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Gorenjak M, Gole B, Goričan L, Jezernik G, Prosenc Zmrzljak U, Pernat C, Skok P, Potočnik U. Single-Cell Transcriptomic and Targeted Genomic Profiling Adjusted for Inflammation and Therapy Bias Reveal CRTAM and PLCB1 as Novel Hub Genes for Anti-Tumor Necrosis Factor Alpha Therapy Response in Crohn's Disease. Pharmaceutics 2024; 16:835. [PMID: 38931955 PMCID: PMC11207411 DOI: 10.3390/pharmaceutics16060835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/11/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND The lack of reliable biomarkers in response to anti-TNFα biologicals hinders personalized therapy for Crohn's disease (CD) patients. The motivation behind our study is to shift the paradigm of anti-TNFα biomarker discovery toward specific immune cell sub-populations using single-cell RNA sequencing and an innovative approach designed to uncover PBMCs gene expression signals, which may be masked due to the treatment or ongoing inflammation; Methods: The single-cell RNA sequencing was performed on PBMC samples from CD patients either naïve to biological therapy, in remission while on adalimumab, or while on ustekinumab but previously non-responsive to adalimumab. Sieves for stringent downstream gene selection consisted of gene ontology and independent cohort genomic profiling. Replication and meta-analyses were performed using publicly available raw RNA sequencing files of sorted immune cells and an association analysis summary. Machine learning, Mendelian randomization, and oligogenic risk score methods were deployed to validate DEGs highly relevant to anti-TNFα therapy response; Results: This study found PLCB1 in CD4+ T cells and CRTAM in double-negative T cells, which met the stringent statistical thresholds throughout the analyses. An additional assessment proved causal inference of both genes in response to anti-TNFα therapy; Conclusions: This study, jointly with an innovative design, uncovered novel candidate genes in the anti-TNFα response landscape of CD, potentially obscured by therapy or inflammation.
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Affiliation(s)
- Mario Gorenjak
- Centre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska ulica 8, SI-2000 Maribor, Slovenia; (B.G.); (L.G.); (G.J.); (U.P.)
| | - Boris Gole
- Centre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska ulica 8, SI-2000 Maribor, Slovenia; (B.G.); (L.G.); (G.J.); (U.P.)
| | - Larisa Goričan
- Centre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska ulica 8, SI-2000 Maribor, Slovenia; (B.G.); (L.G.); (G.J.); (U.P.)
| | - Gregor Jezernik
- Centre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska ulica 8, SI-2000 Maribor, Slovenia; (B.G.); (L.G.); (G.J.); (U.P.)
| | | | - Cvetka Pernat
- Department of Gastroenterology, Division of Internal Medicine, Maribor University Medical Centre, Ljubljanska ulica 5, SI-2000 Maribor, Slovenia; (C.P.); (P.S.)
| | - Pavel Skok
- Department of Gastroenterology, Division of Internal Medicine, Maribor University Medical Centre, Ljubljanska ulica 5, SI-2000 Maribor, Slovenia; (C.P.); (P.S.)
| | - Uroš Potočnik
- Centre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska ulica 8, SI-2000 Maribor, Slovenia; (B.G.); (L.G.); (G.J.); (U.P.)
- Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
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Peterson TE, Hahn VS, Moaddel R, Zhu M, Haberlen SA, Palella FJ, Plankey M, Bader JS, Lima JA, Gerszten RE, Rotter JI, Rich SS, Heckbert SR, Kirk GD, Piggott DA, Ferrucci L, Margolick JB, Brown TT, Wu KC, Post WS. Proteomic Signature of HIV-Associated Subclinical Left Atrial Remodeling and Incident Heart Failure. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.13.24302797. [PMID: 38405757 PMCID: PMC10888991 DOI: 10.1101/2024.02.13.24302797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Background People living with HIV (PLWH) are at higher risk of heart failure (HF) and preceding subclinical cardiac abnormalities, including left atrial dilation, compared to people without HIV (PWOH). Hypothesized mechanisms include premature aging linked to chronic immune activation. We leveraged plasma proteomics to identify potential novel contributors to HIV-associated differences in indexed left atrial volume (LAVi) among PLWH and PWOH and externally validated identified proteomic signatures with incident HF among a cohort of older PWOH. Methods We performed proteomics (Olink Explore 3072) on plasma obtained concurrently with cardiac magnetic resonance imaging among PLWH and PWOH in the United States. Proteins were analyzed individually and as agnostically defined clusters. Cross-sectional associations with HIV and LAVi were estimated using multivariable regression with robust variance. Among an independent general population cohort, we estimated associations between identified signatures and LAVi using linear regression and incident HF using Cox regression. Results Among 352 participants (age 55±6 years; 25% female), 61% were PLWH (88% on ART; 73% with undetectable HIV RNA) and mean LAVi was 29±9 mL/m 2 . Of 2594 analyzed proteins, 439 were associated with HIV serostatus, independent of demographics, hepatitis C virus infection, renal function, and substance use (FDR<0.05). We identified 73 of these proteins as candidate contributors to the independent association between positive HIV serostatus and higher LAVi, enriched in tumor necrosis factor (TNF) signaling and immune checkpoint proteins regulating T cell, B cell, and NK cell activation. We identified one protein cluster associated with LAVi and HIV regardless of HIV viral suppression status, which comprised 42 proteins enriched in TNF signaling, ephrin signaling, and extracellular matrix (ECM) organization. This protein cluster and 30 of 73 individual proteins were associated with incident HF among 2273 older PWOH (age 68±9 years; 52% female; 8.5±1.4 years of follow-up). Conclusion Proteomic signatures that may contribute to HIV-associated LA remodeling were enriched in immune checkpoint proteins, cytokine signaling, and ECM organization. These signatures were also associated with incident HF among older PWOH, suggesting specific markers of chronic immune activation, systemic inflammation, and fibrosis may identify shared pathways in HIV and aging that contribute to risk of HF.
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Walker GT, Gerner RR, Nuccio SP, Raffatellu M. Murine Models of Salmonella Infection. Curr Protoc 2023; 3:e824. [PMID: 37478288 PMCID: PMC10372748 DOI: 10.1002/cpz1.824] [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] [Indexed: 07/23/2023]
Abstract
The pathogen Salmonella enterica encompasses a range of bacterial serovars that cause intestinal inflammation and systemic infections in humans. Mice are a widely used infection model due to their relative simplicity and versatility. Here, we provide standardized protocols for culturing the prolific zoonotic pathogen S. enterica serovar Typhimurium for intragastric inoculation of mice to model colitis or systemic dissemination, along with techniques for direct extraintestinal infection. Furthermore, we present procedures for quantifying pathogen burden and for characterizing the immune response by analyzing tissue pathology, inflammatory markers, and immune cells from intestinal tissues. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Murine colitis model utilizing oral streptomycin pretreatment and oral S. Typhimurium administration Basic Protocol 2: Intraperitoneal injection of S. Typhimurium for modeling extraintestinal infection Support Protocol 1: Preparation of S. Typhimurium inoculum Support Protocol 2: Preparation of mixed S. Typhimurium inoculum for competitive infection Basic Protocol 3: Assessment of S. Typhimurium burden Support Protocol 3: Preservation and pathological assessment of S. Typhimurium-infected tissues Support Protocol 4: Measurement of inflammatory marker expression in intestinal tissues by qPCR Support Protocol 5: Preparation of intestinal content for inflammatory marker quantification by ELISA Support Protocol 6: Immune cell isolation from Salmonella-infected intestinal tissues.
