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Xiao B, Liang Y, Liu G, Wang L, Zhang Z, Qiu L, Xu H, Carr S, Shi X, Reis RL, Kundu SC, Zhu Z. Gas-propelled nanomotors alleviate colitis through the regulation of intestinal immunoenvironment-hematopexis-microbiota circuits. Acta Pharm Sin B 2024; 14:2732-2747. [PMID: 38828144 PMCID: PMC11143748 DOI: 10.1016/j.apsb.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/05/2023] [Accepted: 12/18/2023] [Indexed: 06/05/2024] Open
Abstract
The progression of ulcerative colitis (UC) is associated with immunologic derangement, intestinal hemorrhage, and microbiota imbalance. While traditional medications mainly focus on mitigating inflammation, it remains challenging to address multiple symptoms. Here, a versatile gas-propelled nanomotor was constructed by mild fusion of post-ultrasonic CaO2 nanospheres with Cu2O nanoblocks. The resulting CaO2-Cu2O possessed a desirable diameter (291.3 nm) and a uniform size distribution. It could be efficiently internalized by colonic epithelial cells and macrophages, scavenge intracellular reactive oxygen/nitrogen species, and alleviate immune reactions by pro-polarizing macrophages to the anti-inflammatory M2 phenotype. This nanomotor was found to penetrate through the mucus barrier and accumulate in the colitis mucosa due to the driving force of the generated oxygen bubbles. Rectal administration of CaO2-Cu2O could stanch the bleeding, repair the disrupted colonic epithelial layer, and reduce the inflammatory responses through its interaction with the genes relevant to blood coagulation, anti-oxidation, wound healing, and anti-inflammation. Impressively, it restored intestinal microbiota balance by elevating the proportions of beneficial bacteria (e.g., Odoribacter and Bifidobacterium) and decreasing the abundances of harmful bacteria (e.g., Prevotellaceae and Helicobacter). Our gas-driven CaO2-Cu2O offers a promising therapeutic platform for robust treatment of UC via the rectal route.
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Affiliation(s)
- Bo Xiao
- Department of Gastroenterology, the First Affiliated Hospital of Nanchang University, Nanchang 330006, China
- College of Sericulture, Textile, and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Yuqi Liang
- College of Sericulture, Textile, and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Ga Liu
- College of Sericulture, Textile, and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Lingshuang Wang
- College of Sericulture, Textile, and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Zhan Zhang
- Department of Neurology, School of Medicine, Emory University, Atlanta, GA 30322, USA
- Atlanta Veterans Affairs Medical Center, Decatur, GA 30033, USA
| | - Libin Qiu
- College of Sericulture, Textile, and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Haiting Xu
- College of Sericulture, Textile, and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Sean Carr
- Atlanta Veterans Affairs Medical Center, Decatur, GA 30033, USA
- Department of Surgery, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Xiaoxiao Shi
- College of Sericulture, Textile, and Biomass Sciences, Southwest University, Chongqing 400715, China
| | - Rui L. Reis
- 3Bs Research Group, I3Bs — Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Barco, Guimaraes 4805-017, Portugal
| | - Subhas C. Kundu
- 3Bs Research Group, I3Bs — Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Barco, Guimaraes 4805-017, Portugal
| | - Zhenghua Zhu
- Department of Gastroenterology, the First Affiliated Hospital of Nanchang University, Nanchang 330006, China
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2
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Duraisamy K, Kumar M, Nawabjan A, Lo EKK, Hui Lin M, Lefranc B, Bonnafé E, Treilhou M, El-Nezami H, Leprince J, Chow BKC. MRGPRB2/X2 and the analogous effects of its agonist and antagonist in DSS-induced colitis in mice. Biomed Pharmacother 2024; 174:116471. [PMID: 38547764 DOI: 10.1016/j.biopha.2024.116471] [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: 10/23/2023] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 05/01/2024] Open
Abstract
The mast cell receptor Mrgprb2, a mouse orthologue of human Mrgprx2, is known as an inflammatory receptor and its elevated expression is associated with various diseases such as ulcerative colitis. We aimed to elucidate the role of Mrgprb2/x2 and the effect of its ligands on a chemically induced murine colitis model. We showed that in Mrgprb2-/- mice, there is a differential regulation of cytokine releases in the blood plasma and severe colonic damages after DSS treatment. Unexpectedly, we demonstrated that known Mrgprb2/x2 agonists (peptide P17, P17 analogues and CST-14) and antagonist (GE1111) similarly increased the survival rate of WT mice subjected to 4% DSS-induced colitis, ameliorated the colonic damages of 2.5% DSS-induced colitis, restored major protein mRNA expression involved in colon integrity, reduced CD68+ and F4/80+ immune cell infiltration and restored cytokine levels. Collectively, our findings highlight the eminent role of Mrpgrb2/x2 in conferring a beneficial effect in the colitis model, and this significance is demonstrated by the heightened severity of colitis with altered cytokine releases and inflammatory immune cell infiltration observed in the Mrgprb2 knockout mice. Elevated expression of Mrgprb2 in WT colitis murine models may represent the organism's adaptive protective mechanism since Mrgprb2 knockout results in severe colitis. On the other hand, both agonist and antagonist of Mrgprb2 analogously mitigated the severity of colitis in DSS-induced colitis model by altering Mrgprb2 expression, immune cell infiltration and inflammatory cytokine releases.
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Affiliation(s)
- Karthi Duraisamy
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China; INSERM U1239 NorDiC, PRIMACEN, Université Rouen Normandie, Rouen, France
| | - Mukesh Kumar
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Abdullah Nawabjan
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Emily Kwun Kwan Lo
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Ming Hui Lin
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Benjamin Lefranc
- INSERM U1239 NorDiC, PRIMACEN, Université Rouen Normandie, Rouen, France
| | - Elsa Bonnafé
- EA7417 BTSB, Université Fédérale Toulouse Midi-Pyrénées, INU Champollion, Albi, France
| | - Michel Treilhou
- EA7417 BTSB, Université Fédérale Toulouse Midi-Pyrénées, INU Champollion, Albi, France
| | - Hani El-Nezami
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China; Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Jérôme Leprince
- INSERM U1239 NorDiC, PRIMACEN, Université Rouen Normandie, Rouen, France.
| | - Billy K C Chow
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China.
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3
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Liew F, Efstathiou C, Fontanella S, Richardson M, Saunders R, Swieboda D, Sidhu JK, Ascough S, Moore SC, Mohamed N, Nunag J, King C, Leavy OC, Elneima O, McAuley HJC, Shikotra A, Singapuri A, Sereno M, Harris VC, Houchen-Wolloff L, Greening NJ, Lone NI, Thorpe M, Thompson AAR, Rowland-Jones SL, Docherty AB, Chalmers JD, Ho LP, Horsley A, Raman B, Poinasamy K, Marks M, Kon OM, Howard LS, Wootton DG, Quint JK, de Silva TI, Ho A, Chiu C, Harrison EM, Greenhalf W, Baillie JK, Semple MG, Turtle L, Evans RA, Wain LV, Brightling C, Thwaites RS, Openshaw PJM. Large-scale phenotyping of patients with long COVID post-hospitalization reveals mechanistic subtypes of disease. Nat Immunol 2024; 25:607-621. [PMID: 38589621 PMCID: PMC11003868 DOI: 10.1038/s41590-024-01778-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 02/06/2024] [Indexed: 04/10/2024]
Abstract
One in ten severe acute respiratory syndrome coronavirus 2 infections result in prolonged symptoms termed long coronavirus disease (COVID), yet disease phenotypes and mechanisms are poorly understood1. Here we profiled 368 plasma proteins in 657 participants ≥3 months following hospitalization. Of these, 426 had at least one long COVID symptom and 233 had fully recovered. Elevated markers of myeloid inflammation and complement activation were associated with long COVID. IL-1R2, MATN2 and COLEC12 were associated with cardiorespiratory symptoms, fatigue and anxiety/depression; MATN2, CSF3 and C1QA were elevated in gastrointestinal symptoms and C1QA was elevated in cognitive impairment. Additional markers of alterations in nerve tissue repair (SPON-1 and NFASC) were elevated in those with cognitive impairment and SCG3, suggestive of brain-gut axis disturbance, was elevated in gastrointestinal symptoms. Severe acute respiratory syndrome coronavirus 2-specific immunoglobulin G (IgG) was persistently elevated in some individuals with long COVID, but virus was not detected in sputum. Analysis of inflammatory markers in nasal fluids showed no association with symptoms. Our study aimed to understand inflammatory processes that underlie long COVID and was not designed for biomarker discovery. Our findings suggest that specific inflammatory pathways related to tissue damage are implicated in subtypes of long COVID, which might be targeted in future therapeutic trials.
