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Xue JY, Chen MT, Jian YH, Liang LL, Yang XR, Sun SH, Liu P, Liu QY, Jiang Y, Liu MN. The role of the TREM receptor family in cardiovascular diseases: Functions, mechanisms, and therapeutic target. Life Sci 2025; 369:123555. [PMID: 40068732 DOI: 10.1016/j.lfs.2025.123555] [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: 11/11/2024] [Revised: 03/03/2025] [Accepted: 03/08/2025] [Indexed: 03/15/2025]
Abstract
The Triggering Receptor Expressed in the Myeloid Cells (TREM) family represents an emerging subgroup within the immunoglobulin superfamily, which includes key members such as TREM-1, TREM-2, TREM-3, TREM-like transcript-1 (TLT-1), TLT-2, and TLT-4. TREM-1 serves as a potent amplifier of immune responses, exacerbating atherosclerosis and myocardial injury by enhancing inflammatory reactions. In contrast, TREM-2 exerts protective effects by regulating lipid metabolism, mitigating inflammation, and promoting phagocytic activity, thereby attenuating cardiovascular damage. Both soluble TLT-1 and TLT-4 have been identified as potential biomarkers for cardiovascular risk. In recent years, the roles of the TREM family in the pathogenesis of cardiovascular diseases (CVD) have garnered growing interest within the scientific community. This review aims to illuminate the functional roles, underlying mechanisms, and clinical relevance of TREM family members in the regulation of CVD, while exploring their potential applications in early diagnosis, disease monitoring, and the development of novel therapeutic targets for CVD, ultimately laying a foundation for their clinical translation and advancement in precision medicine.
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Affiliation(s)
- Jin-Yi Xue
- Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou 646000, China
| | - Ming-Tai Chen
- Shenzhen Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, 518000, China
| | - Yu-Hong Jian
- Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou 646000, China
| | - Ling-Ling Liang
- Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou 646000, China
| | - Xin-Rui Yang
- Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou 646000, China
| | - Shi-Han Sun
- Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou 646000, China
| | - Ping Liu
- Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou 646000, China
| | - Qiu-Yu Liu
- School of Pharmacy, Southwest Medical University, Luzhou 646000, China.
| | - Yan Jiang
- Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou 646000, China.
| | - Meng-Nan Liu
- Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou 646000, China.
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2
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Zhevlakova I, Liu H, Dudiki T, Gao D, Yakubenko V, Tkachenko S, Cherepanova O, Podrez EA, Byzova TV. Mechanisms and consequences of myeloid adhesome dysfunction in atherogenesis. Cardiovasc Res 2025; 121:62-76. [PMID: 39393814 PMCID: PMC11999018 DOI: 10.1093/cvr/cvae223] [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: 04/10/2024] [Revised: 07/24/2024] [Accepted: 08/23/2024] [Indexed: 10/13/2024] Open
Abstract
AIMS In the context of atherosclerosis, macrophages exposed to oxidized low-density lipoproteins (oxLDLs) exhibit cellular abnormalities, specifically in adhesome functions, yet the mechanisms and implications of these adhesive dysfunctions remain largely unexplored. METHODS AND RESULTS This study reveals a significant depletion of Kindlin3 (K3) or Fermt3, an essential component of the adhesome regulating integrin functions, in macrophages located within atherosclerotic plaques in vivo and following oxLDL exposure in vitro. To examine the effects of K3 deficiency, the study utilized hyperlipidaemic bone marrow chimeras devoid of myeloid Kindlin3 expression. The absence of myeloid K3 increased atherosclerotic plaque burden in the aortas in vivo and enhanced lipid accumulation and lipoprotein uptake in macrophages from Kindlin3-null chimeric mice in vitro. Importantly, re-expression of K3 in macrophages ameliorated these abnormalities. RNA sequencing of bone marrow-derived macrophages (BMDM) from K3-deficient mice revealed extensive deregulation in adhesion-related pathways, echoing changes observed in wild-type cells treated with oxLDL. Notably, there was an increase in Olr1 expression [encoding the lectin-like oxidized LDL receptor-1 (LOX1)], a gene implicated in atherogenesis. The disrupted K3-integrin axis in macrophages led to a significant elevation in the LOX1 receptor, contributing to increased oxLDL uptake and foam cell formation. Inhibition of LOX1 normalized lipid uptake in Kindlin3-null macrophages. A similar proatherogenic phenotype, marked by increased macrophage LOX1 expression and foam cell formation, was observed in myeloid-specific Itgβ1-deficient mice but not in Itgβ2-deficient mice, underscoring the critical role of K3/Itgβ1 interaction. CONCLUSION This study shows that the loss of Kindlin3 in macrophages upon exposure to oxLDL leads to adhesome dysfunction in atherosclerosis and reveals the pivotal role of Kindlin3 in macrophage function and its contribution to the progression of atherosclerosis, providing valuable insights into the molecular mechanisms that could be targeted for therapeutic interventions.
