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Cui H, Duan R, Niu H, Yu T, Huang K, Chen C, Hao K, Yang T, Wang C. Integrated analysis of mRNA and long noncoding RNA profiles in peripheral blood mononuclear cells of patients with bronchial asthma. BMC Pulm Med 2022; 22:174. [PMID: 35501805 PMCID: PMC9059365 DOI: 10.1186/s12890-022-01945-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 04/11/2022] [Indexed: 12/02/2022] Open
Abstract
Background Bronchial asthma is a heterogeneous disease with distinct disease phenotypes and underlying pathophysiological mechanisms. Long non-coding RNAs (lncRNAs) are involved in numerous functionally different biological and physiological processes. The aim of this study was to identify differentially expressed lncRNAs and mRNAs in patients with asthma and further explore the functions and interactions between lncRNAs and mRNAs. Methods Ten patients with asthma and 9 healthy controls were enrolled in this study. RNA was isolated from peripheral blood mononuclear cells. We performed microarray analysis to evaluate lncRNA and mRNA expression. The functions of the differentially expressed mRNAs were analyzed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses. A global signal transduction network was constructed to identify the core mRNAs. An lncRNA–mRNA network was constructed. Five mRNAs showing the greatest differences in expression levels or high degrees in the gene–gene functional interaction network, with their correlated lncRNAs, were validated by real-time quantitative polymerase chain reaction. Results We identified 2229 differentially expressed mRNAs and 1397 lncRNAs between the asthma and control groups. Kyoto Encyclopedia of Genes and Genomes pathway analysis identified many pathways associated with inflammation and cell survival. The gene–gene functional interaction network suggested that some core mRNAs are involved in the pathogenesis of bronchial asthma. The lncRNA–mRNA co-expression network revealed correlated lncRNAs. CXCL8, FOXO3, JUN, PIK3CA, and G0S2 and their related lncRNAs NONHSAT115963, AC019050.1, MTCYBP3, KB-67B5.12, and HNRNPA1P12 were identified according to their differential expression levels and high degrees in the gene–gene network. Conclusions We identified the core mRNAs and their related lncRNAs and predicted the biological processes and signaling pathways involved in asthma. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-022-01945-9.
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Affiliation(s)
- Han Cui
- Department of Pathophysiology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Department of Geriatric, Beijing Hospital, Beijing, China
| | - Ruirui Duan
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Hongtao Niu
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Tao Yu
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Ke Huang
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Chen Chen
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ting Yang
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China. .,Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China. .,Institute of Respiratory Medicine, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, China.
| | - Chen Wang
- Department of Pathophysiology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China. .,Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China. .,Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China. .,Institute of Respiratory Medicine, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, China.
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Resino S, Jiménez-Sousa MÁ, Blanco J, Pacheco YM, del Romero J, Peraire J, Virseda-Berdices A, Muñoz-Gómez MJ, Galera-Peñaranda C, García-Fraile LJ, Benito JM, Rallón N. DBP rs7041 and DHCR7 rs3829251 are Linked to CD4+ Recovery in HIV Patients on Antiretroviral Therapy. Front Pharmacol 2022; 12:773848. [PMID: 35115928 PMCID: PMC8804497 DOI: 10.3389/fphar.2021.773848] [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: 09/13/2021] [Accepted: 12/09/2021] [Indexed: 12/03/2022] Open
Abstract
Background: The lack of the recovery of CD4+ T-cells (CD4+ recovery) among immunodeficiency virus (HIV)-infected patients on antiretroviral therapy (ART) is not well known. We aimed to analyze the association between single nucleotide polymorphisms (SNPs) underlying vitamin D metabolism and the CD4+ recovery in naïve HIV-infected patients who started ART with low baseline CD4+. Methods: We conducted a retrospective study in 411 naïve individuals with plasma HIV load >200 copies/mL and CD4+ <200 cells/mm3. During 24 months of follow-up, all patients had plasma HIV load <50 copies/mL. DNA genotyping was performed using the Sequenom MassARRAY platform. The outcome variable was the change in CD4+ during the study. Results: CD4+ recovery was higher in patients carrying DBP rs7041 AA genotype (AA versus CC/AC) and DHCR7 rs3829251 AA genotype (AA versus GG/AG) (p-value < 0.05). DBP rs7041 AA genotype was linked to increase in CD4+ (adjusted arithmetic mean ratio (aAMR) = 1.22; q-value = 0.011), increase in CD4+ ≥P75th [adjusted odds ratio (aOR) = 2.31; q-value = 0.005], slope of CD4+ recovery (aAMR = 1.25; q-value = 0.008), slope of CD4+ recovery ≥ P75th (aOR = 2.55; q-value = 0.005) and achievement of CD4+ ≥500 cells/mm3 (aOR = 1.89; q-value = 0.023). Besides, DHCR7 rs3829251 AA genotype was related to increase in CD4+ (aAMR = 1.43; q-value = 0.031), increase in CD4+ ≥P75th (aOR = 3.92; q-value = 0.030), slope of CD4+ recovery (aAMR = 1.40; q-value = 0.036), slope of CD4+ recovery ≥ P75th (aOR = 3.42; q-value = 0.031) and achievement of CD4+ ≥500 cells/mm3 (aOR = 5.68; q-value = 0.015). Conclusion: In summary, DHCR7 rs3829251 and DBP rs7041 polymorphisms were associated with CD4+ recovery in HIV-infected patients who started cART with low CD4+ T-cell counts.
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Affiliation(s)
- Salvador Resino
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- *Correspondence: Salvador Resino,
| | - María Ángeles Jiménez-Sousa
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Julià Blanco
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Virología e Inmunología Celular, IrsiCaixa AIDS Research Institute, Badalona, Spain
| | - Yolanda M. Pacheco
- Laboratorio de Inmunología, Instituto de Biomedicina de Sevilla (IBiS), Sevilla, Spain
| | - Jorge del Romero
- Centro Sanitario Sandoval, Hospital Clínico San Carlos, Madrid, Spain
| | - Joaquim Peraire
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Departamento de Medicina Interna, Hospital Universitari de Tarragona Joan XXIII, Tarragona, Spain
| | - Ana Virseda-Berdices
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - María José Muñoz-Gómez
- Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Galera-Peñaranda
- Departamento de Medicina Interna, Hospital Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Lucio Jesus García-Fraile
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Departamento de Medicina Interna, Hospital Universitario de La Princesa, Madrid, Spain
| | - José M. Benito
- Laboratorio de Investigación Del VIH y la Hepatitis Viral, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | - Norma Rallón
- Laboratorio de Investigación Del VIH y la Hepatitis Viral, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Hospital Universitario Rey Juan Carlos, Móstoles, Spain
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