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Affiliation(s)
- Felicity Liew
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Sara Fontanella
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Matthew Richardson
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Ruth Saunders
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Dawid Swieboda
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Jasmin K Sidhu
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Stephanie Ascough
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Shona C Moore
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Noura Mohamed
- The Imperial Clinical Respiratory Research Unit, Imperial College NHS Trust, London, UK
| | - Jose Nunag
- Cardiovascular Research Team, Imperial College Healthcare NHS Trust, London, UK
| | - Clara King
- Cardiovascular Research Team, Imperial College Healthcare NHS Trust, London, UK
| | - Olivia C Leavy
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Omer Elneima
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Hamish J C McAuley
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Aarti Shikotra
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Amisha Singapuri
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Marco Sereno
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Victoria C Harris
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Linzy Houchen-Wolloff
- Centre for Exercise and Rehabilitation Science, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK
| | - Neil J Greening
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Nazir I Lone
- Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Matthew Thorpe
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - A A Roger Thompson
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Sarah L Rowland-Jones
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Annemarie B Docherty
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - James D Chalmers
- University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Ling-Pei Ho
- MRC Human Immunology Unit, University of Oxford, Oxford, UK
| | - Alexander Horsley
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Betty Raman
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Michael Marks
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
- Hospital for Tropical Diseases, University College London Hospital, London, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Onn Min Kon
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Luke S Howard
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Daniel G Wootton
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jennifer K Quint
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Antonia Ho
- MRC Centre for Virus Research, School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Christopher Chiu
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Ewen M Harrison
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
| | - William Greenhalf
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - J Kenneth Baillie
- Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
- Pandemic Science Hub, University of Edinburgh, Edinburgh, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- The Pandemic Institute, University of Liverpool, Liverpool, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- The Pandemic Institute, University of Liverpool, Liverpool, UK
| | - Rachael A Evans
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Louise V Wain
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Christopher Brightling
- Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Ryan S Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK.
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4
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Tan L, Li X, Qin H, Zhang Q, Wang J, Chen T, Zhang C, Zhang X, Tan Y. Identified S100A9 as a target for diagnosis and treatment of ulcerative colitis by bioinformatics analysis. Sci Rep 2024; 14:5517. [PMID: 38448514 PMCID: PMC10917761 DOI: 10.1038/s41598-024-55944-3] [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: 10/23/2023] [Accepted: 02/29/2024] [Indexed: 03/08/2024] Open
Abstract
Ulcerative colitis (UC) is a chronic, recurrent inflammatory bowel disease. UC confronts with severe challenges including the unclear pathogenesis and lack of specific diagnostic markers, demanding for identifying predictive biomarkers for UC diagnosis and treatment. We perform immune infiltration and weighted gene co-expression network analysis on gene expression profiles of active UC, inactive UC, and normal controls to identify UC related immune cell and hub genes. Neutrophils, M1 macrophages, activated dendritic cells, and activated mast cells are significantly enriched in active UC. MMP-9, CHI3L1, CXCL9, CXCL10, CXCR2 and S100A9 are identified as hub genes in active UC. Specifically, S100A9 is significantly overexpressed in mice with colitis. The receiver operating characteristic curve demonstrates the excellent performance of S100A9 expression in diagnosing active UC. Inhibition of S100A9 expression reduces DSS-induced colonic inflammation. These identified biomarkers associated with activity in UC patients enlighten the new insights of UC diagnosis and treatment.
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Affiliation(s)
- Lulu Tan
- The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People' Hospital, Yichang, 443000, China
| | - Xin Li
- Wuhan Asia Heart Hospital, Wuhan, 430022, China
| | - Hong Qin
- The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People' Hospital, Yichang, 443000, China
| | - Qingqing Zhang
- Haiyan County Hospital of Traditional Chinese Medicine, Jiaxing, 314399, China
| | - Jinfeng Wang
- The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People' Hospital, Yichang, 443000, China
| | - Tao Chen
- The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People' Hospital, Yichang, 443000, China
| | - Chengwu Zhang
- The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People' Hospital, Yichang, 443000, China
| | - Xiaoying Zhang
- The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People' Hospital, Yichang, 443000, China.
| | - Yuyan Tan
- The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People' Hospital, Yichang, 443000, China.
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5
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Chen C, Beloqui A, Xu Y. Oral nanomedicine biointeractions in the gastrointestinal tract in health and disease. Adv Drug Deliv Rev 2023; 203:115117. [PMID: 37898337 DOI: 10.1016/j.addr.2023.115117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/03/2023] [Accepted: 10/21/2023] [Indexed: 10/30/2023]
Abstract
Oral administration is the preferred route of administration based on the convenience for and compliance of the patient. Oral nanomedicines have been developed to overcome the limitations of free drugs and overcome gastrointestinal (GI) barriers, which are heterogeneous across healthy and diseased populations. This review aims to provide a comprehensive overview and comparison of the oral nanomedicine biointeractions in the gastrointestinal tract (GIT) in health and disease (GI and extra-GI diseases) and highlight emerging strategies that exploit these differences for oral nanomedicine-based treatment. We introduce the key GI barriers related to oral delivery and summarize their pathological changes in various diseases. We discuss nanomedicine biointeractions in the GIT in health by describing the general biointeractions based on the type of oral nanomedicine and advanced biointeractions facilitated by advanced strategies applied in this field. We then discuss nanomedicine biointeractions in different diseases and explore how pathological characteristics have been harnessed to advance the development of oral nanomedicine.
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Affiliation(s)
- Cheng Chen
- UCLouvain, Université catholique de Louvain, Louvain Drug Research Institute, Advanced Drug Delivery and Biomaterials, 1200 Brussels, Belgium
| | - Ana Beloqui
- UCLouvain, Université catholique de Louvain, Louvain Drug Research Institute, Advanced Drug Delivery and Biomaterials, 1200 Brussels, Belgium; WEL Research Institute, avenue Pasteur, 6, 1300 Wavre, Belgium.
| | - Yining Xu
- Department of Pharmacy, Institute of Metabolic Diseases and Pharmacotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Department of Clinical Pharmacy and Pharmacy Administration, West China School of Pharmacy, Sichuan University, Chengdu 610041, China.
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6
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Wang F, Su Q, Li C. Identification of cuproptosis-related asthma diagnostic genes by WGCNA analysis and machine learning. J Asthma 2023; 60:2052-2063. [PMID: 37289763 DOI: 10.1080/02770903.2023.2213334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 05/08/2023] [Indexed: 06/10/2023]
Abstract
OBJECTIVE Cuproptosis is the latest novel form of cell death. However, the relationship between asthma and cuproptosis is not fully understood. METHODS In this study, we screened differentially expressed cuproptosis-related genes from the Gene Expression Omnibus (GEO) database and performed immune infiltration analysis. Subsequently, patients with asthma were typed and analyzed by Kyoto Encyclopedia of Genes and Genomes (KEGG). Weighted gene co-expression network analysis (WGCNA) was performed to calculate the module-trait correlations, and the hub genes of the intersection were taken to construct machine learning (XGB, SVM, RF, GLM). Finally, we used TGF-β to establish a BEAS-2B asthma model to observe the expression levels of hub genes. RESULTS Six cuproptosis-related genes were obtained. Immune-infiltration analysis shows that cuproptosis-related genes are associated with a variety of biological functions. We classified asthma patients into two subtypes based on the expression of cuproptosis-related genes and found significant Gene Ontology (GO) and immune function differences between the different subtypes. WGCNA selected 2 significant modules associated with disease features and typing. Finally, we identified TRIM25, DYSF, NCF4, ABTB1, CXCR1 as asthma biomarkers by taking the intersection of the hub genes of the 2 modules and constructing a 5-genes signature, which nomograph, decision curve analysis (DCA) and calibration curves, receiver operating characteristic curve (ROC) showed high efficiency in diagnosing the probability of survival of asthma patients. Finally, in vitro experiments have shown that DYSF and CXCR1 expression is up expressed in asthma. CONCLUSIONS Our study provides further directions for studying the molecular mechanism of asthma.
