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Peng P, Shen Y. Identification of shared disease marker genes and underlying mechanisms between rheumatoid arthritis and Crohn disease through bioinformatics analysis. Medicine (Baltimore) 2024; 103:e38690. [PMID: 38941374 DOI: 10.1097/md.0000000000038690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/30/2024] Open
Abstract
As chronic autoimmune inflammatory diseases, rheumatoid arthritis (RA) and Crohn disease (CD) are closely associated and display a significant positive correlation. However, the underlying mechanisms and disease markers responsible for their cooccurrence remain unknown and have not been systematically studied. Therefore, this study aimed to identify key molecules and pathways commonly involved in both RA and CD through bioinformatic analysis of public sequencing databases. Datasets for RA and CD were downloaded from the GEO database. Overlapping genes were identified using weighted gene co-expression network analysis and differential analysis crossover, and enrichment analysis was conducted for these genes. Protein-protein interaction networks were then constructed using these overlapping genes to identify hub genes. Expression validation and receiver operating characteristic curve validation were performed for these hub genes using different datasets. Additionally, the immune cell correlation, single-cell expression cluster, and the immune cell expression cluster of the core gene were analyzed. Furthermore, upstream shared microRNAs (miRNA) were predicted and a miRNA-gene network was constructed. Finally, drug candidates were analyzed and predicted. These core genes were found to be positively correlated with multiple immune cells that are infiltrated by the disease. Analysis of gene expression clusters revealed that these genes were mostly associated with inflammatory and immune responses. The miRNA-genes network analysis suggested that hsa-miR-31-5p may play an important role in the common mechanism of RA and CD. Finally, tamibarotene, retinoic acid, and benzo[a]pyrene were identified as potential treatment options for patients with both RA and CD. This bioinformatics study has identified ITGB2, LCP2, and PLEK as key diagnostic genes in patients with both RA and CD. The study has further confirmed that inflammation and immune response play a central role in the development of both RA and CD. Interestingly, the study has highlighted hsa-miR-31-5p as a potential key player in the common mechanism of both diseases, representing a new direction in research and a potential therapeutic target. These shared genes, potential mechanisms, and regulatory networks offer new opportunities for further research and may provide hope for future treatment of patients with both RA and CD.
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Affiliation(s)
- Peifei Peng
- Department of Geriatrics, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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2
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Nofi CP, Prince JM, Wang P, Aziz M. Chromatin as alarmins in necrotizing enterocolitis. Front Immunol 2024; 15:1403018. [PMID: 38881893 PMCID: PMC11176418 DOI: 10.3389/fimmu.2024.1403018] [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: 03/18/2024] [Accepted: 05/20/2024] [Indexed: 06/18/2024] Open
Abstract
Necrotizing enterocolitis (NEC) is a severe gastrointestinal disease primarily affecting premature neonates, marked by poorly understood pro-inflammatory signaling cascades. Recent advancements have shed light on a subset of endogenous molecular patterns, termed chromatin-associated molecular patterns (CAMPs), which belong to the broader category of damage-associated molecular patterns (DAMPs). CAMPs play a crucial role in recognizing pattern recognition receptors and orchestrating inflammatory responses. This review focuses into the realm of CAMPs, highlighting key players such as extracellular cold-inducible RNA-binding protein (eCIRP), high mobility group box 1 (HMGB1), cell-free DNA, neutrophil extracellular traps (NETs), histones, and extracellular RNA. These intrinsic molecules, often perceived as foreign, have the potential to trigger immune signaling pathways, thus contributing to NEC pathogenesis. In this review, we unravel the current understanding of the involvement of CAMPs in both preclinical and clinical NEC scenarios. We also focus on elucidating the downstream signaling pathways activated by these molecular patterns, providing insights into the mechanisms that drive inflammation in NEC. Moreover, we scrutinize the landscape of targeted therapeutic approaches, aiming to mitigate the impact of tissue damage in NEC. This in-depth exploration offers a comprehensive overview of the role of CAMPs in NEC, bridging the gap between preclinical and clinical insights.
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Affiliation(s)
- Colleen P. Nofi
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
- Elmezzi Graduate School of Molecular Medicine, Manhasset, NY, United States
- Department of Surgery, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, United States
| | - Jose M. Prince
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
- Department of Surgery, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, United States
| | - Ping Wang
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
- Elmezzi Graduate School of Molecular Medicine, Manhasset, NY, United States
- Department of Surgery, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, United States
- Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, United States
| | - Monowar Aziz
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
- Elmezzi Graduate School of Molecular Medicine, Manhasset, NY, United States
- Department of Surgery, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, United States
- Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, United States
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3
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Chang X, Wang B, Zhao Y, Deng B, Liu P, Wang Y. The role of IFI16 in regulating PANoptosis and implication in heart diseases. Cell Death Discov 2024; 10:204. [PMID: 38693141 PMCID: PMC11063201 DOI: 10.1038/s41420-024-01978-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 05/03/2024] Open
Abstract
Interferon Gamma Inducible Protein 16 (IFI16) belongs to the HIN-200 protein family and is pivotal in immunological responses. Serving as a DNA sensor, IFI16 identifies viral and aberrant DNA, triggering immune and inflammatory responses. It is implicated in diverse cellular death mechanisms, such as pyroptosis, apoptosis, and necroptosis. Notably, these processes are integral to the emergent concept of PANoptosis, which encompasses cellular demise and inflammatory pathways. Current research implies a significant regulatory role for IFI16 in PANoptosis, particularly regarding cardiac pathologies. This review delves into the complex interplay between IFI16 and PANoptosis in heart diseases, including atherosclerosis, myocardial infarction, heart failure, and diabetic cardiomyopathy. It synthesizes evidence of IFI16's impact on PANoptosis, with the intention of providing novel insights for therapeutic strategies targeting heart diseases.
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Affiliation(s)
- Xindi Chang
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China
| | - Bei Wang
- Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China
| | - Yingli Zhao
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China
| | - Bing Deng
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China
| | - Ping Liu
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China.
| | - Yiru Wang
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China.
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Bao HF, She CH, Hou CC, Ji DN, Hu D, Zou J, Shen Y, Jian LL, Cai JF, Ye JF, Luo D, Ma HF, Guan JL. PLK1-activating IFI16-STING-TBK1 pathway induces apoptosis of intestinal epithelial cells in patients with intestinal Behçet's syndrome. FEBS J 2024. [PMID: 38676954 DOI: 10.1111/febs.17147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/28/2023] [Accepted: 04/15/2024] [Indexed: 04/29/2024]
Abstract
Inflammatory signals from immunological cells may cause damage to intestinal epithelial cells (IECs), resulting in intestinal inflammation and tissue impairment. Interferon-γ-inducible protein 16 (IFI16) was reported to be involved in the pathogenesis of Behçet's syndrome (BS). This study aimed to investigate how inflammatory cytokines released by immunological cells and IFI16 participate in the pathogenesis of intestinal BS. RNA sequencing and real-time quantitative PCR (qPCR) showed that the positive regulation of tumor necrosis factor-α (TNF-α) production in peripheral blood mononuclear cells (PBMCs) of intestinal BS patients may be related to the upregulation of polo like kinase 1 (PLK1) in PBMCs (P = 0.012). The plasma TNF-α protein level in intestinal BS was significantly higher than in healthy controls (HCs; P = 0.009). PBMCs of intestinal BS patients and HCs were co-cultured with human normal IECs (NCM460) to explore the interaction between immunological cells and IECs. Using IFI16 knockdown, PBMC-NCM460 co-culture, TNF-α neutralizing monoclonal antibody (mAb), stimulator of interferon genes (STING) agonist 2'3'-cGAMP, and the PLK1 inhibitor SBE 13 HCL, we found that PLK1 promotes the secretion of TNF-α from PBMCs of intestinal BS patients, which causes overexpression of IFI16 and induces apoptosis of IECs via the STING-TBK1 pathway. The expressions of IFI16, TNF-α, cleaved caspase 3, phosphorylated STING (pSTING) and phosphorylated tank binding kinase 1 (pTBK1) in the intestinal ulcer tissue of BS patients were significantly higher than that of HCs (all P < 0.05). PLK1 in PBMCs of intestinal BS patients increased TNF-α secretion, inducing IEC apoptosis via activation of the IFI16-STING-TBK1 pathway. PLK1 and the IFI16-STING-TBK1 pathway may be new therapeutic targets for intestinal BS.
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Affiliation(s)
- Hua-Fang Bao
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| | - Chun-Hui She
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| | - Cheng-Cheng Hou
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| | - Da-Nian Ji
- Department of Gastrointestinal Endoscopy, Huadong Hospital, Fudan University, Shanghai, China
| | - Dan Hu
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| | - Jun Zou
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| | - Yan Shen
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| | - Lei-Lei Jian
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| | - Jian-Fei Cai
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| | - Jing-Fen Ye
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| | - Dan Luo
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| | - Hai-Fen Ma
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
| | - Jian-Long Guan
- Department of Rheumatology and Immunology, Huadong Hospital, Fudan University, Shanghai, China
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Fenton CG, Ray MK, Paulssen RH. Challenges in Defining a Reference Set of Differentially Expressed lncRNAs in Ulcerative Colitis by Meta-Analysis. Curr Issues Mol Biol 2024; 46:3164-3174. [PMID: 38666928 PMCID: PMC11049510 DOI: 10.3390/cimb46040198] [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: 03/05/2024] [Revised: 03/27/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
The study aimed to identify common differentially expressed lncRNAs from manually curated ulcerative colitis (UC) gene expression omnibus (GEO) datasets. Nine UC transcriptomic datasets of clearly annotated human colonic biopsies were included in the study. The datasets were manually curated to select active UC samples and controls. R packages geneknitR, gprofiler, clusterProfiler were used for gene symbol annotation. The R EdgeR package was used to analyze differential expression. This resulted in a total of nineteen lncRNAs that were differentially expressed in at least three datasets of the nine GEO datasets. Several of the differentially expressed lncRNAs found in UC were associated with promoting colorectal cancer (CRC) through regulating gene expression, epithelial to mesenchymal transition (EMT), cell cycle progression, and by promoting tumor proliferation, invasion, and migration. The expression of several lncRNAs varied between disease states and tissue locations within the same disease state. The identified differentially expressed lncRNAs may function as general markers for active UC independent of biopsy location, age, gender, or treatment, thereby representing a comparative resource for future comparisons using available GEO UC datasets.
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Affiliation(s)
- Christopher G. Fenton
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway; (C.G.F.); (M.K.R.)
- Genomic Support Centre Tromsø (GSCT), Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Mithlesh Kumar Ray
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway; (C.G.F.); (M.K.R.)
| | - Ruth H. Paulssen
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway; (C.G.F.); (M.K.R.)
- Genomic Support Centre Tromsø (GSCT), Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
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Arosa L, Camba-Gómez M, Lorenzo-Martín LF, Clavaín L, López M, Conde-Aranda J. RNA Expression of MMP12 Is Strongly Associated with Inflammatory Bowel Disease and Is Regulated by Metabolic Pathways in RAW 264.7 Macrophages. Int J Mol Sci 2024; 25:3167. [PMID: 38542140 PMCID: PMC10970096 DOI: 10.3390/ijms25063167] [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: 02/02/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Macrophage metalloelastase or matrix metalloproteinase-12 (MMP12) is a macrophage-specific proteolytic enzyme involved in the physiopathology of many inflammatory diseases, including inflammatory bowel disease. Although previously published data suggested that the modulation of MMP12 in macrophages could be a determinant for the development of intestinal inflammation, scarce information is available on the mechanisms underlying the regulation of MMP12 expression in those phagocytes. Therefore, in this study, we aimed to delineate the association of MMP12 with inflammatory bowel disease and the molecular events leading to the transcriptional control of this metalloproteinase. For that, we used publicly available transcriptional data. Also, we worked with the RAW 264.7 macrophage cell line for functional experiments. Our results showed a strong association of MMP12 expression with the severity of inflammatory bowel disease and the response to relevant biological therapies. In vitro assays revealed that the inhibition of mechanistic target of rapamycin complex 1 (mTORC1) and the stimulation of the AMP-activated protein kinase (AMPK) signaling pathway potentiated the expression of Mmp12. Additionally, AMPK and mTOR required a functional downstream glycolytic pathway to fully engage with Mmp12 expression. Finally, the pharmacological inhibition of MMP12 abolished the expression of the proinflammatory cytokine Interleukin-6 (Il6) in macrophages. Overall, our findings provide a better understanding of the mechanistic regulation of MMP12 in macrophages and its relationship with inflammation.
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Affiliation(s)
- Laura Arosa
- Molecular and Cellular Gastroenterology Group, Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (L.A.); (M.C.-G.)
| | - Miguel Camba-Gómez
- Molecular and Cellular Gastroenterology Group, Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (L.A.); (M.C.-G.)
| | | | - Laura Clavaín
- EGO Genomics, Scientific Park of the University of Salamanca, Adaja Street 4, Building M2, 37185 Villamayor, Spain;
| | - Miguel López
- NeurObesity Group, Department of Physiology, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain;
- CIBER Fisiopatologia de la Obesidad y Nutrición (CIBERobn), 15706 Santiago de Compostela, Spain
| | - Javier Conde-Aranda
- Molecular and Cellular Gastroenterology Group, Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain; (L.A.); (M.C.-G.)
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Bass K, Sivaprakasam S, Dharmalingam-Nandagopal G, Thangaraju M, Ganapathy V. Colonic ketogenesis, a microbiota-regulated process, contributes to blood ketones and protects against colitis in mice. Biochem J 2024; 481:295-312. [PMID: 38372391 PMCID: PMC10903465 DOI: 10.1042/bcj20230403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 02/01/2024] [Accepted: 02/04/2024] [Indexed: 02/20/2024]
Abstract
Ketogenesis is considered to occur primarily in liver to generate ketones as an alternative energy source for non-hepatic tissues when glucose availability/utilization is impaired. 3-Hydroxy-3-methylglutaryl-CoA synthase-2 (HMGCS2) mediates the rate-limiting step in this mitochondrial pathway. Publicly available databases show marked down-regulation of HMGCS2 in colonic tissues in Crohn's disease and ulcerative colitis. This led us to investigate the expression and function of this pathway in colon and its relevance to colonic inflammation in mice. Hmgcs2 is expressed in cecum and colon. As global deletion of Hmgcs2 showed significant postnatal mortality, we used a conditional knockout mouse with enzyme deletion restricted to intestinal tract. These mice had no postnatal mortality. Fasting blood ketones were lower in these mice, indicating contribution of colonic ketogenesis to circulating ketones. There was also evidence of gut barrier breakdown and increased susceptibility to experimental colitis with associated elevated levels of IL-6, IL-1β, and TNF-α in circulation. Interestingly, many of these phenomena were mostly evident in male mice. Hmgcs2 expression in colon is controlled by colonic microbiota as evidenced from decreased expression in germ-free mice and antibiotic-treated conventional mice and from increased expression in a human colonic epithelial cell line upon treatment with aqueous extracts of cecal contents. Transcriptomic analysis of colonic epithelia from control mice and Hmgcs2-null mice indicated an essential role for colonic ketogenesis in the maintenance of optimal mitochondrial function, cholesterol homeostasis, and cell-cell tight-junction organization. These findings demonstrate a sex-dependent obligatory role for ketogenesis in protection against colonic inflammation in mice.
