1
|
Polonio CM, McHale KA, Sherr DH, Rubenstein D, Quintana FJ. The aryl hydrocarbon receptor: a rehabilitated target for therapeutic immune modulation. Nat Rev Drug Discov 2025:10.1038/s41573-025-01172-x. [PMID: 40247142 DOI: 10.1038/s41573-025-01172-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2025] [Indexed: 04/19/2025]
Abstract
The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor originally identified as the target mediating the toxic effects of environmental pollutants including polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and dioxins. For years, AHR activation was actively avoided during drug development. However, the AHR was later identified as an important physiological regulator of the immune response. These findings triggered a paradigm shift that resulted in identification of the AHR as a regulator of both innate and adaptive immunity and outlined a pathway for its modulation by the diet, commensal flora and metabolism in the context of autoimmunity, cancer and infection. Moreover, the AHR was revealed as a candidate target for the therapeutic modulation of the immune response. Indeed, the first AHR-activating drug (tapinarof) was recently approved for the treatment of psoriasis. Clinical trials are underway to evaluate the effects of tapinarof and other AHR-targeting therapeutics in inflammatory diseases, cancer and infections. This Review outlines the molecular mechanism of AHR action, and describes how it regulates the immune response. We also discuss links to disease and AHR-targeting therapeutics that have been tested in past and ongoing clinical trials.
Collapse
Affiliation(s)
- Carolina M Polonio
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - David H Sherr
- Department of Environmental Health, Boston University School of Public Health, Boston, MA, USA
| | | | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
2
|
Sopić M, Vladimirov S, Munjas J, Mitić T, Hall IF, Jusic A, Ruzic D, Devaux Y. Targeting noncoding RNAs to treat atherosclerosis. Br J Pharmacol 2025; 182:220-245. [PMID: 38720437 DOI: 10.1111/bph.16412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/06/2024] [Accepted: 04/05/2024] [Indexed: 12/13/2024] Open
Abstract
Noncoding RNAs (ncRNAs) are pivotal for various pathological processes, impacting disease progression. The potential for leveraging ncRNAs to prevent or treat atherosclerosis and associated cardiovascular diseases is of great significance, especially given the increasing prevalence of atherosclerosis in an ageing and sedentary population. Together, these diseases impose a substantial socio-economic burden, demanding innovative therapeutic solutions. This review explores the potential of ncRNAs in atherosclerosis treatment. We commence by examining approaches for identifying and characterizing atherosclerosis-associated ncRNAs. We then delve into the functional aspects of ncRNAs in atherosclerosis development and progression. Additionally, we review current RNA and RNA-targeting molecules in development or under approval for clinical use, offering insights into their pharmacological potential. The importance of improved ncRNA delivery strategies is highlighted. Finally, we suggest avenues for advanced research to accelerate the use of ncRNAs in treating atherosclerosis and mitigating its societal impact. LINKED ARTICLES: This article is part of a themed issue Non-coding RNA Therapeutics. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v182.2/issuetoc.
Collapse
Affiliation(s)
- Miron Sopić
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Luxembourg, Luxembourg
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Sandra Vladimirov
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Jelena Munjas
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Tijana Mitić
- BHF/University Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Ignacio Fernando Hall
- BHF/University Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Amela Jusic
- HAYA Therapeutics SA, SuperLab Suisse - Bâtiment Serine, Lausanne, Vaud, Switzerland
| | - Dusan Ruzic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Precision Health, Luxembourg Institute of Health, Luxembourg, Luxembourg
| |
Collapse
|
3
|
Skov-Jeppesen SM, Kobylecki CJ, Jacobsen KK, Bojesen SE. Aryl hydrocarbon receptor repressor ( AHRR ) methylation predicts risk of vascular disease: A cohort study of the general population. Int J Surg 2024; 110:6953-6961. [PMID: 38990298 PMCID: PMC11573105 DOI: 10.1097/js9.0000000000001922] [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: 04/12/2024] [Accepted: 06/25/2024] [Indexed: 07/12/2024]
Abstract
AIMS Smoking is a risk factor for cardiovascular disease, but there is currently no clinically established biomarker for its cardiovascular damage. We aimed to investigate the hypothesis that aryl hydrocarbon receptor repressor ( AHRR ) methylation at CpG site cg05575921, a biomarker of smoking behavior, is associated with the risk of peripheral artery disease (PAD) and aortic aneurysm (AA) in the general population. METHODS AND RESULTS In this prospective cohort study of the general population, we measured AHRR methylation in individuals from three visits to the Copenhagen City Heart Study. Information on risk factors was collected at visits with 10 years intervals; visit 1 (1991-1994), visit 2 (2001-2003), and visit 3 (2011-2015). Individuals were followed up in the Danish National Patient Register for PAD and AA until December 2018. Subhazard ratios were calculated using Fine and Gray competing risk regression. In 11 332 individuals from visit 1 ( n =9234), visit 2 ( n =5384), and visit 3 ( n =4387), there were 613 and 219 events of PAD and AA during up to 26.5 years of follow-up. AHRR hypomethylation was associated with a higher risk of PAD and AA with multivariable-adjusted subhazard ratios of 2.82 (1.91; 4.15) for PAD and 2.88 (1.42; 5.88) for AA in individuals within the lowest versus highest methylation quintile. CONCLUSIONS We found that AHRR methylation, a strong biomarker for smoking, was associated with the risk of PAD and AA. AHRR methylation could be a useful tool in more personalized risk prediction of PAD and AA.
Collapse
Affiliation(s)
- Sune M. Skov-Jeppesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital
| | - Camilla J. Kobylecki
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital
| | - Katja K. Jacobsen
- Department of Technology, Faculty of Health and Technology, University College Copenhagen
| | - Stig E. Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital
- The Copenhagen General Population Study, Copenhagen University Hospital, Herlev and Gentofte Hospital, Herlev
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
4
|
Park SH, Choi HK, Park JH, Hwang JT. Current insights into genome-based personalized nutrition technology: a patent review. Front Nutr 2024; 11:1346144. [PMID: 38318472 PMCID: PMC10838982 DOI: 10.3389/fnut.2024.1346144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
Unlike general nutritional ranges that meet the nutritional needs essential for maintaining the life of an entire population, personalized nutrition is characterised by maintaining health through providing customized nutrition according to individuals' lifestyles or genetic characteristics. The development of technology and services for personalized nutrition is increasing, owing to the acquisition of knowledge about the differences in nutritional requirements according to the diversity of individuals and an increase in health interest. Regarding genetics, technology is being developed to distinguish the various characteristics of individuals and provide customized nutrition. Therefore, to understand the current state of personalized nutrition technology, understanding genomics is necessary to acquire information on nutrition research based on genomics. We reviewed patents related to personalized nutrition-targeting genomics and examined their mechanisms of action. Using the patent database, we searched 694 patents on nutritional genomics and extracted 561 highly relevant valid data points. Furthermore, an in-depth review was conducted by selecting core patents related to genome-based personalized nutrition technology. A marked increase was observed in personalized nutrition technologies using methods such as genetic scoring and disease-specific dietary recommendations.
Collapse
Affiliation(s)
| | | | - Jae Ho Park
- Food Functionality Research Division, Korea Food Research Institute, Wanju-gun, Jeollabuk-do, Republic of Korea
| | - Jin-Taek Hwang
- Food Functionality Research Division, Korea Food Research Institute, Wanju-gun, Jeollabuk-do, Republic of Korea
| |
Collapse
|
5
|
Gheidari ME, Geramifard A, Rafiei M. Dysregulation of LncRNAs ANRIL, MALAT1, and LINC00305 in Coronary Slow Flow Patients: Implications for Inflammation and Endothelial Dysfunction. INTERNATIONAL JOURNAL OF MOLECULAR AND CELLULAR MEDICINE 2024; 13:91-104. [PMID: 39156871 PMCID: PMC11329937 DOI: 10.22088/ijmcm.bums.13.1.91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 06/28/2024] [Accepted: 07/03/2024] [Indexed: 08/20/2024]
Abstract
Coronary Slow Flow (CSF) is observed in individuals who experience delayed blood supply in the coronary arteries. Inflammation and endothelial dysfunction may play a role in the etiology and development of CSF. The current investigation aimed to compare the expression of specific long noncoding RNAs (lncRNAs) associated with endothelial dysfunction and inflammation in CSF patients. This case‒control study enrolled 72 CSF patients and 71 healthy individuals. Blood samples were collected, and serum marker levels were measured. The expression levels of lncRNAs ANRIL, MALAT1, and LINC00305 in peripheral blood mononuclear cells (PBMCs) were assessed using real-time Polymerase Chain Reaction (PCR). All statistical analyses were performed using SPSS 22, with the significance level set at P < 0.05. The study revealed that the relative expression of MALAT1 and LINC00305 was significantly lower in the CSF group (p < 0.01), whereas ANRIL was expressed at higher levels (p < 0.0001). The areas under the ROC curves (AUCs) for MALAT1, LINC00305, and ANRIL were 0.64, 0.66, and 0.75, respectively. Notably, the expression level of LINC00305 exhibited an inverse correlation with CSF incidence (OR: 0.83, p: 0.008) in contrast to that of ANRIL (OR: 1.43, p < 0.0001). Additionally, compared to those in the control group, the average BMI, WBC, RBC, Hb, LDH, LDL, FBS, and percentage of neutrophils in the CSF group were significantly greater (p< 0.05). lncRNA ANRIL is upregulated in CSF patients, whereas MALAT1 and LINC00305 are downregulated. Dysregulation of ANRIL, MALAT1, and LINC00305 may serve as diagnostic and predictive factors for CSF leakage.
Collapse
Affiliation(s)
- Mohammad Esmail Gheidari
- Department of Cardiology, Taleghani Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Asal Geramifard
- Cardiovascular Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mahyar Rafiei
- Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran.
| |
Collapse
|
6
|
Glad HM, Tralamazza SM, Croll D. The expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogen Zymoseptoria tritici. Microb Genom 2023; 9. [PMID: 37991492 DOI: 10.1099/mgen.0.001136] [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] [Indexed: 11/23/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are regulatory molecules interacting in a wide array of biological processes. lncRNAs in fungal pathogens can be responsive to stress and play roles in regulating growth and nutrient acquisition. Recent evidence suggests that lncRNAs may also play roles in virulence, such as regulating pathogenicity-associated enzymes and on-host reproductive cycles. Despite the importance of lncRNAs, only a few model fungi have well-documented inventories of lncRNA. In this study, we apply a recent computational pipeline to predict high-confidence lncRNA candidates in Zymoseptoria tritici, an important global pathogen of wheat impacting global food production. We analyse genomic features of lncRNAs and the most likely associated processes through analyses of expression over a host infection cycle. We find that lncRNAs are frequently expressed during early infection, before the switch to necrotrophic growth. They are mostly located in facultative heterochromatic regions, which are known to contain many genes associated with pathogenicity. Furthermore, we find that lncRNAs are frequently co-expressed with genes that may be involved in responding to host defence signals, such as oxidative stress. Finally, we assess pangenome features of lncRNAs using four additional reference-quality genomes. We find evidence that the repertoire of expressed lncRNAs varies substantially between individuals, even though lncRNA loci tend to be shared at the genomic level. Overall, this study provides a repertoire and putative functions of lncRNAs in Z. tritici enabling future molecular genetics and functional analyses in an important pathogen.