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Affiliation(s)
- Fangwei Wang
- Department of Respiratory Medicine, the First Affiliated Hospital of Guangxi Medical University, Nan'ning, China
| | - Qisheng Su
- Department of Clinical Laboratory, the First Affiliated Hospital of Guangxi Medical University, Nan'ning, China
| | - Chaoqian Li
- Department of Respiratory Medicine, the First Affiliated Hospital of Guangxi Medical University, Nan'ning, China
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7
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Caliendo G, D'Elia G, Makker J, Passariello L, Albanese L, Molinari AM, Vietri MT. Biological, genetic and epigenetic markers in ulcerative colitis. Adv Med Sci 2023; 68:386-395. [PMID: 37813048 DOI: 10.1016/j.advms.2023.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/15/2023] [Accepted: 09/18/2023] [Indexed: 10/11/2023]
Abstract
In this review, we have summarized the existing knowledge of ulcerative colitis (UC) markers based on current literature, specifically, the roles of potential new biomarkers, such as circulating, fecal, genetic, and epigenetic alterations, in UC onset, disease activity, and in therapy response. UC is a complex multifactorial inflammatory disease. There are many invasive and non-invasive diagnostic methods in UC, including several laboratory markers which are employed in diagnosis and disease assessment; however, colonoscopy remains the most widely used method. Common laboratory abnormalities currently used in the clinical practice include inflammation-induced alterations, serum autoantibodies, and antibodies against bacterial antigens. Other new serum and fecal biomarkers are supportive in diagnosis and monitoring disease activity and therapy response; and potential salivary markers are currently being evaluated as well. Several UC-related genetic and epigenetic alterations are implied in its pathogenesis and therapeutic response. Moreover, the use of artificial intelligence in the integration of laboratory biomarkers and big data could potentially be useful in clinical translation and precision medicine in UC management.
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Affiliation(s)
- Gemma Caliendo
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Giovanna D'Elia
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Jasmine Makker
- Department of GKT School of Medical Education, King's College London, London, UK
| | - Luana Passariello
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Luisa Albanese
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Anna Maria Molinari
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Maria Teresa Vietri
- Unity of Clinical and Molecular Pathology, AOU University of Campania "Luigi Vanvitelli", Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.
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8
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Patra R, Dey AK, Mukherjee S. Identification of genes critical for inducing ulcerative colitis and exploring their tumorigenic potential in human colorectal carcinoma. PLoS One 2023; 18:e0289064. [PMID: 37535606 PMCID: PMC10399749 DOI: 10.1371/journal.pone.0289064] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 07/11/2023] [Indexed: 08/05/2023] Open
Abstract
Ulcerative colitis (UC) is a chronic relapsing inflammatory bowel disease leading to continuous mucosal inflammation in the rectum extending proximally towards the colon. Chronic and/or recurrent UC is one of the critical predisposing mediators of the oncogenesis of human colorectal carcinoma (CRC). Perturbations of the differential expression of the UC-critical genes exert an intense impact on the neoplastic transformation of the affected tissue(s). Herein, a comprehensive exploration of the UC-critical genes from the transcriptomic profiles of UC patients was conducted to study the differential expression, functional enrichment, genomic alterations, signal transduction pathways, and immune infiltration level encountered by these genes concerning the oncogenesis of CRC. The study reveals that WFDC2, TTLL12, THRA, and EPHB3 play crucial roles as UC-CRC critical genes and are positively correlated with the molecular transformation of UC to CRC. Taken together, these genes can be used as potential biomarkers and therapeutic targets for combating UC-induced human CRC.
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Affiliation(s)
- Ritwik Patra
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol, West Bengal, India
| | - Amit Kumar Dey
- Biomedical Research Centre, Translational Geroproteomics Unit, National Institute on Aging, National Institute of Health (NIH), Baltimore, MD, United States of America
| | - Suprabhat Mukherjee
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol, West Bengal, India
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9
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Lee Y, Kim SH, Jeong H, Kim KH, Jeon D, Cho Y, Lee D, Nam KT. Role of Nox4 in Mitigating Inflammation and Fibrosis in Dextran Sulfate Sodium-Induced Colitis. Cell Mol Gastroenterol Hepatol 2023; 16:411-429. [PMID: 37207801 PMCID: PMC10372905 DOI: 10.1016/j.jcmgh.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 05/21/2023]
Abstract
BACKGROUND & AIMS Fibrosis development in ulcerative colitis is associated directly with the severity of mucosal inflammation, which increases the risk of colorectal cancer. The transforming growth factor-β (TGF-β) signaling pathway is an important source of tissue fibrogenesis, which is stimulated directly by reactive oxygen species produced from nicotinamide adenine dinucleotide phosphate oxidases (NOX). Among members of the NOX family, NOX4 expression is up-regulated in patients with fibrostenotic Crohn's disease (CD) and in dextran sulfate sodium (DSS)-induced murine colitis. The aim of this study was to determine whether NOX4 plays a role in fibrogenesis during inflammation in the colon using a mouse model. METHODS Acute and recovery models of colonic inflammation were performed by DSS administration to newly generated Nox4-/- mice. Pathologic analysis of colon tissues was performed, including detection of immune cells, proliferation, and fibrotic and inflammatory markers. RNA sequencing was performed to detect differentially expressed genes between Nox4-/- and wild-type mice in both the untreated and DSS-treated conditions, followed by functional enrichment analysis to explore the molecular mechanisms contributing to pathologic differences during DSS-induced colitis and after recovery. RESULTS Nox4-/- mice showed increased endogenous TGF-β signaling in the colon, increased reactive oxygen species levels, intensive inflammation, and an increased fibrotic region after DSS treatment compared with wild-type mice. Bulk RNA sequencing confirmed involvement of canonical TGF-β signaling in fibrogenesis of the DSS-induced colitis model. Up-regulation of TGF-β signaling affects collagen activation and T-cell lineage commitment, increasing the susceptibility for inflammation. CONCLUSIONS Nox4 protects against injury and plays a crucial role in fibrogenesis in DSS-induced colitis through canonical TGF-β signaling regulation, highlighting a new treatment target.
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Affiliation(s)
- Yura Lee
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Sung-Hee Kim
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Haengdueng Jeong
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Kwang H Kim
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Donghun Jeon
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Yejin Cho
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Daekee Lee
- Department of Life Science, Ewha Womans University, Seoul, Korea
| | - Ki Taek Nam
- Severance Biomedical Science Institute, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea.
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Chen Q, Bei S, Zhang Z, Wang X, Zhu Y. Identification of diagnostic biomarks and immune cell infiltration in ulcerative colitis. Sci Rep 2023; 13:6081. [PMID: 37055577 PMCID: PMC10102327 DOI: 10.1038/s41598-023-33388-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/12/2023] [Indexed: 04/15/2023] Open
Abstract
We aimed to explore diagnostic biomarks and immune cell infiltration characteristics in ulcerative colitis (UC). We used the dataset GSE38713 as the training set and dataset GSE94648 as the test set. A total of 402 differentially expressed genes (DEGs) were obtained from GSE38713. Annotating, visualizing, and integrating discovery of these differential genes was performed using Gene Ontology (GO), Kyoto Gene and Genome Encyclopedia Pathway (KEGG), and Gene Set Enrichment Analysis (GSEA). Protein-protein interaction networks were constructed from the STRING database, and protein functional modules were identified using the CytoHubba plugin of Cytoscape. Random forest and LASSO regression were used to screen for UC-related diagnostic markers, and ROC curves were generated to validate their diagnostic value. The composition of 22 immune cells was analyzed, and the immune cell infiltration in UC was analyzed using CIBERSORT. Results: Seven diagnostic markers associated with UC were identified: TLCD3A, KLF9, EFNA1, NAAA,WDR4, CKAP4, and CHRNA1. Immune cell infiltration assessment revealed that macrophages M1, activated dendritic cells, and neutrophil cells infiltrated relatively more compared to normal control samples. Our results suggest a new functional feature of UC and suggest potential biomarkers for UC through comprehensive analysis of integrated gene expression data.
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Affiliation(s)
- Qin Chen
- Department of Anorectal, Kunming Municipal Hospital of Traditional Chinese Medicine, The Third Affiliated Hospital of Yunnan University of Chinese Medicine, No. 25 Dongfeng East Road, Panlong District, Kunming, 650011, Yunnan Province, China.