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Affiliation(s)
- Kevin Bass
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, U.S.A
| | - Sathish Sivaprakasam
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, U.S.A
| | | | - Muthusamy Thangaraju
- Department of Biochemistry and Molecular Biology, Augusta University, Augusta, GA 30912, U.S.A
| | - Vadivel Ganapathy
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, U.S.A
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Kim D, Shah M, Kim JH, Kim J, Baek YH, Jeong JS, Han SY, Lee YS, Park G, Cho JH, Roh YH, Lee SW, Choi GB, Park JH, Yoo KH, Seong RH, Lee YS, Woo HG. Integrative transcriptomic and genomic analyses unveil the IFI16 variants and expression as MASLD progression markers. Hepatology 2024:01515467-990000000-00759. [PMID: 38385945 DOI: 10.1097/hep.0000000000000805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/05/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND AND AIMS Metabolic dysfunction-associated steatotic liver disease (MASLD) encompasses a broad and continuous spectrum of liver diseases ranging from fatty liver to steatohepatitis. The intricate interactions of genetic, epigenetic, and environmental factors in the development and progression of MASLD remain elusive. Here, we aimed to achieve an integrative understanding of the genomic and transcriptomic alterations throughout the progression of MASLD. APPROACH AND RESULTS RNA-Seq profiling (n = 146) and whole-exome sequencing (n = 132) of MASLD liver tissue samples identified 3 transcriptomic subtypes (G1-G3) of MASLD, which were characterized by stepwise pathological and molecular progression of the disease. Macrophage-driven inflammatory activities were identified as a key feature for differentiating these subtypes. This subtype-discriminating macrophage interplay was significantly associated with both the expression and genetic variation of the dsDNA sensor IFI16 (rs6940, A>T, T779S), establishing it as a fundamental molecular factor in MASLD progression. The in vitro dsDNA-IFI16 binding experiments and structural modeling revealed that the IFI16 variant exhibited increased stability and stronger dsDNA binding affinity compared to the wild-type. Further downstream investigation suggested that the IFI16 variant exacerbated DNA sensing-mediated inflammatory signals through mitochondrial dysfunction-related signaling of the IFI16-PYCARD-CASP1 pathway. CONCLUSIONS This study unveils a comprehensive understanding of MASLD progression through transcriptomic classification, highlighting the crucial roles of IFI16 variants. Targeting the IFI16-PYCARD-CASP1 pathway may pave the way for the development of novel diagnostics and therapeutics for MASLD.
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Affiliation(s)
- Doyoon Kim
- Department of Physiology, Ajou University School of Medicine, Suwon, Republic of Korea
- Department of Biomedical Science, Graduate School, Ajou University, Suwon, Republic of Korea
| | - Masaud Shah
- Department of Physiology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Jang Hyun Kim
- Department of Physiology, Ajou University School of Medicine, Suwon, Republic of Korea
- Department of Biomedical Science, Graduate School, Ajou University, Suwon, Republic of Korea
| | - JungMo Kim
- Ajou Translational Omics Center (ATOC), Research Institute for Innovative Medicine, Ajou University Medical Center, Suwon, Republic of Korea
| | - Yang-Hyun Baek
- Department of Internal Medicine, Liver Center, Dong-A University College of Medicine, Busan, Republic of Korea
| | - Jin-Sook Jeong
- Pathology and Laboratory Medicine, St Mary's Hospital, Busan, Republic of Korea
| | | | - Yong Sun Lee
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Republic of Korea
| | - Gaeul Park
- Division of Rare Cancer, Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - Jin-Han Cho
- Department of Diagnostic Radiology, Dong-A University Medical Center, Busan, Republic of Korea
| | - Young-Hoon Roh
- Department of Surgery, Dong-A University Medical Center, Busan, Republic of Korea
| | - Sung-Wook Lee
- Department of Internal Medicine, Liver Center, Dong-A University Medical Center, Busan, Republic of Korea
| | - Gi-Bok Choi
- Department of Radiology, On Hospital, Busan, Republic of Korea
| | - Jong Hoon Park
- Department of Biological Sciences, Sookmyung Women's University, Seoul, Republic of Korea
| | - Kyung Hyun Yoo
- Department of Biological Sciences, Sookmyung Women's University, Seoul, Republic of Korea
| | - Rho Hyun Seong
- Department of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Yeon-Su Lee
- Division of Rare Cancer, Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - Hyun Goo Woo
- Department of Physiology, Ajou University School of Medicine, Suwon, Republic of Korea
- Department of Biomedical Science, Graduate School, Ajou University, Suwon, Republic of Korea
- Ajou Translational Omics Center (ATOC), Research Institute for Innovative Medicine, Ajou University Medical Center, Suwon, Republic of Korea
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Zhao X, Hu C, Chen X, Ren S, Gao F. Drug Repositioning of Inflammatory Bowel Disease Based on Co-Target Gene Expression Signature of Glucocorticoid Receptor and TET2. BIOLOGY 2024; 13:82. [PMID: 38392301 PMCID: PMC10886832 DOI: 10.3390/biology13020082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/16/2024] [Accepted: 01/25/2024] [Indexed: 02/24/2024]
Abstract
The glucocorticoid receptor (GR) and ten-eleven translocation 2 (TET2), respectively, play a crucial role in regulating immunity and inflammation, and GR interacts with TET2. However, their synergetic roles in inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), remain unclear. This study aimed to investigate the co-target gene signatures of GR and TET2 in IBD and provide potential therapeutic interventions for IBD. By integrating public data, we identified 179 GR- and TET2-targeted differentially expressed genes (DEGs) in CD and 401 in UC. These genes were found to be closely associated with immunometabolism, inflammatory responses, and cell stress pathways. In vitro inflammatory cellular models were constructed using LPS-treated HT29 and HCT116 cells, respectively. Drug repositioning based on the co-target gene signatures of GR and TET2 derived from transcriptomic data of UC, CD, and the in vitro model was performed using the Connectivity Map (CMap). BMS-536924 emerged as a top therapeutic candidate, and its validation experiment within the in vitro inflammatory model confirmed its efficacy in mitigating the LPS-induced inflammatory response. This study sheds light on the pathogenesis of IBD from a new perspective and may accelerate the development of novel therapeutic agents for inflammatory diseases including IBD.
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Affiliation(s)
- Xianglin Zhao
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
- School of Life Sciences, Henan University, Kaifeng 475004, China
- Shenzhen Research Institute of Henan University, Henan University, Shenzhen 518000, China
| | - Chenghao Hu
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Xinyu Chen
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Shuqiang Ren
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Fei Gao
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou 310022, China
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
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10
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McAllister MJ, Hall R, Whelan RJ, Fischer LJ, Chuah CS, Cartlidge PD, Drury B, Rutherford DG, Duffin RM, Cartwright JA, Dorward DA, Rossi AG, Ho GT. Formylated Peptide Receptor-1-Mediated Gut Inflammation as a Therapeutic Target in Inflammatory Bowel Disease. CROHN'S & COLITIS 360 2024; 6:otae003. [PMID: 38352118 PMCID: PMC10862654 DOI: 10.1093/crocol/otae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Indexed: 02/16/2024] Open
Abstract
Background Formylated peptide receptor (FPR)-1 is a G-coupled receptor that senses foreign bacterial and host-derived mitochondrial formylated peptides (FPs), leading to innate immune system activation. Aim We sought to investigate the role of FPR1-mediated inflammation and its potential as a therapeutic target in inflammatory bowel disease (IBD). Methods We characterized FPR1 gene and protein expression in 8 human IBD (~1000 patients) datasets with analysis on disease subtype, mucosal inflammation, and drug response. We performed in vivo dextran-sulfate sodium (DSS) colitis in C57/BL6 FPR1 knockout mice. In ex vivo studies, we studied the role of mitochondrial FPs and pharmacological blockade of FPR1 using cyclosporin H in human peripheral blood neutrophils. Finally, we assess mitochondrial FPs as a potential mechanistic biomarker in the blood and stools of patients with IBD. Results Detailed in silico analysis in human intestinal biopsies showed that FPR1 is highly expressed in IBD (n = 207 IBD vs 67 non-IBD controls, P < .001), and highly correlated with gut inflammation in ulcerative colitis (UC) and Crohn's disease (CD) (both P < .001). FPR1 receptor is predominantly expressed in leukocytes, and we showed significantly higher FPR1+ve neutrophils in inflamed gut tissue section in IBD (17 CD and 24 UC; both P < .001). Further analysis in 6 independent IBD (data available under Gene Expression Omnibus accession numbers GSE59071, GSE206285, GSE73661, GSE16879, GSE92415, and GSE235970) showed an association with active gut inflammation and treatment resistance to infliximab, ustekinumab, and vedolizumab. FPR1 gene deletion is protective in murine DSS colitis with lower gut neutrophil inflammation. In the human ex vivo neutrophil system, mitochondrial FP, nicotinamide adenine dinucleotide dehydrogenase subunit-6 (ND6) is a potent activator of neutrophils resulting in higher CD62L shedding, CD63 expression, reactive oxygen species production, and chemotactic capacity; these effects are inhibited by cyclosporin H. We screened for mitochondrial ND6 in IBD (n = 54) using ELISA and detected ND6 in stools with median values of 2.2 gg/mL (interquartile range [IQR] 0.0-4.99; range 0-53.3) but not in blood. Stool ND6 levels, however, were not significantly correlated with paired stool calprotectin, C-reactive protein, and clinical IBD activity. Conclusions Our data suggest that FPR1-mediated neutrophilic inflammation is a tractable target in IBD; however, further work is required to clarify the clinical utility of mitochondrial FPs as a potential mechanistic marker for future stratification.
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Affiliation(s)
- Milly J McAllister
- Edinburgh IBD Science Unit, Centre for Inflammation Research, Queens Medical Research Unit, University of Edinburgh, Edinburgh, Scotland, UK
| | - Rebecca Hall
- Edinburgh IBD Science Unit, Centre for Inflammation Research, Queens Medical Research Unit, University of Edinburgh, Edinburgh, Scotland, UK
| | - Robert J Whelan
- Edinburgh IBD Science Unit, Centre for Inflammation Research, Queens Medical Research Unit, University of Edinburgh, Edinburgh, Scotland, UK
| | - Lena J Fischer
- Edinburgh IBD Science Unit, Centre for Inflammation Research, Queens Medical Research Unit, University of Edinburgh, Edinburgh, Scotland, UK
| | - Cher S Chuah
- Edinburgh IBD Science Unit, Centre for Inflammation Research, Queens Medical Research Unit, University of Edinburgh, Edinburgh, Scotland, UK
| | - Peter D Cartlidge
- Edinburgh IBD Science Unit, Centre for Inflammation Research, Queens Medical Research Unit, University of Edinburgh, Edinburgh, Scotland, UK
| | - Broc Drury
- Edinburgh IBD Science Unit, Centre for Inflammation Research, Queens Medical Research Unit, University of Edinburgh, Edinburgh, Scotland, UK
| | - Duncan G Rutherford
- Edinburgh IBD Science Unit, Centre for Inflammation Research, Queens Medical Research Unit, University of Edinburgh, Edinburgh, Scotland, UK
| | - Rodger M Duffin
- Edinburgh IBD Science Unit, Centre for Inflammation Research, Queens Medical Research Unit, University of Edinburgh, Edinburgh, Scotland, UK
| | - Jennifer A Cartwright
- Edinburgh IBD Science Unit, Centre for Inflammation Research, Queens Medical Research Unit, University of Edinburgh, Edinburgh, Scotland, UK
| | - David A Dorward
- Edinburgh IBD Science Unit, Centre for Inflammation Research, Queens Medical Research Unit, University of Edinburgh, Edinburgh, Scotland, UK
| | - Adriano G Rossi
- Edinburgh IBD Science Unit, Centre for Inflammation Research, Queens Medical Research Unit, University of Edinburgh, Edinburgh, Scotland, UK
| | - Gwo-tzer Ho
- Edinburgh IBD Science Unit, Centre for Inflammation Research, Queens Medical Research Unit, University of Edinburgh, Edinburgh, Scotland, UK
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11
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Ahmad R, Kumar B, Thapa I, Talmon GA, Salomon J, Ramer-Tait AE, Bastola DK, Dhawan P, Singh AB. Loss of claudin-3 expression increases colitis risk by promoting Gut Dysbiosis. Gut Microbes 2023; 15:2282789. [PMID: 38010872 PMCID: PMC10730149 DOI: 10.1080/19490976.2023.2282789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/08/2023] [Indexed: 11/29/2023] Open
Abstract
Dysregulation of both the gut barrier and microbiota (dysbiosis) promotes susceptibility to and severity of Inflammatory Bowel Diseases (IBD). Leaky gut and dysbiosis often coexist; however, potential interdependence and molecular regulation are not well understood. Robust expression of claudin-3 (CLDN3) characterizes the gut epithelium, and studies have demonstrated a positive association between CLDN3 expression and gut barrier maturity and integrity, including in response to probiotics. However, the exact status and causal role of CLDN3 in IBD and regulation of gut dysbiosis remain unknown. Analysis of mouse and human IBD cohorts helped examine CLDN3 expression in IBD. The causal role was determined by modeling CLDN3 loss of expression during experimental colitis. 16S sequencing and in silico analysis helped examine gut microbiota diversity between Cldn3KO and WT mice and potential host metabolic responses. Fecal microbiota transplant (FMT) studies were performed to assess the role of gut dysbiosis in the increased susceptibility of Cldn3KO mice to colitis. A significant decrease in CLDN3 expression characterized IBD and CLDN3 loss of expression promoted colitis. 16S sequencing analysis suggested gut microbiota changes in Cldn3KO mice that were capable of modulating fatty acid metabolism and oxidative stress response. FMT from naïve Cldn3KO mice promoted colitis susceptibility in recipient germ-free mice (GFM) compared with GFM-receiving microbiota from WT mice. Our data demonstrate a critical role of CLDN3 in maintaining normal gut microbiota and inflammatory responses, which can be harnessed to develop novel therapeutic opportunities for patients with IBD.
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Affiliation(s)
- Rizwan Ahmad
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Balawant Kumar
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ishwor Thapa
- School of Interdisciplinary Informatics, College of Information Science & Technology, University of Nebraska at Omaha, Omaha, NE, USA
| | - Geoffrey A. Talmon
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Jeffrey Salomon
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE, USA
| | - Amanda E. Ramer-Tait
- Department of Food Science and Technology and the Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Dhundy K. Bastola
- School of Interdisciplinary Informatics, College of Information Science & Technology, University of Nebraska at Omaha, Omaha, NE, USA
| | - Punita Dhawan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
- Veterans Affairs Nebraska-Western Iowa Health Care System, Omaha, NE, USA
| | - Amar B. Singh
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
- Veterans Affairs Nebraska-Western Iowa Health Care System, Omaha, NE, USA
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12
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El-Deeb OS, Hafez YM, Eltokhy AK, Awad MM, El-shaer RAA, Abdel Ghafar MT, Atef MM. Stimulator of interferon genes/Interferon regulatory factor 3 (STING-IRF3) and inflammasome-activation mediated pyroptosis biomarkers: a network of integrated pathways in diabetic nephropathy. J Diabetes Metab Disord 2023; 22:1471-1480. [PMID: 37975106 PMCID: PMC10638254 DOI: 10.1007/s40200-023-01270-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/25/2023] [Indexed: 11/19/2023]
Abstract
Background Diabetic Nephropathy (DN) is serious diabetic complication affecting the structure and function of the kidney. This study assessed the stimulator of interferon genes/ Interferon regulatory factor 3 (STING/IRF3) signaling pathway roles and inflammasome-activation mediated pyroptosis, being imperative pathways of inordinate importance in disease progression, in DN throughout its different stages. Methods 45 Diabetic cases were categorized into three groups based on their albuminuric status as follow: Normoalbuminuric, Microalbuminuric and Macroalbuminuric diabetic groups and 15 healthy subjects as controls were included. We evaluated STING and absent in melanoma 2 (AIM2) messenger RNA (mRNA) expressions from whole blood using quantitative RT-PCR. Additionally, Serum levels of STING, AIM2, IRF3, Nod like receptor pyrins-3 (NLRP3), interleukin-1β (IL-1β) and caspase-1 were assessed by ELISA technique. Results The study documented that STING and AIM2 mRNA expressions had significantly increased in DN cases with highest value in macroalbuminuric diabetic groups (p < 0.001*). Parallel results were observed concerning serum STING, AIM2, IRF3, NLRP3, Caspase-1 in addition to IL-1β levels (p < 0.001*). Conclusion The study documented the forthcoming role of STING in DN progression and its positive correlation with inflammasome-activation mediated pyroptosis biomarkers throughout its three different stages; launching new horizons in DN pathogenesis by highlighting its role as a reliable prognostic biomarker.