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Affiliation(s)
- Irina Zhevlakova
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Ave, Cleveland, OH 44195, USA
| | - Huan Liu
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Ave, Cleveland, OH 44195, USA
| | - Tejasvi Dudiki
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Ave, Cleveland, OH 44195, USA
| | - Detao Gao
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Ave, Cleveland, OH 44195, USA
| | - Valentin Yakubenko
- Department of Biomedical Sciences, Center of Excellence for Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37684, USA
| | - Svyatoslav Tkachenko
- Department of Genetics and Genome Sciences, Case Western Reserve University, 2109 Adelbert Rd Building, Cleveland, OH 44106, USA
| | - Olga Cherepanova
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Ave, Cleveland, OH 44195, USA
| | - Eugene A Podrez
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Ave, Cleveland, OH 44195, USA
| | - Tatiana V Byzova
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Ave, Cleveland, OH 44195, USA
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Kaur G, Lamb T, Tjitropranoto A, Rahman I. Single-cell transcriptomics identifies a dampened neutrophil function and accentuated T-cell cytotoxicity in tobacco flavored e-cigarette exposed mouse lungs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.17.638715. [PMID: 40027777 PMCID: PMC11870523 DOI: 10.1101/2025.02.17.638715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
E-cigarettes (e-cigs) are a public health concern for young adults due to their popularity and evidence for increased oxidative stress and immunotoxicity. Yet an extensive study defining the cell-specific immune changes upon exposure to flavored e-cigs remains elusive. To understand the immunological lung landscape upon acute nose-only exposure of C57BL/6J to flavored e-cig aerosols we performed single-cell RNA sequencing (scRNA seq). scRNA profiles of 71,725 cells were generated from control and treatment groups (n=2/sex/group). A distinct phenotype of Ly6G-neutrophils was identified in lungs exposed to tobacco flavored e-cig aerosol which demonstrated dampened IL-1 mediated and pattern recognition signaling as compared to air controls. Differential gene expression analyses identified dysregulation of T-cell mediated pro-inflammation ( Cct7 , Cct8 ) and stress-response signals ( Neurl3 , Stap1 , Cirbp and Htr2c) in the lungs of mice exposed to e-cig aerosols, with pronounced effects for tobacco flavor. Flow cytometry analyses and cytokine/chemokine assessments within the lungs corroborated the scRNA seq data, demonstrating a significant increase in T-cell percentages and levels of T-cell associated cytokine/chemokines in the lungs of tobacco-flavored aerosol exposed mice. Increased levels of Klra4 and Klra8 expression also suggest an enhanced natural killer (NK) cell activity in this mouse group. Overall, this is a pilot study identifying increase in the percentages of Ly6G-neutrophils that may be responsible for dampened innate immune responses and heightened T-cell cytotoxicity in lungs of tobacco-flavored e-cig aerosol exposed mice. In addition, we provide preliminary evidence for sex-specific changes in the transcriptional landscape of mouse lungs upon exposure to e-cig aerosol, an area that warrants further study.
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4
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Chowdari Gurram P, Satarker S, Nampoothiri M. Recent advances in the molecular signaling pathways of Substance P in Alzheimer's disease: Link to neuroinflammation associated with toll-like receptors. Biochem Biophys Res Commun 2024; 733:150597. [PMID: 39197195 DOI: 10.1016/j.bbrc.2024.150597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 08/20/2024] [Accepted: 08/22/2024] [Indexed: 09/01/2024]
Abstract
A significant quantity of substance P (SP) and its receptor, the neurokinin 1 (NK1) receptors are found in the brain. SP is a neuropeptide distributed in the central nervous system and functions as a neurotransmitter, neuromodulator, and neurotrophic factor. The concentrations of SP in the brain and cerebrospinal fluid fluctuate in individuals with Alzheimer's disease (AD). SP is an endogenous ligand for NK1 receptor, enhancing the expression of toll-like receptors (TLR) and vice versa. So, both pathways are interconnected, where activation of one pathway activates the second pathway. Researchers have observed the interaction of TLR with SP in the pathophysiology of AD. Thus, this review discusses various TLRs involved in regulating amyloid processing and its interaction with SP in AD. Further, in AD pathology, SP can regulate the non-amyloidogenic pathway. Recent studies have also demonstrated the capacity of SP in regulating voltage-gated potassium channel currents, emphasizing SP's neuroprotective ability. Therefore, we corroborate the findings linking the SP, NK1R, and TLRs in AD.
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Affiliation(s)
- Prasada Chowdari Gurram
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India; KL College of Pharmacy, Koneru Lakshmaiah Education Foundation, Green Fields, Vaddeswaram, A.P, 522302, India
| | - Sairaj Satarker
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Madhavan Nampoothiri
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India.
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Gao Y, Wang B, Hu M, Ma Y, Zheng B. The Role of Iron in Atherosclerosis and its Association with Related Diseases. Curr Atheroscler Rep 2024; 27:1. [PMID: 39520606 DOI: 10.1007/s11883-024-01251-1] [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] [Accepted: 10/08/2024] [Indexed: 11/16/2024]
Abstract
PURPOSE OF REVIEW This review aims to elucidate the multifaceted role of iron in the pathogenesis of atherosclerosis. The primary objective is to summarize recent advances in understanding how iron contributes to atherosclerosis through various cellular mechanisms. Additionally, the review explores the therapeutic implications of targeting iron metabolism in the prevention and treatment of cardiovascular diseases. RECENT FINDINGS A growing body of literature suggests that excess iron accelerates the progression of atherosclerosis, with the deleterious form of iron, non-transferrin-bound iron (NTBI), particularly exacerbating this process. Furthermore, iron overload has been demonstrated to play a pivotal role in endothelial cells, vascular smooth muscle cells, and macrophages, contributing to plaque instability and disease progression by promoting lipid peroxidation, oxidative stress, inflammatory responses, and ferroptosis. Iron plays a complex role in atherosclerosis, influencing multiple cellular processes and promoting disease progression. By promoting oxidative stress, inflammation, and ferroptosis, iron exacerbates endothelial dysfunction, smooth muscle cell calcification, and the formation of macrophage-derived foam cells. Targeted therapies focusing on iron metabolism have proven effective in treating atherosclerosis and other cardiovascular diseases.