Collapse
Affiliation(s)
- Hanna M Glad
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Sabina Moser Tralamazza
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| |
Collapse
|
7
|
Wang B, Shen XY, Pan LY, Li Z, Chen CJ, Yao YS, Tang DF, Gao W. The HDAC2-MTA3 interaction induces nonsmall cell lung cancer cell migration and invasion by targeting c-Myc and cyclin D1. Mol Carcinog 2023; 62:1630-1644. [PMID: 37401867 DOI: 10.1002/mc.23604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 07/05/2023]
Abstract
Genome-wide association studies have identified numerous single-nucleotide polymorphisms (SNPs) associated with lung cancer; however, the functions of histone deacetylase 2 (HDAC2) rs13213007 and HDAC2 in nonsmall cell lung cancer (NSCLC) remain unclear. Here we identified HDAC2 rs13213007 as a risk SNP and showed that HDAC2 was upregulated in both peripheral blood mononuclear cells (PBMCs) and NSCLC tissues with the rs13213007 A/A genotype compared with those with the rs13213007 G/G or G/A genotype. Patient clinical data indicated strong associations between rs13213007 genotype and N classification. Immunohistochemical staining confirmed that higher expression of HDAC2 was associated with NSCLC progression. Furthermore, we generated 293T cells with the rs13213007 A/A genotype using CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 gene editing. Chromatin immunoprecipitation sequencing followed by motif analysis showed that HDAC2 can bind to c-Myc in rs13213007 A/A 293T cells. Cell Counting Kit-8, colony formation, wound-healing, and Transwell assays revealed that HDAC2 upregulates c-Myc and cyclin D1 expression and promotes NSCLC cell proliferation, migration, and invasion. Co-immunoprecipitation, quantitative reverse transcription-polymerase chain reaction, and western blot analysis assays showed that MTA3 interacts with HDAC2, decreases HDAC2 expression, and rescues the migration and invasion abilities of NSCLC cells. Taken together, these findings identify HDAC2 as a potential therapeutic biomarker in NSCLC.
Collapse
Affiliation(s)
- Bin Wang
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Department of Thoracic Surgery, The Affiliated Huadong Hospital of Fudan University, Shanghai, China
| | - Xiao-Yong Shen
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Department of Thoracic Surgery, The Affiliated Huadong Hospital of Fudan University, Shanghai, China
| | - Lin-Yue Pan
- Department of Respiration, The Affiliated Zhongshan Hospital of Fudan University, Shanghai, China
| | - Zheng Li
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Department of Thoracic Surgery, The Affiliated Huadong Hospital of Fudan University, Shanghai, China
| | - Chun-Ji Chen
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Department of Thoracic Surgery, The Affiliated Huadong Hospital of Fudan University, Shanghai, China
| | - Yuan-Shan Yao
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Department of Thoracic Surgery, The Affiliated Huadong Hospital of Fudan University, Shanghai, China
| | - Dong-Fang Tang
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Department of Thoracic Surgery, The Affiliated Huadong Hospital of Fudan University, Shanghai, China
| | - Wen Gao
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Department of Thoracic Surgery, The Affiliated Huadong Hospital of Fudan University, Shanghai, China
| |
Collapse
|
8
|
Alluli A, Rijnbout St James W, Eidelman DH, Baglole CJ. Dynamic relationship between the aryl hydrocarbon receptor and long noncoding RNA balances cellular and toxicological responses. Biochem Pharmacol 2023; 216:115745. [PMID: 37597813 DOI: 10.1016/j.bcp.2023.115745] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/21/2023]
Abstract
The aryl hydrocarbon receptor (AhR) is a cytosolic transcription factor activated by endogenous ligands and xenobiotic chemicals. Once the AhR is activated, it translocates to the nucleus, dimerizes with the AhR nuclear translator (ARNT) and binds to xenobiotic response elements (XRE) to promote gene transcription, notably the cytochrome P450 CYP1A1. The AhR not only mediates the toxic effects of environmental chemicals, but also has numerous putative physiological functions. This dichotomy in AhR biology may be related to reciprocal regulation of long non-coding RNA (lncRNA). lncRNA are defined as transcripts more than 200 nucleotides in length that do not encode a protein but are implicated in many physiological processes such as cell differentiation, cell proliferation, and apoptosis. lncRNA are also linked to disease pathogenesis, particularly the development of cancer. Recent studies have revealed that AhR activation by environmental chemicals affects the expression and function of lncRNA. In this article, we provide an overview of AhR signaling pathways activated by diverse ligands and highlight key differences in the putative biological versus toxicological response of AhR activation. We also detail the functions of lncRNA and provide current data on their regulation by the AhR. Finally, we outline how overlap in function between AhR and lncRNA may be one way in which AhR can be both a regulator of endogenous functions but also a mediator of toxicological responses to environmental chemicals. Overall, more research is still needed to fully understand the dynamic interplay between the AhR and lncRNA.
Collapse
Affiliation(s)
- Aeshah Alluli
- Meakins-Christie Laboratories, McGill University, Canada; Translational Research in Respiratory Diseases Program at the Research Institute of the McGill University Health Centre, Canada; Department of Pathology, McGill University, Canada
| | - Willem Rijnbout St James
- Meakins-Christie Laboratories, McGill University, Canada; Translational Research in Respiratory Diseases Program at the Research Institute of the McGill University Health Centre, Canada; Department of Pathology, McGill University, Canada
| | - David H Eidelman
- Meakins-Christie Laboratories, McGill University, Canada; Department of Medicine, McGill University, Canada
| | - Carolyn J Baglole
- Meakins-Christie Laboratories, McGill University, Canada; Translational Research in Respiratory Diseases Program at the Research Institute of the McGill University Health Centre, Canada; Department of Pathology, McGill University, Canada; Department of Medicine, McGill University, Canada; Department of Pharmacology and Therapeutics, McGill University, Canada.
| |
Collapse
|
9
|
El-Haddad NW, El Kawak M, El Asmar K, Jabbour ME, Moussa MA, Habib RR, Dhaini HR. AhRR methylation contributes to disease progression in urothelial bladder cancer. Cancer Biomark 2022; 35:167-177. [PMID: 36093686 DOI: 10.3233/cbm-220002] [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: 11/15/2022]
Abstract
BACKGROUND Bladder Cancer (BCa) is the tenth most incidental malignancy worldwide. BCa is mostly attributed to environmental exposure and lifestyle, particularly tobacco smoking. The Aryl Hydrocarbon Receptor Repressor (AhRR) participates in the induction of many enzymes involved in metabolizing carcinogens, including tobacco smoke components. Additionally, studies have shown that smoking demethylates the (AhRR) gene in blood, suggesting AhRR demethylation as a specific serum smoking biomarker. OBJECTIVE This study aimed to validate AhRR demethylation as a smoking biomarker in the target tissue and investigate its contribution to bladder carcinogenesis. METHODS AhRR percent methylation was tested for its association with patient smoking status and oncogenic outcome indicators, particularly p53, RB1, and FGFR3 activating mutations, muscle-invasiveness, and tumor grade, in 180 BCa tissue-based DNA. RESULTS Results showed significantly higher AhRR percent methylation in muscle-invasive compared to non-muscle invasive tumors (42.86% vs. 33.98%; p= 0.011), while lower AhRR methylation was significantly associated with FGFR3 Codon 248 mutant genotype compared to wild-type (28.11% ± 9.44 vs. 37.87% ± 22.53; p= 0.036). All other tested associations were non-statistically significant. CONCLUSIONS Although AhRR methylation did not predict smoking status in BCa tumors, it seems to play a role in carcinogenesis and disease progression. Our findings make a basis for further research.
Collapse
Affiliation(s)
- Nataly W El-Haddad
- Department of Environmental Health, American University of Beirut, Beirut, Lebanon
| | - Michelle El Kawak
- Department of Environmental Health, American University of Beirut, Beirut, Lebanon
| | - Khalil El Asmar
- Department of Epidemiology and Population Health, American University of Beirut, Beirut, Lebanon
| | - Michel E Jabbour
- Department of Urology, St George Hospital University Medical Center, Beirut, Lebanon.,Faculty of Medicine, University of Balamand, Beirut, Lebanon
| | - Mohamad A Moussa
- Department of Urology, Lebanese University, Beirut, Lebanon.,Department of Surgery, Division of Urology, Al-Zahraa University Hospital, Beirut, Lebanon
| | - Rima R Habib
- Department of Environmental Health, American University of Beirut, Beirut, Lebanon
| | - Hassan R Dhaini
- Department of Environmental Health, American University of Beirut, Beirut, Lebanon
| |
Collapse
|
10
|
Scheurer T, Steffens J, Markert A, Du Marchie Sarvaas M, Roderburg C, Rink L, Tacke F, Luedde T, Kraus T, Baumann R. The human long noncoding RNAs CoroMarker, MALAT1, CDR1as, and LINC00460 in whole blood of individuals after controlled short-term exposure with ultrafine metal fume particles at workplace conditions, and in human macrophages in vitro. J Occup Med Toxicol 2022; 17:15. [PMID: 35915466 PMCID: PMC9344619 DOI: 10.1186/s12995-022-00356-0] [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] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 07/12/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Short-term inhalation of occupationally relevant ultrafine zinc/copper (Zn/Cu) containing welding fumes has been shown to induce subclinical systemic inflammation, associated with an elevated risk for cardiovascular diseases. The involvement of noncoding RNAs (lncRNAs) in this setting is currently unknown. However, lncRNAs have been reported to fulfill essential roles in, e.g., cardiovascular diseases, inflammation, infectious diseases, and pollution-related lung disorders. METHODS In this study, the specific lncRNAs levels of the 4 lncRNAs CoroMarker, MALAT1, CDR1as and LINC00460 were determined by RT-qPCR in THP-1 macrophages exposed to Zn/Cu metal fume suspensions for 1, 2, and 4 hours in vitro. Furthermore, 14 subjects were exposed to Zn/Cu containing welding fumes (at 2.5 mg/m3) for 6 hours. Before, 6, 10, and 29 hours after exposure start, whole blood cell lncRNAs levels were determined by RT-qPCR. RESULTS In THP-1 macrophages, we observed a 2.3-fold increase of CDR1as at 1 h (Wilcoxon p = 0.03), a non-significant increase of CoroMarker at 1 h, and an increase of LINC00460 at 2 h (p = 0.03) and at 4 h (p = 0.06). In whole blood cells, we determined a non-significant upregulation of CDR1as at 6 h (p = 0.2), a significant downregulation of CoroMarker at 6 h (p = 0.04), and a significant upregulation of LINC00460 levels at 10 h (p = 0.04) and 29 h (p = 0.04). MALAT-1 remained unchanged in both settings. CONCLUSION The orientation of regulation of the lncRNAs is (except for CoroMarker) similar in the in vitro and in vivo experiments and in line with their described functions. Therefore, these results, e.g. the upregulation of the potential risk marker for cardiovascular diseases, CDR1as, contribute to understanding the underlying mechanisms of Zn/Cu-induced subclinical inflammation in metal workers.
Collapse
Affiliation(s)
- Theresa Scheurer
- Institute for Occupational, Social and Environmental Medicine, Medical Faculty, University Hospital RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Jan Steffens
- Institute for Occupational, Social and Environmental Medicine, Medical Faculty, University Hospital RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany.