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Affiliation(s)
- Omnia Safwat El-Deeb
- Medical Biochemistry Department, Faculty of Medicine, Tanta University, El Geesh Street, Tanta, 31511 Egypt
| | - Yasser Mostafa Hafez
- Internal Medicine Department, Faculty of Medicine, Tanta University, Tanta, Egypt
| | - Amira Kamel Eltokhy
- Medical Biochemistry Department, Faculty of Medicine, Tanta University, El Geesh Street, Tanta, 31511 Egypt
| | - Marwa Mahmoud Awad
- Physiology Department, Faculty of Medicine, Tanta University, Tanta, Egypt
| | | | | | - Marwa Mohamed Atef
- Medical Biochemistry Department, Faculty of Medicine, Tanta University, El Geesh Street, Tanta, 31511 Egypt
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13
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Ahmad R, Kumar B, Thapa I, Tamang RL, Yadav SK, Washington MK, Talmon GA, Yu AS, Bastola DK, Dhawan P, Singh AB. Claudin-2 protects against colitis-associated cancer by promoting colitis-associated mucosal healing. J Clin Invest 2023; 133:e170771. [PMID: 37815870 PMCID: PMC10688979 DOI: 10.1172/jci170771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 10/05/2023] [Indexed: 10/12/2023] Open
Abstract
Patients with inflammatory bowel disease (IBD) are susceptible to colitis-associated cancer (CAC). Chronic inflammation promotes the risk for CAC. In contrast, mucosal healing predicts improved prognosis in IBD and reduced risk of CAC. However, the molecular integration among colitis, mucosal healing, and CAC remains poorly understood. Claudin-2 (CLDN2) expression is upregulated in IBD; however, its role in CAC is not known. The current study was undertaken to examine the role for CLDN2 in CAC. The AOM/DSS-induced CAC model was used with WT and CLDN2-modified mice. High-throughput expression analyses, murine models of colitis/recovery, chronic colitis, ex vivo crypt culture, and pharmacological manipulations were employed in order to increase our mechanistic understanding. The Cldn2KO mice showed significant inhibition of CAC despite severe colitis compared with WT littermates. Cldn2 loss also resulted in impaired recovery from colitis and increased injury when mice were subjected to intestinal injury by other methods. Mechanistic studies demonstrated a possibly novel role of CLDN2 in promotion of mucosal healing downstream of EGFR signaling and by regulation of Survivin expression. An upregulated CLDN2 expression protected from CAC and associated positively with crypt regeneration and Survivin expression in patients with IBD. We demonstrate a potentially novel role of CLDN2 in promotion of mucosal healing in patients with IBD and thus regulation of vulnerability to colitis severity and CAC, which can be exploited for improved clinical management.
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Affiliation(s)
- Rizwan Ahmad
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Balawant Kumar
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Ishwor Thapa
- School of Interdisciplinary Informatics, University of Nebraska Omaha, Omaha, Nebraska, USA
| | - Raju Lama Tamang
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Santosh K. Yadav
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Mary K. Washington
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Geoffrey A. Talmon
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Alan S. Yu
- Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Dhundy K. Bastola
- School of Interdisciplinary Informatics, University of Nebraska Omaha, Omaha, Nebraska, USA
| | - Punita Dhawan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
- VA Nebraska-Western Iowa Health Care System, Omaha, Nebraska, USA
| | - Amar B. Singh
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
- VA Nebraska-Western Iowa Health Care System, Omaha, Nebraska, USA
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14
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Wan T, Wang Y, He K, Zhu S. Microbial sensing in the intestine. Protein Cell 2023; 14:824-860. [PMID: 37191444 PMCID: PMC10636641 DOI: 10.1093/procel/pwad028] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023] Open
Abstract
The gut microbiota plays a key role in host health and disease, particularly through their interactions with the immune system. Intestinal homeostasis is dependent on the symbiotic relationships between the host and the diverse gut microbiota, which is influenced by the highly co-evolved immune-microbiota interactions. The first step of the interaction between the host and the gut microbiota is the sensing of the gut microbes by the host immune system. In this review, we describe the cells of the host immune system and the proteins that sense the components and metabolites of the gut microbes. We further highlight the essential roles of pattern recognition receptors (PRRs), the G protein-coupled receptors (GPCRs), aryl hydrocarbon receptor (AHR) and the nuclear receptors expressed in the intestinal epithelial cells (IECs) and the intestine-resident immune cells. We also discuss the mechanisms by which the disruption of microbial sensing because of genetic or environmental factors causes human diseases such as the inflammatory bowel disease (IBD).
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Affiliation(s)
- Tingting Wan
- Division of Life Sciences and Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Institute of Immunology, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Yalong Wang
- Division of Life Sciences and Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Institute of Immunology, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Kaixin He
- Division of Life Sciences and Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Institute of Immunology, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Shu Zhu
- Division of Life Sciences and Medicine, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Institute of Immunology, School of Basic Medical Sciences, University of Science and Technology of China, Hefei 230027, China
- Department of Digestive Disease, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei 230001, China
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei 230601, China
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15
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Xiong Z, Fang Y, Lu S, Sun Q, Huang J. Identification and Validation of Signature Genes and Potential Therapy Targets of Inflammatory Bowel Disease and Periodontitis. J Inflamm Res 2023; 16:4317-4330. [PMID: 37795494 PMCID: PMC10545806 DOI: 10.2147/jir.s426004] [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: 07/05/2023] [Accepted: 09/12/2023] [Indexed: 10/06/2023] Open
Abstract
Background Inflammatory bowel disease (IBD) and periodontitis (PD) are correlated, although the pathogenic mechanism behind their correlation has not been clarified. This study aims to explore the common signature genes and potential therapeutic targets of IBD and PD using transcriptomic analysis. Methods The GEO database was used to download datasets of IBD and PD, and differential expression analysis was used to identify DEGs. We then conducted GO and KEGG enrichment analyses of the shared genes. Next, we applied 4 machine learning (ML) algorithms (GLM, RF, GBM, and SVM) to select the best prediction model for diagnosing the disease and obtained the hub genes of IBD and PD. The diagnostic value of the signature genes was verified by a validation set and qRT‒PCR experiments. Subsequently, immune cell infiltration in IBD samples and PD samples was analyzed by ssGSEA. Finally, we investigated and validated the response of hub genes to infliximab therapy. Results We identified 43 upregulated genes as shared genes by intersecting the DEGs of IBD and PD. Functional enrichment analysis suggested that the shared genes were closely associated with immunity and inflammation. The ML algorithm and qRT‒PCR results indicated that IGKC and COL4A1 were the hub genes with the most diagnostic value for IBD and PD. Subsequently, through immune infiltration analysis, CD4 T cells, NK cells and neutrophils were identified to play crucial roles in the pathogenesis of IBD and PD. Finally, through in vivo and in vitro experiments, we found that IGKC and COL4A1 were significantly downregulated during the treatment of patients with IBD using infliximab. Conclusion We investigated the potential association between IBD and PD using transcriptomic analysis. The IGKC and COL4A1 genes were identified as characteristic genes and novel intervention targets for these two diseases. Infliximab may be used to treat or prevent IBD and PD.
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Affiliation(s)
- Zhe Xiong
- Department of Gastroenterology, the Affiliated Changzhou No.2 People’s Hospital of Nanjing Medical University, Changzhou, Jiangsu Province, People’s Republic of China
- Graduate School of Dalian Medical University, Dalian, Liaoning Province, People’s Republic of China
| | - Ying Fang
- Department of Gastroenterology, the Affiliated Changzhou No.2 People’s Hospital of Nanjing Medical University, Changzhou, Jiangsu Province, People’s Republic of China
- Graduate School of Dalian Medical University, Dalian, Liaoning Province, People’s Republic of China
| | - Shuangshuang Lu
- Department of Gastroenterology, the Affiliated Changzhou No.2 People’s Hospital of Nanjing Medical University, Changzhou, Jiangsu Province, People’s Republic of China
| | - Qiuyue Sun
- Department of Gastroenterology, the Affiliated Changzhou No.2 People’s Hospital of Nanjing Medical University, Changzhou, Jiangsu Province, People’s Republic of China
- Graduate School of Nanjing Medical University, Nanjing, Jiangsu Province, People’s Republic of China
| | - Jin Huang
- Department of Gastroenterology, the Affiliated Changzhou No.2 People’s Hospital of Nanjing Medical University, Changzhou, Jiangsu Province, People’s Republic of China
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16
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Singh AK, Kumar R, Yin J, Brooks Ii JF, Kathania M, Mukherjee S, Kumar J, Conlon KP, Basrur V, Chen Z, Han X, Hooper LV, Burstein E, Venuprasad K. RORγt-Raftlin1 complex regulates the pathogenicity of Th17 cells and colonic inflammation. Nat Commun 2023; 14:4972. [PMID: 37591835 PMCID: PMC10435467 DOI: 10.1038/s41467-023-40622-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/03/2023] [Indexed: 08/19/2023] Open
Abstract
Th17 cells that produce Interleukin IL-17 are pathogenic in many human diseases, including inflammatory bowel disease, but are, paradoxically, essential for maintaining the integrity of the intestinal barrier in a non-inflammatory state. However, the intracellular mechanisms that regulate distinct transcriptional profiles and functional diversity of Th17 cells remain unclear. Here we show Raftlin1, a lipid raft protein, specifically upregulates and forms a complex with RORγt in pathogenic Th17 cells. Disruption of the RORγt-Raftlin1 complex results in the reduction of pathogenic Th17 cells in response to Citrobacter rodentium; however, there is no effect on nonpathogenic Th17 cells in response to commensal segmented filamentous bacteria. Mechanistically, we show that Raftlin1 recruits distinct phospholipids to RORγt and promotes the pathogenicity of Th17 cells. Thus, we have identified a mechanism that drives the pathogenic function of Th17 cells, which could provide a platform for advanced therapeutic strategies to dampen Th17-mediated inflammatory diseases.
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Affiliation(s)
- Amir Kumar Singh
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ritesh Kumar
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jianyi Yin
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - John F Brooks Ii
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Mahesh Kathania
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Sandip Mukherjee
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jitendra Kumar
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kevin P Conlon
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Zhe Chen
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Xianlin Han
- University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Lora V Hooper
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
- The Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ezra Burstein
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - K Venuprasad
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
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17
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Hosseini-Abgir A, Naghizadeh MM, Igder S, Miladpour B. Insilco prediction of the role of the FriZZled5 gene in colorectal cancer. Cancer Treat Res Commun 2023; 36:100751. [PMID: 37595345 DOI: 10.1016/j.ctarc.2023.100751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 07/27/2023] [Accepted: 08/14/2023] [Indexed: 08/20/2023]
Abstract
INTRODUCTION In this study, we aimed to elucidate the crosstalk between the Wnt/β-catenin signaling pathway and colorectal cancer (CRC) associated with inflammatory bowel disease (IBD) using a bioinformatics analysis of putative common biomarkers and a systems biology approach. MATERIALS AND METHODS The following criteria were used to search the GEO and ArrayExpress databases for terms related to CRC and IBD: 1. The dataset containing the transcriptomic data, and 2. Untreated samples by medications or drugs. A total of 42 datasets were selected for additional analysis. The GEO2R identified the differentially expressed genes. The genes involved in the Wnt signaling pathway were extracted from the KEGG database. Enrichment analysis and miRNA target prediction were conducted through the ToppGene online tool. RESULTS In CRC datasets, there were 1168 up- and 998 down-regulated probes, whereas, in IBD datasets, there were 256 up- and 200 down-regulated probes. There were 65 upregulated and 57 downregulated genes shared by CRC and IBD. According to KEGG, there were 166 genes in the Wnt pathway. FriZZled5 (FZD5) was a down-regulated gene in both CRC and IBD, as determined by the intersection of CRC- and IBD-related DEGs with the Wnt pathway. It was also demonstrated that miR-191, miR-885-5p, miR-378a-3p, and miR-396-3p affect the FriZZled5 gene expression. CONCLUSION It is possible that increased expression of miR-191 and miR-885-5p, or decreased expression of miR-378a -3p and miR396-3, in IBD and CRC results in decreased expression of the FZD5 gene. Based on the function of this gene, FZD5 may be a potential therapeutic target in IBD that progresses to CRC.
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Affiliation(s)
| | | | - Somayeh Igder
- Department of Clinical Biochemistry, Faculty of Medicine, Ahvaz Jundishapur University of Medical Science, Ahvaz, Iran
| | - Behnoosh Miladpour
- Department of Clinical Biochemistry, Fasa University of Medical Sciences, Fasa, Iran.
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18
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Tang X, Hu W, You W, Fang T. Exploration of key ferroptosis-related genes and immune infiltration in Crohn's disease using bioinformatics. Sci Rep 2023; 13:12769. [PMID: 37550393 PMCID: PMC10406931 DOI: 10.1038/s41598-023-40093-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 08/04/2023] [Indexed: 08/09/2023] Open
Abstract
Crohn's disease (CD) is a type of inflammatory bowel disease (IBD) that manifests mainly as chronic inflammation in different parts of the gastrointestinal tract, and its incidence has come to be increasing in recent years. Ferroptosis, a novel type of programmed cell death, it seems the role of ferroptosis-related biomarkers in CD has not been mentioned. Thus, the role of ferroptosis in CD and its relationship with immune infiltration were explored in this study. The CD dataset was downloaded from the Gene Expression Omnibus database. The validated ferroptosis genes (FRGs) were retrieved from the public FerrDb database. The gene expression matrix of the CD dataset was analyzed with the "limma" package in R language to obtain differentially expressed genes (DEGs) between diseased and healthy samples. Then, intersecting genes between DEGs and FRGs were identified as differentially expressed ferroptosis-associated genes (DE-FRGs). Protein-protein interaction (PPI) network analysis and visualization were carried out with STRING and Cytoscape, and key CD ferroptosis-related genes (CD-FRGs) were identified along with their Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways using the clusterProfiler package. Immune cell infiltration was analyzed with CIBERSORT. The correlation between key CD-FRGs and immune-infiltrated cells in CD was studied by Spearman's correlation method. A total of 37 DE-FRGs and 6 key CD-FRGs (CAV1, CD44, HIF1A, IFNG, TIMP1 and TLR4) were identified. GO and KEGG functional analysis indicated these genes enrichment in programmed cell death and apoptotic process, HIF-1 signaling pathway and IBD. Infiltration matrix analysis of immune cells showed abundant T cells CD4 memory activated, M1 macrophages, M2 macrophages, Mast cells activated and Neutrophils in CD intestinal tissues. The 6 key CD-FRGs were correlated with immune-infiltrated cells in CD based on correlation analysis. Taken together, immune cells with abnormal infiltration can be implicated in CD due to ferroptosis. This study identified 6 key CD-FRGs that may be key biomarkers of ferroptosis in CD; they include CAV1, CD44, HIF1A, IFNG, TIMP1 and TLR4. These findings suggest that the immune response is critical in CD caused by ferroptosis through the interaction between key CD-FRGs and immune infiltrating cells.
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Affiliation(s)
- Xiaoting Tang
- Department of Gastroenterology, The Second Affiliated Hospital of Fujian Medical University, 34 North Zhongshan Road, Licheng District, Quanzhou, 362000, Fujian, People's Republic of China
| | - Weitao Hu
- Department of Rheumatology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, Fujian, People's Republic of China
| | - Wei You
- Department of Neurosurgery, Zhangzhou Municipal Hospital of Fujian Province and Zhangzhou Affiliated Hospital of Fujian Medical University, Zhangzhou, 363000, Fujian Province, People's Republic of China
| | - Taiyong Fang
- Department of Gastroenterology, The Second Affiliated Hospital of Fujian Medical University, 34 North Zhongshan Road, Licheng District, Quanzhou, 362000, Fujian, People's Republic of China.