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Affiliation(s)
- Yingbo Gao
- Department of Biochemistry and Molecular Biology, Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang, 050017, China
| | - Boda Wang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang, 050017, China
| | - Mengrui Hu
- Department of Biochemistry and Molecular Biology, Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang, 050017, China
| | - Yuhan Ma
- Department of Biochemistry and Molecular Biology, Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang, 050017, China
| | - Bin Zheng
- Department of Biochemistry and Molecular Biology, Key Laboratory of Neural and Vascular Biology, Ministry of Education, Hebei Medical University, Shijiazhuang, 050017, China.
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Ertel MV, da Silva ABA, de Sousa DF, Dos Santos CJ, da Silva TM, da Silva-Sales MFM, de Oliveira Matos A, Sales-Campos H. Who is who within the universe of TREM-like transcripts (TREML)? Life Sci 2024; 348:122696. [PMID: 38710279 DOI: 10.1016/j.lfs.2024.122696] [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: 11/16/2023] [Revised: 04/29/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024]
Abstract
The Triggering Receptor Expressed on Myeloid Cells (TREM) family of receptors plays a crucial role in the immune response across various species. Particularly, TREM-1 and TREM-2 have been extensively studied, both in terms of their applications and their expression sites and signaling pathways. However, the same is not observed for the other family members collectively known as TREM-like-transcripts (TREML). The TREML family consists of eight receptors, with TREML1-5 identified in humans and mice, TREML-6 exclusive found in mice, TREML-7 in dogs and horses, and TREML-8 in rabbits and opossums. Despite the limited data available on the TREML members, they have been implicated in different immune and non-immune activities, which have been proposed to display both pro and anti-inflammatory activities, and to influence fundamental biological processes such as coagulation, bone and neurological development. In this review, we have compiled available information regarding the already discovered members of the family and provided foundational framework for understanding the function, localization, and therapeutic potential of all TREML members. Additionally, we hope that this review may shed light on this family of receptors, whose underlying mechanisms are still awaiting elucidation, while emphasizing the need for future studies to explore their functions and potential therapeutic application.
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Affiliation(s)
- Márcia Verônica Ertel
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil.
| | | | - Daniel Francisco de Sousa
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil.
| | - Cairo José Dos Santos
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil.
| | - Tatiane Mendonça da Silva
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil.
| | | | - Amanda de Oliveira Matos
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil.
| | - Helioswilton Sales-Campos
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Goiás, Brazil.
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7
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Tong Q, Ling Y. A prognostic model based on regulatory T-cell-related genes in gastric cancer: Systematic construction and validation. Int J Exp Pathol 2023; 104:226-236. [PMID: 37350375 PMCID: PMC10500170 DOI: 10.1111/iep.12487] [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: 09/29/2022] [Revised: 12/22/2022] [Accepted: 06/01/2023] [Indexed: 06/24/2023] Open
Abstract
Human gastrointestinal tumours have been shown to contain massive numbers of tumour infiltrating regulatory T cells (Tregs), the presence of which are closely related to tumour immunity. This study was designed to develop new Treg-related prognostic biomarkers to monitor the prognosis of patients with gastric cancer (GC). Treg-related prognostic genes were screened from Treg-related differentially expressed genes in GC patients by using Cox regression analysis, based on which a prognostic model was constructed. Then, combined with RiskScore, survival curve, survival status assessment and ROC analysis, these genes were used to verify the accuracy of the model, whose independent prognostic ability was also evaluated. Six Treg-related prognostic genes (CHRDL1, APOC3, NPTX1, TREML4, MCEMP1, GH2) in GC were identified, and a 6-gene Treg-related prognostic model was constructed. Survival analysis revealed that patients had a higher survival rate in the low-risk group. Combining clinicopathological features, we performed univariate and multivariate regression analyses, with results establishing that the RiskScore was an independent prognostic factor. Predicted 1-, 3- and 5-year survival rates of GC patients had a good fit with the actual survival rates according to nomogram results. In addition patients in the low-risk group had higher tumour mutational burden (TMB) values. Gene Set Enrichment Analysis (GSEA) demonstrated that genes in the high-risk group were significantly enriched in pathways related to immune inflammation, tumour proliferation and migration. In general, we constructed a 6-gene Treg-associated GC prognostic model with good prediction accuracy, where RiskScore could act as an independent prognostic factor. This model is expected to provide a reference for clinicians to estimate the prognosis of GC patients.
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Affiliation(s)
- Qin Tong
- Department of Gastrointestinal SurgeryJinhua Guangfu HospitalJinhuaChina
| | - Yingjie Ling
- Department of Gastrointestinal SurgeryJinhua Guangfu HospitalJinhuaChina
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8
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Kim A, Ortega-Ribera M, McMullen MR, Bellar A, Taiwo M, Pathak V, Streem D, Dasarathy J, Welch N, Dasarathy S, Vachharajani V, Nagy LE. Altered Anti-Viral Immune Responses in Monocytes in Overweight Heavy Drinkers. iScience 2023; 26:107133. [PMID: 37361874 PMCID: PMC10268809 DOI: 10.1016/j.isci.2023.107133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/08/2023] [Accepted: 06/12/2023] [Indexed: 06/28/2023] Open
Abstract
Alcohol abuse causes increased susceptibility to respiratory syndromes like bacterial pneumonia and viral infections like SARS-CoV-2. Heavy drinkers (HD) are at higher risk of severe COVID-19 if they are also overweight, yet the molecular mechanisms are unexplored. Single-cell RNA-seq (scRNA-seq) was performed on peripheral blood mononuclear cells from lean or overweight HD and healthy controls (HC) after challenge with a dsRNA homopolymer (PolyI:C) to mimic a viral infection and/or with lipopolysaccharide (LPS). All monocyte populations responded to both PolyI:C and LPS with pro-inflammatory gene expression. However, expression of interferon stimulated genes, essential for inhibiting viral pathogenesis, was greatly reduced in overweight patients. Interestingly, the number of upregulated genes in response to PolyI:C challenge was far greater in monocytes from HD compared to HC, including much stronger pro-inflammatory cytokine and interferon-γ signaling responses. These results suggest increased body weight reduced anti-viral responses while heavy drinking increased pro-inflammatory cytokines.