| | - Shaosheng Bei
- Department of Anorectal, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhiyun Zhang
- Department of Anorectal, Kunming Municipal Hospital of Traditional Chinese Medicine, The Third Affiliated Hospital of Yunnan University of Chinese Medicine, No. 25 Dongfeng East Road, Panlong District, Kunming, 650011, Yunnan Province, China
| | - Xiaofeng Wang
- Department of Colorectal Surgery, Guang'an Men Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yunying Zhu
- Department of Anorectal, Kunming Municipal Hospital of Traditional Chinese Medicine, The Third Affiliated Hospital of Yunnan University of Chinese Medicine, No. 25 Dongfeng East Road, Panlong District, Kunming, 650011, Yunnan Province, China
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Li L, Gao L, Zhou H, Shi C, Zhang X, Zhang D, Liu H. High Expression Level of BRD4 Is Associated with a Poor Prognosis and Immune Infiltration in Esophageal Squamous Cell Carcinoma. Dig Dis Sci 2023:10.1007/s10620-023-07907-3. [PMID: 36933111 DOI: 10.1007/s10620-023-07907-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023]
Abstract
BACKGROUND Bromodomain-containing protein 4 (BRD4) is a reader of histone acetylation and is associated with a variety of diseases. AIM To investigate the expression level of BRD4 in esophageal squamous cell carcinoma (ESCC), its prognostic value and its relationship with immune infiltration. METHODS The study included 94 ESCC patients from The Cancer Genome Atlas (TCGA) database and 179 ESCC patients from Affiliated Hospital 2 of Nantong University. The expression levels of proteins in tissue microarray were detected by immunohistochemistry. The prognostic factors were analyzed by Kaplan-Meier curve and univariate and multivariate cox regression. The ESTIMATE website was used to calculate the stromal, immune and ESTIMATE score. CIBERSORT was used to calculate the abundance of immune infiltrates. Spearman and Phi coefficient were used for correlation analysis. The TIDE algorithm was used to predict treatment response to immune checkpoint blockade. RESULTS BRD4 is up-regulated in ESCC, and high BRD4 expression level is associated with poor prognosis and adverse clinicopathological features. In addition, the monocyte count, systemic inflammatory-immunologic index, platelet-lymphocyte ratio, and monocyte-lymphocyte ratio in the BRD4 high expression level group were higher than in the low expression level group. Finally, we found that BRD4 expression level correlated with immune infiltration and that it was inversely correlated with infiltration of CD8 + T cells. Higher TIDE scores in the BRD4 high expression group than in the low expression group. CONCLUSION BRD4 is associated with poor prognosis and immune infiltration in ESCC, and may be a potential biomarker for prognosis and immunotherapy application.
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Affiliation(s)
- Li Li
- Department of Pathology, Affiliated Hospital 2 of Nantong University and First People's Hospital of Nantong City, Shengli Road No. 666, Nantong, 226001, Jiangsu, People's Republic of China
| | - Lin Gao
- Medical Research Center, Affiliated Hospital 2 of Nantong University and First People's Hospital of Nantong City, Nantong, 226001, People's Republic of China
| | - Hong Zhou
- Department of Pathology, Affiliated Hospital 2 of Nantong University and First People's Hospital of Nantong City, Shengli Road No. 666, Nantong, 226001, Jiangsu, People's Republic of China
| | - Chao Shi
- Department of Pathology, Affiliated Hospital 2 of Nantong University and First People's Hospital of Nantong City, Shengli Road No. 666, Nantong, 226001, Jiangsu, People's Republic of China
| | - Xiaojuan Zhang
- Department of Pathology, Affiliated Hospital 2 of Nantong University and First People's Hospital of Nantong City, Shengli Road No. 666, Nantong, 226001, Jiangsu, People's Republic of China
| | - Dongmei Zhang
- Medical Research Center, Affiliated Hospital 2 of Nantong University and First People's Hospital of Nantong City, Nantong, 226001, People's Republic of China
| | - Hongbin Liu
- Department of Pathology, Affiliated Hospital 2 of Nantong University and First People's Hospital of Nantong City, Shengli Road No. 666, Nantong, 226001, Jiangsu, People's Republic of China.
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Heng H, Liu J, Hu M, Li D, Su W, Li J. WDR43 is a potential diagnostic biomarker and therapeutic target for osteoarthritis complicated with Parkinson’s disease. Front Cell Neurosci 2022; 16:1013745. [DOI: 10.3389/fncel.2022.1013745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
Osteoarthritis (OA) and Parkinson’s disease (PD) are on the rise and greatly impact the quality of individuals’ lives. Although accumulating evidence indicates a relationship between OA and PD, the particular interactions connecting the two diseases have not been thoroughly examined. Therefore, this study explored the association through genetic characterization and functional enrichment. Four datasets (GSE55235, GSE12021, GSE7621, and GSE42966) were chosen for assessment and validation from the Gene Expression Omnibus (GEO) database. Weighted Gene Co-Expression Network Analysis (WGCNA) was implemented to determine the most relevant genes for clinical features. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were carried out to explore the biological processes of common genes, and to display the interrelationships between common genes, the STRING database and the application Molecular Complex Detection Algorithm (MCODE) of Cytoscape software were leveraged to get hub genes. By intersecting the common genes with the differentially expressed genes (DEGs) acquired from GSE12021 and GSE42966, the hub genes were identified. Finally, we validated the diagnostic efficacy of hub genes and explored their correlation with 22 immune infiltrating cells. As a consequence, we discovered 71 common genes, most of which were functionally enriched in antigen processing and presentation, mitochondrial translation, the mRNA surveillance pathway, and nucleocytoplasmic transport. Furthermore, WDR43 was found by intersecting eight hub genes with 28 DEGs from the two validation datasets. Receiver Operating Characteristic (ROC) implied the diagnostic role of WDR43 in OA and PD. Immune infiltration research revealed that T-cell regulatory (Tregs), monocytes, and mast cells resting were associated with the pathogenesis of OA and PD. WDR43 may provide key insights into the relationship between OA and PD.
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Jiang Z, Huang L, Chen L, Zhou J, Liang B, Bai X, Wu L, Huang H. Circular RNA profile in Graves' disease and potential function of hsa_circ_0090364. Endocr Connect 2022; 11:e220030. [PMID: 36018563 PMCID: PMC9578071 DOI: 10.1530/ec-22-0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/25/2022] [Indexed: 11/25/2022]
Abstract
Background Graves' disease is a common autoimmune disease. Cytokines and their signalling pathways play a major part in the pathogenesis of Graves' disease; however, the underlying mechanism needs to be clarified. Aims The aim of this study was to explore whether circular RNAs participate in the immunological pathology of Graves' disease via cytokine-related signalling pathways. Methods Bioinformatics analysis was performed to identify differentially expressed circular RNAs and their targets and associated pathways. A total of three patients with Graves' disease and three sex- and age-matched healthy controls were enrolled for validation with microarray analysis and real-time quantitative PCR (qPCR). An additional 24 patients with Graves' disease and 24 gender- and age-matched controls were included for validation by real-time fluorescent qPCR. Flow cytometry and CCK8 assays were used to detect the apoptotic and proliferative levels of Jurkat cells (T lymphocytes) with the silenced expression of circRNA. ELISA was performed to detect the growth and apoptosis-related proteins. The competition mechanism of endogenous RNA was explored by real-time fluorescence qPCR. Results A total of 366 significantly differentially expressed circular RNAs were identified in the Graves' disease group compared to healthy controls. The level of hsa_circ_0090364 was elevated in Graves' disease patients and positively correlated with thyroid-stimulating hormone receptor antibodies. Further analyses suggested that hsa_circ_0090364 may regulate the JAK-STAT pathway via the hsa-miR-378a-3p/IL-6ST/IL21R axis to promote cell growth. Conclusions These results provide novel clues into the pathophysiological mechanisms of Graves' disease and potential targets for drug treatment.
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Affiliation(s)
- Zhengrong Jiang
- Department of Endocrinology, The Second affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
| | - Linghong Huang
- Department of Endocrinology, The Second affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
| | - Lijun Chen
- Department of Endocrinology, The Second affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
| | - Jingxiong Zhou
- Department of Endocrinology, The Second affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
| | - Bo Liang
- Department of Endocrinology, The Second affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
| | - Xuefeng Bai
- Department of Endocrinology, The Second affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
| | - Lizhen Wu
- Department of Endocrinology, The Second affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
| | - Huibin Huang
- Department of Endocrinology, The Second affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
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Peng Y, Hong H, Gao N, Wan A, Ma Y. Bioinformatics methods in biomarkers of preeclampsia and associated potential drug applications. BMC Genomics 2022; 23:711. [PMID: 36258174 PMCID: PMC9580137 DOI: 10.1186/s12864-022-08937-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/28/2022] [Indexed: 11/23/2022] Open
Abstract
Background Preeclampsia is a pregnancy-related condition that causes high blood pressure and proteinuria after 20 weeks of pregnancy. It is linked to increased maternal mortality, organ malfunction, and foetal development limitation. In this view, there is a need critical to identify biomarkers for the early detection of preeclampsia. The objective of this study is to discover critical genes and explore medications for preeclampsia treatment that may influence these genes. Methods Four datasets, including GSE10588, GSE25906, GSE48424 and GSE60438 were retrieved from the Gene Expression Omnibus database. The GSE10588, GSE25906, and GSE48424 datasets were then removed the batch effect using the “sva” R package and merged into a complete dataset. The differentially expressed genes (DEGs) were identified using the “limma” R package. The potential small-molecule agents for the treatment of PE was further screened using the Connective Map (CMAP) drug database based on the DEGs. Further, Weight gene Co-expression network (WGNCA) analysis was performed to identified gene module associated with preeclampsia, hub genes were then identified using the logistic regression analysis. Finally, the immune cell infiltration level of genes was evaluated through the single sample gene set enrichment analysis (ssGSEA). Results A total of 681 DEGs (376 down-regulated and 305 up-regulated genes) were identified between normal and preeclampsia samples. Then, Dexamethasone, Prednisone, Rimexolone, Piretanide, Trazodone, Buflomedil, Scoulerin, Irinotecan, and Camptothecin drugs were screened based on these DEGs through the CMAP database. Two modules including yellow and brown modules were the most associated with disease through the WGCNA analysis. KEGG analysis revealed that the chemokine signaling pathway, Th1 and Th2 cell differentiation, B cell receptor signalling pathway and oxytocin signalling pathway were significantly enriched in these modules. Moreover, two key genes, PLEK and LEP were evaluated using the univariate and multivariate logistic regression analysis from the hub modules. These two genes were further validated in the external validation cohort GSE60438 and qRT-PCR experiment. Finally, we evaluated the relationship between immune cell and two genes. Conclusion In conclusion, the present study investigated key genes associated with PE pathogenesis that may contribute to identifying potential biomarkers, therapeutic agents and developing personalized treatment for PE. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08937-3.