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19
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Liu D, Lum KK, Treen N, Núñez CT, Yang J, Howard T, Levine M, Cristea I. IFI16 phase separation via multi-phosphorylation drives innate immune signaling. Nucleic Acids Res 2023; 51:6819-6840. [PMID: 37283074 PMCID: PMC10359621 DOI: 10.1093/nar/gkad449] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/11/2023] [Accepted: 05/12/2023] [Indexed: 06/08/2023] Open
Abstract
The interferon inducible protein 16 (IFI16) is a prominent sensor of nuclear pathogenic DNA, initiating innate immune signaling and suppressing viral transcription. However, little is known about mechanisms that initiate IFI16 antiviral functions or its regulation within the host DNA-filled nucleus. Here, we provide in vitro and in vivo evidence to establish that IFI16 undergoes liquid-liquid phase separation (LLPS) nucleated by DNA. IFI16 binding to viral DNA initiates LLPS and induction of cytokines during herpes simplex virus type 1 (HSV-1) infection. Multiple phosphorylation sites within an intrinsically disordered region (IDR) function combinatorially to activate IFI16 LLPS, facilitating filamentation. Regulated by CDK2 and GSK3β, IDR phosphorylation provides a toggle between active and inactive IFI16 and the decoupling of IFI16-mediated cytokine expression from repression of viral transcription. These findings show how IFI16 switch-like phase transitions are achieved with temporal resolution for immune signaling and, more broadly, the multi-layered regulation of nuclear DNA sensors.
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Affiliation(s)
- Dawei Liu
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Krystal K Lum
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Nicholas Treen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Corazón T Núñez
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jinhang Yang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Timothy R Howard
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Michael Levine
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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20
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Wang X, Fu S, Yu J, Ma F, Zhang L, Wang J, Wang L, Tan Y, Yi H, Wu H, Xu Z. Renal interferon-inducible protein 16 expression is associated with disease activity and prognosis in lupus nephritis. Arthritis Res Ther 2023; 25:112. [PMID: 37393341 PMCID: PMC10314472 DOI: 10.1186/s13075-023-03094-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/19/2023] [Indexed: 07/03/2023] Open
Abstract
BACKGROUND Lupus nephritis (LN) is one of the most severe complications of systemic lupus erythematosus (SLE). However, the current management of LN remains unsatisfactory due to sneaky symptoms during early stages and lack of reliable predictors of disease progression. METHODS Bioinformatics and machine learning algorithms were initially used to explore the potential biomarkers for LN development. Identified biomarker expression was evaluated by immunohistochemistry (IHC) and multiplex immunofluorescence (IF) in 104 LN patients, 12 diabetic kidney disease (DKD) patients, 12 minimal change disease (MCD) patients, 12 IgA nephropathy (IgAN) patients and 14 normal controls (NC). The association of biomarker expression with clinicopathologic indices and prognosis was analyzed. Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA) were utilized to explore potential mechanisms. RESULTS Interferon-inducible protein 16 (IFI16) was identified as a potential biomarker for LN. IFI16 was highly expressed in the kidneys of LN patients compared to those with MCD, DKD, IgAN or NC. IFI16 co-localized with certain renal and inflammatory cells. Glomerular IFI16 expression was correlated with pathological activity indices of LN, while tubulointerstitial IFI16 expression was correlated with pathological chronicity indices. Renal IFI16 expression was positively associated with systemic lupus erythematosus disease activity index (SLEDAI) and serum creatinine while negatively related to baseline eGFR and serum complement C3. Additionally, higher IFI16 expression was closely related to poorer prognosis of LN patients. GSEA and GSVA suggested that IFI16 expression was involved in adaptive immune-related processes of LN. CONCLUSION Renal IFI16 expression is a potential biomarker for disease activity and clinical prognosis in LN patients. Renal IFI16 levels may be used to shed light on predicting the renal response and develop precise therapy for LN.
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Affiliation(s)
- Xueyao Wang
- Department of Nephrology, The First Hospital of Jilin University, Changchun, China
| | - Shaojie Fu
- Department of Nephrology, The First Hospital of Jilin University, Changchun, China
| | - Jinyu Yu
- Department of Renal Pathology, The First Hospital of Jilin University, Changchun, China
| | - Fuzhe Ma
- Department of Nephrology, The First Hospital of Jilin University, Changchun, China
| | - Lihong Zhang
- Department of Pathology, Basic Medical College of Jilin University, Changchun, China
| | - Jiahui Wang
- Department of Nephrology, The First Hospital of Jilin University, Changchun, China
| | - Luyu Wang
- Department of Nephrology, The First Hospital of Jilin University, Changchun, China
| | - Yue Tan
- Department of Nephrology, The First Hospital of Jilin University, Changchun, China
| | - Huanfa Yi
- Central Laboratory, The First Hospital of Jilin University, Changchun, China
| | - Hao Wu
- Department of Nephrology, The First Hospital of Jilin University, Changchun, China.
| | - Zhonggao Xu
- Department of Nephrology, The First Hospital of Jilin University, Changchun, China.
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21
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Zhao XH, Zhao P, Deng Z, Yang T, Qi YX, An LY, Sun DL, He HY. Integrative analysis reveals marker genes for intestinal mucosa barrier repairing in clinical patients. iScience 2023; 26:106831. [PMID: 37250791 PMCID: PMC10212979 DOI: 10.1016/j.isci.2023.106831] [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: 11/01/2022] [Revised: 03/21/2023] [Accepted: 05/03/2023] [Indexed: 05/31/2023] Open
Abstract
This study aims to identify biomarkers of intestinal repair and provide potential therapeutic clues for improving functional recovery and prognostic performance after intestinal inflammation or injury. Here, we conducted a large-scale screening of multiple transcriptomic and scRNA-seq datasets of patients with inflammatory bowel disease (IBD), and identified 10 marker genes that potentially contribute to intestinal barrier repairing: AQP8, SULT1A1, HSD17B2, PADI2, SLC26A2, SELENBP1, FAM162A, TNNC2, ACADS, and TST. Analysis of a published scRNA-seq dataset revealed that expression of these healing markers were specific to absorptive cell types in intestinal epithelium. Furthermore, we conducted a clinical study where 11 patients underwent ileum resection demonstrating that upregulation of post-operative AQP8 and SULT1A1 expression were associated with improved recovery of bowel functions after surgery-induced intestinal injury, making them confident biomarkers of intestinal healing as well as potential prognostic markers and therapeutic targets for patients with impaired intestinal barrier functions.
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Affiliation(s)
- Xiao-Hu Zhao
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Kunming Medical University / Second Faculty of Clinical Medicine, Kunming Medical University, Kunming 650101, China
| | - Peinan Zhao
- Department of Medicine (Alfred Hospital), Central Clinical School, Monash University, 99 Commercial Rd, Melbourne, VIC 3004, Australia
| | - Zihao Deng
- Department of Medicine (Alfred Hospital), Central Clinical School, Monash University, 99 Commercial Rd, Melbourne, VIC 3004, Australia
| | - Ting Yang
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Kunming Medical University / Second Faculty of Clinical Medicine, Kunming Medical University, Kunming 650101, China
| | - Yu-Xing Qi
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Kunming Medical University / Second Faculty of Clinical Medicine, Kunming Medical University, Kunming 650101, China
| | - Li-Ya An
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Kunming Medical University / Second Faculty of Clinical Medicine, Kunming Medical University, Kunming 650101, China
| | - Da-Li Sun
- Department of Gastrointestinal Surgery, Second Affiliated Hospital of Kunming Medical University / Second Faculty of Clinical Medicine, Kunming Medical University, Kunming 650101, China
| | - Hai-Yu He
- Department of Gastroenterology, Second Affiliated Hospital of Kunming Medical University / Second Faculty of Clinical Medicine, Kunming Medical University, Kunming 650101, China
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22
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Valková N, Kratochvilová L, Martinková L, Brázda V. Dual mode of IFI16 binding to supercoiled and linear DNA: A closer insight. Biochem Biophys Res Commun 2023; 667:89-94. [PMID: 37209567 DOI: 10.1016/j.bbrc.2023.05.049] [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: 05/09/2023] [Accepted: 05/14/2023] [Indexed: 05/22/2023]
Abstract
IFI16 (Interferon inducible protein 16) is a DNA sensor responsible for innate immune response stimulation and a direct viral restriction by modulating gene expression and replication. Many IFI16-DNA binding properties were described - length-dependent and sequence-independent binding, oligomerization of IFI16 upon recognition, sliding on the DNA, and preference for supercoiled DNA. However, the question of the role of IFI16-DNA binding in distinct IFI16 functions remains unclear. Here we demonstrate two modes of IFI16 binding to DNA using atomic force microscopy and electrophoretic mobility shift assays. In our study, we show that IFI16 can bind to DNA in the form of globular complexes or oligomers depending on DNA topology and molar ratios. The stability of the complexes is different in higher salt concentrations. In addition, we observed no preferential binding with the HIN-A or HIN-B domains to supercoiled DNA, revealing the importance of the whole protein for this specificity. These results provide more profound insight into IFI16-DNA interactions and may be important in answering the question of self- and non-self-DNA binding by the IFI16 protein and potentially could shed light on the role of DNA binding in distinct IFI16 functions.
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Affiliation(s)
- Natália Valková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 65, Brno, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Libuše Kratochvilová
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00, Brno, Czech Republic
| | - Lucia Martinková
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53, Brno, Czech Republic
| | - Václav Brázda
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 65, Brno, Czech Republic.
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23
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Lee M, Kim YS, Lim S, Shin SH, Kim I, Kim J, Choi M, Kim JH, Koh SJ, Park JW, Shin HW. Protein stabilization of ITF2 by NF-κB prevents colitis-associated cancer development. Nat Commun 2023; 14:2363. [PMID: 37185280 PMCID: PMC10130090 DOI: 10.1038/s41467-023-38080-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Chronic colonic inflammation is a feature of cancer and is strongly associated with tumorigenesis, but its underlying molecular mechanisms remain poorly understood. Inflammatory conditions increased ITF2 and p65 expression both ex vivo and in vivo, and ITF2 and p65 showed positive correlations. p65 overexpression stabilized ITF2 protein levels by interfering with the binding of Parkin to ITF2. More specifically, the C-terminus of p65 binds to the N-terminus of ITF2 and inhibits ubiquitination, thereby promoting ITF2 stabilization. Parkin acts as a E3 ubiquitin ligase for ITF2 ubiquitination. Intestinal epithelial-specific deletion of ITF2 facilitated nuclear translocation of p65 and thus increased colitis-associated cancer tumorigenesis, which was mediated by Azoxymethane/Dextran sulfate sodium or dextran sulfate sodium. Upregulated ITF2 expression was lost in carcinoma tissues of colitis-associated cancer patients, whereas p65 expression much more increased in both dysplastic and carcinoma regions. Therefore, these findings indicate a critical role for ITF2 in the repression of colitis-associated cancer progression and ITF2 would be an attractive target against inflammatory diseases including colitis-associated cancer.
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Affiliation(s)
- Mingyu Lee
- Division of Allergy and Clinical Immunology, Brigham and Women's Hospital and Department of Medicine, Harvard Medical School, Boston, USA
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, South Korea
- Obstructive Upper airway Research (OUaR) Laboratory, Department of Pharmacology, Seoul National University College of Medicine, Seoul, South Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Yi-Sook Kim
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, South Korea
- Obstructive Upper airway Research (OUaR) Laboratory, Department of Pharmacology, Seoul National University College of Medicine, Seoul, South Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Suha Lim
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, South Korea
- Obstructive Upper airway Research (OUaR) Laboratory, Department of Pharmacology, Seoul National University College of Medicine, Seoul, South Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Seung-Hyun Shin
- Hanmi Research Center, Hanmi Pharmaceutical Co. Ltd., 550 Dongtangiheung-ro, Hwaseong-si, 18469, Gyeonggi-do, South Korea
| | - Iljin Kim
- Department of Pharmacology, Inha University College of Medicine, Incheon, South Korea
| | - Jiyoung Kim
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, South Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Min Choi
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, South Korea
- Obstructive Upper airway Research (OUaR) Laboratory, Department of Pharmacology, Seoul National University College of Medicine, Seoul, South Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Jung Ho Kim
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Seong-Joon Koh
- Liver Research Institute and Seoul National University College of Medicine, Seoul, South Korea
| | - Jong-Wan Park
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, South Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyun-Woo Shin
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, South Korea.
- Obstructive Upper airway Research (OUaR) Laboratory, Department of Pharmacology, Seoul National University College of Medicine, Seoul, South Korea.
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea.
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, South Korea.
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, South Korea.
- Sensory Organ Research Institute, Seoul National University College of Medicine, Seoul, South Korea.
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24
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Baran M, Feriotti C, McGinley A, Carlile SR, Jiang Z, Calderon-Gonzalez R, Dumigan A, Sá-Pessoa J, Sutton CE, Kearney J, McLoughlin RM, Mills KHG, Fitzgerald KA, Bengeochea JA, Bowie AG. PYHIN protein IFI207 regulates cytokine transcription and IRF7 and contributes to the establishment of K. pneumoniae infection. Cell Rep 2023; 42:112341. [PMID: 37018072 DOI: 10.1016/j.celrep.2023.112341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 02/02/2023] [Accepted: 03/20/2023] [Indexed: 04/06/2023] Open
Abstract
PYHIN proteins AIM2 and IFI204 sense pathogen DNA, while other PYHINs have been shown to regulate host gene expression through as-yet unclear mechanisms. We characterize mouse PYHIN IFI207, which we find is not involved in DNA sensing but rather is required for cytokine promoter induction in macrophages. IFI207 co-localizes with both active RNA polymerase II (RNA Pol II) and IRF7 in the nucleus and enhances IRF7-dependent gene promoter induction. Generation of Ifi207-/- mice shows no role for IFI207 in autoimmunity. Rather, IFI207 is required for the establishment of a Klebsiella pneumoniae lung infection and for Klebsiella macrophage phagocytosis. These insights into IFI207 function illustrate that PYHINs can have distinct roles in innate immunity independent of DNA sensing and highlight the need to better characterize the whole mouse locus, one gene at a time.
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Affiliation(s)
- Marcin Baran
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2 Dublin, Ireland
| | - Claudia Feriotti
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queens University Belfast, 97 Lisburn Road, Belfast, UK
| | - Aoife McGinley
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2 Dublin, Ireland
| | - Simon R Carlile
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2 Dublin, Ireland
| | - Zhaozhao Jiang
- Division of Innate Immunity, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ricardo Calderon-Gonzalez
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queens University Belfast, 97 Lisburn Road, Belfast, UK
| | - Amy Dumigan
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queens University Belfast, 97 Lisburn Road, Belfast, UK
| | - Joana Sá-Pessoa
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queens University Belfast, 97 Lisburn Road, Belfast, UK
| | - Caroline E Sutton
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2 Dublin, Ireland
| | - Jay Kearney
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2 Dublin, Ireland
| | - Rachel M McLoughlin
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2 Dublin, Ireland
| | - Kingston H G Mills
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2 Dublin, Ireland
| | - Katherine A Fitzgerald
- Division of Innate Immunity, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jose A Bengeochea
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queens University Belfast, 97 Lisburn Road, Belfast, UK
| | - Andrew G Bowie
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2 Dublin, Ireland.