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Affiliation(s)
- Adam Kim
- - Northern Ohio Alcohol Center, Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH
- - Department of Medicine, University of Connecticut Health Center, Farmington, CT
| | - Martí Ortega-Ribera
- - Northern Ohio Alcohol Center, Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH
| | - Megan R McMullen
- - Northern Ohio Alcohol Center, Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH
| | - Annette Bellar
- - Northern Ohio Alcohol Center, Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH
| | - Moyinoluwa Taiwo
- - Northern Ohio Alcohol Center, Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH
| | - Vai Pathak
- - Northern Ohio Alcohol Center, Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH
| | - David Streem
- - Lutheran Hospital, Cleveland Clinic, Cleveland, OH
| | | | - Nicole Welch
- - Northern Ohio Alcohol Center, Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH
- - Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, OH
- - Department of Molecular Medicine, Case Western Reserve University, Cleveland, OH
| | - Srinivasan Dasarathy
- - Northern Ohio Alcohol Center, Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH
- - Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, OH
- - Department of Molecular Medicine, Case Western Reserve University, Cleveland, OH
| | - Vidula Vachharajani
- - Northern Ohio Alcohol Center, Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH
- - Department of Critical Care Medicine Cleveland Clinic Respiratory Institute, Cleveland, OH
| | - Laura E Nagy
- - Northern Ohio Alcohol Center, Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH
- - Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, OH
- - Department of Molecular Medicine, Case Western Reserve University, Cleveland, OH
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TREML4 polymorphisms increase the mRNA in blood leukocytes in the progression of atherosclerosis. Sci Rep 2022; 12:18612. [PMID: 36329152 PMCID: PMC9633690 DOI: 10.1038/s41598-022-22040-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
TREML4 and other members of the triggering receptor expressed in the myeloid cell family are associated with a risk of atherosclerosis and progression in coronary artery disease, acute coronary syndrome, and coronary artery calcification. Herein, the relationship between TREML4 expression and its polymorphisms (rs2803495 and rs280396) was evaluated in patients with subclinical atherosclerosis (n = 340) and heart failure post-acute myocardial infarction (MI) (n = 68) for the first time. TREML4 variants rs2803495 (A > G) and rs2803496 (T > C) and leukocyte mRNA expression was analyzed by qRT-PCR. The rs2803495 G allele was associated with TREML4 expression (OR 8.01, CI 3.78-16.99, p < 0.001). Patients carrying the rs2803496 C minor allele (TC/CC genotypes) were more likely to express TREML4 than those without the C allele (OR 10.42, CI 4.76-22.78, p < 0.001), as well as having higher levels of TREML4 expression (OR 4.88, CI 2.35-10.12, p < 0.001). Thus, we report for the first time that TREML4 is not associated with the early stages of atherosclerotic plaque formation and later stages after MI. In conclusion, TREML4 mRNA expression in blood leukocytes is influenced by minor alleles (G and C) and may regulate differently during the atherosclerosis progression stages, but not in asymptomatic atherosclerosis disease and post-MI.
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Han S, Zhuang H, Arja RD, Reeves WH. A novel monocyte differentiation pattern in pristane-induced lupus with diffuse alveolar hemorrhage. eLife 2022; 11:e76205. [PMID: 36264674 PMCID: PMC9584606 DOI: 10.7554/elife.76205] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 10/10/2022] [Indexed: 11/29/2022] Open
Abstract
Pristane causes chronic peritoneal inflammation resulting in lupus, which in C57BL/6 mice is complicated by lung microvascular injury and diffuse alveolar hemorrhage (DAH). Mineral oil (MO) also causes inflammation, but not lupus or DAH. Since monocyte depletion prevents DAH, we examined the role of monocytes in the disease. Impaired bone marrow (BM) monocyte egress in Ccr2-/- mice abolished DAH, confirming the importance of monocyte recruitment to the lung. Circulating Ly6Chi monocytes from pristane-treated mice exhibited increased annexin-V staining in comparison with MO-treated controls without evidence of apoptosis, suggesting that pristane alters the distribution of phosphatidylserine in the plasma membrane before or shortly after monocyte egress from the BM. Plasma membrane asymmetry also was impaired in Nr4a1-regulated Ly6Clo/- 'patrolling' monocytes, which are derived from Ly6Chi precursors. Patrolling Ly6Clo/- monocytes normally promote endothelial repair, but their phenotype was altered in pristane-treated mice. In contrast to MO-treated controls, Nr4a1-regulated Ly6Clo/- monocytes from pristane-treated mice were CD138+, expressed more TremL4, a protein that amplifies TLR7 signaling, and exuberantly produced TNFα in response to TLR7 stimulation. TremL4 expression on these novel CD138+ monocytes was regulated by Nr4a1. Thus, monocyte CD138, high TremL4 expression, and annexin-V staining may define an activated/inflammatory subtype of patrolling monocytes associated with DAH susceptibility. By altering monocyte development, pristane exposure may generate activated Ly6Chi and Ly6Clo/- monocytes, contributing to lung microvascular endothelial injury and DAH susceptibility.
