates and vertebrates, revealing how far the described features of GBPs can be transferred to other species.
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Affiliation(s)
- Luca Schelle
- Faculty of Medicine, Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - João Vasco Côrte-Real
- Faculty of Medicine, Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany.,CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, 4485-661, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, 4169-007, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Pedro José Esteves
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, 4485-661, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, 4169-007, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,CITS-Center of Investigation in Health Technologies, CESPU, 4585-116, Gandra, Portugal
| | - Joana Abrantes
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, 4485-661, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, 4169-007, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Hanna-Mari Baldauf
- Faculty of Medicine, Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany.
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Côrte-Real JV, Baldauf HM, Melo-Ferreira J, Abrantes J, Esteves PJ. Evolution of Guanylate Binding Protein ( GBP) Genes in Muroid Rodents (Muridae and Cricetidae) Reveals an Outstanding Pattern of Gain and Loss. Front Immunol 2022; 13:752186. [PMID: 35222365 PMCID: PMC8863968 DOI: 10.3389/fimmu.2022.752186] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 01/20/2022] [Indexed: 01/05/2023] Open
Abstract
Guanylate binding proteins (GBPs) are paramount in the host immunity by providing defense against invading pathogens. Multigene families related to the immune system usually show that the duplicated genes can either undergo deletion, gain new functions, or become non-functional. Here, we show that in muroids, the Gbp genes followed an unusual pattern of gain and loss of genes. Muroids present a high diversity and plasticity regarding Gbp synteny, with most species presenting two Gbp gene clusters. The phylogenetic analyses revealed seven different Gbps groups. Three of them clustered with GBP2, GBP5 and GBP6 of primates. Four new Gbp genes that appear to be exclusive to muroids were identified as Gbpa, b, c and d. A duplication event occurred in the Gbpa group in the common ancestor of Muridae and Cricetidae (~20 Mya), but both copies were deleted from the genome of Mus musculus, M. caroli and Cricetulus griseus. The Gbpb gene emerged in the ancestor of Muridae and Cricetidae and evolved independently originating Gbpb1 in Muridae, Gbpb2 and Gbpb3 in Cricetidae. Since Gbpc appears only in three species, we hypothesize that it was present in the common ancestor and deleted from most muroid genomes. The second Gbp gene cluster, Gbp6, is widespread across all muroids, indicating that this cluster emerged before the Muridae and Cricetidae radiation. An expansion of Gbp6 occurred in M. musculus and M. caroli probably to compensate the loss of Gbpa and b. Gbpd is divided in three groups and is present in most muroids suggesting that a duplication event occurred in the common ancestor of Muridae and Cricetidae. However, in Grammomys surdaster and Mus caroli, Gbpd2 is absent, and in Arvicanthis niloticus, Gbpd1 appears to have been deleted. Our results further demonstrated that primate GBP1, GBP3 and GBP7 are absent from the genome of muroids and showed that the Gbp gene annotations in muroids were incorrect. We propose a new classification based on the phylogenetic analyses and the divergence between the groups. Extrapolations to humans based on functional studies of muroid Gbps should be re-evaluated. The evolutionary analyses of muroid Gbp genes provided new insights about the evolution and function of these genes.