- Institute for Translational Medicine (ITM), Medical School Hamburg (MSH) - Am Kaiserkai 1, 20457, Hamburg, Germany.
| | - Agnieszka Markert
- Institute for Occupational, Social and Environmental Medicine, Medical Faculty, University Hospital RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Miriam Du Marchie Sarvaas
- Institute for Occupational, Social and Environmental Medicine, Medical Faculty, University Hospital RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Christoph Roderburg
- Department of Medicine III, Medical Faculty, University Hospital RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
- Department of Hepatology and Gastroenterology, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Lothar Rink
- Institute of Immunology, Medical Faculty, University Hospital RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Frank Tacke
- Department of Medicine III, Medical Faculty, University Hospital RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
- Department of Hepatology and Gastroenterology, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Tom Luedde
- Department of Medicine III, Medical Faculty, University Hospital RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Thomas Kraus
- Institute for Occupational, Social and Environmental Medicine, Medical Faculty, University Hospital RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Ralf Baumann
- Institute for Occupational, Social and Environmental Medicine, Medical Faculty, University Hospital RWTH Aachen University, Pauwelsstr. 30, 52074, Aachen, Germany
- Institute for Translational Medicine (ITM), Medical School Hamburg (MSH) - Am Kaiserkai 1, 20457, Hamburg, Germany
| |
Collapse
|
11
|
Qureshi AA. Tocotrienols: Exciting Biological and Pharmacological Properties of Tocotrienols and Naturally Occurring Compounds, Part II. ANNALS OF CLINICAL CASE REPORTS 2022; 7:2258. [PMID: 36540866 PMCID: PMC9762682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
δ-Tocotrienol plus AHA Step-1 diet in hypercholesterolemic subjects caused reductions in lipid parameters (14% to 18%) with 250 mg/d dose, and 500 mg/d resulted induction in these parameters. Although, α-tocopherol is the most bioavailable form of vitamin E. There are few reports on bioavailability of tocotrienols in humans. Pharmacokinetics and bioavailability of δ-tocotrienol was quantified on plasma levels of tocol isomers, cytokines, and microRNAs. Subjects were fed doses of 125 mg/d to 500 mg/d. Plasma samples collected between 0 h to 10 h, levels of tocols estimated by HPLC, which resulted dose-dependent increases in AUC0-10, Cmax0-∞, Tmaxh, t1/2h, Cl-T 1/h, Vd/f, keh-1. Maximum plasma levels of δ-tocotrienol were at 3 h (125 mg/d to 250 mg/d), 6 h (500 mg/d). Effects of 32 compounds were evaluated on TNF-α secretion, nitric oxide production, and gene expression (TNF-α, IL-1β, IL-6, iNOS activity) in PPAR-α knockout mice. Anticancer activities of thiostrepton, dexamethasone, 2-methoxyestradiol, δ-tocotrienol, quercetin, amiloride, quinine sulfate showed significant anti-proliferative properties in Hela cells, pancreatic, prostate, breast, lungs, melanoma, B-lymphocytes, T-cells (40% to 95%). Results of plasma total mRNAs after δ-tocotrienol feeding to hepatitis C patients revealed significant down-regulated gene expression of pro-inflammatory cytokines. A mixture of δ-tocotrienol, resveratrol, vitamin D3 (NS-3) were given two capsules/d or cellulose/olive oil as placebo to individuals with T2DM (24-weeks). Significant down-regulation (15% to 74%) of gene expression in diabetes biomarkers and decreases i n serum levels of fasting-glucose, HbA1c, hs-CRP, fasting-insulin, HOMA-IR, MDA (9% to 23%) were observed with NS-3 treated T2DM. Pure plasma mRNAs and miRNAs of pre-dose vs. post-dose of NS-3 treated samples were analyzed by Next Generation Sequencing (NGS). Venn diagrams have established genetic regulatory network images and canonical signaling pathways for mRNA, miRNA, and paired mRNA-miRNA.
Collapse
Affiliation(s)
- Asaf A Qureshi
- Department of Biomedical Science, School of Medicine, University of Missouri, Kansas City, USA
| |
Collapse
|
12
|
Zhang T, Feng C, Zhang X, Sun B, Bian Y. Abnormal expression of long non-coding RNA rhabdomyosarcoma 2-associated transcript (RMST) participates in the pathological mechanism of atherosclerosis by regulating miR-224-3p. Bioengineered 2022; 13:2648-2657. [PMID: 35067166 PMCID: PMC8974166 DOI: 10.1080/21655979.2021.2023995] [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] [Indexed: 11/28/2022] Open
Abstract
Study shows that long non-coding RNA (lncRNA) plays a regulatory role in cardiovascular diseases, and the mechanism of rhabdomyosarcoma 2-associated transcript (RMST) in atherosclerosis (AS) is still unclear. This study aimed to evaluate the expression of RMST and its possible role in the occurrence of AS. RMST and miR-224-3p level in serum and human umbilical vein endothelial cells (HUVECs) were determined by real-time quantitative PCR (RT-qPCR). In vitro atherosclerotic cell model was achieved by treating HUVECs with ox-LDL. Receiver operating characteristic (ROC) curve assessed the diagnostic value of RMST in AS, and Pearson correlation coefficient estimated the correlation of RMST with carotid intima-media thickness (CIMT) and carotid-femoral pulse wave velocity (cfPWV). Cell counting kit-8 (CCK-8) assay and Enzyme-linked immunosorbent assay (ELISA) were performed to evaluate the effect of RMST on cell viability and inflammatory response. The luciferase analysis was used to validate the relationship between RMST and miR-224-3p. The results showed that in serum and HUVECs, RMST levels were increased, while miR-224-3p level was decreased. ROC curve suggested that RMST had clinical diagnostic value for AS. Besides, CIMT and cfPWV were positively correlated with RMST levels, respectively. In HUVECs, RMST-knockdown notably improved the cell viability and inhibited the production of inflammatory factors. Moreover, miR-224-3p was the target of RMST. In conclusion, RMST has the potential to be a diagnostic marker for AS. RMST-knockdown contributes to the enhancement of cell viability and the inhibition of inflammatory response, which may provide new insights into the conquest of AS.
Collapse
Affiliation(s)
- Tao Zhang
- Department of Endocrinology, People’s Hospital of Rizhao, Shandong, China
| | - Cuina Feng
- Department of Cardiology, Affiliated Hospital of Hebei University, Hebei, China
| | - Xiang Zhang
- Department of Cardiology, People’s Hospital of Rizhao, Shandong, China
| | - Bin Sun
- Department of Emergency, Yidu Central Hospital of Weifang, Shandong, China
| | - Ying Bian
- Department of General Breast Surgery, Affiliated Hospital of Hebei University, Hebei, China
| |
Collapse
|
13
|
Functional Implications of Intergenic GWAS SNPs in Immune-Related LncRNAs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1363:147-160. [DOI: 10.1007/978-3-030-92034-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
14
|
Aryl Hydrocarbon Receptor Repressor Is Hypomethylated in Psoriasis and Promotes Psoriasis-like Inflammation in HaCaT Cells. Int J Mol Sci 2021; 22:ijms222312715. [PMID: 34884515 PMCID: PMC8657998 DOI: 10.3390/ijms222312715] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022] Open
Abstract
It is known that DNA hypomethylation of aryl hydrocarbon receptor repressor (AhRR), one of the epigenetic markers of environmental pollutants, causes skin diseases. However, the function and mechanisms are still unknown. We aimed to determine whether AhRR is hypomethylated in PBMC of psoriasis patients, as well as to examine the expression of psoriasis-related inflammatory cytokines and antimicrobial peptides after 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treatment in HaCaT cells overexpressing or silencing AhRR. AhRR was determined by qPCR, Western blot, immunohistochemistry, and immunocytochemistry in skin tissue and HaCaT cells. DNA methylation of AhRR was performed by Infinium Human Methylation450 BeadChip in PBMC of psoriasis patients and methylation-specific PCR (MSP) in HaCaT cells. NF-κB pp50 translocation and activity were performed by immunocytochemistry and luciferase reporter assay, respectively. We verified AhRR gene expression in the epidermis from psoriasis patients and healthy controls. AhRR hypomethylation in PBMC of psoriasis patients and pAhRR-HaCaT cells was confirmed. The expression level of AhRR was increased in both TCDD-treated HaCaT cells and pAhRR-HaCaT cells. NF-κB pp50 translocation and activity increased with TCDD. Our results showed that AhRR was hypomethylated and overexpressed in the lesional skin of patients with psoriasis, thereby increasing AhRR gene expression and regulating pro-inflammatory cytokines through the NF-κB signaling pathway in TCDD-treated HaCaT cells.
Collapse
|
15
|
Ding Y, Yin R, Zhang S, Xiao Q, Zhao H, Pan X, Zhu X. The Combined Regulation of Long Non-coding RNA and RNA-Binding Proteins in Atherosclerosis. Front Cardiovasc Med 2021; 8:731958. [PMID: 34796209 PMCID: PMC8592911 DOI: 10.3389/fcvm.2021.731958] [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: 06/30/2021] [Accepted: 10/07/2021] [Indexed: 12/31/2022] Open
Abstract
Atherosclerosis is a complex disease closely related to the function of endothelial cells (ECs), monocytes/macrophages, and vascular smooth muscle cells (VSMCs). Despite a good understanding of the pathogenesis of atherosclerosis, the underlying molecular mechanisms are still only poorly understood. Therefore, atherosclerosis continues to be an important clinical issue worthy of further research. Recent evidence has shown that long non-coding RNAs (lncRNAs) and RNA-binding proteins (RBPs) can serve as important regulators of cellular function in atherosclerosis. Besides, several studies have shown that lncRNAs are partly dependent on the specific interaction with RBPs to exert their function. This review summarizes the important contributions of lncRNAs and RBPs in atherosclerosis and provides novel and comprehensible interaction models of lncRNAs and RBPs.
Collapse
Affiliation(s)
- Yuanyuan Ding
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ruihua Yin
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Shuai Zhang
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Qi Xiao
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hongqin Zhao
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xudong Pan
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaoyan Zhu
- Department of Critical Care Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
| |
Collapse
|
16
|
The diversity of lipocalin receptors. Biochimie 2021; 192:22-29. [PMID: 34534611 DOI: 10.1016/j.biochi.2021.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 11/23/2022]
Abstract
Lipocalins are important carriers of preferentially hydrophobic molecules, but they can also bind other ligands, like highly polar siderophores or intact proteins. Consequently, they are involved in a variety of physiological processes in many species. Since lipocalins are mainly extracellular proteins, they have to interact with cell receptors to exert their biological effects. In contrast to the large number of lipocalins identified in the last years, the number of receptors known is still limited. Nevertheless, some novel findings concerning the molecules involved in cellular uptake or signaling effects of lipocalins have been made recently. This review presents a detailed overview of the receptors identified so far. The methods used for isolation or identification are described and structural as well as functional information on these proteins is presented essentially in chronological order of their initial discovery.
Collapse
|
17
|
Sansonetti M, De Windt LJ. Non-coding RNAs in cardiac inflammation: key drivers in the pathophysiology of heart failure. Cardiovasc Res 2021; 118:2058-2073. [PMID: 34097013 DOI: 10.1093/cvr/cvab192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 06/04/2021] [Indexed: 12/15/2022] Open
Abstract
Heart failure is among the most progressive diseases and a leading cause of morbidity. Despite several advances in cardiovascular therapies, pharmacological treatments are limited to relieve symptoms without curing cardiac injury. Multiple observations point to the involvement of immune cells as key drivers in the pathophysiology of heart failure. In particular, there is a growing recognition that heart failure is related to a prolonged and insufficiently repressed inflammatory response leading to molecular, cellular, and functional cardiac alterations. Over the last decades, non-coding RNAs are recognized as prominent mediators of the cardiac inflammation, affecting the function of several immune cells. In the current review, we explore the contribution of the diverse immune cells in the progression of heart failure, revealing mechanistic functions for non-coding RNAs in cardiac immune cells as a new and exciting field of investigation.