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Affiliation(s)
- Shuhong Han
- Division of Rheumatology, Allergy, & Clinical Immunology, University of FloridaGainesvilleUnited States
| | - Haoyang Zhuang
- Division of Rheumatology, Allergy, & Clinical Immunology, University of FloridaGainesvilleUnited States
| | - Rawad Daniel Arja
- Division of Rheumatology, Allergy, & Clinical Immunology, University of FloridaGainesvilleUnited States
| | - Westley H Reeves
- Division of Rheumatology, Allergy, & Clinical Immunology, University of FloridaGainesvilleUnited States
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Hoenow S, Yan K, Noll J, Groneberg M, Casar C, Lory NC, Vogelsang M, Hansen C, Wolf V, Fehling H, Sellau J, Mittrücker HW, Lotter H. The Properties of Proinflammatory Ly6Chi Monocytes Are Differentially Shaped by Parasitic and Bacterial Liver Infections. Cells 2022; 11:cells11162539. [PMID: 36010615 PMCID: PMC9406626 DOI: 10.3390/cells11162539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022] Open
Abstract
In the past, proinflammatory CD11b+Ly6Chi monocytes were predominantly considered as a uniform population. However, recent investigations suggests that this population is far more diverse than previously thought. For example, in mouse models of Entamoeba (E.) histolytica and Listeria (L.) monocytogenes liver infections, it was shown that their absence had opposite effects. In the former model, it ameliorated parasite-dependent liver injury, whereas in the listeria model it exacerbated liver pathology. Here, we analyzed Ly6Chi monocytes from the liver of both infection models at transcriptome, protein, and functional levels. Paralleled by E. histolytica- and L. monocytogenes-specific differences in recruitment-relevant chemokines, both infections induced accumulation of Ly6C+ monocytes at infection sites. Transcriptomic analysis revealed a high similarity between monocytes from naïve and parasite-infected mice and a clear proinflammatory phenotype of listeria-induced monocytes. This was further reflected by the upregulation of M2-related transcription factors (e.g., Mafb, Nr4a1, Fos) and higher CD14 expression by Ly6Chi monocytes in the E. histolytica infection model. In contrast, monocytes from the listeria infection model expressed M1-related transcription factors (e.g., Irf2, Mndal, Ifi204) and showed higher expression of CD38, CD74, and CD86, as well as higher ROS production. Taken together, proinflammatory Ly6Chi monocytes vary considerably depending on the causative pathogen. By using markers identified in the study, Ly6Chi monocytes can be further subdivided into different populations.
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Affiliation(s)
- Stefan Hoenow
- Department of Molecular Parasitology and Immunology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Karsten Yan
- Institute for Immunology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Jill Noll
- Department of Molecular Parasitology and Immunology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Marie Groneberg
- Department of Molecular Parasitology and Immunology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Christian Casar
- Bioinformatic Facility, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Niels Christian Lory
- Institute for Immunology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Malte Vogelsang
- Department of Molecular Parasitology and Immunology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Charlotte Hansen
- Department of Molecular Parasitology and Immunology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Vincent Wolf
- Department of Molecular Parasitology and Immunology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Helena Fehling
- Department of Molecular Parasitology and Immunology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Julie Sellau
- Department of Molecular Parasitology and Immunology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Hans-Willi Mittrücker
- Institute for Immunology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Hannelore Lotter
- Department of Molecular Parasitology and Immunology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
- Correspondence:
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12
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Beneš N, Brim L, Kadlecaj J, Pastva S, Šafránek D. Exploring attractor bifurcations in Boolean networks. BMC Bioinformatics 2022; 23:173. [PMID: 35546394 PMCID: PMC9092939 DOI: 10.1186/s12859-022-04708-9] [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: 11/23/2021] [Accepted: 04/19/2022] [Indexed: 11/10/2022] Open
Abstract
Background Boolean networks (BNs) provide an effective modelling formalism for various complex biochemical phenomena. Their long term behaviour is represented by attractors–subsets of the state space towards which the BN eventually converges. These are then typically linked to different biological phenotypes. Depending on various logical parameters, the structure and quality of attractors can undergo a significant change, known as a bifurcation. We present a methodology for analysing bifurcations in asynchronous parametrised Boolean networks. Results In this paper, we propose a computational framework employing advanced symbolic graph algorithms that enable the analysis of large networks with hundreds of Boolean variables. To visualise the results of this analysis, we developed a novel interactive presentation technique based on decision trees, allowing us to quickly uncover parameters crucial to the changes in the attractor landscape. As a whole, the methodology is implemented in our tool AEON. We evaluate the method’s applicability on a complex human cell signalling network describing the activity of type-1 interferons and related molecules interacting with SARS-COV-2 virion. In particular, the analysis focuses on explaining the potential suppressive role of the recently proposed drug molecule GRL0617 on replication of the virus. Conclusions The proposed method creates a working analogy to the concept of bifurcation analysis widely used in kinetic modelling to reveal the impact of parameters on the system’s stability. The important feature of our tool is its unique capability to work fast with large-scale networks with a relatively large extent of unknown information. The results obtained in the case study are in agreement with the recent biological findings.