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Affiliation(s)
- João Vasco Côrte-Real
- Research Center in Biodiversity and Genetic Resources (CIBIO-InBIO), University of Porto, Vairão, Portugal.,Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU) München, Munich, Germany.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Research Center in Biodiversity and Genetic Resources (CIBIO), Vairão, Portugal
| | - Hanna-Mari Baldauf
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU) München, Munich, Germany
| | - José Melo-Ferreira
- Research Center in Biodiversity and Genetic Resources (CIBIO-InBIO), University of Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Research Center in Biodiversity and Genetic Resources (CIBIO), Vairão, Portugal
| | - Joana Abrantes
- Research Center in Biodiversity and Genetic Resources (CIBIO-InBIO), University of Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Research Center in Biodiversity and Genetic Resources (CIBIO), Vairão, Portugal
| | - Pedro José Esteves
- Research Center in Biodiversity and Genetic Resources (CIBIO-InBIO), University of Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Research Center in Biodiversity and Genetic Resources (CIBIO), Vairão, Portugal.,Center of Investigation in Health Technologies (CITS), CESPU, Gandra, Portugal
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95
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Wang H, Zhou Y, Zhang Y, Fang S, Zhang M, Li H, Xu F, Liu L, Liu J, Zhao Q, Wang F. Subtyping of microsatellite stability colorectal cancer reveals guanylate binding protein 2 (GBP2) as a potential immunotherapeutic target. J Immunother Cancer 2022; 10:jitc-2021-004302. [PMID: 35383115 PMCID: PMC8984016 DOI: 10.1136/jitc-2021-004302] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2022] [Indexed: 12/12/2022] Open
Abstract
Backgrounds Proficient-mismatch-repair or microsatellite stability (pMMR/MSS) colorectal cancer (CRC) has limited efficacy for immune checkpoint blockade (ICB) therapy and its underlying mechanism remains unclear. Guanylate binding protein 2 (GBP2) is a member of the GTPase family and is crucial to host immunity against pathogens. However, the correlations between GBP2 and immunosurveillance and immunotherapy for pMMR/MSS CRC have not been reported. Methods Unsupervised clustering was employed to classify immune class and non-immune class in 1424 pMMR/MSS patients from six independent public datasets. This binary classification was validated using immune cells or response related signatures. The correlation between GBP2 and immune microenvironment was explored using well-established biological algorithms, multiplex immunohistochemistry (mIHC), in vitro and in vivo experiments. Results We classified 1424 pMMR/MSS CRC patients into two classes, ‘immune’ and ‘non-immune’, and GBP2 was identified as a gene of interest. We found that lower GBP2 expression was correlated with poor prognosis and metastasis. GBP2 expression was also upregulated in the immune class and highly associated with interferon-γ (IFN-γ) signaling pathway and CD8 +T cell infiltration using gene set enrichment analysis, gene ontology analysis, single-cell sequencing and mIHC. Moreover, reduced GBP2 expression inhibited the antigen processing and presentation machinery and CXCL10/11 expression in MSS CRC cells on IFN-γ stimulation. A Transwell assay revealed that deletion of GBP2 in murine MSS CRC cells reduced CD8 +T cell migration. Mechanistically, GBP2 promoted signal transducer and transcription activator 1 (STAT1) phosphorylation by competing with SHP1 for binding to STAT1 in MSS CRC cells. Finally, an unsupervised subclass mapping (SubMap) algorithm showed that pMMR/MSS patients with high GBP2 expression may correlate with a favorable response to anti-PD-1 therapy. We further confirmed that GBP2 knockout reduced CD8 +T cell infiltration and blunted the efficacy of PD-1 blockade in tumor-bearing mice. Conclusions Our study reveals that pMMR/MSS CRC is immunogenically heterogeneous and that GBP2 is a promising target for combinatorial therapy with ICB.
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Affiliation(s)
- Haizhou Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Yabo Zhou
- Department of Immunology & National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, China
| | - Yangyang Zhang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Shilin Fang
- Department of Pain, Renmin Hospital of Wuhan University, Wuhan, China
| | - Meng Zhang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Haiou Li
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Fei Xu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Lan Liu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Jing Liu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China .,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China .,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
| | - Fan Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China .,Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, China
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96
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Sasai M, Yamamoto M. Anti-toxoplasma host defense systems and the parasitic counterdefense mechanisms. Parasitol Int 2022; 89:102593. [DOI: 10.1016/j.parint.2022.102593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 04/12/2022] [Accepted: 04/26/2022] [Indexed: 10/18/2022]
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97
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8-Oxoguanine DNA Glycosylase (OGG1) Deficiency Exacerbates Doxorubicin-Induced Cardiac Dysfunction. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:9180267. [PMID: 35391931 PMCID: PMC8981022 DOI: 10.1155/2022/9180267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 02/13/2022] [Accepted: 03/01/2022] [Indexed: 12/13/2022]
Abstract
Doxorubicin is an anthracycline widely used for the treatment of various cancers; however, the drug has a common deleterious side effect, namely a dose-dependent cardiotoxicity. Doxorubicin treatment increases the generation of reactive oxygen species, which leads to oxidative stress in the cardiac cells and ultimately DNA damage and cell death. The most common DNA lesion produced by oxidative stress is 7,8-dihydro-8-oxoguanine (8-oxoguanine), and the enzyme responsible for its repair is the 8-oxoguanine DNA glycosylase (OGG1), a base excision repair enzyme. Here, we show that the OGG1 deficiency has no major effect on cardiac function at baseline or with pressure overload; however, we found an exacerbation of cardiac dysfunction as well as a higher mortality in Ogg1 knockout mice treated with doxorubicin. Our transcriptomic analysis also showed a more extensive dysregulation of genes in the hearts of Ogg1 knockout mice with an enrichment of genes involved in inflammation. These results demonstrate that OGG1 attenuates doxorubicin-induced cardiotoxicity and thus plays a role in modulating drug-induced cardiomyopathy.