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25
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Sirt1 Negatively Regulates Cellular Antiviral Responses by Preventing the Cytoplasmic Translocation of Interferon-Inducible Protein 16 in Human Cells. J Virol 2023; 97:e0197522. [PMID: 36749073 PMCID: PMC9973000 DOI: 10.1128/jvi.01975-22] [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: 02/08/2023] Open
Abstract
Interferon-inducible protein 16 (IFI16) plays a critical role in antiviral innate immune responses against DNA viruses. Although the acetylation of IFI16 is crucial to its cytoplasmic translocation and downstream signal transduction, the regulation of IFI16 acetylation remains unclear. In this study, we demonstrated that the NAD-dependent deacetylase silent information regulatory 1 (Sirtuin1, Sirt1) interacted with IFI16 and decreased the acetylation of IFI16, resulting in the inhibition of IFI16 cytoplasmic localization and antiviral responses against DNA virus and viral DNA in human cells. Meantime, Sirt1 could not inhibit RNA virus-triggered signal transduction. Interestingly, even p204, the murine ortholog of human IFI16, barely interacted with Sirt1. Thus, Sirt1 could not negatively regulate the acetylation of p204 and subsequent signal transduction upon herpes simplex virus 1 (HSV-1) infection in mouse cells. Taken together, our research work showed a new mechanism by which Sirt1 manipulated IFI16-mediated host defense. Our study also demonstrated a difference in the regulation of antiviral host defense between humans and mice, which might be considered in preclinical studies for antiviral treatment. IMPORTANCE DNA viruses, such as hepatitis B virus (HBV), human papillomavirus (HPV), human cytomegalovirus (HCMV), Epstein-Barr virus (EBV), and herpes simplex virus (HSV), can cause a wide range of diseases and are considered a global threat to human health. Interferon-inducible protein 16 (IFI16) binds virus DNA and triggers antiviral innate immune responses to restrict viral infection. In this study, we identified that silent information regulatory 1 (Sirtuin1, Sirt1) interacted with IFI16 and regulated IFI16-mediated innate host defense. Therefore, the activator or inhibitor of Sirt1 may have the potential to be used as a novel strategy to treat DNA virus-associated diseases. We also found that Sirt1 barely interacted with p204, the murine ortholog of human IFI16, and could not negatively regulate innate immune responses upon HSV-1 infection in mouse cells. This difference between humans and mice in the regulation of antiviral host defense might be considered in preclinical studies for antiviral treatment.
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26
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Sharma BR, Kanneganti TD. Inflammasome signaling in colorectal cancer. Transl Res 2023; 252:45-52. [PMID: 36150688 PMCID: PMC9839553 DOI: 10.1016/j.trsl.2022.09.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/29/2022] [Accepted: 09/15/2022] [Indexed: 01/17/2023]
Abstract
Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths in the world. Inflammation is often an underlying risk factor for developing CRC. Maintaining gut homeostasis and balancing inflammation is therefore critical to prevent CRC development. One key class of molecular complexes that impact gut homeostasis are inflammasomes, cytosolic multiprotein immune complexes that assemble upon sensing various intracellular alterations. Inflammasomes regulate inflammation, cell death, cytokine release, signaling cascades, and other cellular processes. Roles for inflammasomes in colitis and colitis-associated CRC have been shown in multiple animal models. The activation of inflammasomes leads to the release of the bioactive forms of interleukin (IL)-1β and IL-18, the inflammasome effector cytokines. These cytokines ensure an optimal inflammatory immune response during colitis and colitis-associated CRC. The activation of some inflammasome sensors, including NLRP3, NLRP1, NLRP6, and Pyrin, provides protection from colitis-associated CRC via effector cytokine-dependent mechanisms. Additionally, activation of other inflammasome sensors, such as AIM2, NLRC4, and NAIPs, provides mostly effector cytokine-independent protection. Inflammasomes can also act as integral components of PANoptosomes, which are multifaceted complexes that integrate components from other cell death pathways and regulate a unique form of innate immune inflammatory cell death called PANoptosis. Furthermore, IRF1, a key regulator of some inflammasomes and PANoptosomes, has been implicated in CRC. It is therefore critical to consider the role of inflammasomes in effector cytokine-dependent and -independent protection as well as their role in PANoptosis to modulate CRC for therapeutic targeting. Here, we discuss the mechanisms of inflammasome activation, the functions of inflammasomes in CRC, and current obstacles and future perspectives in inflammasome and CRC research.
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Affiliation(s)
- Bhesh Raj Sharma
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee
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27
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Yarani R, Palasca O, Doncheva NT, Anthon C, Pilecki B, Svane CAS, Mirza AH, Litman T, Holmskov U, Bang-Berthelsen CH, Vilien M, Jensen LJ, Gorodkin J, Pociot F. Cross-species high-resolution transcriptome profiling suggests biomarkers and therapeutic targets for ulcerative colitis. Front Mol Biosci 2023; 9:1081176. [PMID: 36685283 PMCID: PMC9850088 DOI: 10.3389/fmolb.2022.1081176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/08/2022] [Indexed: 01/07/2023] Open
Abstract
Background: Ulcerative colitis (UC) is a disorder with unknown etiology, and animal models play an essential role in studying its molecular pathophysiology. Here, we aim to identify common conserved pathological UC-related gene expression signatures between humans and mice that can be used as treatment targets and/or biomarker candidates. Methods: To identify differentially regulated protein-coding genes and non-coding RNAs, we sequenced total RNA from the colon and blood of the most widely used dextran sodium sulfate Ulcerative colitis mouse. By combining this with public human Ulcerative colitis data, we investigated conserved gene expression signatures and pathways/biological processes through which these genes may contribute to disease development/progression. Results: Cross-species integration of human and mouse Ulcerative colitis data resulted in the identification of 1442 genes that were significantly differentially regulated in the same direction in the colon and 157 in blood. Of these, 51 genes showed consistent differential regulation in the colon and blood. Less known genes with importance in disease pathogenesis, including SPI1, FPR2, TYROBP, CKAP4, MCEMP1, ADGRG3, SLC11A1, and SELPLG, were identified through network centrality ranking and validated in independent human and mouse cohorts. Conclusion: The identified Ulcerative colitis conserved transcriptional signatures aid in the disease phenotyping and future treatment decisions, drug discovery, and clinical trial design.
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Affiliation(s)
- Reza Yarani
- Translational Type 1 Diabetes Research, Department of Clinical Research, Steno Diabetes Center Copenhagen, Gentofte, Denmark,*Correspondence: Reza Yarani, ; Flemming Pociot,
| | - Oana Palasca
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark,Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nadezhda T. Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark,Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Anthon
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bartosz Pilecki
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Cecilie A. S. Svane
- Translational Type 1 Diabetes Research, Department of Clinical Research, Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Aashiq H. Mirza
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, United States
| | - Thomas Litman
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Uffe Holmskov
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Claus H. Bang-Berthelsen
- Research Group for Microbial Biotechnology and Biorefining, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark,Department of Gastroenterology, North Zealand Hillerød Hospital, Hillerød, Denmark
| | - Mogens Vilien
- Department of Surgery, North Zealand Hospital, Hillerød, Denmark
| | - Lars J. Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark,Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Flemming Pociot
- Translational Type 1 Diabetes Research, Department of Clinical Research, Steno Diabetes Center Copenhagen, Gentofte, Denmark,Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark,Copenhagen Diabetes Research Center, Department of Pediatrics, Herlev University Hospital, Herlev, Denmark,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark,*Correspondence: Reza Yarani, ; Flemming Pociot,
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28
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Pan Z, Lin H, Fu Y, Zeng F, Gu F, Niu G, Fang J, Gu B. Identification of gene signatures associated with ulcerative colitis and the association with immune infiltrates in colon cancer. Front Immunol 2023; 14:1086898. [PMID: 36742294 PMCID: PMC9893113 DOI: 10.3389/fimmu.2023.1086898] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/04/2023] [Indexed: 01/21/2023] Open
Abstract
Background Inflammatory bowel diseases, including ulcerative colitis (UC) and Crohn's disease, are some of the most common inflammatory disorders of the gastrointestinal tract. The dysfunction of the immune system in the intestines is suggested to be the underlying cause of the pathogenesis of UC. However, the mechanisms regulating these dysfunctional immune cells and inflammatory phenotypes are still unclear. Methods The differential expression analysis on microarray datasets were performed including GSE24287, GSE87466, GSE102133, and GSE107499, including 376 samples. "Gene Ontology" and "Kyoto Encyclopedia of Genes and Genomes" pathway enrichment analyses were conducted to identify the common differentially expressed genes (DEGs) in these datasets and explore their underlying biological mechanisms. Further algorithms like "Cell-type Identification by Estimating Relative Subsets of RNA Transcripts" were used to determine the infiltration status of immune cells in patients with UC. "Cytoscape" and "Gene Set Enrichment Analysis" were used to screen for hub genes and to investigate their biological mechanisms. The Tumor Immune Estimation Resource database was used to study the correlation between hub genes and infiltrating immune cells in patients with UC. A total of three hub genes, CCL3, MMP3, and TIMP1, were identified using Cytoscape. Results A positive correlation was observed between these hub genes and patients with active UC. These genes served as a biomarker for active UC. Moreover, a decrease in CCL3, MMP3, and TIMP1 expression was observed in the mucosa of the intestine of patients with active UC who responded to Golimumab therapy. In addition, results show a significant positive correlation between CCL3, MMP3, and TIMP1 expression and different immune cell types including dendritic cells, macrophages, CD8+ T cells, and neutrophils in patients with colon cancer. Moreover, CCL3, MMP3, and TIMP1 expression were strongly correlated with different immune cell markers. Conclusion Study results show the involvement of hub genes like CCL3, MMP3, and TIMP1 in the pathogenesis of UC. These genes could serve as a novel pharmacological regulator of UC. These could be used as a therapeutic target for treating patients with UC and may serve as biomarkers for immune cell infiltration in colon cancer.
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Affiliation(s)
- Zhaoji Pan
- Department of Clinical Laboratory, Xuzhou Central Hospital, Xuzhou Institute of Medical Sciences, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Hao Lin
- Department of Gastrointestinal Surgery, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yanyan Fu
- Department of Cell Biology and Neurobiology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Fanpeng Zeng
- Department of Clinical Laboratory, Xuzhou Central Hospital, Xuzhou Institute of Medical Sciences, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Feng Gu
- Department of Clinical Laboratory, Xuzhou Central Hospital, Xuzhou Institute of Medical Sciences, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Guoping Niu
- Department of Clinical Laboratory, Xuzhou Central Hospital, Xuzhou Institute of Medical Sciences, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jian Fang
- Department of Blood Transfusion, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Bing Gu
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
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29
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Dovrolis N, Filidou E, Tarapatzi G, Kokkotis G, Spathakis M, Kandilogiannakis L, Drygiannakis I, Valatas V, Arvanitidis K, Karakasiliotis I, Vradelis S, Manolopoulos VG, Paspaliaris V, Bamias G, Kolios G. Co-expression of fibrotic genes in inflammatory bowel disease; A localized event? Front Immunol 2022; 13:1058237. [PMID: 36632136 PMCID: PMC9826764 DOI: 10.3389/fimmu.2022.1058237] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/08/2022] [Indexed: 12/27/2022] Open
Abstract
Introduction Extracellular matrix turnover, a ubiquitous dynamic biological process, can be diverted to fibrosis. The latter can affect the intestine as a serious complication of Inflammatory Bowel Diseases (IBD) and is resistant to current pharmacological interventions. It embosses the need for out-of-the-box approaches to identify and target molecular mechanisms of fibrosis. Methods and results In this study, a novel mRNA sequencing dataset of 22 pairs of intestinal biopsies from the terminal ileum (TI) and the sigmoid of 7 patients with Crohn's disease, 6 with ulcerative colitis and 9 control individuals (CI) served as a validation cohort of a core fibrotic transcriptomic signature (FIBSig), This signature, which was identified in publicly available data (839 samples from patients and healthy individuals) of 5 fibrotic disorders affecting different organs (GI tract, lung, skin, liver, kidney), encompasses 241 genes and the functional pathways which derive from their interactome. These genes were used in further bioinformatics co-expression analyses to elucidate the site-specific molecular background of intestinal fibrosis highlighting their involvement, particularly in the terminal ileum. We also confirmed different transcriptomic profiles of the sigmoid and terminal ileum in our validation cohort. Combining the results of these analyses we highlight 21 core hub genes within a larger single co-expression module, highly enriched in the terminal ileum of CD patients. Further pathway analysis revealed known and novel inflammation-regulated, fibrogenic pathways operating in the TI, such as IL-13 signaling and pyroptosis, respectively. Discussion These findings provide a rationale for the increased incidence of fibrosis at the terminal ileum of CD patients and highlight operating pathways in intestinal fibrosis for future evaluation with mechanistic and translational studies.
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Affiliation(s)
- Nikolas Dovrolis
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece,Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece,Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), Alexandroupolis, Greece,*Correspondence: George Kolios, ; Nikolas Dovrolis,
| | - Eirini Filidou
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece,Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), Alexandroupolis, Greece
| | - Gesthimani Tarapatzi
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece,Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), Alexandroupolis, Greece
| | - Georgios Kokkotis
- Gastrointestinal (GI) Unit, 3 Department of Internal Medicine, Sotiria Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Michail Spathakis
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece,Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), Alexandroupolis, Greece
| | - Leonidas Kandilogiannakis
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece,Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), Alexandroupolis, Greece
| | - Ioannis Drygiannakis
- Gastroenterology and Hepatology Research Laboratory, Medical School, University of Crete, Heraklion, Greece
| | - Vassilis Valatas
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece,Gastroenterology and Hepatology Research Laboratory, Medical School, University of Crete, Heraklion, Greece
| | - Konstantinos Arvanitidis
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece,Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), Alexandroupolis, Greece
| | - Ioannis Karakasiliotis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Stergios Vradelis
- Second Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Vangelis G. Manolopoulos
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece,Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), Alexandroupolis, Greece
| | | | - Giorgos Bamias
- Gastrointestinal (GI) Unit, 3 Department of Internal Medicine, Sotiria Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - George Kolios
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece,Individualised Medicine & Pharmacological Research Solutions Center (IMPReS), Alexandroupolis, Greece,*Correspondence: George Kolios, ; Nikolas Dovrolis,
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30
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A shared tissue transcriptome signature and pathways in psoriasis and ulcerative colitis. Sci Rep 2022; 12:19740. [PMID: 36396672 PMCID: PMC9671879 DOI: 10.1038/s41598-022-22465-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/14/2022] [Indexed: 11/18/2022] Open
Abstract
Despite multiple efficacious therapies in common between psoriasis (PS) and Ulcerative Colitis (UC), mechanisms underlying their common pathophysiology remain largely unclear. Here we sought to establish a link by evaluating expression differences and pathway alterations in diseased tissues. We identified two sets of differentially expressed genes (DEGs) between lesional and nonlesional tissues in meta-analyses of data collected from baseline samples in 3 UC and then 3 PS available clinical studies from Pfizer. A shared gene signature was defined by 190 DEGs common to both diseases. Commonly dysregulated pathways identified via enrichment analysis include interferon signaling, partly driven by genes IFI6, CXCL9, CXCL10 and CXCL11, which may attract chemotaxis of Th1 cells to inflammatory sites; IL-23 pathway (IL-23A, CCL20, PI3, CXCL1, LCN2); and Th17 pathway except IL-17A. Elevated expression of costimulatory molecules ICOS and CTLA4 suggests ongoing T-cell activation in both diseases. The clinical value of the shared signature is demonstrated by a gene set improvement score reflecting post-treatment molecular improvement for each disease. This is the first study using transcriptomic meta-analysis to define a tissue gene signature and pathways dysregulated in both PS and UC. These findings suggest immune mechanisms may initiate and sustain inflammation similarly in the two diseases.