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Affiliation(s)
- Nikola Beneš
- Faculty of Informatics, Masaryk University, Brno, Czechia.
| | - Luboš Brim
- Faculty of Informatics, Masaryk University, Brno, Czechia
| | - Jakub Kadlecaj
- Faculty of Informatics, Masaryk University, Brno, Czechia
| | - Samuel Pastva
- Faculty of Informatics, Masaryk University, Brno, Czechia
| | - David Šafránek
- Faculty of Informatics, Masaryk University, Brno, Czechia
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13
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Chen J, Zhang X, Millican R, Lynd T, Gangasani M, Malhotra S, Sherwood J, Hwang PT, Cho Y, Brott BC, Qin G, Jo H, Yoon YS, Jun HW. Recent Progress in in vitro Models for Atherosclerosis Studies. Front Cardiovasc Med 2022; 8:790529. [PMID: 35155603 PMCID: PMC8829969 DOI: 10.3389/fcvm.2021.790529] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/21/2021] [Indexed: 12/13/2022] Open
Abstract
Atherosclerosis is the primary cause of hardening and narrowing arteries, leading to cardiovascular disease accounting for the high mortality in the United States. For developing effective treatments for atherosclerosis, considerable efforts have been devoted to developing in vitro models. Compared to animal models, in vitro models can provide great opportunities to obtain data more efficiently, economically. Therefore, this review discusses the recent progress in in vitro models for atherosclerosis studies, including traditional two-dimensional (2D) systems cultured on the tissue culture plate, 2D cell sheets, and recently emerged microfluidic chip models with 2D culture. In addition, advanced in vitro three-dimensional models such as spheroids, cell-laden hydrogel constructs, tissue-engineered blood vessels, and vessel-on-a-chip will also be covered. Moreover, the functions of these models are also summarized along with model discussion. Lastly, the future perspectives of this field are discussed.
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Affiliation(s)
- Jun Chen
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Xixi Zhang
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL, United States
| | | | - Tyler Lynd
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Manas Gangasani
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Shubh Malhotra
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL, United States
| | | | | | - Younghye Cho
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL, United States
- Family Medicine Clinic, Obesity, Metabolism, and Nutrition Center and Research Institute of Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, South Korea
| | - Brigitta C. Brott
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL, United States
- Endomimetics, LLC., Birmingham, AL, United States
- Division of Cardiovascular Disease, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Gangjian Qin
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Hanjoong Jo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
| | - Young-sup Yoon
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA, United States
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Ho-Wook Jun
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL, United States
- Endomimetics, LLC., Birmingham, AL, United States
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14
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Checkouri E, Blanchard V, Meilhac O. Macrophages in Atherosclerosis, First or Second Row Players? Biomedicines 2021; 9:biomedicines9091214. [PMID: 34572399 PMCID: PMC8465019 DOI: 10.3390/biomedicines9091214] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/08/2021] [Accepted: 09/11/2021] [Indexed: 12/24/2022] Open
Abstract
Macrophages represent a cell type that has been widely described in the context of atherosclerosis since the earliest studies in the 17th century. Their role has long been considered to be preponderant in the onset and aggravation of atherosclerosis, in particular by participating in the establishment of a chronic inflammatory state by the release of pro-inflammatory cytokines and by uncontrolled engorgement of lipids resulting in the formation of foam cells and later of the necrotic core. However, recent evidence from mouse models using an elegant technique of tracing vascular smooth muscle cells (VSMCs) during plaque development revealed that resident VSMCs display impressive plastic properties in response to an arterial injury, allowing them to switch into different cell types within the plaque, including mesenchymal-like cells, macrophage-like cells and osteochondrogenic-like cells. In this review, we oppose the arguments in favor or against the influence of macrophages versus VSMCs in all stages of atherosclerosis including pre-atherosclerosis, formation of lipid-rich foam cells, development of the necrotic core and the fibrous cap as well as calcification and rupture of the plaque. We also analyze the relevance of animal models for the investigation of the pathophysiological mechanisms of atherosclerosis in humans, and discuss potential therapeutic strategies targeting either VSMCs or macrophage to prevent the development of cardiovascular events. Overall, although major findings have been made from animal models, efforts are still needed to better understand and therefore prevent the development of atherosclerotic plaques in humans.
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Affiliation(s)
- Eloïse Checkouri
- INSERM, UMR 1188 Diabète Athérothrombose Thérapies Réunion Océan Indien (DéTROI), Université de La Réunion, 97400 Sainte-Clotilde, France; (E.C.); (V.B.)
- Habemus Papam, Food Industry, 97470 Saint-Benoit, France
| | - Valentin Blanchard
- INSERM, UMR 1188 Diabète Athérothrombose Thérapies Réunion Océan Indien (DéTROI), Université de La Réunion, 97400 Sainte-Clotilde, France; (E.C.); (V.B.)
- Departments of Medicine, Centre for Heart Lung Innovation, Providence Healthcare Research Institute, St Paul’s Hospital, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Olivier Meilhac
- INSERM, UMR 1188 Diabète Athérothrombose Thérapies Réunion Océan Indien (DéTROI), Université de La Réunion, 97400 Sainte-Clotilde, France; (E.C.); (V.B.)
- CHU de La Réunion, INSERM, CIC1410, 97500 Saint-Pierre, France
- Correspondence: ; Tel.: +33-262-93-8811
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15
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Heath O, Berlato C, Maniati E, Lakhani A, Pegrum C, Kotantaki P, Elorbany S, Böhm S, Barry ST, Annibaldi A, Barton DP, Balkwill FR. Chemotherapy Induces Tumor-Associated Macrophages that Aid Adaptive Immune Responses in Ovarian Cancer. Cancer Immunol Res 2021; 9:665-681. [PMID: 33839687 DOI: 10.1158/2326-6066.cir-20-0968] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/27/2021] [Accepted: 03/22/2021] [Indexed: 01/01/2023]
Abstract
Neoadjuvant chemotherapy (NACT) may stimulate anticancer adaptive immune responses in high-grade serous ovarian cancer (HGSOC), but little is known about effects on innate immunity. Using omental biopsies from HGSOC, and omental tumors from orthotopic mouse HGSOC models that replicate the human tumor microenvironment, we studied the impact of platinum-based NACT on tumor-associated macrophages (TAM). We found that chemotherapy reduces markers associated with alternative macrophage activation while increasing expression of proinflammatory pathways, with evidence of inflammasome activation. Further evidence of a shift in TAM functions came from macrophage depletion via CSF1R inhibitors (CSF1Ri) in the mouse models. Although macrophage depletion in established disease had no impact on tumor weight or survival, CSF1Ri treatment after chemotherapy significantly decreased disease-free and overall survival. This decrease in survival was accompanied by significant inhibition of adaptive immune response pathways in the tumors. We conclude that chemotherapy skews the TAM population in HSGOC toward an antitumor phenotype that may aid adaptive immune responses, and therapies that enhance or sustain this during remission may delay relapse.