Collapse
Affiliation(s)
- Marida Sansonetti
- Department of Molecular Genetics, Faculty of Science and Engineering; Faculty of Health, Medicine and Life Sciences; Maastricht University, Maastricht, The Netherlands
| | - Leon J De Windt
- Department of Molecular Genetics, Faculty of Science and Engineering; Faculty of Health, Medicine and Life Sciences; Maastricht University, Maastricht, The Netherlands
| |
Collapse
|
18
|
Yan H, Liu G, Liang Y, Wu W, Xia R, Jiao L, Shen H, Jia Z, Wang Q, Wang Z, Kong Y, Ying B, Wang H, Wang C. Up-regulated long noncoding RNA AC007128.1 and its genetic polymorphisms associated with Tuberculosis susceptibility. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1018. [PMID: 34277818 PMCID: PMC8267308 DOI: 10.21037/atm-21-2724] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/17/2021] [Indexed: 02/05/2023]
Abstract
Background Tuberculosis (TB) remains a major public health problem. Long non-coding RNAs (lncRNAs) are important regulators of gene expression. In this study, we explored the association between the expression of lncRNA AC007128.1 and TB susceptibility. Methods Three single-nucleotide polymorphisms (SNPs) (rs12333784, rs6463794, and rs720964) of lncRNA AC007128.1 were selected using the 1000 Genomes Project database and offline software Haploview V4.2, and were genotyped by a customized 2×48-Plex SNPscan™ Kit. Results We identified two differentially expressed lncRNA including AC007128.1 and AP001065.3 in comparisons of expression profiles between ATB vs. LTBI, LTBI vs. HCs, and AC700128.1 expression was specifically and significantly up-regulated in TB patients by verification of external data. Gene Ontology functional enrichment analysis and co-expression network showed up-regulated mRNA was mainly involved in negative regulation of the G protein-coupled receptor (GPCR) signaling pathway, and FPR1 and CYP27B1 were involved in the co-expression of AC007128.1. Using the 1000 Genomes Project, software Haploview V4.2, and SNP genotype, we screened out SNP rs12333784 which locus at 7p21.3 in AC007128.1 associated with TB susceptibility. The G carrier of rs12333784 was then finally verified to be significantly associated with pulmonary TB (PTB) and extrapulmonary tuberculosis (EPTB) susceptibility (pBonferroni =0.03878), and a similar but more significant effect was observed under the dominant model analysis (pBonferroni =0.013, OR =1.349, 95% CI, 1.065–1.709). In addition, the GG + GA genotype of SNP rs12333784 was significantly correlated with higher glucose (GLU) (P=0.03), higher gamma-glutamyl transferase (GGT) (P=0.05), and higher erythrocyte sedimentation rate (ESR) (P=0.05). Conclusions Our findings show lncRNA AC007128.1 can be regarded as biomarkers discriminating between ATB and LTBI and may also be a diagnostic biomarker for LBTI. These findings may aid clinical decision making in the management of TB.
Collapse
Affiliation(s)
- Hong Yan
- Department of Clinical Laboratory Medicine, the First Medical Center, Chinese PLA General Hospital, Beijing, China.,Laboratory Medicine Center, the Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Guoye Liu
- Department of Laboratory Medicine, Affiliated Brain Hospital of Nanjing Medical University (Chest Branch), Nanjing, China
| | - Yuan Liang
- The Affiliated Cancer Hospital & Hepatobiliary Center, First Affiliated Hospital, Nanjing Medical University, Nanjing, China.,Department of Bioinformatics, Nanjing Medical University, Nanjing, China
| | - Wei Wu
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China.,Research Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Rui Xia
- Department of Laboratory Medicine, Affiliated Brain Hospital of Nanjing Medical University (Chest Branch), Nanjing, China
| | - Lin Jiao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Han Shen
- Department of Clinical Laboratory, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Zhijun Jia
- Department of Nuclear Medicine, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Qian Wang
- Department of Laboratory Medicine, Affiliated Brain Hospital of Nanjing Medical University (Chest Branch), Nanjing, China
| | - Zhiqiang Wang
- Department of Laboratory Medicine, Affiliated Brain Hospital of Nanjing Medical University (Chest Branch), Nanjing, China
| | - Yi Kong
- Department of Clinical Laboratory Medicine, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Hualiang Wang
- Department of Molecular Biology, Shanghai Centre for Clinical Laboratory, Shanghai, China
| | - Chengbin Wang
- Department of Clinical Laboratory Medicine, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| |
Collapse
|
19
|
Li J, Ren L, Li M, Yang C, Chen J, Chen Q. Screening of Potential Key Genes Related to Tubal Factor Infertility Based on Competitive Endogenous RNA Network. Genet Test Mol Biomarkers 2021; 25:325-333. [PMID: 34003694 DOI: 10.1089/gtmb.2020.0083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: The molecular biological mechanism of tubal factor infertility (TFI) is still unclear. Long noncoding RNAs (lncRNAs) are considered a major part of the competitive endogenous RNA (ceRNA) network and have attracted growing attention. Our study aimed to explore the regulatory mechanisms of lncRNAs associated with TFI and screen potential key genes related to TFI. Materials and Methods: Differentially expressed lncRNAs (DELs) and differentially expressed genes (DEGs) were identified by comparing normal and TFI expression patterns of lncRNAs and mRNAs in eutopic endometrial tissues obtained from 3 normal and 3 TFI patients during implantation. These data were used to develop a protein-protein interaction (PPI) network of DEGs using the STRING online software. The identified DELs and DEGs were then used to construct a ceRNA network, and the Network Analyzer Tool Kit in Cytoscape was used to analyze the ceRNA network topology and stability. Finally, the overlapping genes present in both the ceRNA and PPI networks were selected as the potential key genes related to TFI. Results: Ninety-six DEGs (59 up and 37 down) and 45 DELs (28 up and 17 down) were identified. Thirty-four DEGs were mapped in a PPI network. A ceRNA network, including two lncRNAs (LINC00305 and DLX6-AS1), four microRNAs (hsa-miR-20b-5p, hsa-miR-17-5p, hsa-miR-107, and hsa-miR-24-3p), and four mRNAs (MAP3K3, HMGB3, FAM103A1, and TMEM209), was successfully constructed. Importantly, a potential key gene (TMEM209) related to TFI was identified. Conclusion: The construction of a ceRNA network related to TFI may help elucidate the regulatory mechanism by which genes and lncRNAs function as ceRNA networks. Importantly, TMEM209 may be further evaluated as potential therapeutic targets for TFI.
Collapse
Affiliation(s)
- Junzui Li
- School of Medicine, Xiamen University, Fujian, P.R. China.,First Affiliated Hospital of Xiamen University, Fujian, P.R. China
| | - Lulu Ren
- First Affiliated Hospital of Xiamen University, Fujian, P.R. China
| | - Meina Li
- College of the Environment and Ecology, Xiamen University, Fujian, P.R. China
| | - Cui Yang
- School of Medicine, Xiamen University, Fujian, P.R. China
| | - Jiahao Chen
- School of Medicine, Xiamen University, Fujian, P.R. China
| | - Qionghua Chen
- School of Medicine, Xiamen University, Fujian, P.R. China.,First Affiliated Hospital of Xiamen University, Fujian, P.R. China
| |
Collapse
|
20
|
Long Non-Coding RNAs (lncRNAs) in Cardiovascular Disease Complication of Type 2 Diabetes. Diagnostics (Basel) 2021; 11:diagnostics11010145. [PMID: 33478141 PMCID: PMC7835902 DOI: 10.3390/diagnostics11010145] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/14/2021] [Accepted: 01/18/2021] [Indexed: 02/07/2023] Open
Abstract
The discovery of non-coding RNAs (ncRNAs) has opened a new paradigm to use ncRNAs as biomarkers to detect disease progression. Long non-coding RNAs (lncRNA) have garnered the most attention due to their specific cell-origin and their existence in biological fluids. Type 2 diabetes patients will develop cardiovascular disease (CVD) complications, and CVD remains the top risk factor for mortality. Understanding the lncRNA roles in T2D and CVD conditions will allow the future use of lncRNAs to detect CVD complications before the symptoms appear. This review aimed to discuss the roles of lncRNAs in T2D and CVD conditions and their diagnostic potential as molecular biomarkers for CVD complications in T2D.
Collapse
|
21
|
Aznaourova M, Schmerer N, Schmeck B, Schulte LN. Disease-Causing Mutations and Rearrangements in Long Non-coding RNA Gene Loci. Front Genet 2020; 11:527484. [PMID: 33329688 PMCID: PMC7735109 DOI: 10.3389/fgene.2020.527484] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022] Open
Abstract
The classic understanding of molecular disease-mechanisms is largely based on protein-centric models. During the past decade however, genetic studies have identified numerous disease-loci in the human genome that do not encode proteins. Such non-coding DNA variants increasingly gain attention in diagnostics and personalized medicine. Of particular interest are long non-coding RNA (lncRNA) genes, which generate transcripts longer than 200 nucleotides that are not translated into proteins. While most of the estimated ~20,000 lncRNAs currently remain of unknown function, a growing number of genetic studies link lncRNA gene aberrations with the development of human diseases, including diabetes, AIDS, inflammatory bowel disease, or cancer. This suggests that the protein-centric view of human diseases does not capture the full complexity of molecular patho-mechanisms, with important consequences for molecular diagnostics and therapy. This review illustrates well-documented lncRNA gene aberrations causatively linked to human diseases and discusses potential lessons for molecular disease models, diagnostics, and therapy.
Collapse
Affiliation(s)
- Marina Aznaourova
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany
| | - Nils Schmerer
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany
| | - Bernd Schmeck
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany.,Systems Biology Platform, German Center for Lung Research (DZL), Philipps University Marburg, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
| | - Leon N Schulte
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany.,Systems Biology Platform, German Center for Lung Research (DZL), Philipps University Marburg, Marburg, Germany
| |
Collapse
|
22
|
Ma X, Liu H, Chen F. Functioning of Long Noncoding RNAs Expressed in Macrophage in the Development of Atherosclerosis. Front Pharmacol 2020; 11:567582. [PMID: 33381026 PMCID: PMC7768882 DOI: 10.3389/fphar.2020.567582] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 09/22/2020] [Indexed: 12/26/2022] Open
Abstract
Chronic inflammation is part of the pathological process during atherosclerosis (AS). Due to the abundance of monocytes/macrophages within the arterial plaque, monocytes/macrophages have become a critical cellular target in AS studies. In recent decades, a number of long noncoding RNAs (lncRNAs) have been found to exert regulatory roles on the macrophage metabolism and macrophage plasticity, consequently promoting or suppressing atherosclerotic inflammation. In this review, we provide a comprehensive overview of lncRNAs in macrophage biology, highlighting the potential role of lncRNAs in AS based on recent findings, with the aim to identify disease biomarkers and future therapeutic interventions for AS.
Collapse
Affiliation(s)
- Xirui Ma
- Department of Endocrinology and Metabolism, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huifang Liu
- Department of Endocrinology and Metabolism, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fengling Chen
- Department of Endocrinology and Metabolism, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
23
|
Feng T, Feng N, Zhu T, Li Q, Zhang Q, Wang Y, Gao M, Zhou B, Yu H, Zheng M, Qian B. A SNP-mediated lncRNA (LOC146880) and microRNA (miR-539-5p) interaction and its potential impact on the NSCLC risk. J Exp Clin Cancer Res 2020; 39:157. [PMID: 32795333 PMCID: PMC7427888 DOI: 10.1186/s13046-020-01652-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Many cancer-associated single nucleotide polymorphisms (SNPs) are located in the genomic regions of long non-coding RNAs (lncRNAs). Mechanisms of these SNPs in connection to cancer risk are not fully understood. METHODS Association of SNP (rs140618127) in lncRNA LOC146880 with non-small cell lung cancer (NSCLC) was evaluated in a case-control study of 2707 individuals. The mechanism of the SNP's biologic influence was explored with in vitro and in vivo experiments, including plasmid transfection, siRNA knockdown, flow cytometry assessment, and assays of cell proliferation, migration, invasion, and colony formation. RESULTS Association analysis showed that A allele of SNP rs140618127 was associated with low risk of NSCLC in the Chinese population. Lab experiments indicated that SNP rs140618127 contained a binding site for miR-539-5p and the binding between miR-539-5p and LOC146880 resulted in declined phosphorylation of an oncogene, ENO1. The reduced phosphorylation of ENO1 led to decreased phosphorylation of PI3K and Akt, which is further linked to the decline in cell proliferation and tumor progression. CONCLUSION The study demonstrates that SNP rs140618127 in lncRNA loc146880 provides an alternate binding site for microRNA miR-539-5p which affects the phosphorylation of ENO1 and activation of the PI3K and Akt pathway.