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Affiliation(s)
- Ying Peng
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong, China.,Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine,University of Science and Technology of China, Hefei, Anhui, China
| | - Hui Hong
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine,University of Science and Technology of China, Hefei, Anhui, China
| | - Na Gao
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan Shandong, 250012, China
| | - An Wan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine,University of Science and Technology of China, Hefei, Anhui, China
| | - Yuyan Ma
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan Shandong, 250012, China.
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Wang F, Su Q, Li C. Identidication of novel biomarkers in non-small cell lung cancer using machine learning. Sci Rep 2022; 12:16693. [PMID: 36202977 PMCID: PMC9537298 DOI: 10.1038/s41598-022-21050-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
Lung cancer is one of the leading causes of cancer-related deaths worldwide, and non-small cell lung cancer (NSCLC) accounts for a large proportion of lung cancer cases, with few diagnostic and therapeutic targets currently available for NSCLC. This study aimed to identify specific biomarkers for NSCLC. We obtained three gene-expression profiles from the Gene Expression Omnibus database (GSE18842, GSE21933, and GSE32863) and screened for differentially expressed genes (DEGs) between NSCLC and normal lung tissue. Enrichment analyses were performed using Gene Ontology, Disease Ontology, and the Kyoto Encyclopedia of Genes and Genomes. Machine learning methods were used to identify the optimal diagnostic biomarkers for NSCLC using least absolute shrinkage and selection operator logistic regression, and support vector machine recursive feature elimination. CIBERSORT was used to assess immune cell infiltration in NSCLC and the correlation between biomarkers and immune cells. Finally, using western blot, small interfering RNA, Cholecystokinin-8, and transwell assays, the biological functions of biomarkers with high predictive value were validated. A total of 371 DEGs (165 up-regulated genes and 206 down-regulated genes) were identified, and enrichment analysis revealed that these DEGs might be linked to the development and progression of NSCLC. ABCA8, ADAMTS8, ASPA, CEP55, FHL1, PYCR1, RAMP3, and TPX2 genes were identified as novel diagnostic biomarkers for NSCLC. Monocytes were the most visible activated immune cells in NSCLC. The knockdown of the TPX2 gene, a biomarker with a high predictive value, inhibited A549 cell proliferation and migration. This study identified eight potential diagnostic biomarkers for NSCLC. Further, the TPX2 gene may be a therapeutic target for NSCLC.
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Affiliation(s)
- Fangwei Wang
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Qisheng Su
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Chaoqian Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China.
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FABP6 Expression Correlates with Immune Infiltration and Immunogenicity in Colorectal Cancer Cells. J Immunol Res 2022; 2022:3129765. [PMID: 36033394 PMCID: PMC9403257 DOI: 10.1155/2022/3129765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
Abstract
Background Immune checkpoint inhibitors (ICIs) have rapidly revolutionized colorectal cancer (CRC) treatment, but resistance caused by the heterogeneous tumor microenvironment (TME) still presents a challenge. Therefore, it is necessary to characterize TME immune infiltration and explore new targets to improve immunotherapy. Methods The compositions of 64 types of infiltrating immune cells and their relationships with CRC patient clinical characteristics were assessed. Differentially expressed genes (DEGs) between “hot” and “cold” tumors were used for functional analysis. A prediction model was constructed to explore the survival of CRC patients treated with and without immunotherapy. Finally, fatty acid-binding protein (FABP6) was selected for in vitro experiments, which revealed its roles in the proliferation, apoptosis, migration, and immunogenicity of CRC tissues and cell lines. Results The infiltration levels of several immune cells were associated with CRC tumor stage and prognosis. Different cell types showed the synergistic or antagonism infiltration patterns. Enrichment analysis of DEGs revealed that immune-related signaling was significantly activated in hot tumors, while metabolic process pathways were altered in cold tumors. In addition, the constructed model effectively predicted the survival of CRC patients treated with and without immunotherapy. FABP6 knockdown did not significantly alter tumor cell proliferation, apoptosis, and migration. FABP6 was negatively correlated with immune infiltration, and knockdown of FABP6 increased major histocompatibility complex (MHC) class 1 expression and promoted immune-related chemokine secretion, indicating the immunogenicity enhancement of tumor cells. Finally, knockdown of FABP6 could promote the recruitment of CD8+ T cells. Conclusion Collectively, we described the landscape of immune infiltration in CRC and identified FABP6 as a potential immunotherapeutic target for treatment.
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An Immune-Related Prognostic Risk Model in Colon Cancer by Bioinformatics Analysis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:3640589. [PMID: 36065262 PMCID: PMC9440785 DOI: 10.1155/2022/3640589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/11/2022] [Accepted: 08/13/2022] [Indexed: 11/17/2022]
Abstract
Colon cancer is one of the leading malignancies with poor prognosis worldwide. Immune cell infiltration has a potential prognostic value for colon cancer. This study aimed to establish an immune-related prognostic risk model for colon cancer by bioinformatics analysis. A total of 1670 differentially expressed genes (DEGs), including 177 immune-related genes, were identified from The Cancer Genome Atlas (TCGA) dataset. A prognostic risk model was constructed based on six critical immune-related genes (C-X-C motif chemokine ligand 1 (CXCL1), epiregulin (EREG), C-C motif chemokine ligand 24 (CCL24), fatty acid binding protein 4 (FABP4), tropomyosin 2 (TPM2), and semaphorin 3G (SEMA3G)). This model was validated using the microarray dataset GSE35982. In addition, Cox regression analysis showed that age and clinical stage were correlated with prognostic risk scores. Kaplan–Meier survival analysis showed that high risk scores correlated with low survival probabilities in patients with colon cancer. Downregulated TPM2, FABP4, and SEMA3G levels were positively associated with the activated mast cells, monocytes, and macrophages M2. Upregulated CXCL1 and EREG were positively correlated with macrophages M1 and activated T cells CD4 memory, respectively. Based on these results, we can conclude that the proposed prognostic risk model presents promising novel signatures for the diagnosis and prognosis prediction of colon cancer. This model may provide therapeutic benefits for the development of immunotherapy for colon cancer.
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Identification of a Novel Risk Model: A Five-Gene Prognostic Signature for Pancreatic Cancer. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:3660110. [PMID: 35845587 PMCID: PMC9286972 DOI: 10.1155/2022/3660110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 12/24/2022]
Abstract
Objective. Biomarkers for pancreatic cancer (PCa) prognosis provide evidence for improving the survival outcome of this disease. This study aimed to identify a prognostic risk model based on gene expression profiling of microarray bioinformatics analysis. Methods. Prognostic immune genes in the TCGA-PAAD cohort were identified using the univariate Cox regression and Kaplan–Meier survival analysis. Multivariate Cox regression (stepAIC) was used to identify prognostic genes from the top 20 hub genes in the protein-protein interaction (PPI) network. A prognostic risk model was established and its performance in predicting the overall survival in PCa was validated in GSE62452. Gene mutations and infiltration immune cells in PCa tumors were analyzed using online databases. Results. Univariate Cox regression and Kaplan–Meier survival analyses identified 128 prognostic genes. Multivariate Cox regression (stepAIC) identified five prognostic genes (PLCG1, MET, TNFSF10, CXCL9, and TLR3) out of the 20 hub genes in the PPI network. A prognostic risk model was established using the signature of five genes. This model had moderate to high accuracies (AUC > 0.700) in predicting 3-year and 5-year overall survival in TCGA and GSE62452 cohorts. The Kaplan–Meier survival analysis showed that high-risk scores were correlated with poor survival outcomes in PCa (
). Also, mutations in the five genes were related to poor survival. The five genes were related to multiple immune cells. Conclusions. The prognostic risk model was significantly correlated with the survival in PCa patients. This model modulated PCa tumor progression and prognosis by regulating immune cell infiltration.
