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Li Q, Xin T, Liu Z, Wang Q, Ma L. Construction of ceRNA regulatory networks for active pulmonary tuberculosis. Sci Rep 2024; 14:10595. [PMID: 38719908 PMCID: PMC11079045 DOI: 10.1038/s41598-024-61451-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 05/06/2024] [Indexed: 05/12/2024] Open
Abstract
Delayed diagnosis in patients with pulmonary tuberculosis (PTB) often leads to serious public health problems. High throughput sequencing was used to determine the expression levels of lncRNAs, mRNAs, and miRNAs in the lesions and adjacent health lung tissues of patients with PTB. Their differential expression profiles between the two groups were compared, and 146 DElncRs, 447 DEmRs, and 29 DEmiRs were obtained between lesions and adjacent health tissues in patients with PTB. Enrichment analysis for mRNAs showed that they were mainly involved in Th1, Th2, and Th17 cell differentiation. The lncRNAs, mRNAs with target relationship with miRNAs were predicted respectively, and correlation analysis was performed. The ceRNA regulatory network was obtained by comparing with the differentially expressed transcripts (DElncRs, DEmRs, DEmiRs), then 2 lncRNAs mediated ceRNA networks were established. The expression of genes within the network was verified by quantitative real-time PCR (qRT-PCR). Flow cytometric analysis revealed that the proportion of Th1 cells and Th17 cells was lower in PTB than in controls, while the proportion of Th2 cells increased. Our results provide rich transcriptome data for a deeper investigation of PTB. The ceRNA regulatory network we obtained may be instructive for the diagnosis and treatment of PTB.
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Affiliation(s)
- Qifeng Li
- Xinjiang Institute of Pediatrics, Children's Hospital of Xinjiang Uygur Autonomous Region, NO. 393, Aletai Road, Shayibake District, Urumqi, 830054, Xinjiang, China.
| | - Tao Xin
- Department of Pediatrics, The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, 830049, China
| | - Zhigang Liu
- Department of Thoracic Surgery, The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, 830049, China
| | - Quan Wang
- Department of Clinical Laboratory, The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, 830049, China
| | - Lanhong Ma
- Department of Pediatrics, Children's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, 830054, China
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Akbar NU, Ahmad S, Khan TA, Tayyeb M, Akhter N, Shafiq L, Khan SN, Alam MM, Abdullah AM, Rehman MFU, Bajaber MA, Akram MS. Consanguineous marriages increase the incidence of recurrent tuberculosis: Evidence from whole exome sequencing. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 118:105559. [PMID: 38266757 DOI: 10.1016/j.meegid.2024.105559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 01/26/2024]
Abstract
BACKGROUND In this study, we have identified multiple mutations in the IL-12R1 gene among Pakistani patients who have inherited them through consanguineous marriages. These patients have experienced severe Bacille-Calmette-Guérin (BCG) infection as well as recurrent tuberculosis. We will demonstrate the pivotal role of interleukin (IL)-12/interferon (IFN)-γ axis in the regulation of mycobacterial diseases. METHODOLOGY First, we checked the patients' medical records, and then afterward, we assessed interferon-gamma (IFN-γ) production through ELISA. Following that, DNA was extracted to investigate IL-12/IFN- abnormalities. Whole exome sequencing was conducted through Sanger sequencing. Secretory cytokine levels were compared from healthy control of the same age groups and they were found to be considerably less in the disease cohort. To evaluate the probable functional impact of these alterations, an in silico study was performed. RESULTS The study found that the patients' PBMCs produced considerably less IFN-γ than expected. Analysis using flow cytometry showed that activated T cells lacked surface expression of IL-12Rβ1. Exon 7 of the IL-12Rβ1 gene, which encodes a portion of the cytokine binding region (CBR), and exon 10, which encodes the fibronectin-type III (FNIII) domain, were found to have the mutations c.641 A > G; p.Q214R and c.1094 T > C; p.M365T, respectively. In silico analysis showed that these mutations likely to have a deleterious effect on protein function. CONCLUSION Our findings indicate the significant contribution of the IL-12/IFN-γ is in combating infections due to mycobacterium. Among Pakistani patients born to consanguineous marriages, the identified mutations in the IL-12Rβ-1 gene provide insights into the genetic basis of severe BCG infections and recurrent tuberculosis. The study highlights the potential utility of newborn screening in regions with mandatory BCG vaccination, enabling early detection and intervention for primary immunodeficiencies associated with mycobacterial infections. Moreover, the study suggests at the potential role of other related genes such as IL-23Rβ1, TYK2, or JAK2 in IFN-γ production, warranting further investigation.