Collapse
MESH Headings
- Animals
- Apoptosis
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- Carcinoma, Non-Small-Cell Lung/pathology
- Case-Control Studies
- Cell Movement
- Cell Proliferation
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- MicroRNAs/genetics
- Middle Aged
- Phosphopyruvate Hydratase/genetics
- Phosphopyruvate Hydratase/metabolism
- Polymorphism, Single Nucleotide
- Prognosis
- RNA, Long Noncoding/genetics
- Tumor Cells, Cultured
- Tumor Suppressor Proteins/genetics
- Tumor Suppressor Proteins/metabolism
- Xenograft Model Antitumor Assays
Collapse
Affiliation(s)
- Tienan Feng
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Clinical Research Promotion and Development Center, Shanghai Shenkang Hospital Development Center, Shanghai, 200041, China
| | - Nannan Feng
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Tengteng Zhu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Qiang Li
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Qi Zhang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yu Wang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ming Gao
- Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Baosen Zhou
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, 110013, China
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI, 96813, USA
| | - Min Zheng
- Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China
| | - Biyun Qian
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Second Affiliated hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, 610051, Sichuan, China.
| |
Collapse
|
24
|
Safa A, Arsang-Jang S, Taheri M, Omrani MD, Ghafouri-Fard S. Dysregulation of NF-κB-Associated lncRNAs in Multiple Sclerosis Patients. J Mol Neurosci 2020; 71:80-88. [DOI: 10.1007/s12031-020-01628-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 06/08/2020] [Indexed: 12/22/2022]
|
25
|
Linnenkamp BDW, Raskin S, Esposito SE, Herai RH. A comprehensive analysis of AHRR gene as a candidate for cleft lip with or without cleft palate. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 785:108319. [PMID: 32800270 DOI: 10.1016/j.mrrev.2020.108319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 02/06/2023]
Abstract
Cleft lip and palate (CL/P) is among the most common congenital malformations and affects 1 in 700 newborns. CL/P is caused by genetic and environmental factors (maternal smoking, alcohol or drug use and others). Many genes and loci were associated with cleft lip/palate but the amount of heterogeneity justifies identifying new causal genes and variants. AHRR (Aryl-Hydrocarbon Receptor Repressor) gene has recently been related to CL/P however, few functional studies analyze the genotypephenotype interaction of AHRR with CL/P. Several studies associate the molecular pathway of AHRR to CL/P which indicates this gene as a functional candidate in CL/P etiology. METHODS Systematic Literature Review was performed using PUBMED database with the keywords cleft lip, cleft palate, orofacial cleft, AHRR and synonyms. SLR resulted in 37 included articles. RESULTS AHRR is a positional and functional candidate gene for CL/P. In silico analysis detected interactions with other genes previously associated to CL/P like ARNT and CYP1A1. AHRR protein regulates cellular toxicity through TCDD mediated AHR pathway. Exposure to TCDD in animal embryos is AHR mediated and lead to cleft palate due to palate fusion failure and post fusion rupture. AHRR regulates cellular growth and differentiation, fundamental to lip and palatogenesis. AHRR decreases carcinogenesis and recently a higher tumor risk has been described in CL/P patients and families. AHRR is also a smoking biomarker due to changed methylation sites found in smokers DNA although folate intake may partially revert these methylation alterations. This corroborates the role of maternal smoking and lack of folate supplementation as risk factors for CL/P. CONCLUSION This research identified the importance of AHRR in dioxin response and demonstrated an example of genetic and environmental interaction, indispensable in the development of many complex diseases.
Collapse
Affiliation(s)
- Bianca Domit Werner Linnenkamp
- Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, Brazil
| | - Salmo Raskin
- School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, Brazil
| | - Selene Elifio Esposito
- Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, Brazil; School of Life Sciences, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, Brazil
| | - Roberto Hirochi Herai
- Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, Brazil; Research Department, Lico Kaesemodel Institute (ILK), Curitiba, Paraná, Brazil.
| |
Collapse
|
26
|
Abstract
Currently, cardiovascular diseases continue to be the leading cause of death worldwide; therefore, atherosclerosis remains one of the most crucial public health problems. This chronic and complex disease is considered to be a result of aberrant lipid homeostasis and inflammation of the inner wall of arteries that leads to plaque development. In recent years, a specific class of non-coding RNAs that are characterised by transcript lengths longer than 200 nucleotides, called long non-coding RNAs (lncRNAs), has emerged. Moreover, a growing body of evidence indicates that deregulation of lncRNA expression may contribute to the development of many diseases. Despite continuous efforts in deciphering the molecular basis of atherosclerotic plaque (AP) formation, many aspects of this process remain elusive. Therefore, continuing efforts in this area should remain the highest priority in the coming years. Establishment of a standardised experimental pipeline and validation of lncRNAs as possible relevant biomarkers for cardiovascular disease would enable the translation of gathered findings into clinical practice.
Collapse
Affiliation(s)
- Weronika Kraczkowska
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Science, 6 Święcickiego Street, 60-781, Poznan, Poland.
| | - Paweł Piotr Jagodziński
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Science, 6 Święcickiego Street, 60-781, Poznan, Poland
| |
Collapse
|
27
|
Wahba AS, Ibrahim ME, Mesbah NM, Saleh SM, Abo-Elmatty DM, Mehanna ET. Serum LINC00305 expression and its genetic variant rs2850711 are associated with clinical and laboratory features of rheumatoid arthritis. Br J Biomed Sci 2020; 77:142-147. [PMID: 32188348 DOI: 10.1080/09674845.2020.1744942] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Long intergenic non-protein coding (lnc) RNA 00305 (LINC00305) is a pro-inflammatory atherosclerosis-associated lncRNA. We hypothesised that LINC00305 expression and its variant rs2850711 (A/T) are implicated in rheumatoid arthritis (RA) and linked with clinical and routine laboratory markers. METHODS 100 RA patients and 100 healthy controls were recruited. LINC00305 genotyping and expression were performed using allelic-discrimination PCR and quantitative real-time PCR. LINC00305 diagnostic power was evaluated using area under the receiver operating characteristic curve (AUC). Serum nuclear factor- κB (NF-κB) and matrix metalloproteinase-3 (MMP-3) levels were determined by ELISA, standard laboratory markers by routine methods. RESULTS LINC00305 expression was significantly increased in RA patients and positively correlated with DAS28, C-reactive protein, erythrocyte sedimentation rate, rheumatoid factor and anti-cyclic citrullinated peptide antibody. In multivariate analysis, NF-κB, MMP-3 and LINC00305 were significant predictors of RA (P< 0.0001). Individuals carrying AT and TT genotypes of rs2850711 polymorphism had significantly more likely to have RA than AA genotype carriers (P< 0.05). LINC00305 expression, DAS28 score and serum levels of NF-κB and MMP-3 were significantly increased in the patients carrying LINC00305 AT and TT genotypes as compared with AA genotype patients (P< 0.01). CONCLUSION Increased expression level of LINC00305 and its rs2850711 genetic variant may play a role in the diagnosis and management of RA, and its severity and activity.
Collapse
Affiliation(s)
- A S Wahba
- Department of Biochemistry, Faculty of Pharmacy, Suez Canal University , Ismailia, Egypt
| | - M E Ibrahim
- Department of Physical Medicine, Rheumatology and Rehabilitation, Faculty of Medicine, Suez Canal University , Ismailia, Egypt
| | - N M Mesbah
- Department of Biochemistry, Faculty of Pharmacy, Suez Canal University , Ismailia, Egypt
| | - S M Saleh
- Department of Biochemistry, Faculty of Pharmacy, Suez Canal University , Ismailia, Egypt
| | - D M Abo-Elmatty
- Department of Biochemistry, Faculty of Pharmacy, Suez Canal University , Ismailia, Egypt
| | - E T Mehanna
- Department of Biochemistry, Faculty of Pharmacy, Suez Canal University , Ismailia, Egypt
| |
Collapse
|
28
|
Robinson EK, Covarrubias S, Carpenter S. The how and why of lncRNA function: An innate immune perspective. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194419. [PMID: 31487549 PMCID: PMC7185634 DOI: 10.1016/j.bbagrm.2019.194419] [Citation(s) in RCA: 209] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/21/2019] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing has provided a more complete picture of the composition of the human transcriptome indicating that much of the "blueprint" is a vastness of poorly understood non-protein-coding transcripts. This includes a newly identified class of genes called long noncoding RNAs (lncRNAs). The lack of sequence conservation for lncRNAs across species meant that their biological importance was initially met with some skepticism. LncRNAs mediate their functions through interactions with proteins, RNA, DNA, or a combination of these. Their functions can often be dictated by their localization, sequence, and/or secondary structure. Here we provide a review of the approaches typically adopted to study the complexity of these genes with an emphasis on recent discoveries within the innate immune field. Finally, we discuss the challenges, as well as the emergence of new technologies that will continue to move this field forward and provide greater insight into the biological importance of this class of genes. This article is part of a Special Issue entitled: ncRNA in control of gene expression edited by Kotb Abdelmohsen.
Collapse
Affiliation(s)
- Elektra K Robinson
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Sergio Covarrubias
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America.
| |
Collapse
|
29
|
Long non-coding RNAs in immune regulation and their potential as therapeutic targets. Int Immunopharmacol 2020; 81:106279. [PMID: 32058929 DOI: 10.1016/j.intimp.2020.106279] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/30/2020] [Accepted: 02/01/2020] [Indexed: 12/18/2022]
Abstract
Long non-coding RNAs (lncRNAs) are potent regulators of immune cell development and function. Their implication in multiple immune-mediated disorders highlights lncRNAs as exciting biomarkers and potential drug targets. Recent technological innovations in oligo-based therapeutics, development of RNA-targeting small molecules, and CRISPR-based approaches, position RNA as the next therapeutic frontier. Here, we review the latest advances made toward understanding the role of lncRNAs in human immunological disorders and further discuss RNA-targeting approaches that could be potentially exploited to manipulate lncRNA function as a clinical intervention.