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Chen P, Yao M, Fang T, Ye C, Du Y, Jin Y, Wu R. Identification of NFASC and CHL1 as Two Novel Hub Genes in Endometriosis Using Integrated Bioinformatic Analysis and Experimental Verification. Pharmgenomics Pers Med 2022; 15:377-392. [PMID: 35496348 PMCID: PMC9041605 DOI: 10.2147/pgpm.s354957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/11/2022] [Indexed: 11/23/2022] Open
Abstract
Background Endometriosis (EMS) is a common and highly recurrent gynecological disease characterized by chronic pain and infertility. There are no definitive therapies for endometriosis since the pathogenesis remains undetermined. This study aimed to identify EMS-related functional modules and hub genes by integrated bioinformatics analysis. Methods Three endometriosis expression profiling series (GSE25628, GSE23339, and GSE7305) were obtained from Gene Expression Omnibus (GEO). The EMS-related module was constructed by weighted gene co-expression network analysis (WGCNA), followed by Gene Ontology (GO) enrichment analyses. Cytohubba and the MCODE plug-ins of Cytoscape were used to screen out the hub genes, which were verified via receiver operating characteristic (ROC) curves. Immunohistochemistry was performed to verify the protein expression of the hub genes in ectopic endometrial tissues. Moreover, CIBERSORT was used to analyze the relationship between the abundance of immune cells infiltration and the expression of hub genes. Results Among the 18 modules obtained, the darkmagenta module was identified as the EMS-related module, genes of which were significantly enriched to terms referring to cell migration and neurogenesis. NFASC and CHL1 were screened out and prioritized as hub genes through Cytoscape and confirmed to be differentially upregulated in ectopic endometrial samples. Finally, the expression of hub genes was related to the abundance of immune cells infiltration. The higher expression of NFASC or CHL1 correlated with increased M2 macrophages and decreased natural killer (NK) cells in ectopic lesions. Conclusion This study provided new insights into the molecular factors underlying the pathogenesis of endometriosis and provided a theoretical basis for the potential that the two hub genes, NFASC and CHL1, might be novel biomarkers and therapeutic targets in the future.
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Affiliation(s)
- Pei Chen
- Department of Obstetrics and Gynecology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Mengyun Yao
- Department of Obstetrics and Gynecology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Tao Fang
- Department of Obstetrics and Gynecology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Chaoshuang Ye
- Department of Obstetrics and Gynecology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Yongjiang Du
- Department of Obstetrics and Gynecology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Yang Jin
- Department of Obstetrics and Gynecology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Ruijin Wu
- Department of Obstetrics and Gynecology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Correspondence: Ruijin Wu, Department of Obstetrics and Gynecology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People’s Republic of China, Tel +86 571-8706223, Email
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20
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Wang H, Zhang J. Identification of DTL as Related Biomarker and Immune Infiltration Characteristics of Nasopharyngeal Carcinoma via Comprehensive Strategies. Int J Gen Med 2022; 15:2329-2345. [PMID: 35264872 PMCID: PMC8901051 DOI: 10.2147/ijgm.s352330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/02/2022] [Indexed: 11/25/2022] Open
Abstract
Purpose Although considerable progress has been made in basic and clinical research on nasopharyngeal carcinoma (NPC), the biomarkers of the progression of NPC have not been fully studied and described. This study was designed to identify potential novel biomarkers for NPC using integrated analyses and explore the immune cell infiltration in this pathological process. Methods Five GEO data sets were downloaded from gene expression omnibus database (GEO) and analysed to identify differentially expressed genes (DEGs), followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. The four algorithms were adopted for screening of novel and key biomarkers for NPC, including random forest (RF) machine learning algorithm, least absolute shrinkage and selection operator (LASSO) logistic regression, support vector machine-recursive feature elimination (SVM-RFE), and weighted gene co-expression network analysis (WGCNA). Lastly, CIBERSORT was used to assess the infiltration of immune cells in NPC, and the correlation between diagnostic markers and infiltrating immune cells was analyzed. Results Herein, we identified 46 DEGs, and enrichment analysis results showed that DEGs and several kinds of signaling pathways might be closely associated with the occurrence and progression of NPC. DTL was recognized as NPC-related biomarker. DTL, also known as retinoic acid-regulated nuclear matrix-associated protein (RAMP), or DNA replication factor 2 (CDT2), is reported to be correlated with the cell proliferation, cell cycle arrest and cell invasion in hepatocellular carcinoma, breast cancer and gastric cancer. Immune infiltration analysis demonstrated that macrophages M0, macrophages M1 and T cells CD4 memory activated were linked to pathogenesis of NPC. Conclusion In summary, we adopted a comprehensive strategy to screen DTL as biomarkers related to NPC and explore the critical role of immune cell infiltration in NPC.
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Affiliation(s)
- Hehe Wang
- Department of Otolaryngology, Head and Neck Surgery, Ningbo First Hospital, Ningbo, Zhejiang, People’s Republic of China
- Correspondence: Hehe Wang, Department of Otolaryngology Head and Neck Surgery, Ningbo First Hospital, Ningbo, Zhejiang, 315010, People’s Republic of China, Email
| | - Junge Zhang
- Department of Anesthesiology, Ningbo First Hospital, Ningbo, Zhejiang, People’s Republic of China
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21
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Screening of Potential Biomarkers in the Peripheral Serum for Steroid-Induced Osteonecrosis of the Femoral Head Based on WGCNA and Machine Learning Algorithms. DISEASE MARKERS 2022; 2022:2639470. [PMID: 35154510 PMCID: PMC8832155 DOI: 10.1155/2022/2639470] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/27/2021] [Indexed: 12/24/2022]
Abstract
Background. Steroid-induced osteonecrosis of the femoral head (SONFH) has produced a substantial burden of medical and social experience. However, the current diagnosis is still limited. Thus, this study is aimed at identifying potential biomarkers in the peripheral serum of patients with SONFH. Methods. The expression profile data of SONFH (number: GSE123568) was acquired from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) in SONFH were identified and used for weighted gene coexpression network analysis (WGCNA). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to investigate the biological functions. The protein-protein interaction (PPI) network and machine learning algorithms were employed to screen for potential biomarkers. Gene set enrichment analysis (GSEA), transcription factor (TF) enrichment analysis, and competing endogenous RNA (ceRNA) network were used to determine the biological functions and regulatory mechanisms of the potential biomarkers. Results. A total of 562 DEGs, including 318 upregulated and 244 downregulated genes, were identified between SONFH and control samples, and 94 target genes were screened based on WGCNA. Moreover, biological function analysis suggested that target genes were mainly involved in erythrocyte differentiation, homeostasis and development, and myeloid cell homeostasis and development. Furthermore, GYPA, TMCC2, and BPGM were identified as potential biomarkers in the peripheral serum of patients with SONFH based on machine learning algorithms and showed good diagnostic values. GSEA revealed that GYPA, TMCC2, and BPGM were mainly involved in immune-related biological processes (BPs) and signaling pathways. Finally, we found that GYPA might be regulated by hsa-miR-3137 and that BPGM might be regulated by hsa-miR-340-3p. Conclusion. GYPA, TMCC2, and BPGM are potential biomarkers in the peripheral serum of patients with SONFH and might affect SONFH by regulating erythrocytes and immunity.
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22
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Zhang Q, Liu Y, Chen P, Shi X, Liu Y, Shi L, Cong P, Mao S, Tong C, Du C, Hou M. Solute carrier family 12 member 8 (SLC12A8) is a potential biomarker and related to tumor immune cell infiltration in bladder cancer. Bioengineered 2021; 12:4946-4961. [PMID: 34365894 PMCID: PMC8806707 DOI: 10.1080/21655979.2021.1962485] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 01/10/2023] Open
Abstract
The solute carrier family has been reported to play critical roles in the progression of several cancers; however, the relationship between solute carrier family 12 member 8 (SLC12A8) and bladder cancer (BC) has not been clearly confirmed. This study explores the prognostic value of SLC12A8 for BC and its correlation with immune cell infiltration. We found that the expression of SLC12A8 mRNA was significantly overexpressed in BC tissues compared with noncancerous tissues in multiple public databases, and the result was validated using real-time PCR and immunohistochemistry (IHC). The Kaplan-Meier method and Cox proportional hazards models were used to evaluate the prognostic value of SLC12A8 for BC. The high expression of SLC12A8 led to a shorter overall survival time and was an unfavorable prognostic biomarker for BC. The mechanisms of SLC12A8 promoting tumorigenesis were investigated by Gene Set Enrichment Analysis (GSEA). Moreover, the correlations of SLC12A8 expression with the tumor-infiltrating immune cells (TICs) in BC were explored using TIMER 2.0 and CIBERSORT. SLC12A8 was associated with CD4+ T cells, dendritic cells, neutrophils, and macrophages infiltration. The expression of SLC12A8 was positively correlated with crucial immune checkpoint molecules. In conclusion, SLC12A8 might be an unfavorable prognostic biomarker in BC related to tumor immune cell infiltration.