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31
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Zhou Z, Plug LG, Patente TA, de Jonge-Muller ESM, Elmagd AA, van der Meulen-de Jong AE, Everts B, Barnhoorn MC, Hawinkels LJAC. Increased stromal PFKFB3-mediated glycolysis in inflammatory bowel disease contributes to intestinal inflammation. Front Immunol 2022; 13:966067. [PMID: 36405760 PMCID: PMC9670190 DOI: 10.3389/fimmu.2022.966067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 10/17/2022] [Indexed: 08/10/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic relapsing inflammation of the intestinal tract with currently not well-understood pathogenesis. In addition to the involvement of immune cells, increasing studies show an important role for fibroblasts in the pathogenesis of IBD. Previous work showed that glycolysis is the preferred energy source for fibroblasts in fibrotic diseases. 6-phosphofructo-2-kinase/fructose-2, 6-bisphosphatase 3 (PFKFB3) is a key kinase supporting glycolysis. Increased expression of PFKFB3 in several cancers and inflammatory diseases has been previously reported, but the metabolic status of fibroblasts and the role of PFKFB3 in patients with IBD are currently unknown. Therefore, in this study, we evaluated the role of glycolysis and PFKFB3 expression in IBD. Single-sample gene set enrichment analysis (ssGSEA) revealed that glycolysis was significantly higher in IBD intestinal samples, compared to healthy controls, which was confirmed in the validation cohorts of IBD patients. Single-cell sequencing data indicated that PFKFB3 expression was higher in IBD-derived stromal cells. In vitro, PFKFB3 expression in IBD-derived fibroblasts was increased after the stimulation with pro-inflammatory cytokines. Using seahorse real-time cell metabolic analysis, inflamed fibroblasts were shown to have a higher extracellular acidification rate and a lower oxygen consumption rate, which could be reversed by inhibition of JAK/STAT pathway. Furthermore, increased expression of pro-inflammatory cytokines and chemokines in fibroblasts could be reverted by PFK15, a specific inhibitor of PFKFB3. In vivo experiments showed that PFK15 reduced the severity of dextran sulfate sodium (DSS)- and Tcell transfer induced colitis, which was accompanied by a reduction in immune cell infiltration in the intestines. These findings suggest that increased stromal PFKFB3 expression contributes to inflammation and the pathological function of fibroblasts in IBD. Inhibition of PFKFB3 suppressed their inflammatory characteristics.
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Affiliation(s)
- Zhou Zhou
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Leonie G. Plug
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Thiago A. Patente
- Department of Parasitology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Amir Abou Elmagd
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Bart Everts
- Department of Parasitology, Leiden University Medical Center, Leiden, Netherlands
| | - Marieke C. Barnhoorn
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Lukas J. A. C. Hawinkels
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands
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32
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Chen K, Shang S, Yu S, Cui L, Li S, He N. Identification and exploration of pharmacological pyroptosis-related biomarkers of ulcerative colitis. Front Immunol 2022; 13:998470. [PMID: 36311726 PMCID: PMC9606687 DOI: 10.3389/fimmu.2022.998470] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/26/2022] [Indexed: 11/25/2022] Open
Abstract
Ulcerative colitis (UC) is a chronic inflammatory bowel disease (IBD). Its etiology is unclear. Much evidence suggests that the death of abnormal intestinal epithelial cells (IECs) leads to intestinal barrier disruption, and the subsequent inflammatory response plays a vital role in UC. Pyroptosis is a form of programmed inflammatory cell death, and the role of pyroptosis in UC etiology remains to be explored. This study identified 10 hub genes in pyroptosis by gene expression profiles obtained from the GSE87466 dataset. Meanwhile, the biomarkers were screened based on gene significance (GS) and module membership (MM) through the Weighted Gene Co-Expression Network Analysis (WGCNA). The following analysis indicated that hub genes were closely associated with the UC progression and therapeutic drug response. The single-cell RNA (scRNA) sequencing data from UC patients within the GSE162335 dataset indicated that macrophages were most related to pyroptosis. Finally, the expression of hub genes and response to the therapeutic drug [5-aminosalicylic acid (5-ASA)] were verified in dextran sulfate sodium (DSS)-induced colitis mice. Our study identified IL1B as the critical pyroptosis-related biomarker in UC. The crosstalk between macrophage pyroptosis and IEC pyroptosis may play an essential role in UC, deserving further exploration.
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Affiliation(s)
| | | | | | | | | | - Ningning He
- *Correspondence: Shangyong Li, ; Ningning He,
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33
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Pavlidis P, Tsakmaki A, Pantazi E, Li K, Cozzetto D, Digby-Bell J, Yang F, Lo JW, Alberts E, Sa ACC, Niazi U, Friedman J, Long AK, Ding Y, Carey CD, Lamb C, Saqi M, Madgwick M, Gul L, Treveil A, Korcsmaros T, Macdonald TT, Lord GM, Bewick G, Powell N. Interleukin-22 regulates neutrophil recruitment in ulcerative colitis and is associated with resistance to ustekinumab therapy. Nat Commun 2022; 13:5820. [PMID: 36192482 PMCID: PMC9530232 DOI: 10.1038/s41467-022-33331-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 09/14/2022] [Indexed: 11/28/2022] Open
Abstract
The function of interleukin-22 (IL-22) in intestinal barrier homeostasis remains controversial. Here, we map the transcriptional landscape regulated by IL-22 in human colonic epithelial organoids and evaluate the biological, functional and clinical significance of the IL-22 mediated pathways in ulcerative colitis (UC). We show that IL-22 regulated pro-inflammatory pathways are involved in microbial recognition, cancer and immune cell chemotaxis; most prominently those involving CXCR2+ neutrophils. IL-22-mediated transcriptional regulation of CXC-family neutrophil-active chemokine expression is highly conserved across species, is dependent on STAT3 signaling, and is functionally and pathologically important in the recruitment of CXCR2+ neutrophils into colonic tissue. In UC patients, the magnitude of enrichment of the IL-22 regulated transcripts in colonic biopsies correlates with colonic neutrophil infiltration and is enriched in non-responders to ustekinumab therapy. Our data provide further insights into the biology of IL-22 in human disease and highlight its function in the regulation of pathogenic immune pathways, including neutrophil chemotaxis. The transcriptional networks regulated by IL-22 are functionally and clinically important in UC, impacting patient trajectories and responsiveness to biological intervention. Mechanisms of non-response to ustekinumab, a biologic targeting IL-23, are currently unclear. Here, the authors show that the transcriptional program regulated by IL-22, an IL-23 responsive cytokine, is enriched in patients with ulcerative colitis unresponsive to ustekinumab and associated with higher colon neutrophil recruitment and activation of upstream IL-22 regulators.
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Affiliation(s)
| | - Anastasia Tsakmaki
- Diabetes Research Group, School of Life Course Sciences, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Eirini Pantazi
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Katherine Li
- Janssen Research & Development, 1400 McKean Rd, Spring House, PA, 19477, USA
| | - Domenico Cozzetto
- Translational Bioinformatics, National Institute for Health Research Biomedical Centre, Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
| | - Jonathan Digby-Bell
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Feifei Yang
- Janssen Research & Development, 1400 McKean Rd, Spring House, PA, 19477, USA
| | - Jonathan W Lo
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Elena Alberts
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | | | - Umar Niazi
- Translational Bioinformatics, National Institute for Health Research Biomedical Centre, Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
| | - Joshua Friedman
- Janssen Research & Development, 1400 McKean Rd, Spring House, PA, 19477, USA
| | - Anna K Long
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Yuchun Ding
- Translational and Clinical Research Institute, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
| | - Christopher D Carey
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.,Translational and Clinical Research Institute, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
| | - Christopher Lamb
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.,Translational and Clinical Research Institute, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
| | - Mansoor Saqi
- Translational Bioinformatics, National Institute for Health Research Biomedical Centre, Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
| | - Matthew Madgwick
- Earlham Institute, Norwich Research Park, Norwich, UK.,Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Leila Gul
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, UK.,Earlham Institute, Norwich Research Park, Norwich, UK.,Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Agatha Treveil
- Earlham Institute, Norwich Research Park, Norwich, UK.,Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Tamas Korcsmaros
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, UK.,Earlham Institute, Norwich Research Park, Norwich, UK.,Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Thomas T Macdonald
- Centre for Immunobiology, Barts and the London School of Medicine and Dentistry, QMUL, London, UK
| | - Graham M Lord
- School of Immunology and Microbial Sciences, King's College London, London, UK.,Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Gavin Bewick
- Diabetes Research Group, School of Life Course Sciences, Faculty of Life Science and Medicine, King's College London, London, UK
| | - Nick Powell
- Division of Digestive Diseases, Faculty of Medicine, Imperial College London, London, UK.
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34
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Swanson KV, Girnary M, Alves T, Ting JPY, Divaris K, Beck J, Pucinelli CM, da Silva RAB, Uyan D, Wilson J, Seaman WT, Webster-Cyriaque J, Vias N, Jiao Y, Cantley L, Marlier A, Arnold RR, Marchesan JT. Interferon activated gene 204 protects against bone loss in experimental periodontitis. J Periodontol 2022; 93:1366-1377. [PMID: 35404474 PMCID: PMC9489626 DOI: 10.1002/jper.21-0668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/03/2022] [Accepted: 03/31/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Periodontal destruction can be the result of different known and yet-to-be-discovered biological pathways. Recent human genetic association studies have implicated interferon-gamma inducible protein 16 (IFI16) and absent in melanoma 2 (AIM2) with high periodontal interleukin (IL)-1β levels and more destructive disease, but mechanistic evidence is lacking. Here, we sought to experimentally validate these observational associations and better understand IFI16 and AIM2's roles in periodontitis. METHODS Periodontitis was induced in Ifi204-/- (IFI16 murine homolog) and Aim2-/- mice using the ligature model. Chimeric mice were created to identify the main source cells of Ifi204 in the periodontium. IFI16-silenced human endothelial cells were treated with periodontal pathogens in vitro. Periodontal tissues from Ifi204-/- mice were evaluated for alveolar bone (micro-CT), cell inflammatory infiltration (MPO+ staining), Il1b (qRT-PCR), and osteoclast numbers (cathepsin K+ staining). RESULTS Ifi204-deficient mice> exhibited >20% higher alveolar bone loss than wild-type (WT) (P < 0.05), while no significant difference was found in Aim2-/- mice. Ifi204's effect on bone loss was primarily mediated by a nonbone marrow source and was independent of Aim2. Ifi204-deficient mice had greater neutrophil/macrophage trafficking into gingival tissues regardless of periodontitis development compared to WT. In human endothelial cells, IFI16 decreased the chemokine response to periodontal pathogens. In murine periodontitis, Ifi204 depletion elevated gingival Il1b and increased osteoclast numbers at diseased sites (P < 0.05). CONCLUSIONS These findings support IFI16's role as a novel regulator of inflammatory cell trafficking to the periodontium that protects against bone loss and offers potential targets for the development of new periodontal disease biomarkers and therapeutics.
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Affiliation(s)
- Karen V Swanson
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Mustafa Girnary
- Curriculum in Doctor of Dental Surgery, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tomaz Alves
- Division of Comprehensive Oral Health, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - Jenny PY Ting
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kimon Divaris
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - Jim Beck
- Division of Comprehensive Oral Health, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - Carolina Maschietto Pucinelli
- Department of Pediatric Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Raquel Assed Bezerra da Silva
- Department of Pediatric Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Dilek Uyan
- Division of Comprehensive Oral Health, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - Justin Wilson
- Department of Immunobiology, College of Medicine, The University of Arizona, Tucson, AZ, USA
| | - William T. Seaman
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - Jennifer Webster-Cyriaque
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - Nishma Vias
- Curriculum in Doctor of Dental Surgery, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yizu Jiao
- Curriculum in Doctor of Dental Surgery, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lloyd Cantley
- Department of Internal Medicine, Yale University, New Haven, CT, USA
| | - Arnaud Marlier
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Roland R. Arnold
- Division of Diagnostic Sciences, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - Julie T. Marchesan
- Division of Comprehensive Oral Health, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
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35
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Pucinelli CM, Lima RB, Almeida LKY, Lucisano MP, Córdoba AZ, Marchesan JT, da Silva LAB, da Silva RAB. Interferon‐gamma inducible protein 16 and type I interferon receptors expression in experimental apical periodontitis induced in wild type mice. Int Endod J 2022; 55:1042-1052. [DOI: 10.1111/iej.13802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/30/2022]
Affiliation(s)
- C. M. Pucinelli
- Department of Pediatric Dentistry ‐ University of São Paulo School of Dentistry of Ribeirão Preto Ribeirão Preto SP Brazil
| | - R. B. Lima
- Department of Pediatric Dentistry ‐ University of São Paulo School of Dentistry of Ribeirão Preto Ribeirão Preto SP Brazil
| | - L. K. Y. Almeida
- Department of Pediatric Dentistry ‐ University of São Paulo School of Dentistry of Ribeirão Preto Ribeirão Preto SP Brazil
| | - M. P. Lucisano
- Department of Pediatric Dentistry ‐ University of São Paulo School of Dentistry of Ribeirão Preto Ribeirão Preto SP Brazil
| | - A. Z. Córdoba
- Department of Pediatric Dentistry ‐ University of São Paulo School of Dentistry of Ribeirão Preto Ribeirão Preto SP Brazil
| | - J. T. Marchesan
- Department of Periodontology ‐ University of North Carolina at Chapel Hill School of Dentistry Chapel Hill NC EUA
| | - L. A. B. da Silva
- Department of Pediatric Dentistry ‐ University of São Paulo School of Dentistry of Ribeirão Preto Ribeirão Preto SP Brazil
| | - R. A. B. da Silva
- Department of Pediatric Dentistry ‐ University of São Paulo School of Dentistry of Ribeirão Preto Ribeirão Preto SP Brazil
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Al-Mustanjid M, Mahmud SMH, Akter F, Rahman MS, Hossen MS, Rahman MH, Moni MA. Systems biology models to identify the influence of SARS-CoV-2 infections to the progression of human autoimmune diseases. INFORMATICS IN MEDICINE UNLOCKED 2022; 32:101003. [PMID: 35818398 PMCID: PMC9259025 DOI: 10.1016/j.imu.2022.101003] [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: 02/17/2022] [Revised: 06/25/2022] [Accepted: 06/25/2022] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been circulating since 2019, and its global dominance is rising. Evidences suggest the respiratory illness SARS-CoV-2 has a sensitive affect on causing organ damage and other complications to the patients with autoimmune diseases (AD), posing a significant risk factor. The genetic interrelationships and molecular appearances between SARS-CoV-2 and AD are yet unknown. We carried out the transcriptomic analytical framework to delve into the SARS-CoV-2 impacts on AD progression. We analyzed both gene expression microarray and RNA-Seq datasets from SARS-CoV-2 and AD affected tissues. With neighborhood-based benchmarks and multilevel network topology, we obtained dysfunctional signaling and ontological pathways, gene disease (diseasesome) association network and protein-protein interaction network (PPIN), uncovered essential shared infection recurrence connectivities with biological insights underlying between SARS-CoV-2 and AD. We found a total of 77, 21, 9, 54 common DEGs for SARS-CoV-2 and inflammatory bowel disorder (IBD), SARS-CoV-2 and rheumatoid arthritis (RA), SARS-CoV-2 and systemic lupus erythematosus (SLE) and SARS-CoV-2 and type 1 diabetes (T1D). The enclosure of these common DEGs with bimolecular networks revealed 10 hub proteins (FYN, VEGFA, CTNNB1, KDR, STAT1, B2M, CD3G, ITGAV, TGFB3). Drugs such as amlodipine besylate, vorinostat, methylprednisolone, and disulfiram have been identified as a common ground between SARS-CoV-2 and AD from drug repurposing investigation which will stimulate the optimal selection of medications in the battle against this ongoing pandemic triggered by COVID-19.