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98
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The genetics behind inflammasome regulation. Mol Immunol 2022; 145:27-42. [PMID: 35278849 DOI: 10.1016/j.molimm.2022.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/10/2022] [Accepted: 03/01/2022] [Indexed: 12/14/2022]
Abstract
The inflammasome is a cytosolic multiproteic complex that promotes proinflammatory events through the release of the cytokines IL-1β and IL-18, and in some context by the induction of a lytic cell death called pyroptosis, in response to damage, infections, or changes in the homeostasis. Due to the powerful inflammatory effect, there are several regulatory mechanisms that are essential to modulate or limit the activation of the inflammasome. When these mechanisms fail, the deregulation of the complex leads or contributes to the development of a plethora of diseases characterized by constitutive and/or chronic inflammation, such as autoinflammatory, autoimmune, cardiovascular, neurodegenerative, and metabolic diseases, cancer, or even severe complications of infectious diseases. Either environmental or genetic factors may affect the threshold and/or the level of inflammasome activation, such as hyperglycemia, hyperuricemia, auto-antibodies, unfolded proteins and fibrils, or individual genetic variants in genes coding for inflammasome receptors or effector molecules, and also in regulators. While the genetics of inflammasome itself has been elsewhere characterized and also recently reviewed by our group, less is known about how genetic variants in regulatory molecules could affect inflammatory diseases. Therefore in this work, we selected a group of known or possible regulators of the inflammasome, and through the review of genetic association studies we tried to depict the contribution of these regulators in the development of multifactorial diseases.
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99
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Sun G, Qiu L, Yu L, An Y, Ding Y, Zhou L, Wu J, Yang X, Zhang Z, Tang X, Xia H, Cao L, You F, Zhao X, Du H. Loss of Function Mutation in ELF4 Causes Autoinflammatory and Immunodeficiency Disease in Human. J Clin Immunol 2022; 42:798-810. [PMID: 35266071 DOI: 10.1007/s10875-022-01243-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 02/28/2022] [Indexed: 02/04/2023]
Abstract
Monogenic autoinflammatory diseases (mAIDs) are a heterogeneous group of diseases affecting primarily innate immunity, with various genetic causes. Genetic diagnosis of mAIDs can assist in the patient's management and therapy. However, a large number of sporadic and familial cases remain genetically uncharacterized. Deficiency in ELF4, X-linked (DEX) is recently identified as a novel mAID. Here, we described a pediatric patient suffering from recurrent viral and bacterial respiratory infection, refractory oral ulcer, constipation, and arthritis. Whole-exome sequencing found a hemizygous variant in ELF4 (chrX:129205133 A > G, c.691 T > C, p.W231R). Using cells from patient and point mutation mice, we showed mutant cells failed to restrict viral replication effectively and produced more pro-inflammatory cytokines. RNA-seq identified several potential critical antiviral and anti-inflammation genes with decreased expression, and ChIP-qPCR assay suggested mutant ELF4 failed to bind to the promoters of these genes. Thus, we presented the second report of DEX.