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Affiliation(s)
- Qian Zhang
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, Liaoning, P.R. China
| | - Yunen Liu
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, Liaoning, P.R. China
| | - Peng Chen
- Department of Urology, General Hospital of Northern Theater Command, Shenyang, Liaoning, P.R. China
| | - Xiuyun Shi
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, Liaoning, P.R. China
| | - Ying Liu
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, Liaoning, P.R. China
| | - Lin Shi
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, Liaoning, P.R. China
| | - Peifang Cong
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, Liaoning, P.R. China
| | - Shun Mao
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, Liaoning, P.R. China
| | - Cangci Tong
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, Liaoning, P.R. China
| | - Cheng Du
- Department of Oncology, General Hospital of Northern Theater Command, Shenyang, Liaoning, P.R. China
| | - Mingxiao Hou
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, Liaoning, P.R. China
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, Liaoning, P.R. China
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23
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Li Y, Deng Y, He J. Monocyte-related gene biomarkers for latent and active tuberculosis. Bioengineered 2021; 12:10799-10811. [PMID: 34751089 PMCID: PMC8809927 DOI: 10.1080/21655979.2021.2003931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Monocytes are closely associated with tuberculosis (TB). Latent tuberculosis in some patients gradually develops into its active state. This study aimed to investigate the role of hub monocyte-associated genes in distinguishing latent TB infection (LTBI) from active TB. The gene expression profiles of 15 peripheral blood mononuclear cells (PBMCs) samples were downloaded from the gene expression omnibus (GEO) database, GSE54992. The monocyte abundance was high in active TB as evaluated by the Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) algorithm. The limma test and correlation analysis documented 165 differentially expressed monocyte-related genes (DEMonRGs) between latent TB and active TB. Functional annotation and enrichment analyses of the DEMonRGs using the database for annotation, visualization, and integration discovery (DAVID) tools showed enrichment of inflammatory response mechanisms and immune-related pathways. A protein-protein interaction network was constructed with a node degree ≥10. The expression levels of these hub DEMonRGs (SERPINA1, FUCA2, and HP) were evaluated and verified using several independent datasets and clinical settings. Finally, a single sample scoring method was used to establish a gene signature for the three DEMonRGs, distinguishing active TB from latent TB. The findings of the present study provide a better understanding of monocyte-related molecular fundamentals in TB progression and contribute to the identification of new potential biomarkers for the diagnosis of active TB.
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Affiliation(s)
- Yu Li
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning Guangxi, China
| | - Yaju Deng
- Emergency Department, Guangxi District Maternal and Child Health Hospital, Nanning, Guangxi, China
| | - Jie He
- Clinical Medical College of Chengdu Medical College, Chengdu, Sichuan, China.,Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
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24
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Gamah M, Alahdal M, Zhang Y, Zhou Y, Ji Q, Yuan Z, Han Y, Shen X, Ren Y, Zhang W. High-altitude hypoxia exacerbates dextran sulfate sodium (DSS)-induced colitis by upregulating Th1 and Th17 lymphocytes. Bioengineered 2021; 12:7985-7994. [PMID: 34666625 PMCID: PMC8806510 DOI: 10.1080/21655979.2021.1975017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
High altitude hypoxia (HAH) involves the pathogenesis of ulcerative colitis (UC) and gastrointestinal erosions. However, the mechanism of effects of HAH in colitis remains controversial. This study reports the immunomodulation mediated by HAH to enhancing the severity of UC in the mice model. BALB/c mice were used to establish the UC model by dextran sulfate sodium (DSS) compared to wild type mice. Mice groups were exposed to hypoxic conditions in a hypobaric chamber with an altitude of 5000 m for 7 days. Then, Spleen, mesenteric lymph nodes and colon tissues were collected. The activity of UC, the infiltration of the immune cells, and the released cytokines were investigated. Results showed that the severity of DSS-induced UC significantly increased in mice exposed to HAH. The analysis of pathological changes showed increased weight loss and decreased colon length accompanied by diarrhea and bloody feces in the hypobaric hypoxia group. Interestingly, the levels of inflammatory cytokines IL-17, TNF-α, and IFN-γ in the spleen and mesenteric lymph node showed a significant increase within the colon of the hypobaric hypoxia group. The population of Th 1 and Th 17 cells in the spleen was significantly increased in mice exposed to hypobaric hypoxia compared NC group. Suggesting that high altitude hypoxia enhances colitis in mice through activating the increase of inflammatory Th1 and Th17 lymphocytes. In conclusion, this study revealed that hypobaric hypoxia directly increases the severity of UC in the mice model via increasing the activity of inflammatory CD4+ Th1 and Th 17 lymphocytes.
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Affiliation(s)
- Mohammed Gamah
- Research Center for High Altitude Medicine, Key Laboratory for High Altitude Medicine, Ministry of Education, Qinghai University, Xining, Qinghai, 810001, China.,Medical College of Qinghai University, Xining, Qinghai, 810001, China
| | - Murad Alahdal
- Shenzhen Key Laboratory of Tissue Engineering, Shenzhen Laboratory of Digital Orthopedic Engineering, Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University, Health Science Center), Shenzhen P. R. China.,Medical Laboratory Department, Faculty of Medicine and Health Sciences, Hodeidah University, Al Hudaydah, Yemen
| | - Yu Zhang
- Medical College of Qinghai University, Xining, Qinghai, 810001, China
| | - Yiling Zhou
- Research Center for High Altitude Medicine, Key Laboratory for High Altitude Medicine, Ministry of Education, Qinghai University, Xining, Qinghai, 810001, China
| | - Qiaorong Ji
- Department of Pathophysiology, School of Basic Medical Sciences, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Zhouyang Yuan
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Ying Han
- Medical College of Qinghai University, Xining, Qinghai, 810001, China
| | - Xiangqun Shen
- Research Center for High Altitude Medicine, Key Laboratory for High Altitude Medicine, Ministry of Education, Qinghai University, Xining, Qinghai, 810001, China
| | - Yanming Ren
- Medical College of Qinghai University, Xining, Qinghai, 810001, China
| | - Wei Zhang
- Research Center for High Altitude Medicine, Key Laboratory for High Altitude Medicine, Ministry of Education, Qinghai University, Xining, Qinghai, 810001, China.,Medical College of Qinghai University, Xining, Qinghai, 810001, China
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25
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Wang B, Gong S, Shao W, Han L, Li Z, Zhang Z, Zheng Y, Ouyang F, Ma Y, Xu W, Feng Y. Comprehensive analysis of pivotal biomarkers, immune cell infiltration and therapeutic drugs for steroid-induced osteonecrosis of the femoral head. Bioengineered 2021; 12:5971-5984. [PMID: 34488536 PMCID: PMC8815624 DOI: 10.1080/21655979.2021.1972081] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Steroid-induced osteonecrosis of the femoral head (SONFH) is a progressive disease that leads to an increased disability rate. This study aimed to ascertain biomarkers, infiltrating immune cells, and therapeutic drugs for SONFH. The gene expression profile of the GSE123568 dataset was downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified using the NetworkAnalyst platform. Functional enrichment, protein-protein interaction network (PPI), and module analyses were performed using Metascape tools. An immune cell abundance identifier was used to explore immune cell infiltration. Furthermore, hub genes were identified based on maximal clique centrality (MCC) evaluation using cytoHubba application and confirmed by qRT-PCR using clinical samples. Finally, the L1000 platform was used to determine potential drugs for SONFH treatment. The SONFH mouse model was used to determine the therapeutic effects of aspirin. In total, 429 DEGs were identified in SONFH samples. Functional enrichment analysis showed that these DEGs were enriched in myeloid leukocyte activation and osteoclast differentiation processes. A set of nine immune cell types was confirmed to be markedly different between the SONFH and control samples. All 10 hub genes were significantly highly expressed in the serum of SONFH patients, as shown by qRT-PCR. Finally, the therapeutic effect of aspirin on SONFH was examined in animal experiments. Taken together, our data revealed the hub genes and infiltrating immune cells in SONFH, and we also screened potential drugs for use in SONFH treatment.