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Affiliation(s)
- Md Al-Mustanjid
- Department of Software Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - S M Hasan Mahmud
- Department of Computer Science, American International University-Bangladesh, Dhaka, 1229, Bangladesh
| | - Farzana Akter
- Department of Software Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - Md Shazzadur Rahman
- Department of Computer Science & Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - Md Sajid Hossen
- Department of Software Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia-7003, Bangladesh
| | - Mohammad Ali Moni
- Department of Computer Science and Engineering, Pabna Science & Technology University, Pabna, 6600, Bangladesh
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Ye B, Lu Z. Role of TRIM22 in ulcerative colitis and its underlying mechanisms. Mol Med Rep 2022; 26:249. [PMID: 35674157 PMCID: PMC9218723 DOI: 10.3892/mmr.2022.12765] [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: 11/02/2021] [Accepted: 03/16/2022] [Indexed: 12/03/2022] Open
Abstract
Ulcerative colitis (UC) is a common chronic recurrent inflammatory disease, which seriously threatens human life and health. Therefore, the present study aimed to explore the role of tripartite motif-containing (TRIM)22 in UC and its potential mechanism. C57BL/6 mice and HT-29 cell models of UC were constructed using 2% dextran sulphate sodium (DSS). The protein and mRNA expression levels were detected by western blotting and reverse transcription-quantitative PCR, respectively. Cell transfection was performed to overexpress Kruppel-like factor 2 (KLF2), or knockdown KLF2, TRIM22 and TRIM30 expression. The levels of inflammatory factors were evaluated by enzyme-linked immunosorbent assays. Cell Counting Kit-8 and TUNEL staining assay were employed to assess cell viability and apoptosis. Dual-luciferase reporter assay and chromatin immunoprecipitation assay were performed to determine the binding ability of the TRIM22 promoter to KLF2. The results revealed that DSS increased the expression levels of TRIM22 in HT-29 cells and TRIM30 in mice. Short hairpin RNA (sh)-TRIM30 could inhibit the NF-κB pathway, and reduce the levels of TNF-α, IL-6 and IFN-γ. Furthermore, KLF2 expression was downregulated in the cell model of UC, and the luciferase assay confirmed that the 3′ untranslated region of TRIM22 was a direct target of KLF2. The ChIP assay also verified the binding of KLF2 with the TRIM22 promoter. Notably, knockdown of KLF2 reversed the enhancing effects of sh-TRIM22 on the viability of DSS-treated HT-29 cells. In addition, compared with in the DSS + sh-TRIM22 group, the protein expression levels of phosphorylated (p)-NF-κB and p-IκBα were increased in the DSS + sh-TRIM22 + sh-KLF2 group, as were the levels of TNF-α, IL-6 and IFN-γ. In conclusion, TRIM22 was upregulated in DSS-induced HT-29 cells. TRIM22 knockdown increased DSS-induced HT-29 cell viability and decreased apoptosis and inflammation; this was reversed by knockdown of KLF2. These findings suggested that TRIM22 may promote disease development through the NF-κB signaling pathway in UC and could be inhibited by KLF2 transcription.
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Affiliation(s)
- Bin Ye
- Department of Gastroenterology, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310000, P.R. China
| | - Zhongkai Lu
- Department of Gastroenterology, Suzhou Municipal Hospital, Suzhou Hospital Affiliated to Nanjing Medical University, Suzhou, Jiangsu 215001, P.R. China
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Dysbiosis in Inflammatory Bowel Disease: Pathogenic Role and Potential Therapeutic Targets. Int J Mol Sci 2022; 23:ijms23073464. [PMID: 35408838 PMCID: PMC8998182 DOI: 10.3390/ijms23073464] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 12/12/2022] Open
Abstract
Microbe-host communication is essential to maintain vital functions of a healthy host, and its disruption has been associated with several diseases, including Crohn's disease and ulcerative colitis, the two major forms of inflammatory bowel disease (IBD). Although individual members of the intestinal microbiota have been associated with experimental IBD, identifying microorganisms that affect disease susceptibility and phenotypes in humans remains a considerable challenge. Currently, the lack of a definition between what is healthy and what is a dysbiotic gut microbiome limits research. Nevertheless, although clear proof-of-concept of causality is still lacking, there is an increasingly evident need to understand the microbial basis of IBD at the microbial strain, genomic, epigenomic, and functional levels and in specific clinical contexts. Recent information on the role of diet and novel environmental risk factors affecting the gut microbiome has direct implications for the immune response that impacts the development of IBD. The complexity of IBD pathogenesis, involving multiple distinct elements, suggests the need for an integrative approach, likely utilizing computational modeling of molecular datasets to identify more specific therapeutic targets.
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Periodontal infectogenomics: a systematic review update of associations between host genetic variants and subgingival microbial detection. Clin Oral Investig 2022; 26:2209-2221. [PMID: 35122548 PMCID: PMC8898234 DOI: 10.1007/s00784-021-04233-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 10/16/2021] [Indexed: 12/20/2022]
Abstract
Objective The aim of this study was to systematically update the evidence for associations between host genetic variants and subgingival microbial detection and counts. Materials and methods Following a previous systematic review (Nibali et al. J Clin Periodontol 43(11): 889-900, 15), an update of a systematic search of the literature was conducted in Ovid Medline, Embase, LILACS, and Cochrane Library for studies reporting data on host genetic variants and detection of microbes subgingivally published in the last 6 years. Results A total of 19 studies were included in the review, from an initial search of 2797 titles. Studies consisted mainly of candidate gene studies and of one genome-wide analysis. A total of 62 studies were considered for summary findings, including 43 identified in the previous systematic review of studies published up to 2015. Meta-analyses were done when appropriate including both papers in the original review and in the update. Meta-analyses revealed lack of associations between IL1 composite genotype and subgingival detection of Aggregatibacter acinomycetemcomitans, Poprhyromonas gingivalis, Tannerella forsythia, Treponema denticola, and Prevotella intermedia. Promising evidence is emerging from other genetic variants and from sub-analyses of data from genome-association studies. Among other studies with candidate-gene, target SNPs were mainly within the IL10, IL6, IL4, IL8, IL17A, and VDR gene. Conclusions IL1 composite genotype does not seem to be associated with subgingival microbial detection. Promising associations should be pursued by future studies, including studies employing -OMICS technologies. Clinical relevance A better knowledge of which host genetic variant predispose to subgingival microbial colonization and to the development of progression of periodontal disease could potentially help to better understand periodontal disease pathogenesis and help with its management. Supplementary Information The online version contains supplementary material available at 10.1007/s00784-021-04233-8.
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PKCλ/ι inhibition activates an ULK2-mediated interferon response to repress tumorigenesis. Mol Cell 2021; 81:4509-4526.e10. [PMID: 34560002 DOI: 10.1016/j.molcel.2021.08.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/19/2021] [Accepted: 08/27/2021] [Indexed: 01/05/2023]
Abstract
The interferon (IFN) pathway is critical for cytotoxic T cell activation, which is central to tumor immunosurveillance and successful immunotherapy. We demonstrate here that PKCλ/ι inactivation results in the hyper-stimulation of the IFN cascade and the enhanced recruitment of CD8+ T cells that impaired the growth of intestinal tumors. PKCλ/ι directly phosphorylates and represses the activity of ULK2, promoting its degradation through an endosomal microautophagy-driven ubiquitin-dependent mechanism. Loss of PKCλ/ι results in increased levels of enzymatically active ULK2, which, by direct phosphorylation, activates TBK1 to foster the activation of the STING-mediated IFN response. PKCλ/ι inactivation also triggers autophagy, which prevents STING degradation by chaperone-mediated autophagy. Thus, PKCλ/ι is a hub regulating the IFN pathway and three autophagic mechanisms that serve to maintain its homeostatic control. Importantly, single-cell multiplex imaging and bioinformatics analysis demonstrated that low PKCλ/ι levels correlate with enhanced IFN signaling and good prognosis in colorectal cancer patients.
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Hong Y, Lee SO, Oh C, Kang K, Ryoo J, Kim D, Ahn K. USP21 Deubiquitinase Regulates AIM2 Inflammasome Activation. THE JOURNAL OF IMMUNOLOGY 2021; 207:1926-1936. [PMID: 34470856 DOI: 10.4049/jimmunol.2100449] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/01/2021] [Indexed: 12/11/2022]
Abstract
Innate immune sensing of cytosolic DNA via absent in melanoma 2 (AIM2) is a key mechanism leading to inflammatory responses. As aberrant immune responses by dysregulated AIM2 are associated with autoinflammatory diseases, activation of the AIM2 inflammasome should be tightly controlled. In this study, we discovered that ubiquitination and deubiquitination of AIM2 are critical events that regulate AIM2 inflammasome activation. In resting human macrophage cells, AIM2 is constitutively ubiquitinated and undergoes proteasomal degradation to avoid autoinflammation. Upon DNA stimulation, USP21 binds to AIM2 and deubiquitinates it, thereby increasing its protein stability. In addition to the role of USP21 in regulating AIM2 turnover, we uncovered that USP21-mediated deubiquitination of AIM2 is required for the assembly of the AIM2 inflammasome. Depletion of USP21 does not affect the DNA-binding ability of AIM2 but inhibits the formation of the AIM2-ASC complex. Our findings establish that fine-tuning of AIM2 by the ubiquitin system is important for regulating AIM2 inflammasome activation.
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Affiliation(s)
- Yujin Hong
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.,Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; and
| | - Seong-Ok Lee
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.,Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; and
| | - Changhoon Oh
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.,Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; and
| | - Kwonyoon Kang
- College of Medicine, The Catholic University, Seoul, Republic of Korea
| | - Jeongmin Ryoo
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Dongyoung Kim
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.,Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; and
| | - Kwangseog Ahn
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea; .,Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea; and
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Zhu H, Zhao M, Chang C, Chan V, Lu Q, Wu H. The complex role of AIM2 in autoimmune diseases and cancers. Immun Inflamm Dis 2021; 9:649-665. [PMID: 34014039 PMCID: PMC8342223 DOI: 10.1002/iid3.443] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/09/2021] [Indexed: 12/13/2022] Open
Abstract
Absent in melanoma 2 (AIM2) is a novel member of interferon (IFN)-inducible PYHIN proteins. In innate immune cells, AIM2 servers as a cytoplasmic double-stranded DNA sensor, playing a crucial role in the initiation of the innate immune response as a component of the inflammasome. AIM2 expression is increased in patients with systemic lupus erythematosus (SLE), psoriasis, and primary Sjogren's syndrome, indicating that AIM2 might be involved in the pathogenesis of autoimmune diseases. Meanwhile, AIM2 also plays an antitumorigenesis role in an inflammasome independent-manner. In melanoma, AIM2 is initially identified as a tumor suppressor factor. However, AIM2 is also found to contribute to lung tumorigenesis via the inflammasome-dependent release of interleukin 1β and regulation of mitochondrial dynamics. Additionally, AIM2 reciprocally dampening the cGAS-STING pathway causes immunosuppression of macrophages and evasion of antitumor immunity during antibody treatment. To summarize the complicated effect and role of AIM2 in autoimmune diseases and cancers, herein, we provide an overview of the emerging research progress on the function and regulatory pathway of AIM2 in innate and adaptive immune cells, as well as tumor cells, and discuss its pathogenic role in autoimmune diseases, such as SLE, psoriasis, primary Sjogren's syndrome, and cancers, such as melanomas, non-small-cell lung cancer, colon cancer, hepatocellular carcinoma, renal carcinoma, and so on, hopefully providing potential therapeutic and diagnostic strategies for clinical use.
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Affiliation(s)
- Huan Zhu
- Department of Dermatology, Hunan Key Laboratory of Medical EpigenomicsThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Ming Zhao
- Department of Dermatology, Hunan Key Laboratory of Medical EpigenomicsThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Christopher Chang
- Division of Rheumatology, Allergy and Clinical ImmunologyUniversity of California at Davis School of MedicineDavisCaliforniaUSA
| | - Vera Chan
- Division of Rheumatology and Clinical Immunology, Department of MedicineThe University of Hong KongHong KongChina
| | - Qianjin Lu
- Department of Dermatology, Hunan Key Laboratory of Medical EpigenomicsThe Second Xiangya Hospital of Central South UniversityChangshaChina
- Institute of DermatologyChinese Academy of Medical Sciences and Peking Union Medical CollegeNanjingChina
| | - Haijing Wu
- Department of Dermatology, Hunan Key Laboratory of Medical EpigenomicsThe Second Xiangya Hospital of Central South UniversityChangshaChina
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Artificial intelligence guided discovery of a barrier-protective therapy in inflammatory bowel disease. Nat Commun 2021; 12:4246. [PMID: 34253728 PMCID: PMC8275683 DOI: 10.1038/s41467-021-24470-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/21/2021] [Indexed: 12/19/2022] Open
Abstract
Modeling human diseases as networks simplify complex multi-cellular processes, helps understand patterns in noisy data that humans cannot find, and thereby improves precision in prediction. Using Inflammatory Bowel Disease (IBD) as an example, here we outline an unbiased AI-assisted approach for target identification and validation. A network was built in which clusters of genes are connected by directed edges that highlight asymmetric Boolean relationships. Using machine-learning, a path of continuum states was pinpointed, which most effectively predicted disease outcome. This path was enriched in gene-clusters that maintain the integrity of the gut epithelial barrier. We exploit this insight to prioritize one target, choose appropriate pre-clinical murine models for target validation and design patient-derived organoid models. Potential for treatment efficacy is confirmed in patient-derived organoids using multivariate analyses. This AI-assisted approach identifies a first-in-class gut barrier-protective agent in IBD and predicted Phase-III success of candidate agents. Traditional drug discovery process use differential, Bayesian and other network based approaches. We developed a Boolean approach for building disease maps and prioritizing pre-clinical models to discover a first-in-class therapy to restore and protect the leaky gut barrier in inflammatory bowel disease.
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Chen ZA, Sun YF, Wang QX, Ma HH, Ma ZZ, Yang CJ. Integrated Analysis of Multiple Microarray Studies to Identify Novel Gene Signatures in Ulcerative Colitis. Front Genet 2021; 12:697514. [PMID: 34306038 PMCID: PMC8299473 DOI: 10.3389/fgene.2021.697514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/07/2021] [Indexed: 12/30/2022] Open
Abstract
Background: Ulcerative colitis (UC) is a chronic, complicated, inflammatory disease with an increasing incidence and prevalence worldwide. However, the intrinsic molecular mechanisms underlying the pathogenesis of UC have not yet been fully elucidated. Methods: All UC datasets published in the GEO database were analyzed and summarized. Subsequently, the robust rank aggregation (RRA) method was used to identify differentially expressed genes (DEGs) between UC patients and controls. Gene functional annotation and PPI network analysis were performed to illustrate the potential functions of the DEGs. Some important functional modules from the protein-protein interaction (PPI) network were identified by molecular complex detection (MCODE), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG), and analyses were performed. The results of CytoHubba, a plug for integrated algorithm for biomolecular interaction networks combined with RRA analysis, were used to identify the hub genes. Finally, a mouse model of UC was established by dextran sulfate sodium salt (DSS) solution to verify the expression of hub genes. Results: A total of 6 datasets met the inclusion criteria (GSE38713, GSE59071, GSE73661, GSE75214, GSE87466, GSE92415). The RRA integrated analysis revealed 208 significant DEGs (132 upregulated genes and 76 downregulated genes). After constructing the PPI network by MCODE plug, modules with the top three scores were listed. The CytoHubba app and RRA identified six hub genes: LCN2, CXCL1, MMP3, IDO1, MMP1, and S100A8. We found through enrichment analysis that these functional modules and hub genes were mainly related to cytokine secretion, immune response, and cancer progression. With the mouse model, we found that the expression of all six hub genes in the UC group was higher than that in the control group (P < 0.05). Conclusion: The hub genes analyzed by the RRA method are highly reliable. These findings improve the understanding of the molecular mechanisms in UC pathogenesis.