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Affiliation(s)
- Gregory T. Walker
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Romana R. Gerner
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Technical University Munich, TUM School of Life Sciences Weihenstephan, ZIEL – Institute for Food & Health, Freising, Germany
- Department of Internal Medicine III, School of Medicine, University Hospital rechts der Isar, Technical University of Munich, Munich, Germany
| | - Sean-Paul Nuccio
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Manuela Raffatellu
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy, and Vaccines (CU-UCSD cMAV), La Jolla, CA 92093, USA
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Nectin Family Ligands Trigger Immune Effector Functions in Health and Autoimmunity. BIOLOGY 2023; 12:biology12030452. [PMID: 36979144 PMCID: PMC10045777 DOI: 10.3390/biology12030452] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/06/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023]
Abstract
The superfamily of immunoglobulin cell-adhesion molecules (IgCAMs) is a well-known family of cell-adhesion molecules used for immune-cell extravasation and cell–cell interaction. Amongst others, this family includes DNAX accessory molecule 1 (DNAM-1/CD226), class-I-restricted T-cell-associated molecule (CRTAM/CD355), T-cell-activated increased late expression (Tactile/CD96), T-cell immunoreceptor with Ig and ITIM domains (TIGIT), Nectins and Nectin-like molecules (Necls). Besides using these molecules to migrate towards inflammatory sites, their interactions within the immune system can support the immunological synapse with antigen-presenting cells or target cells for cytotoxicity, and trigger diverse effector functions. Although their role is generally described in oncoimmunity, this review emphasizes recent advances in the (dys)function of Nectin-family ligands in health, chronic inflammatory conditions and autoimmune diseases. In addition, this review provides a detailed overview on the expression pattern of Nectins and Necls and their ligands on different immune-cell types by focusing on human cell systems.
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Forgie AJ, Pepin DM, Ju T, Tollenaar S, Sergi CM, Gruenheid S, Willing BP. Over supplementation with vitamin B12 alters microbe-host interactions in the gut leading to accelerated Citrobacter rodentium colonization and pathogenesis in mice. MICROBIOME 2023; 11:21. [PMID: 36737826 PMCID: PMC9896722 DOI: 10.1186/s40168-023-01461-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 01/04/2023] [Indexed: 05/29/2023]
Abstract
BACKGROUND Vitamin B12 supplements typically contain doses that far exceed the recommended daily amount, and high exposures are generally considered safe. Competitive and syntrophic interactions for B12 exist between microbes in the gut. Yet, to what extent excessive levels contribute to the activities of the gut microbiota remains unclear. The objective of this study was to evaluate the effect of B12 on microbial ecology using a B12 supplemented mouse model with Citrobacter rodentium, a mouse-specific pathogen. Mice were fed a standard chow diet and received either water or water supplemented with B12 (cyanocobalamin: ~120 μg/day), which equates to approximately 25 mg in humans. Infection severity was determined by body weight, pathogen load, and histopathologic scoring. Host biomarkers of inflammation were assessed in the colon before and after the pathogen challenge. RESULTS Cyanocobalamin supplementation enhanced pathogen colonization at day 1 (P < 0.05) and day 3 (P < 0.01) postinfection. The impact of B12 on gut microbial communities, although minor, was distinct and attributed to the changes in the Lachnospiraceae populations and reduced alpha diversity. Cyanocobalamin treatment disrupted the activity of the low-abundance community members of the gut microbiota. It enhanced the amount of interleukin-12 p40 subunit protein (IL12/23p40; P < 0.001) and interleukin-17a (IL-17A; P < 0.05) in the colon of naïve mice. This immune phenotype was microbe dependent, and the response varied based on the baseline microbiota. The cecal metatranscriptome revealed that excessive cyanocobalamin decreased the expression of glucose utilizing genes by C. rodentium, a metabolic attribute previously associated with pathogen virulence. CONCLUSIONS Oral vitamin B12 supplementation promoted C. rodentium colonization in mice by altering the activities of the Lachnospiraceae populations in the gut. A lower abundance of select Lachnospiraceae species correlated to higher p40 subunit levels, while the detection of Parasutterella exacerbated inflammatory markers in the colon of naïve mice. The B12-induced change in gut ecology enhanced the ability of C. rodentium colonization by impacting key microbe-host interactions that help with pathogen exclusion. This research provides insight into how B12 impacts the gut microbiota and highlights potential consequences of disrupting microbial B12 competition/sharing through over-supplementation. Video Abstract.
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Affiliation(s)
- Andrew J Forgie
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Deanna M Pepin
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Tingting Ju
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Stephanie Tollenaar
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Consolato M Sergi
- Division of Anatomic Pathology, Children's Hospital of Eastern Ontario (CHEO), Ottawa, Ontario, Canada
| | - Samantha Gruenheid
- Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Benjamin P Willing
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada.