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Affiliation(s)
- Bo Wang
- Department of Rehabilitation, Wuhan No. 1 Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan China
| | - Song Gong
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan China
| | - Wenkai Shao
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan China
| | - Lizhi Han
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan China
| | - Zilin Li
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan China
| | - Zhichao Zhang
- Department of Rehabilitation, Wuhan No. 1 Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan China
| | - Yang Zheng
- Department of Rehabilitation, Wuhan No. 1 Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan China
| | - Fang Ouyang
- Department of Rehabilitation, Wuhan No. 1 Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan China
| | - Yan Ma
- Department of Rehabilitation, Wuhan No. 1 Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan China
| | - Weihua Xu
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan China
| | - Yong Feng
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan China
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26
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Lai X, Chen J. C-X-C motif chemokine ligand 12: a potential therapeutic target in Duchenne muscular dystrophy. Bioengineered 2021; 12:5428-5439. [PMID: 34424816 PMCID: PMC8806931 DOI: 10.1080/21655979.2021.1967029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked recessive disease caused by a mutant dystrophin protein. DMD patients undergo gradual progressive paralysis until death. Chronic glucocorticoid therapy remains one of the main treatments for DMD, despite the significant side effects. However, its mechanisms of action remain largely unknown. We used bioinformatics tools to identify pathogenic genes involved in DMD and glucocorticoid target genes. Two gene expression profiles containing data from DMD patients and healthy controls (GSE38417 and GSE109178) were downloaded for further analysis. Differentially expressed genes (DEGs) between DMD patients and controls were identified using GEO2R, and glucocorticoid target genes were predicted from the Pharmacogenetics and Pharmacogenomics Knowledge Base. Surprisingly, only one gene, CXCL12 (C-X-C motif chemokine ligand 12), was both a glucocorticoid target and a DEG. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, Gene Ontology term enrichment analysis, and gene set enrichment analysis were performed. A protein-protein interaction network was constructed and hub genes identified using the Search Tool for the Retrieval of Interacting Genes (STRING) database and Cytoscape. Enriched pathways involving the DEGs, including CXCL12, were associated with the immune response and inflammation. Levels of CXCL12 and its receptor CXCR4 (C-X-C motif chemokine receptor 4) were increased in X-linked muscular dystrophy (mdx) mice (DMD models) but became significantly reduced after prednisone treatment. Metformin also reduced the expression of CXCL12 and CXCR4 in mdx mice. In conclusion, the CXCL12-CXCR4 pathway may be a potential target for DMD therapy.
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Affiliation(s)
- Xinsheng Lai
- School of Life Science, Nanchang University, Nanchang, Jiangxi, China.,Laboratory of Synaptic Development and Plasticity, Institute of Life Science, Nanchang University, Nanchang, Jiangxi, China
| | - Jie Chen
- School of Life Science, Nanchang University, Nanchang, Jiangxi, China.,Laboratory of Synaptic Development and Plasticity, Institute of Life Science, Nanchang University, Nanchang, Jiangxi, China
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27
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Zhang J, Yu R, Guo X, Zou Y, Chen S, Zhou K, Chen Y, Li Y, Gao S, Wu Y. Identification of TYR, TYRP1, DCT and LARP7 as related biomarkers and immune infiltration characteristics of vitiligo via comprehensive strategies. Bioengineered 2021; 12:2214-2227. [PMID: 34107850 PMCID: PMC8806433 DOI: 10.1080/21655979.2021.1933743] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
This study aims to explore biomarkers associated with vitiligo and analyze the pathological role of immune cell infiltration in the disease. We used the robust rank aggregation (RRA) method to integrate three vitiligo data sets downloaded from gene expression omnibus database, identify the differentially expressed genes (DEGs) and analyze the functional correlation. Then, the comprehensive strategy of combined weighted gene coexpression network analysis (WGCNA) and logical regression of the selection operator (LASSO), support vector machine recursive feature elimination (SVM-RFE), and random forest (RF) machine learning algorithm are employed to screen and biomarkers associated with vitiligo. Finally, the immune cell infiltration of vitiligo was evaluated by CIBERSORT, and the correlation between biomarkers and infiltrating immune cells was analyzed. Herein, we identified 131 robust DEGs, and enrichment analysis results showed that robust DEGs and melanogenesis were closely associated with vitiligo development and progression. TYR, TYRP1, DCT and LARP7 were identified as vitiligo-related biomarkers. Immune infiltration analysis demonstrated that CD4 T Cell, CD8 T Cell, Tregs, NK cells, dendritic cells, and macrophages were involved in vitiligo’s pathogenesis. In summary, we adopted a comprehensive strategy to screen biomarkers related to vitiligo and explore the critical role of immune cell infiltration in vitiligo. Abbreviations: TYR, Tyrosinase; TYRP1, Tyrosinase-related protein-1; DCT, dopachrome tautomerase; LARP7, La ribonucleoprotein domain family, member-7; RRA, robust rank aggregation; DEGs, differentially expressed genes; WGCNA, weighted gene coexpression network analysis; LASSO, logical regression of the selection operator; SVM-RFE, support vector machine recursive feature elimination; RF, random forest; GWAS, Genome-wide association study; FasL, Fas-Fas ligand; Tregs, T-regulatory cells; NK, natural killer; GEPCs, gene expression profiling chips; GO, gene ontology; GSEA, gene set enrichment analysis; FDR, false discovery rate; AUC, area under the curve; ROC, receiver-operating characteristic; BP, biological process; CC, cellular component; MF, molecular function.
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Affiliation(s)
- Jiayu Zhang
- Department of Dermatology, the First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China.,Department of Dermatology, The First Clinical Medical College of Yunnan University of Traditional Chinese Medicine, Kunming, Yunnan, China
| | - Rongguo Yu
- Department of Orthopedics, Fuzhou the Second Hospital Affiliated to Xiamen University, Fujian, China
| | - Xiaoyu Guo
- Department of Neurosurgery/Neuro-oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Yuanxia Zou
- Department of Newborn Medicine, Hospital (T.C.M) Affiliated to Southwest Medical University, Luzhou, Sichuan, China
| | - Sixuan Chen
- Department of Dermatology, The First Clinical Medical College of Yunnan University of Traditional Chinese Medicine, Kunming, Yunnan, China
| | - Kai Zhou
- Department of Dermatology, The First Clinical Medical College of Yunnan University of Traditional Chinese Medicine, Kunming, Yunnan, China
| | - Yi Chen
- Department of Dermatology, the First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - YongRong Li
- Department of Dermatology, the First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Su Gao
- Department of Dermatology, the First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yifei Wu
- Department of Dermatology, the First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
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28
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Yang Y, Long X, Li G, Yu X, Liu Y, Li K, Tian X. Prediction of clinical prognosis in cutaneous melanoma using an immune-related gene pair signature. Bioengineered 2021; 12:1803-1812. [PMID: 34047683 PMCID: PMC8806557 DOI: 10.1080/21655979.2021.1924556] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Cutaneous melanoma (CM) is a malignant and aggressive skin cancer that is the leading cause of skin cancer-related deaths. Increasing evidence shows that immunity plays a vital role in the prognosis of CM. In this study, we developed an immune-related gene pair (IRGP) signature to predict the clinical prognosis of patients with CM. Immune-related genes from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases were selected to construct the IRGPs, and patients with CM in these two cohorts were assigned to low- and high-risk subgroups. Moreover, we investigated the IRGPs and their individualized prognostic signatures using Kaplan-Meier survival analysis, univariate and multivariate Cox analyses, and analysis of immune cell infiltration in CM. A 41-IRGP signature was constructed from 2498 immune genes that could significantly predict the overall survival of patients with CM in both the TCGA and GEO cohorts. Immune infiltration analysis indicated that several immune cells, especially M1 macrophages and activated CD4 T cells, were significantly associated with the prognostic effect of the IRGP signature in patients with CM. Overall, the IRGP signature constructed in this study was useful for determining the prognosis of patients with CM and for providing further understanding of CM immunotherapy.
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Affiliation(s)
- Yu Yang
- Department of Emergency, The Second People's Hospital of Guiyang, Guiyang, China
| | - Xuan Long
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Guiyun Li
- Department of Emergency, The Second People's Hospital of Guiyang, Guiyang, China
| | - Xiaohong Yu
- Department of Emergency, The Second People's Hospital of Guiyang, Guiyang, China
| | - Yu Liu
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Kun Li
- Department of Emergency, The Second People's Hospital of Guiyang, Guiyang, China
| | - Xiaobin Tian
- Department of Orthopedics, Clinical Medical College, Guizhou Medical University, Guiyang, China
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29
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Kitani T, Maddipatla SC, Madupuri R, Greco C, Hartmann J, Baraniuk JN, Vasudevan S. In Search of Newer Targets for Inflammatory Bowel Disease: A Systems and a Network Medicine Approach. NETWORK AND SYSTEMS MEDICINE 2021. [DOI: 10.1089/nsm.2020.0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Takashi Kitani
- Department of Neurology, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia, USA
| | - Sushma C. Maddipatla
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia, USA
| | - Ramya Madupuri
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia, USA
| | - Christopher Greco
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia, USA
| | - Jonathan Hartmann
- Dahlgren Memorial Library, Graduate Health and Life Sciences Research Library, Georgetown University Medical Center, Washington, District of Columbia, USA
| | - James N. Baraniuk
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Georgetown University Medical Center, Washington, District of Columbia, USA
| | - Sona Vasudevan
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia, USA
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