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Affiliation(s)
- Owen Heath
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
- Division of Gynaecological Oncology, St. George's University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Chiara Berlato
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Eleni Maniati
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Anissa Lakhani
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Colin Pegrum
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Panoraia Kotantaki
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Samar Elorbany
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Steffen Böhm
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Simon T Barry
- Bioscience, Early Oncology, AstraZeneca, Cambridge, United Kingdom
| | - Alessandro Annibaldi
- Center for Molecular Medicine Cologne, CMMC Research Center (Building 66), Cologne, Germany
| | - Desmond P Barton
- Division of Gynaecological Oncology, St. George's University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Frances R Balkwill
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom.
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16
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Patel D, Zhang X, Farrell JJ, Lunetta KL, Farrer LA. Set-Based Rare Variant Expression Quantitative Trait Loci in Blood and Brain from Alzheimer Disease Study Participants. Genes (Basel) 2021; 12:419. [PMID: 33804025 PMCID: PMC7999141 DOI: 10.3390/genes12030419] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/04/2021] [Accepted: 03/10/2021] [Indexed: 12/12/2022] Open
Abstract
Because studies of rare variant effects on gene expression have limited power, we investigated set-based methods to identify rare expression quantitative trait loci (eQTL) related to Alzheimer disease (AD). Gene-level and pathway-level cis rare-eQTL mapping was performed genome-wide using gene expression data derived from blood donated by 713 Alzheimer's Disease Neuroimaging Initiative participants and from brain tissues donated by 475 Religious Orders Study/Memory and Aging Project participants. The association of gene or pathway expression with a set of all cis potentially regulatory low-frequency and rare variants within 1 Mb of genes was evaluated using SKAT-O. A total of 65 genes expressed in the brain were significant targets for rare expression single nucleotide polymorphisms (eSNPs) among which 17% (11/65) included established AD genes HLA-DRB1 and HLA-DRB5. In the blood, 307 genes were significant targets for rare eSNPs. In the blood and the brain, GNMT, LDHC, RBPMS2, DUS2, and HP were targets for significant eSNPs. Pathway enrichment analysis revealed significant pathways in the brain (n = 9) and blood (n = 16). Pathways for apoptosis signaling, cholecystokinin receptor (CCKR) signaling, and inflammation mediated by chemokine and cytokine signaling were common to both tissues. Significant rare eQTLs in inflammation pathways included five genes in the blood (ALOX5AP, CXCR2, FPR2, GRB2, IFNAR1) that were previously linked to AD. This study identified several significant gene- and pathway-level rare eQTLs, which further confirmed the importance of the immune system and inflammation in AD and highlighted the advantages of using a set-based eQTL approach for evaluating the effect of low-frequency and rare variants on gene expression.
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Affiliation(s)
- Devanshi Patel
- Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA;
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA; (X.Z.); (J.J.F.)
| | - Xiaoling Zhang
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA; (X.Z.); (J.J.F.)
| | - John J. Farrell
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA; (X.Z.); (J.J.F.)
| | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA;
| | - Lindsay A. Farrer
- Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA;
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA; (X.Z.); (J.J.F.)
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA;
- Department of Ophthalmology, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
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17
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Hu S, Uniken Venema WT, Westra HJ, Vich Vila A, Barbieri R, Voskuil MD, Blokzijl T, Jansen BH, Li Y, Daly MJ, Xavier RJ, Dijkstra G, Festen EA, Weersma RK. Inflammation status modulates the effect of host genetic variation on intestinal gene expression in inflammatory bowel disease. Nat Commun 2021; 12:1122. [PMID: 33602935 PMCID: PMC7892863 DOI: 10.1038/s41467-021-21458-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
More than 240 genetic risk loci have been associated with inflammatory bowel disease (IBD), but little is known about how they contribute to disease development in involved tissue. Here, we hypothesized that host genetic variation affects gene expression in an inflammation-dependent way, and investigated 299 snap-frozen intestinal biopsies from inflamed and non-inflamed mucosa from 171 IBD patients. RNA-sequencing was performed, and genotypes were determined using whole exome sequencing and genome wide genotyping. In total, 28,746 genes and 6,894,979 SNPs were included. Linear mixed models identified 8,881 independent intestinal cis-expression quantitative trait loci (cis-eQTLs) (FDR < 0.05) and interaction analysis revealed 190 inflammation-dependent intestinal cis-eQTLs (FDR < 0.05), including known IBD-risk genes and genes encoding immune-cell receptors and antibodies. The inflammation-dependent cis-eQTL SNPs (eSNPs) mainly interact with prevalence of immune cell types. Inflammation-dependent intestinal cis-eQTLs reveal genetic susceptibility under inflammatory conditions that can help identify the cell types involved in and the pathways underlying inflammation, knowledge that may guide future drug development and profile patients for precision medicine in IBD.
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Affiliation(s)
- Shixian Hu
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Werna T Uniken Venema
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Harm-Jan Westra
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Ruggero Barbieri
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Michiel D Voskuil
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Tjasso Blokzijl
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Bernadien H Jansen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Yanni Li
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Mark J Daly
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ramnik J Xavier
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Microbiome Informatics and Therapeutic, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Eleonora A Festen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.