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Andrade-Meza A, Arias-Romero LE, Armas-López L, Ávila-Moreno F, Chirino YI, Delgado-Buenrostro NL, García-Castillo V, Gutiérrez-Cirlos EB, Juárez-Avelar I, Leon-Cabrera S, Mendoza-Rodríguez MG, Olguín JE, Perez-Lopez A, Pérez-Plasencia C, Reyes JL, Sánchez-Pérez Y, Terrazas LI, Vaca-Paniagua F, Villamar-Cruz O, Rodríguez-Sosa M. Mexican Colorectal Cancer Research Consortium (MEX-CCRC): Etiology, Diagnosis/Prognosis, and Innovative Therapies. Int J Mol Sci 2023; 24:ijms24032115. [PMID: 36768437 PMCID: PMC9917340 DOI: 10.3390/ijms24032115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 01/25/2023] Open
Abstract
In 2013, recognizing that Colorectal Cancer (CRC) is the second leading cause of death by cancer worldwide and that it was a neglected disease increasing rapidly in Mexico, the community of researchers at the Biomedicine Research Unit of the Facultad de Estudios Superiores Iztacala from the Universidad Nacional Autónoma de México (UNAM) established an intramural consortium that involves a multidisciplinary group of researchers, technicians, and postgraduate students to contribute to the understanding of this pathology in Mexico. This article is about the work developed by the Mexican Colorectal Cancer Research Consortium (MEX-CCRC): how the Consortium was created, its members, and its short- and long-term goals. Moreover, it is a narrative of the accomplishments of this project. Finally, we reflect on possible strategies against CRC in Mexico and contrast all the data presented with another international strategy to prevent and treat CRC. We believe that the Consortium's characteristics must be maintained to initiate a national strategy, and the reported data could be useful to establish future collaborations with other countries in Latin America and the world.
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Affiliation(s)
- Antonio Andrade-Meza
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores-Iztacala (FES-I), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico
| | - Luis E. Arias-Romero
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores-Iztacala (FES-I), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
| | - Leonel Armas-López
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores-Iztacala (FES-I), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
| | - Federico Ávila-Moreno
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores-Iztacala (FES-I), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
| | - Yolanda I. Chirino
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores-Iztacala (FES-I), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
| | - Norma L. Delgado-Buenrostro
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores-Iztacala (FES-I), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
| | - Verónica García-Castillo
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores-Iztacala (FES-I), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
| | - Emma B. Gutiérrez-Cirlos
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores-Iztacala (FES-I), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
| | - Imelda Juárez-Avelar
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores-Iztacala (FES-I), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
- Programa de Doctorado en Ciencias Biológicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico
| | - Sonia Leon-Cabrera
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores-Iztacala (FES-I), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
- Carrera de Médico Cirujano, Facultad de Estudios Superiores-Iztacala (FES-I), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
| | - Mónica G. Mendoza-Rodríguez
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores-Iztacala (FES-I), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
| | - Jonadab E. Olguín
- Laboratorio Nacional en Salud: Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores-Iztacala (FES-I), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
| | - Araceli Perez-Lopez
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores-Iztacala (FES-I), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
| | - Carlos Pérez-Plasencia
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores-Iztacala (FES-I), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Ciudad de México 14080, Mexico
| | - José L. Reyes
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores-Iztacala (FES-I), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
| | - Yesennia Sánchez-Pérez
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Ciudad de México 14080, Mexico
| | - Luis I. Terrazas
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores-Iztacala (FES-I), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
- Laboratorio Nacional en Salud: Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores-Iztacala (FES-I), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
| | - Felipe Vaca-Paniagua
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores-Iztacala (FES-I), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
- Laboratorio Nacional en Salud: Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores-Iztacala (FES-I), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Ciudad de México 14080, Mexico
| | - Olga Villamar-Cruz
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores-Iztacala (FES-I), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