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Affiliation(s)
- Gan Sun
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Luyao Qiu
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Lang Yu
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yunfei An
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
- Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yuan Ding
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Lina Zhou
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Junfeng Wu
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
- Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xi Yang
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
- Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Zhiyong Zhang
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
- Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xuemei Tang
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
- Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Huawei Xia
- Beijing Key Laboratory of Tumor Systems Biology, Department of Immunology, School of Basic Medical Sciences, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, 100000, China
| | - Lili Cao
- Beijing Key Laboratory of Tumor Systems Biology, Department of Immunology, School of Basic Medical Sciences, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, 100000, China
| | - Fuping You
- Beijing Key Laboratory of Tumor Systems Biology, Department of Immunology, School of Basic Medical Sciences, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, 100000, China
| | - Xiaodong Zhao
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China.
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China.
- The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400014, China.
| | - Hongqiang Du
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China.
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China.
- Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China.
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100
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Zhao Y, Wu J, Li L, Zhang H, Zhang H, Li J, Zhong H, Lei T, Jin Y, Xu B, Song Q. Guanylate-Binding Protein 1 as a Potential Predictor of Immunotherapy: A Pan-Cancer Analysis. Front Genet 2022; 13:820135. [PMID: 35222540 PMCID: PMC8867058 DOI: 10.3389/fgene.2022.820135] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/11/2022] [Indexed: 01/14/2023] Open
Abstract
Background: Mainstream application of cancer immunotherapy is hampered by the low response rate of most cancer patients. A novel immunotherapeutic target or a biomarker predicting response to immunotherapy needs to be developed. Guanylate-binding protein 1 (GBP1) is an interferon (IFN)-inducible guanosine triphosphatases (GTPases) involving inflammation and infection. However, the immunological effects of GBP1 in pan-cancer patients are still obscure. Methods: Using large-scale public data, we delineated the landscape of GBP1 across 33 cancer types. The correlation between GBP1 expression or mutation and immune cell infiltration was estimated by ESTIMATE, TIMER, xCell, and quanTIseq algorithms. GBP1-related genes and proteins were subjected to function enrichment analysis. Clustering analysis explored the relationship between GBP1 expression and anti-tumor immune phenotypes. We assessed the patient’s response to immunotherapy using the tumor immune dysfunction and exclusion (TIDE) score and immunophenoscore (IPS). Furthermore, we validated the predictive power of GBP1 expression in four independent immunotherapy cohorts. Results: GBP1 was differentially expressed in tumors and normal tissues in multiple cancer types. Distinct correlations existed between GBP1 expression and prognosis in cancer patients. GBP1 expression and mutation were positively associated with immune cell infiltration. Function enrichment analysis showed that GBP1-related genes were enriched in immune-related pathways. Positive correlations were also observed between GBP1 expression and the expression of immune checkpoints, as well as tumor mutation burden (TMB). Pan-cancer patients with higher GBP1 expression were more inclined to display “hot” anti-tumor immune phenotypes and had lower TIDE scores and higher immunophenoscore, suggesting that these patients had better responses to immunotherapy. Patients with higher GBP1 expression exhibited improved overall survival and clinical benefits in immunotherapy cohorts, including the Gide et al. cohort [area under the curve (AUC): 0.813], the IMvigor210 cohort (AUC: 0.607), the Lauss et al. cohort (AUC: 0.740), and the Kim et al. cohort (AUC: 0.793). Conclusion: This study provides comprehensive insights into the role of GBP1 in a pan-cancer manner. We identify GBP1 expression as a predictive biomarker for immunotherapy, potentially enabling more precise and personalized immunotherapeutic strategies in the future.
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Affiliation(s)
- Yaqi Zhao
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jie Wu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lan Li
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Huibo Zhang
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technical University of Munich, Freising, Germany
| | - Haohan Zhang
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jing Li
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Hao Zhong
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Tianyu Lei
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yan Jin
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Bin Xu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Bin Xu, ; Qibin Song,
| | - Qibin Song
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Bin Xu, ; Qibin Song,
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