Collapse
|
30
|
Lu H, Wen D, Sun J, Zeng L, Du J, Du D, Zhang L, Deng J, Jiang J, Zhang A. Enhancer polymorphism rs10865710 associated with traumatic sepsis is a regulator of PPARG gene expression. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2019; 23:430. [PMID: 31888703 PMCID: PMC6938012 DOI: 10.1186/s13054-019-2707-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/16/2019] [Indexed: 12/18/2022]
Abstract
Background Peroxisome proliferator-activated receptor gamma (PPARγ) is a major regulator in sepsis. Our previous study identified the enhancer polymorphism rs10865710C/G to be associated with susceptibility to sepsis in trauma patients. We performed two-stage cohort studies integrating biological experiments of potential functional variants that modify susceptibility to traumatic sepsis. Methods Improved multiplex ligation detection reaction (iMLDR) was used to genotype rs10865710 in 797 Han Chinese trauma patients in Chongqing. Clinical relevance was validated in 334 patients in Guizhou. The potential function of rs10865710 in transcriptional regulation was explored through a dual luciferase reporter assay and electrophoretic mobility shift assay (EMSA). Expression of PPARγ was assessed by expression quantitative trait locus (e-QTL) and western blot analyses. Results The association results confirmed rs10865710 to be significantly strongly associated with sepsis risk in trauma patients of the Chongqing and Guizhou cohorts (OR = 1.41 (1.11–1.79), P = 0.004 and OR = 1.45 (1.01–2.09), P = 0.046, both for allele-dose effect, respectively). A meta-analysis of both cohorts and a previous study indicated strong evidence for this association (OR = 1.41 (1.17–1.71), P = 0.0004 for the dominant model, OR = 1.78 (1.34–2.36), P < 0.0001 for the recessive model and OR = 1.38 (1.20–1.58), P < 0.0001 for the allelic model). Functional experiments verified that rs10865710 was a causative variant influencing enhancer activity (G vs. C, 0.068 ± 0.004 vs. 0.096 ± 0.002, P = 0.0005) and CREB2 binding. Expression analysis also indicatevd rs10865710 genotypes to be associated with levels of PPARγ expression (P = 9.2 × 10−5 for dominant effect and P = 0.005 for recessive effect). Conclusions Our study provides evidence that the enhancer-region polymorphism rs10865710 might influence transcription factor binding and regulate PPARγ expression, thus conferring susceptibility to traumatic sepsis. Trial registration ClinicalTrials.gov, NCT01713205. Registered 18 October 2012, retrospectively registered.
Collapse
Affiliation(s)
- Hongxiang Lu
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping Hospital, Army Medical University, Changjiang Branch Road 10, Daping Street, Yuzhong District, Chongqing, 400042, China
| | - Dalin Wen
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping Hospital, Army Medical University, Changjiang Branch Road 10, Daping Street, Yuzhong District, Chongqing, 400042, China
| | - Jianhui Sun
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping Hospital, Army Medical University, Changjiang Branch Road 10, Daping Street, Yuzhong District, Chongqing, 400042, China
| | - Ling Zeng
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping Hospital, Army Medical University, Changjiang Branch Road 10, Daping Street, Yuzhong District, Chongqing, 400042, China
| | - Juan Du
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping Hospital, Army Medical University, Changjiang Branch Road 10, Daping Street, Yuzhong District, Chongqing, 400042, China
| | - Dingyuan Du
- Department of Cardiothoracic Surgery, Chongqing Emergency Medical Center, The Affiliated Central Hospital of Chongqing University, Chongqing, 400042, China
| | - Lianyang Zhang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping Hospital, Army Medical University, Changjiang Branch Road 10, Daping Street, Yuzhong District, Chongqing, 400042, China
| | - Jin Deng
- Department of Emergency Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Jianxin Jiang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping Hospital, Army Medical University, Changjiang Branch Road 10, Daping Street, Yuzhong District, Chongqing, 400042, China.
| | - Anqiang Zhang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping Hospital, Army Medical University, Changjiang Branch Road 10, Daping Street, Yuzhong District, Chongqing, 400042, China.
| |
Collapse
|
31
|
|
32
|
Jordahl KM, Phipps AI, Randolph TW, Tindle HA, Liu S, Tinker LF, Kelsey KT, White E, Bhatti P. Differential DNA methylation in blood as a mediator of the association between cigarette smoking and bladder cancer risk among postmenopausal women. Epigenetics 2019; 14:1065-1073. [PMID: 31232174 DOI: 10.1080/15592294.2019.1631112] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Smoking accounts for approximately 52% of bladder cancer incidence among postmenopausal women, but the underlying mechanism is poorly understood. Our study investigates whether changes in DNA methylation, as measured in blood, mediate the impact of smoking on bladder cancer risk among postmenopausal women. We conducted analyses among 206 cases and 251 controls that were current or never smokers at baseline from a previous case-control study of bladder cancer and genome-wide DNA methylation nested within the Women's Health Initiative. Separate mediation analyses were conducted for three CpG sites demonstrating robust associations with smoking in prior methylome-wide association studies: cg05575921 (AhRR), cg03636183 (F2RL3), and cg19859270 (GPR15). We estimated causal effects using the regression-based, four-way decomposition approach, which addresses the interaction between smoking and each CpG site. The overall proportion of the excess relative risk mediated by cg05575921 was 92% (p-value = 0.004) and by cg19859270 was 79% (p-value = 0.02). The largest component of the excess relative risk of bladder cancer due to 30 pack-years of smoking history in current smokers was the mediated interaction for both cg05575921 (72%, p = 0.02) and cg19859270 (72%, p-value = 0.04), where the mediated interaction is the effect of smoking on bladder cancer that both acts through differential methylation and depends on smoking history. There was little evidence that smoking was mediated through cg03636183. Our results suggest that differential methylation of cg05575921 and cg19859270 mediate the effects of smoking on bladder cancer, potentially revealing downstream effects of smoking relevant for carcinogenesis.
Collapse
Affiliation(s)
- Kristina M Jordahl
- Department of Epidemiology, School of Public Health, University of Washington , Seattle , WA , USA.,Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Amanda I Phipps
- Department of Epidemiology, School of Public Health, University of Washington , Seattle , WA , USA.,Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Timothy W Randolph
- Program in Biostatistics, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Hilary A Tindle
- Department of Medicine, Vanderbilt University Medical Center , Nashville , TN , USA
| | - Simin Liu
- Departments of Epidemiology, Medicine, and Surgery, Brown University , Providence , RI , USA
| | - Lesley F Tinker
- Cancer Prevention Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Karl T Kelsey
- Departments of Epidemiology and Pathology and Laboratory Medicine, Brown University , Providence , RI , USA
| | - Emily White
- Department of Epidemiology, School of Public Health, University of Washington , Seattle , WA , USA.,Cancer Prevention Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA
| | - Parveen Bhatti
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center , Seattle , WA , USA.,Cancer Control Research, BC Cancer , Vancouver , BC , Canada
| |
Collapse
|
33
|
Li X, Yu M, Han L, Chen L, Zhang D, Zhou G, Zhao Q, Sun T. LINC00305 represses miR-124 expression to trigger inflammatory insults in the presence of lipopolysaccharide. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 47:2352-2360. [PMID: 31190561 DOI: 10.1080/21691401.2019.1624559] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Xiaoyan Li
- Department of Orthopaedics, Affiliated Hospital of Jining Medical University, Jining, China
| | - Manqiu Yu
- Department of Trauma Reconstruction, Shandong Wendeng Orthopaedic & Traumatic Hospital Weihai, China
| | - Liang Han
- Department of Orthopaedics, Affiliated Hospital of Jining Medical University, Jining, China
| | - Lei Chen
- Department of Orthopaedics, Affiliated Hospital of Jining Medical University, Jining, China
| | - Daxue Zhang
- Department of Orthopaedics, Affiliated Hospital of Jining Medical University, Jining, China
| | - Guannan Zhou
- Emergency Department, Jining No. 1 People’s Hospital, Jining, China
| | - Qiang Zhao
- Department of Orthopaedics, Jining No.1 People’s Hospital, Jining, China
| | - Taitao Sun
- Department of Orthopaedics, Jining No.1 People’s Hospital, Jining, China
- Department of Orthopaedics, Affiliated Jining No.1 People's Hospital of Jining Medical University, Jining Medical University, Jining, China
| |
Collapse
|
34
|
Castellanos-Rubio A, Ghosh S. Disease-Associated SNPs in Inflammation-Related lncRNAs. Front Immunol 2019; 10:420. [PMID: 30906297 PMCID: PMC6418042 DOI: 10.3389/fimmu.2019.00420] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 02/18/2019] [Indexed: 02/06/2023] Open
Abstract
Immune-mediated diseases, such as celiac disease, type 1 diabetes or multiple sclerosis, are a clinically heterogeneous group of diseases that share many key genetic triggers. Although the pathogenic mechanisms responsible for the development of immune mediated disorders is not totally understood, high-throughput genomic studies, such as GWAS and Immunochip, performed in the past few years have provided intriguing hints about underlying mechanisms and pathways that lead to disease. More than a hundred gene variants associated with disease susceptibility have been identified through such studies, but the progress toward understanding the underlying mechanisms has been slow. The majority of the identified risk variants are located in non-coding regions of the genome making it difficult to assign a molecular function to the SNPs. However, recent studies have revealed that many of the non-coding regions bearing disease-associated SNPs generate long non-coding RNAs (lncRNAs). LncRNAs have been implicated in several inflammatory diseases, and many of them have been shown to function as regulators of gene expression. Many of the disease associated SNPs located in lncRNAs modify their secondary structure, or influence expression levels, thereby affecting their regulatory function, hence contributing to the development of disease.
Collapse
Affiliation(s)
- Ainara Castellanos-Rubio
- Immunogenetics Research Laboratory, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, UPV/EHU, Leioa, Spain
- Functional Studies in Celiac Disease Group, BioCruces Health Research Institute, Barakaldo, Spain
| | - Sankar Ghosh
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
| |
Collapse
|
35
|
Miano JM, Long X, Lyu Q. CRISPR links to long noncoding RNA function in mice: A practical approach. Vascul Pharmacol 2019; 114:1-12. [PMID: 30822570 PMCID: PMC6435418 DOI: 10.1016/j.vph.2019.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/29/2022]
Abstract
Next generation sequencing has uncovered a trove of short noncoding RNAs (e.g., microRNAs) and long noncoding RNAs (lncRNAs) that act as molecular rheostats in the control of diverse homeostatic processes. Meanwhile, the tsunamic emergence of clustered regularly interspaced short palindromic repeats (CRISPR) editing has transformed our influence over all DNA-carrying entities, heralding global CRISPRization. This is evident in biomedical research where the ease and low-cost of CRISPR editing has made it the preferred method of manipulating the mouse genome, facilitating rapid discovery of genome function in an in vivo context. Here, CRISPR genome editing components are updated for elucidating lncRNA function in mice. Various strategies are highlighted for understanding the function of lncRNAs residing in intergenic sequence space, as host genes that harbor microRNAs or other genes, and as natural antisense, overlapping or intronic genes. Also discussed is CRISPR editing of mice carrying human lncRNAs as well as the editing of competing endogenous RNAs. The information described herein should assist labs in the rigorous design of experiments that interrogate lncRNA function in mice where complex disease processes can be modeled thus accelerating translational discovery.
Collapse
Affiliation(s)
- Joseph M Miano
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States of America.
| | - Xiaochun Long
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, United States of America
| | - Qing Lyu
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States of America
| |
Collapse
|
36
|
Jung M, Dodsworth M, Thum T. Inflammatory cells and their non-coding RNAs as targets for treating myocardial infarction. Basic Res Cardiol 2018; 114:4. [PMID: 30523422 PMCID: PMC6290728 DOI: 10.1007/s00395-018-0712-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 11/29/2018] [Indexed: 12/22/2022]
Abstract
Myocardial infarction triggers infiltration of several types of immune cells that coordinate both innate and adaptive immune responses. These play a dual role in post-infarction cardiac remodeling by initiating and resolving inflammatory processes, which needs to occur in a timely and well-orchestrated way to ensure a reestablishment of normalized cardiac functions. Thus, therapeutic modulation of immune responses might have benefits for infarct patients. While such strategies have shown great potential in treating cancer, applications in the post-infarction context have been disappointing. One challenge has been the complexity and plasticity of immune cells and their functions in cardiac regulation and healing. The types appear in patterns that are temporally and spatially distinct, while influencing each other and the surrounding tissue. A comprehensive understanding of the immune cell repertoire and their regulatory functions following infarction is sorely needed. Processes of cardiac remodeling trigger additional genetic changes that may also play critical roles in the aftermath of cardiovascular disease. Some of these changes involve non-coding RNAs that play crucial roles in the regulation of immune cells and may, therefore, be of therapeutic interest. This review summarizes what is currently known about the functions of immune cells and non-coding RNAs during post-infarction wound healing. We address some of the challenges that remain and describe novel therapeutic approaches under development that are based on regulating immune responses through non-coding RNAs in the aftermath of the disease.