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Qian Y, Li L, Sun Z, Liu J, Yuan W, Wang Z. A multi-omics view of the complex mechanism of vascular calcification. Biomed Pharmacother 2021; 135:111192. [PMID: 33401220 DOI: 10.1016/j.biopha.2020.111192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 12/19/2020] [Accepted: 12/26/2020] [Indexed: 02/07/2023] Open
Abstract
Vascular calcification is a high incidence and high risk disease with increasing morbidity and high mortality, which is considered the consequence of smooth muscle cell transdifferentiation initiating the mechanism of accumulation of hydroxyl calcium phosphate. Vascular calcification is also thought to be strongly associated with poor outcomes in diabetes and chronic kidney disease. Numerous studies have been accomplished; however, the specific mechanism of the disease remains unclear. Development of the genome project enhanced the understanding of life science and has entered the post-genomic era resulting in a variety of omics techniques used in studies and a large amount of available data; thus, a new perspective on data analysis has been revealed. Omics has a broader perspective and is thus advantageous over a single pathway analysis in the study of complex vascular calcification mechanisms. This paper reviews in detail various omics studies including genomics, proteomics, transcriptomics, metabolomics and multiple group studies on vascular calcification. Advances and deficiencies in the use of omics to study vascular calcification are presented in a comprehensive view. We also review the methodology of the omics studies and omics data analysis and processing. In addition, the methodology and data processing presented here can be applied to other areas. An omics landscape perspective across the boundaries between genomics, transcriptomics, proteomics and metabolomics is used to examine the mechanisms of vascular calcification. The perspective combined with various technologies also provides a direction for the subsequent exploration of clinical significance.
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Affiliation(s)
- Yongjiang Qian
- Department of Cardiology, Affiliated Hospital of Jiangsu University, 212000, Zhenjiang, China
| | - Lihua Li
- Department of Pathology, Affiliated Hospital of Jiangsu University, 212000, Zhenjiang, China
| | - Zhen Sun
- Department of Cardiology, Affiliated Hospital of Jiangsu University, 212000, Zhenjiang, China
| | - Jia Liu
- Department of Cardiology, Affiliated Hospital of Jiangsu University, 212000, Zhenjiang, China
| | - Wei Yuan
- Department of Cardiology, Affiliated Hospital of Jiangsu University, 212000, Zhenjiang, China
| | - Zhongqun Wang
- Department of Cardiology, Affiliated Hospital of Jiangsu University, 212000, Zhenjiang, China.
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The Role of miRNA-146a and Proinflammatory Cytokines in Carotid Atherosclerosis. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6657734. [PMID: 33376728 PMCID: PMC7746461 DOI: 10.1155/2020/6657734] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 12/02/2022]
Abstract
The aim of this study was to investigate the expression and significance of miRNA-146a in peripheral blood of patients with carotid atherosclerosis (CAS). Patients with CAS were selected as the stenosis (CAS) group (n = 180). According to the degree of stenosis, they were divided into the mild stenosis group (MS group, n = 64), moderate stenosis group (M group, n = 62 cases), and severe stenosis group (SS group, n = 54). According to the plaque type, patients were divided into a stable plaque group (SP group, n = 96) and a vulnerable plaque group (VP group, n = 84). Patients without CAS represented the normal group (n = 90). The expression levels of miRNA-146a as well as IL-6 and TNF-α in peripheral blood were detected by RT-PCR and ELISA, respectively. The expression levels of miRNA-146a, IL-6, and TNF-α in the CAS group were higher than those in the normal group and positively correlated with the degree of stenosis and plaque vulnerability. The expression levels of miRNA-146a, IL-6, and TNF-α in the stable plaque group were lower than those in the vulnerable plaque group. The area under the curve of miRNA-146a predicting the vulnerability of plaques was significant at 0.641. The expression level of miRNA-146a in the CAS group was positively correlated with IL-6 and TNF-α levels. Our results indicate that miRNA-146a may participate in the occurrence and development of CAS by regulating the expression of IL-6 and TNF-α, which may be potential biomarkers of CAS.
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20
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Behmoaras J. The versatile biochemistry of iron in macrophage effector functions. FEBS J 2020; 288:6972-6989. [PMID: 33354925 DOI: 10.1111/febs.15682] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 01/01/2023]
Abstract
Macrophages are mononuclear phagocytes with remarkable polarization ability that allow them to have tissue-specific functions during development, homeostasis, inflammatory and infectious disease. One particular trophic factor in the tissue environment is iron, which is intimately linked to macrophage effector functions. Macrophages have a well-described role in the control of systemic iron levels, but their activation state is also depending on iron-containing proteins/enzymes. Haemoproteins, dioxygenases and iron-sulphur (Fe-S) enzymes are iron-binding proteins that have bactericidal, metabolic and epigenetic-related functions, essential to shape the context-dependent macrophage polarization. In this review, I describe mainly pro-inflammatory macrophage polarization focussing on the role of iron biochemistry in selected haemoproteins and Fe-S enzymes. I show how iron, as part of haem or Fe-S clusters, participates in the cellular control of pro-inflammatory redox reactions in parallel with its role as enzymatic cofactor. I highlight a possible coordinated regulation of haemoproteins and Fe-S enzymes during classical macrophage activation. Finally, I describe tryptophan and α-ketoglutarate metabolism as two essential effector pathways in macrophages that use diverse iron biochemistry at different enzymatic steps. Through these pathways, I show how iron participates in the regulation of essential metabolites that shape macrophage function.
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