| | - Miriam Rodríguez-Sosa
- Unidad de Investigación en Biomedicina, Facultad de Estudios Superiores-Iztacala (FES-I), Universidad Nacional Autónoma de México (UNAM), Tlalnepantla 54090, Mexico
- Correspondence: ; Tel.: +52-55-5623-1333
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Identification and Validation of Hub Genes for Predicting Treatment Targets and Immune Landscape in Rheumatoid Arthritis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:8023779. [PMID: 36317112 PMCID: PMC9617710 DOI: 10.1155/2022/8023779] [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: 06/27/2022] [Accepted: 09/27/2022] [Indexed: 11/17/2022]
Abstract
Background Rheumatoid arthritis (RA) is recognized as a chronic inflammatory disease featured by pathological synovial inflammation. Currently, the underlying pathophysiological mechanisms of RA remain unclear. In the study, we attempted to explore the underlying mechanisms of RA and provide potential targets for the therapy of RA via bioinformatics analysis. Methods We downloaded four microarray datasets (GSE77298, GSE55235, GSE12021, and GSE55457) from the GEO database. Firstly, GSE77298 and GSE55457 were identified DEGs by the “limma” and “sva” packages of R software. Then, we performed GO, KEGG, and GSEA enrichment analyses to further analyze the function of DEGs. Hub genes were screened using LASSO analysis and SVM-RFE analysis. To further explore the differences of the expression of hub genes in healthy control and RA patient synovial tissues, we calculated the ROC curves and AUC. The expression levels of hub genes were verified in synovial tissues of normal and RA rats by qRT-PCR and western blot. Furthermore, the CIBERSORTx was implemented to assess the differences of infiltration in 22 immune cells between normal and RA synovial tissues. We explored the association between hub genes and infiltrating immune cells. Results CRTAM, CXCL13, and LRRC15 were identified as RA's potential hub genes by machine learning and LASSO algorithms. In addition, we verified the expression levels of three hub genes in the synovial tissue of normal and RA rats by PCR and western blot. Moreover, immune cell infiltration analysis showed that plasma cells, T follicular helper cells, M0 macrophages, M1 macrophages, and gamma delta T cells may be engaged in the development and progression of RA. Conclusions In brief, our study identified and validated that three hub genes CRTAM, CXCL13, and LRRC15 might involve in the pathological development of RA, which could provide novel perspectives for the diagnosis and treatment with RA.
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Corley MJ, Pang APS, Rasmussen TA, Tolstrup M, Søgaard OS, Ndhlovu LC. Candidate host epigenetic marks predictive for HIV reservoir size, responsiveness to latency reversal, and viral rebound. AIDS 2021; 35:2269-2279. [PMID: 34482353 PMCID: PMC8563431 DOI: 10.1097/qad.0000000000003065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
OBJECTIVE This study aimed to identify candidate host epigenetic biomarkers predicting latency reversal agents (LRA) efficacy and HIV-1 rebound kinetics during analytical treatment interruption (ATI). DESIGN Retrospective longitudinal epigenetic profiling study from 13 people with HIV (PWH) on virologically suppressive antiretroviral therapy (ART) that participated in a LRA (HDAC inhibitor) clinical trial (NCT01680094) and a subsequent optional ATI to monitor for viral recrudescence after ART cessation. METHODS Genome-wide DNA methylation (DNAm) in purified CD4+ T cells was measured at single-nucleotide resolution using the Infinium MethylationEPIC array. HIV-1 DNA and RNA measures were previously assessed by PCR-based methods and the association of DNAm levels at regulatory sites of the human genome were examined with reservoir size, responsiveness to LRA, and time to viral rebound following ATI. RESULTS A distinct set of 15 candidate DNAm sites in purified CD4+ T cells at baseline pre-LRA and pre-ATI significantly correlated with time to viral rebound. Eight of these DNAm sites occurred in genes linked to HIV-1 replication dynamics including (SEPSECS, cg19113954), (MALT1, cg15968021), (CPT1C, cg14318858), (CRTAM, cg10977115), (B4GALNT4, cg04663285), (IL10, cg16284789), (TFPI2, cg19645693), and (LIFR, cg26437306); with the remaining sites at intergenic regions containing regulatory elements. Moreover, baseline DNAm states related to total HIV-1 DNA levels and the fold change in unspliced cell-associated HIV RNA following LRA treatment. CONCLUSION Preexisting host epigenetic states may determine HIV-1 rebound kinetics and reservoir maintenance. These findings suggest integrating a suite of DNA methylation markers to improve optimal participant selection and drug regimen in future HIV cure clinical trials.
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Affiliation(s)
- Michael J. Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Alina PS Pang
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Thomas A. Rasmussen
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC 3000, Australia
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Martin Tolstrup
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Ole S. Søgaard
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Lishomwa C. Ndhlovu
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
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