Collapse
Affiliation(s)
- Mira Jung
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Michael Dodsworth
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
- National Heart and Lung Institute, Imperial College London, London, UK.
| |
Collapse
|
37
|
Wang H, Jin Z, Pei T, Song W, Gong Y, Chen D, Zhang L, Zhang M, Zhang G. Long noncoding RNAs C2dat1 enhances vascular smooth muscle cell proliferation and migration by targeting MiR‐34a‐5p. J Cell Biochem 2018; 120:3001-3008. [PMID: 30474870 DOI: 10.1002/jcb.27070] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 04/26/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Hairong Wang
- Department of Cardiology Zhongnan Hospital of Wuhan University Wuhan China
| | - Zhili Jin
- Hubei Univesity of Science and Technology Xianning Hubei China
| | - Tu Pei
- Department of Cardiology Zhongnan Hospital of Wuhan University Wuhan China
| | - Wenhao Song
- Department of Cardiology Zhongnan Hospital of Wuhan University Wuhan China
| | - Yao Gong
- Department of Cardiology Zhongnan Hospital of Wuhan University Wuhan China
| | - Deliang Chen
- Department of Cardiology Zhongnan Hospital of Wuhan University Wuhan China
| | - Lin Zhang
- Department of Cardiology Zhongnan Hospital of Wuhan University Wuhan China
| | - Meichun Zhang
- Department of Cardiology Zhongnan Hospital of Wuhan University Wuhan China
| | - Gangchen Zhang
- Asia Heart Disease Hospital, Wuhan University Wuhan China
| |
Collapse
|
38
|
Gary MA, Tanner EA, Davis AA, McFarlin BK. Combined bead-based multiplex detection of RNA and protein biomarkers: Implications for understanding the time course of skeletal muscle injury and repair. Methods 2018; 158:92-96. [PMID: 30472250 DOI: 10.1016/j.ymeth.2018.11.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/15/2018] [Accepted: 11/21/2018] [Indexed: 01/14/2023] Open
Abstract
Biological response to skeletal muscle injury time course is generally classified as initial (elevated within first 4-h), delayed (elevated at 24-h), and/or prolonged (elevated at 4-h and sustained to 24-h). Accurate description of this process requires the ability to measure a robust set of RNA and protein biomarkers, yet such an approach is not common and not always feasible. This method proposes a novel experimental approach that focuses on the use of bead-based multiplex detection to measure mRNA, lncRNA, cytokines, soluble cytokine receptors, and myokines at 4-h and 24-h post muscle injury. We used an extreme aerobic exercise session (half-marathon race) to create a consistent muscle injury stimulus via oxidative stress and eccentric contractions. Venous blood samples were analyzed to determine the change in 90 targets. Specifically, we identified 14 mRNA, 2 lncRNA, 4 cytokines, and 5 myokines that had only an initial response (change at 4-h). We identified 2 mRNA, 2 cytokines, 13 soluble cytokine receptors, and 1 myokine that had only a delayed response (change at 24-h). Finally, we identified 18 mRNA, 4 lncRNA, 6 myokines and 15 cytokines that had a prolonged response (change at 4-h and sustained at 24-h). We found 4 targets to be undetectable or having no response relative to muscle injury recovery. These findings demonstrate the interplay between RNA and protein biomarkers in response to skeletal muscle injury. This novel experimental application of bead-based multiplexing is applicable to a variety of clinical models that involve muscle injury and/or wasting.
Collapse
Affiliation(s)
- Melody A Gary
- Applied Physiology Laboratory, University of North Texas, Denton, TX, USA; Department of Biological Sciences, University of North Texas, Denton, TX, USA
| | - Elizabeth A Tanner
- Applied Physiology Laboratory, University of North Texas, Denton, TX, USA; Department of Biological Sciences, University of North Texas, Denton, TX, USA
| | - Asheal A Davis
- Applied Physiology Laboratory, University of North Texas, Denton, TX, USA
| | - Brian K McFarlin
- Applied Physiology Laboratory, University of North Texas, Denton, TX, USA; Department of Biological Sciences, University of North Texas, Denton, TX, USA.
| |
Collapse
|
39
|
Wang Z, Zhu T, Ma W, Wang N, Qu G, Zhang S, Wang J. Genome-wide analysis of long non-coding RNAs in Catalpa bungei and their potential function in floral transition using high-throughput sequencing. BMC Genet 2018; 19:86. [PMID: 30236060 PMCID: PMC6149005 DOI: 10.1186/s12863-018-0671-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 09/10/2018] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) have crucial roles in various biological regulatory processes. However, the study of lncRNAs is limited in woody plants. Catalpa bungei is a valuable ornamental tree with a long cultivation history in China, and a deeper understanding of the floral transition mechanism in C. bungei would be interesting from both economic and scientific perspectives. RESULTS In this study, we categorized C. bungei buds from early flowering (EF) and normal flowering (NF) varieties into three consecutive developmental stages. These buds were used to systematically study lncRNAs during floral transition using high-throughput sequencing to identify molecular regulatory networks. Quantitative real-time PCR was performed to study RNA expression changes in different stages. In total, 12,532 lncRNAs and 26,936 messenger RNAs (mRNAs) were detected. Moreover, 680 differentially expressed genes and 817 differentially expressed lncRNAs were detected during the initiation of floral transition. The results highlight the mRNAs and lncRNAs that may be involved in floral transition, as well as the many lncRNAs serving as microRNA precursors. We predicted the functions of lncRNAs by analysing the relationships between lncRNAs and mRNAs. Seven lncRNA-mRNA interaction pairs may participate in floral transition. CONCLUSIONS This study is the first to identify lncRNAs and their potential functions in floral transition, providing a starting point for detailed determination of the functions of lncRNAs in C. bungei.
Collapse
Affiliation(s)
- Zhi Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Haidian District, Dongxiaofu 1#, Beijing, 100091 People’s Republic of China
| | - Tianqing Zhu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Haidian District, Dongxiaofu 1#, Beijing, 100091 People’s Republic of China
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Haidian District, Dongxiaofu 1#, Beijing, 100091 People’s Republic of China
| | - Nan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Haidian District, Dongxiaofu 1#, Beijing, 100091 People’s Republic of China
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, Harbin, 150040 People’s Republic of China
| | - Shougong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Haidian District, Dongxiaofu 1#, Beijing, 100091 People’s Republic of China
| | - Junhui Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Haidian District, Dongxiaofu 1#, Beijing, 100091 People’s Republic of China
| |
Collapse
|
40
|
He J, Tu C, Liu Y. Role of lncRNAs in aging and age-related diseases. Aging Med (Milton) 2018; 1:158-175. [PMID: 31942494 PMCID: PMC6880696 DOI: 10.1002/agm2.12030] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/28/2018] [Accepted: 07/03/2018] [Indexed: 01/10/2023] Open
Abstract
Aging is progressive physiological degeneration and consequently declined function, which is linked to senescence on both cellular and organ levels. Accumulating studies indicate that long noncoding RNAs (lncRNAs) play important roles in cellular senescence at all levels-transcriptional, post-transcriptional, translational, and post-translational. Understanding the molecular mechanism of lncRNAs underlying senescence could facilitate interpretation and intervention of aging and age-related diseases. In this review, we describe categories of known and novel lncRNAs that have been involved in the progression of senescence. We also identify the lncRNAs implicated in diseases arising from age-driven degeneration or dysfunction in some representative organs and systems (brains, liver, muscle, cardiovascular system, bone pancreatic islets, and immune system). Improved comprehension of lncRNAs in the aging process on all levels, from cell to organismal, may provide new insights into the amelioration of age-related pathologies and prolonged healthspan.
Collapse
Affiliation(s)
- Jieyu He
- Department of GeriatricsThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Chao Tu
- Department of OrthopedicsThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Youshuo Liu
- Department of GeriatricsThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| |
Collapse
|
41
|
Donaldson CJ, Lao KH, Zeng L. The salient role of microRNAs in atherogenesis. J Mol Cell Cardiol 2018; 122:98-113. [DOI: 10.1016/j.yjmcc.2018.08.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 08/05/2018] [Accepted: 08/06/2018] [Indexed: 12/17/2022]
|
42
|
Qureshi AA, Khan DA, Mushtaq S, Ye SQ, Xiong M, Qureshi N. δ-Tocotrienol feeding modulates gene expression of EIF2, mTOR, protein ubiquitination through multiple-signaling pathways in chronic hepatitis C patients. Lipids Health Dis 2018; 17:167. [PMID: 30031388 PMCID: PMC6054847 DOI: 10.1186/s12944-018-0804-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 06/26/2018] [Indexed: 12/12/2022] Open
Abstract
Background δ-Tocotrienol is a naturally occurring proteasome inhibitor, which has the capacity to inhibit proliferation and induce apoptosis in several cancer cells obtained from several organs of humans, and other cancer cell lines. Moreover, results of plasma total mRNAs after δ-tocotrienol feeding to hepatitis C patients revealed significant inhibition in the expression of pro-inflammatory cytokines (TNF-α, VCAM1, proteasome subunits) and induction in the expression of ICAM1 and IFN-γ after post-treatment. This down-regulation of proteasome subunits leads to autophagy, apoptosis of immune cells and several genes. The present study describes RNA-sequence analysis of plasma total mRNAs obtained from δ-tocotrienol treatment of hepatitis C patients on gene expression regulated by proteasome. Methods Pooled specimens of plasma total mRNAs of pre-dose versus post-dose of δ-tocotrienol treatment of hepatitis C patients were submitted to RNA-sequence analyses. The data based on > 1 and 8-fold expression changes of 2136 genes were uploaded into “Ingenuity Pathway Analyses (IPA)” for core analysis, which describes possible canonical pathways, upstream regulators, diseases and functional metabolic networks. Results The IPA of “molecules” indicated fold change in gene expression of 953 molecules, which covered several categories of biological biomarkers. Out of these, gene expression of 220 related to present study, 12 were up-regulated, and 208 down-regulated after δ-tocotrienol treatment. The gene expression of transcription regulators (ceramide synthase 3 and Mohawk homeobox) were up-regulated, and gene expression of 208 molecules were down-regulated, involved in several biological functions (HSP90AB1, PSMC3, CYB5R4, NDUFB1, CYP2R1, TNFRF1B, VEGFA, GPR65, PIAS1, SFPQ, GPS2, EIF3F, GTPBP8, EIF4A1, HSPA14, TLR8, TUSSC2). IPA of “causal network” indicated gene regulators (676), in which 76 down-regulated (26 s proteasomes, interleukin cytokines, and PPAR-ligand-PPA-Retinoic acid-RXRα, PPARγ-ligand-PPARγ-Retinoic acid-RARα, IL-21, IL-23) with significant P-values. The IPA of “diseases and functions” regulators (85) were involved with cAMP, STAT2, 26S proteasome, CSF1, IFNγ, LDL, TGFA, and microRNA-155-5p, miR-223, miR-21-5p. The IPA of “upstream analysis” (934) showed 57 up-regulated (mainly 38 microRNAs) and 64 gene regulators were down-regulated (IL-2, IL-5, IL-6, IL-12, IL-13, IL-15, IL-17, IL-18, IL-21, IL-24, IL-27, IL-32), interferon β-1a, interferon γ, TNF-α, STAT2, NOX1, prostaglandin J2, NF-κB, 1κB, TCF3, and also miRNA-15, miRNA-124, miRNA-218-5P with significant activation of Z-Score (P < 0.05). Conclusions This is first report describing RNA-sequence analysis of δ-tocotrienol treated plasma total mRNAs obtained from chronic hepatitis C patients, that acts via multiple-signaling pathways without any side-effects. These studies may lead to development of novel classes of drugs for treatment of chronic hepatitis C patients. Electronic supplementary material The online version of this article (10.1186/s12944-018-0804-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Asaf A Qureshi
- Department of Biomedical Science, School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA.