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Affiliation(s)
- Zi-An Chen
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yu-Feng Sun
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Quan-Xu Wang
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Hui-Hui Ma
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhi-Zhao Ma
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Chuan-Jie Yang
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
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Patankar JV, Müller TM, Kantham S, Acera MG, Mascia F, Scheibe K, Mahapatro M, Heichler C, Yu Y, Li W, Ruder B, Günther C, Leppkes M, Mathew MJ, Wirtz S, Neufert C, Kühl AA, Paquette J, Jacobson K, Atreya R, Zundler S, Neurath MF, Young RN, Becker C. E-type prostanoid receptor 4 drives resolution of intestinal inflammation by blocking epithelial necroptosis. Nat Cell Biol 2021; 23:796-807. [PMID: 34239062 DOI: 10.1038/s41556-021-00708-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 06/06/2021] [Indexed: 02/06/2023]
Abstract
Inflammatory bowel diseases present with elevated levels of intestinal epithelial cell (IEC) death, which compromises the gut barrier, activating immune cells and triggering more IEC death. The endogenous signals that prevent IEC death and break this vicious cycle, allowing resolution of intestinal inflammation, remain largely unknown. Here we show that prostaglandin E2 signalling via the E-type prostanoid receptor 4 (EP4) on IECs represses epithelial necroptosis and induces resolution of colitis. We found that EP4 expression correlates with an improved IBD outcome and that EP4 activation induces a transcriptional signature consistent with resolution of intestinal inflammation. We further show that dysregulated necroptosis prevents resolution, and EP4 agonism suppresses necroptosis in human and mouse IECs. Mechanistically, EP4 signalling on IECs converges on receptor-interacting protein kinase 1 to suppress tumour necrosis factor-induced activation and membrane translocation of the necroptosis effector mixed-lineage kinase domain-like pseudokinase. In summary, our study indicates that EP4 promotes the resolution of colitis by suppressing IEC necroptosis.
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Affiliation(s)
- Jay V Patankar
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Tanja M Müller
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Srinivas Kantham
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Miguel Gonzalez Acera
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Fabrizio Mascia
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Kristina Scheibe
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Mousumi Mahapatro
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Christina Heichler
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Yuqiang Yu
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Wei Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, People's Republic of China
| | - Barbara Ruder
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Claudia Günther
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Moritz Leppkes
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Mano J Mathew
- INSERM, Cordeliers Research Centre, Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, Paris, France
- Allianstic Research Laboratory, EFREI Paris, Villejuif, France
| | - Stefan Wirtz
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Clemens Neufert
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Anja A Kühl
- Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Medizinische Klinik für Gastroenterologie, Infektiologie und Rheumatologie, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt Universität zu Berlin and Berlin Institute of Health, iPATH.Berlin, Berlin, Germany
| | - Jay Paquette
- Centre for Drug Research and Development, Vancouver, BC, Canada
- adMare BioInnovations, Vancouver, British Columbia, Canada
| | - Kevan Jacobson
- Department of Pediatrics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Raja Atreya
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Sebastian Zundler
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Markus F Neurath
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Robert N Young
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Christoph Becker
- Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany.
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany.
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Hirokawa M, Takahashi K, Miyajima M, Furukawa R, Sugita K, Kondo H, Ohmori K. Expression of genes encoding inflammasome sensor subunits in the duodenal and colonic mucosae of dogs with chronic enteropathy. J Vet Med Sci 2021; 83:1161-1166. [PMID: 34078756 PMCID: PMC8349800 DOI: 10.1292/jvms.20-0519] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Inflammasomes play a pivotal role in gastrointestinal homeostasis and inflammation. However, it remains elusive whether the nucleotide-binding oligomerization
domain-like receptor (NLR) family inflammasomes, such as NLR family pyrin domain-containing (NLRP) 3, NLRP6, and NLRP12, are involved in the pathogenesis of
canine chronic enteropathy (CE), which includes antibiotic-responsive enteropathy (ARE), food-responsive enteropathy (FRE), immunosuppressant-responsive
enteropathy (IRE), and non-responsive enteropathy (NRE). Thus, we measured mRNA expression of NLRP3, NLRP6, and
NLRP12 in the intestinal mucosa of 35 dogs with CE (ARE, four dogs; FRE, 11 dogs; IRE and NRE, 20 dogs) and seven healthy dogs. As per
real-time PCR analysis, significant increases in mRNA expression of NLRP3 and NLRP12 were noted in the colonic but not in the
duodenal mucosa of dogs with FRE compared to healthy dogs. These findings suggested that the NLRP3 and NLRP12 inflammasomes might contribute to the development
of colitis in dogs with FRE.
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Affiliation(s)
- Marin Hirokawa
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Kaho Takahashi
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Masaki Miyajima
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Rintaro Furukawa
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.,Advanced Animal Medical Center, 1075 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka 411-0934, Japan
| | - Koji Sugita
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.,Sugita Animal Hospital, 3-55-10 Shinshiraoka, Shiraoka, Saitama 349-0212, Japan
| | - Hirotaka Kondo
- Laboratory of Veterinary Pathology, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Keitaro Ohmori
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
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47
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Penrose HM, Iftikhar R, Collins ME, Toraih E, Ruiz E, Ungerleider N, Nakhoul H, Flemington EF, Kandil E, Shah SB, Savkovic SD. Ulcerative colitis immune cell landscapes and differentially expressed gene signatures determine novel regulators and predict clinical response to biologic therapy. Sci Rep 2021; 11:9010. [PMID: 33907256 PMCID: PMC8079702 DOI: 10.1038/s41598-021-88489-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/08/2021] [Indexed: 12/27/2022] Open
Abstract
The heterogeneous pathobiology underlying Ulcerative Colitis (UC) is not fully understood. Using publicly available transcriptomes from adult UC patients, we identified the immune cell landscape, molecular pathways, and differentially expressed genes (DEGs) across patient cohorts and their association with treatment outcomes. The global immune cell landscape of UC tissue included increased neutrophils, T CD4 memory activated cells, active dendritic cells (DC), and M0 macrophages, as well as reduced trends in T CD8, Tregs, B memory, resting DC, and M2 macrophages. Pathway analysis of DEGs across UC cohorts demonstrated activated bacterial, inflammatory, growth, and cellular signaling. We identified a specific transcriptional signature of one hundred DEGs (UC100) that distinctly separated UC inflamed from uninflamed transcriptomes. Several UC100 DEGs, with unidentified roles in UC, were validated in primary tissue. Additionally, non-responders to anti-TNFα and anti-α4β7 therapy displayed distinct profiles of immune cells and pathways pertaining to inflammation, growth, and metabolism. We identified twenty resistant DEGs in UC non-responders to both therapies of which four had significant predictive power to treatment outcome. We demonstrated the global immune landscape and pathways in UC tissue, highlighting a unique UC signature across cohorts and a UC resistant signature with predictive performance to biologic therapy outcome.
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Affiliation(s)
- Harrison M Penrose
- Department of Pathology and Laboratory Medicine, Tulane University, 1430 Tulane Ave SL-79, New Orleans, LA, 70112, USA
| | - Rida Iftikhar
- Department of Pathology and Laboratory Medicine, Tulane University, 1430 Tulane Ave SL-79, New Orleans, LA, 70112, USA
| | - Morgan E Collins
- Department of Pathology and Laboratory Medicine, Tulane University, 1430 Tulane Ave SL-79, New Orleans, LA, 70112, USA
| | - Eman Toraih
- Division of Endocrine and Oncologic Surgery, Department of Surgery, Tulane University, New Orleans, LA, 70112, USA
| | - Emmanuelle Ruiz
- Division of Endocrine and Oncologic Surgery, Department of Surgery, Tulane University, New Orleans, LA, 70112, USA
| | - Nathan Ungerleider
- Department of Pathology and Laboratory Medicine, Tulane University, 1430 Tulane Ave SL-79, New Orleans, LA, 70112, USA
| | - Hani Nakhoul
- Department of Pathology and Laboratory Medicine, Tulane University, 1430 Tulane Ave SL-79, New Orleans, LA, 70112, USA
| | - Erik F Flemington
- Department of Pathology and Laboratory Medicine, Tulane University, 1430 Tulane Ave SL-79, New Orleans, LA, 70112, USA
| | - Emad Kandil
- Division of Endocrine and Oncologic Surgery, Department of Surgery, Tulane University, New Orleans, LA, 70112, USA
| | - Shamita B Shah
- Division of Gastroenterology, Ochsner Clinic Foundation, New Orleans, LA, 70121, USA
| | - Suzana D Savkovic
- Department of Pathology and Laboratory Medicine, Tulane University, 1430 Tulane Ave SL-79, New Orleans, LA, 70112, USA.
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48
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Beaurivage C, Kanapeckaite A, Loomans C, Erdmann KS, Stallen J, Janssen RAJ. Development of a human primary gut-on-a-chip to model inflammatory processes. Sci Rep 2020; 10:21475. [PMID: 33293676 PMCID: PMC7722760 DOI: 10.1038/s41598-020-78359-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/23/2020] [Indexed: 12/11/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a complex multi-factorial disease for which physiologically relevant in vitro models are lacking. Existing models are often a compromise between biological relevance and scalability. Here, we integrated intestinal epithelial cells (IEC) derived from human intestinal organoids with monocyte-derived macrophages, in a gut-on-a-chip platform to model the human intestine and key aspects of IBD. The microfluidic culture of IEC lead to an increased polarization and differentiation state that closely resembled the expression profile of human colon in vivo. Activation of the model resulted in the polarized secretion of CXCL10, IL-8 and CCL-20 by IEC and could efficiently be prevented by TPCA-1 exposure. Importantly, upregulated gene expression by the inflammatory trigger correlated with dysregulated pathways in IBD patients. Finally, integration of activated macrophages offers a first-step towards a multi-factorial amenable IBD platform that could be scaled up to assess compound efficacy at early stages of drug development or in personalized medicine.
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Affiliation(s)
- Claudia Beaurivage
- Galapagos BV, Leiden, South Holland, 2333CL, The Netherlands
- Department of Biomedical Science, Faculty of Science, University of Sheffield, Sheffield, S10 2TN, South Yorkshire, UK
| | | | - Cindy Loomans
- Galapagos BV, Leiden, South Holland, 2333CL, The Netherlands
| | - Kai S Erdmann
- Department of Biomedical Science, Faculty of Science, University of Sheffield, Sheffield, S10 2TN, South Yorkshire, UK
| | - Jan Stallen
- Galapagos BV, Leiden, South Holland, 2333CL, The Netherlands
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49
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Iannucci A, Caneparo V, Raviola S, Debernardi I, Colangelo D, Miggiano R, Griffante G, Landolfo S, Gariglio M, De Andrea M. Toll-like receptor 4-mediated inflammation triggered by extracellular IFI16 is enhanced by lipopolysaccharide binding. PLoS Pathog 2020; 16:e1008811. [PMID: 32903274 PMCID: PMC7505474 DOI: 10.1371/journal.ppat.1008811] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 09/21/2020] [Accepted: 07/14/2020] [Indexed: 02/06/2023] Open
Abstract
Damage-associated molecular patterns (DAMPs) are endogenous molecules activating the immune system upon release from injured cells. Here we show that the IFI16 protein, once freely released in the extracellular milieu of chronically inflamed tissues, can function as a DAMP either alone or upon binding to lipopolysaccharide (LPS). Specifically, using pull-down and saturation binding experiments, we show that IFI16 binds with high affinity to the lipid A moiety of LPS. Remarkably, IFI16 DAMP activity is potentiated upon binding to subtoxic concentrations of strong TLR4-activating LPS variants, as judged by TLR4-MD2/TIRAP/MyD88-dependent IL-6, IL-8 and TNF-α transcriptional activation and release in stimulated monocytes and renal cells. Consistently, using co-immunoprecipitation (co-IP) and surface plasmon resonance (SPR) approaches, we show that IFI16 is a specific TLR4-ligand and that IFI16/LPS complexes display a faster stimulation turnover on TLR4 than LPS alone. Altogether, our findings point to a novel pathomechanism of inflammation involving the formation of multiple complexes between extracellular IFI16 and subtoxic doses of LPS variants, which then signal through TLR4.
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Affiliation(s)
- Andrea Iannucci
- CAAD—Center for Translational Research on Autoimmune and Allergic Disease, University of Eastern Piedmont, Novara, Italy
- Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Valeria Caneparo
- CAAD—Center for Translational Research on Autoimmune and Allergic Disease, University of Eastern Piedmont, Novara, Italy
- Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Stefano Raviola
- CAAD—Center for Translational Research on Autoimmune and Allergic Disease, University of Eastern Piedmont, Novara, Italy
- Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Isacco Debernardi
- Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Donato Colangelo
- Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | - Riccardo Miggiano
- Department of Pharmaceutical Sciences, University of Eastern Piedmont, Novara, Italy
| | - Gloria Griffante
- Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, Turin, Italy
| | - Santo Landolfo
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, Turin, Italy
| | - Marisa Gariglio
- CAAD—Center for Translational Research on Autoimmune and Allergic Disease, University of Eastern Piedmont, Novara, Italy
- Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Marco De Andrea
- CAAD—Center for Translational Research on Autoimmune and Allergic Disease, University of Eastern Piedmont, Novara, Italy
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, Turin, Italy
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50
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Lee HS, Vancamelbeke M, Verstockt S, Wilms T, Verstockt B, Sabino J, Ferrante M, Vermeire S, Cleynen I. Molecular Changes in the Non-Inflamed Terminal Ileum of Patients with Ulcerative Colitis. Cells 2020; 9:cells9081793. [PMID: 32731480 PMCID: PMC7464680 DOI: 10.3390/cells9081793] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 12/19/2022] Open
Abstract
Ulcerative colitis is a chronic inflammatory disease confined to the colon. Although the etiopathogenesis remains unknown, small bowel dysfunctions like histological and permeability alterations have been described in ulcerative colitis. We evaluated the molecular gene signature in the non-inflamed terminal ileum of 36 ulcerative colitis patients (7 active, with Mayo endoscopic subscore ≥2, and 29 inactive) as compared to 15 non-inflammatory bowel disease controls. Differential gene expression analysis with DESeq2 showed distinct expression patterns depending on disease activity and maximal disease extent. We found 84 dysregulated genes in patients with active extensive colitis and 20 in inactive extensive colitis, compared to controls. There was an overlap of 5 genes: REG1B, REG1A, MUC4, GRAMD2, and CASP10. In patients with left-sided colitis, ileal gene expression levels were similar to controls. Based on gene co-expression analysis, ileal changes in active ulcerative colitis patients were related to immune functions. The ileal changes in the inactive ulcerative colitis subjects converged into the maintenance of the intestinal barrier through increased mitochondrial function and dampened immune functions. In conclusion, we identified molecular changes in the non-inflamed ileum of ulcerative colitis that are dependent on colonic inflammation.
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Affiliation(s)
- Ho-Su Lee
- Laboratory of Complex Genetics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium; (H.-S.L.); (S.V.); (T.W.)
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Maaike Vancamelbeke
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department Chronic Diseases, Metabolism & Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (M.V.); (B.V.); (J.S.); (M.F.); (S.V.)
| | - Sare Verstockt
- Laboratory of Complex Genetics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium; (H.-S.L.); (S.V.); (T.W.)
| | - Tom Wilms
- Laboratory of Complex Genetics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium; (H.-S.L.); (S.V.); (T.W.)
| | - Bram Verstockt
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department Chronic Diseases, Metabolism & Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (M.V.); (B.V.); (J.S.); (M.F.); (S.V.)
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - João Sabino
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department Chronic Diseases, Metabolism & Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (M.V.); (B.V.); (J.S.); (M.F.); (S.V.)
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Marc Ferrante
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department Chronic Diseases, Metabolism & Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (M.V.); (B.V.); (J.S.); (M.F.); (S.V.)
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Séverine Vermeire
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department Chronic Diseases, Metabolism & Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium; (M.V.); (B.V.); (J.S.); (M.F.); (S.V.)
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Isabelle Cleynen
- Laboratory of Complex Genetics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium; (H.-S.L.); (S.V.); (T.W.)
- Correspondence: ; Tel.: +32-1637-7480
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