| | - Dilshad A Khan
- Department of Chemical Pathology and Endocrinology, Armed Forces Institute of Pathology (AFIP), National University of Medical Sciences, Rawalpindi, 64000, Pakistan
| | - Shahida Mushtaq
- Department of Chemical Pathology and Endocrinology, Armed Forces Institute of Pathology (AFIP), National University of Medical Sciences, Rawalpindi, 64000, Pakistan
| | - Shui Qing Ye
- Department of Biomedical Science, School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA.,Division of Experimental and Translational Genetics, Department of Pediatrics, Childern's Mercy Hospital, 2401 Gillham Road, Kansas City, MO, 64108, USA.,Department of Biomedical and Health Informatics, School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA
| | - Min Xiong
- Department of Biomedical Science, School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA.,Division of Experimental and Translational Genetics, Department of Pediatrics, Childern's Mercy Hospital, 2401 Gillham Road, Kansas City, MO, 64108, USA
| | - Nilofer Qureshi
- Department of Biomedical Science, School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA.,Pharmacology/Toxicology, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO, 64108, USA
| |
Collapse
|
43
|
Wan M, Bennett BD, Pittman GS, Campbell MR, Reynolds LM, Porter DK, Crowl CL, Wang X, Su D, Englert NA, Thompson IJ, Liu Y, Bell DA. Identification of Smoking-Associated Differentially Methylated Regions Using Reduced Representation Bisulfite Sequencing and Cell type-Specific Enhancer Activation and Gene Expression. ENVIRONMENTAL HEALTH PERSPECTIVES 2018; 126:047015. [PMID: 29706059 PMCID: PMC6071796 DOI: 10.1289/ehp2395] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 03/22/2018] [Accepted: 03/22/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Cigarette smoke is a causal factor in cancers and cardiovascular disease. Smoking-associated differentially methylated regions (SM-DMRs) have been observed in disease studies, but the causal link between altered DNA methylation and transcriptional change is obscure. OBJECTIVE Our objectives were to finely resolve SM-DMRs and to interrogate the mechanistic link between SM-DMRs and altered transcription of enhancer noncoding RNA (eRNA) and mRNA in human circulating monocytes. METHOD We integrated SM-DMRs identified by reduced representation bisulfite sequencing (RRBS) of circulating CD14+ monocyte DNA collected from two independent human studies [n=38 from Clinical Research Unit (CRU) and n=55 from the Multi-Ethnic Study of Atherosclerosis (MESA), about half of whom were active smokers] with gene expression for protein-coding genes and noncoding RNAs measured by RT-PCR or RNA sequencing. Candidate SM-DMRs were compared with RRBS of purified CD4+ T cells, CD8+ T cells, CD15+ granulocytes, CD19+ B cells, and CD56+ NK cells (n=19 females, CRU). DMRs were validated using pyrosequencing or bisulfite amplicon sequencing in up to 85 CRU volunteers, who also provided saliva DNA. RESULTS RRBS identified monocyte SM-DMRs frequently located in putative gene regulatory regions. The most significant monocyte DMR occurred at a poised enhancer in the aryl-hydrocarbon receptor repressor gene (AHRR) and it was also detected in both granulocytes and saliva DNA. To our knowledge, we identify for the first time that SM-DMRs in or near AHRR, C5orf55-EXOC-AS, and SASH1 were associated with increased noncoding eRNA as well as mRNA in monocytes. Functionally, the AHRR SM-DMR appeared to up-regulate AHRR mRNA through activating the AHRR enhancer, as suggested by increased eRNA in the monocytes, but not granulocytes, from smokers compared with nonsmokers. CONCLUSIONS Our findings suggest that AHRR SM-DMR up-regulates AHRR mRNA in a monocyte-specific manner by activating the AHRR enhancer. Cell type-specific activation of enhancers at SM-DMRs may represent a mechanism driving smoking-related disease. https://doi.org/10.1289/EHP2395.
Collapse
Affiliation(s)
- Ma Wan
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Brian D Bennett
- Integrative Bioinformatics Support Group, NIEHS, NIH, DHHS, Research Triangle Park, North Carolina, USA
| | - Gary S Pittman
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Michelle R Campbell
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Lindsay M Reynolds
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Devin K Porter
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Christopher L Crowl
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Xuting Wang
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Dan Su
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Neal A Englert
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Isabel J Thompson
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Douglas A Bell
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| |
Collapse
|
44
|
Ishihara Y, Tsuji M, Vogel CFA. Suppressive effects of aryl-hydrocarbon receptor repressor on adipocyte differentiation in 3T3-L1 cells. Arch Biochem Biophys 2018; 642:75-80. [PMID: 29432714 DOI: 10.1016/j.abb.2018.01.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/16/2018] [Accepted: 01/31/2018] [Indexed: 12/28/2022]
Abstract
The aryl-hydrocarbon receptor repressor (AhRR) negatively regulates aryl-hydrocarbon receptor (AhR) signaling via its inhibitory transactivation. AhR is well known to suppress adipocyte differentiation, but the function of AhRR during adipogenesis is unclear. The purpose of this study was to investigate the role of AhRR in adipocyte differentiation using 3T3-L1 cells. During the early phase of differentiation, AhRR expression was transiently induced, but throughout the entire differentiation process, low levels of AhR expression were maintained. AhRR knockdown significantly increased not only glycerol-3-phosphate dehydrogenase (GPDH) activity but also lipid accumulation inside the cells. AhRR overexpression clearly reduced GPDH activity and lipid accumulation, indicating that AhRR upregulation during the early stage of adipogenesis suppresses adipocyte differentiation. Since AhRR knockdown increases the expression and activity of peroxisome proliferator-activated receptor γ (PPARγ), AhRR negatively regulates PPARγ during adipogenesis. In summary, similar to AhR, AhRR acts as an inhibitor of adipocyte differentiation. In addition to controlling the negative feedback loop of AhR, AhRR might be involved in other functions, especially in adipocyte differentiation processes.
Collapse
Affiliation(s)
- Yasuhiro Ishihara
- Center for Health and the Environment, University of California, Davis, Davis, CA, 95616, USA; Graduate School of Integrated Arts and Sciences, Hiroshima University, Hiroshima, 739-8521, Japan.
| | - Mayumi Tsuji
- Center for Health and the Environment, University of California, Davis, Davis, CA, 95616, USA; Department of Environmental Health, University of Occupational and Environmental Health, Fukuoka, 807-8555, Japan
| | - Christoph F A Vogel
- Center for Health and the Environment, University of California, Davis, Davis, CA, 95616, USA; Department of Environmental Toxicology, University of California, Davis, Davis, CA, 95616, USA
| |
Collapse
|
45
|
Simion V, Haemmig S, Feinberg MW. LncRNAs in vascular biology and disease. Vascul Pharmacol 2018; 114:145-156. [PMID: 29425892 DOI: 10.1016/j.vph.2018.01.003] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 01/09/2018] [Accepted: 01/16/2018] [Indexed: 12/14/2022]
Abstract
Accumulating studies indicate that long non-coding RNAs (lncRNAs) play important roles in the regulation of diverse biological processes involved in homeostatic control of the vessel wall in health and disease. However, our knowledge of the mechanisms by which lncRNAs control gene expression and cell signaling pathways is still nascent. Furthermore, only a handful of lncRNAs has been functionally evaluated in response to pathophysiological stimuli or in vascular disease states. For example, lncRNAs may regulate endothelial dysfunction by modulating endothelial cell proliferation (e.g. MALAT1, H19) or angiogenesis (e.g. MEG3, MANTIS). LncRNAs have also been implicated in modulating vascular smooth muscle cell (VSMC) phenotypes or vascular remodeling (e.g. ANRIL, SMILR, SENCR, MYOSLID). Finally, emerging studies have implicated lncRNAs in leukocytes activation (e.g. lincRNA-Cox2, linc00305, THRIL), macrophage polarization (e.g. GAS5), and cholesterol metabolism (e.g. LeXis). This review summarizes recent findings on the expression, mechanism, and function of lncRNAs implicated in a range of vascular disease states from mice to human subjects. An improved understanding of lncRNAs in vascular disease may provide new pathophysiological insights and opportunities for the generation of a new class of RNA-based biomarkers and therapeutic targets.
Collapse
Affiliation(s)
- Viorel Simion
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stefan Haemmig
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mark W Feinberg
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
46
|
Shi Z, Pan B, Feng S. The emerging role of long non-coding RNA in spinal cord injury. J Cell Mol Med 2018; 22:2055-2061. [PMID: 29392896 PMCID: PMC5867120 DOI: 10.1111/jcmm.13515] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 11/16/2017] [Indexed: 12/13/2022] Open
Abstract
Spinal cord injury (SCI) is a significant health burden worldwide which causes permanent neurological deficits, and there are approximately 17,000 new cases each year. However, there are no effective and current treatments that lead to functional recovery because of the limited understanding of the pathogenic mechanism of SCI. In recent years, the biological roles of long non-coding RNAs (lncRNAs) in SCI have attracted great attention from the researchers all over the world, and an increasing number of studies have investigated the regulatory roles of lncRNAs in SCI. In this review, we summarized the biogenesis, classification and function of lncRNAs and focused on the investigations on the roles of lncRNAs involved in the pathogenic processes of SCI, including neuronal loss, astrocyte proliferation and activation, demyelination, microglia activation, inflammatory reaction and angiogenesis. This review will help understand the molecular mechanisms of SCI and facilitate the potential use of lncRNAs as diagnostic markers and therapeutic targets for SCI treatment.
Collapse
Affiliation(s)
- Zhongju Shi
- Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Bin Pan
- Department of Orthopaedics, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Shiqing Feng
- Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, China
| |
Collapse
|
47
|
Emerging Roles for Epigenetic Programming in the Control of Inflammatory Signaling Integration in Heath and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1024:63-90. [PMID: 28921465 DOI: 10.1007/978-981-10-5987-2_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Macrophages and dendritic cells initiate the innate immune response to infection and injury and contribute to inflammatory signaling to maintain the homeostasis of various tissues, which includes resident macrophages for the elimination of invading microorganisms and tissue damage. Inappropriate inflammatory signaling can lead to persistent inflammation and further develop into autoimmune and inflammation-associated diseases. Inflammatory signaling pathways have been well characterized, but how these signaling pathways are converted into sustained and diverse patterns of expression of cytokines, chemokines, and other genes in response to environmental challenges is unclear. Emerging evidence suggests the important role of epigenetic mechanisms in finely tuning the outcome of the host innate immune response. An understanding of epigenetic regulation of innate immune cell identity and function will enable the identification of the mechanism between gene-specific host defenses and inflammatory disease and will also allow for exploration of the program of innate immune memory in health and disease. This information could be used to develop therapeutic agents to enhance the host response, preventing chronic inflammation through preserving tissues and signaling integrity.
Collapse
|