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Affiliation(s)
- Noor Ul Akbar
- Department of Zoology, Kohat University of Science and Technology, Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Sajjad Ahmad
- Institute of Pathology and Diagnostic Medicine, Khyber Medical University, Peshawar 25160, Pakistan
| | - Taj Ali Khan
- Institute of Pathology and Diagnostic Medicine, Khyber Medical University, Peshawar 25160, Pakistan; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Muhammad Tayyeb
- Institute of Pathology and Diagnostic Medicine, Khyber Medical University, Peshawar 25160, Pakistan
| | - Naheed Akhter
- Department of Biochemistry, Faculty of life Sciences, Government College University, Faisalabad 38000, Pakistan
| | - Laraib Shafiq
- Institute of Pathology and Diagnostic Medicine, Khyber Medical University, Peshawar 25160, Pakistan
| | - Shahid Niaz Khan
- Department of Zoology, Kohat University of Science and Technology, Kohat 26000, Khyber Pakhtunkhwa, Pakistan.
| | - Mohammad Mahtab Alam
- Department of Basic Medical Sciences, College of Applied Medical Science, King Khalid University, Abha 61421, Saudi Arabia
| | - Alduwish Manal Abdullah
- Department of Biology, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia
| | | | - Majed A Bajaber
- Department of Chemistry, Faculty of Science, King Khalid University, Abha 61413, Saudi Arabia
| | - Muhammad Safwan Akram
- School of Health and Life Sciences, Teesside University, Middlesbrough TS1 3BX, UK; National Horizons Centre, Teesside University, Darlington DL1 1HG, UK.
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Mokhtari L, Hosseinzadeh F, Nourazarian A. Biochemical implications of robotic surgery: a new frontier in the operating room. J Robot Surg 2024; 18:91. [PMID: 38401027 DOI: 10.1007/s11701-024-01861-6] [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: 11/23/2023] [Accepted: 02/01/2024] [Indexed: 02/26/2024]
Abstract
Robotic surgery represents a milestone in surgical procedures, offering advantages such as less invasive methods, elimination of tremors, scaled motion, and 3D visualization. This in-depth analysis explores the complex biochemical effects of robotic methods. The use of pneumoperitoneum and steep Trendelenburg positioning can decrease pulmonary compliance and splanchnic perfusion while increasing hypercarbia. However, robotic surgery reduces surgical stress and inflammation by minimizing tissue trauma. This contributes to faster recovery but may limit immune function. Robotic procedures also limit ischemia-reperfusion injury and oxidative damage compared to open surgery. They also help preserve native antioxidant defenses and coagulation. In a clinical setting, robotic procedures reduce blood loss, pain, complications, and length of stay compared to traditional procedures. However, risks remain, including device failure, the need for conversion to open surgery and increased costs. On the oncology side, there is still debate about margins, recurrence, and long-term survival. The advent of advanced technologies, such as intraoperative biosensors, localized drug delivery systems, and the incorporation of artificial intelligence, may further improve the efficiency of robotic surgery. However, ethical dilemmas regarding patient consent, privacy, access, and regulation of this disruptive innovation need to be addressed. Overall, this review sheds light on the complex biochemical implications of robotic surgery and highlights areas that require additional mechanistic investigation. It presents a comprehensive approach to responsibly maximize the potential of robotic surgery to improve patient outcomes, integrating technical skill with careful consideration of physiological and ethical issues.
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Affiliation(s)
- Leila Mokhtari
- Department of Nursing, Khoy University of Medical Sciences, Khoy, Iran
| | | | - Alireza Nourazarian
- Department of Basic Medical Sciences, Khoy University of Medical Sciences, Khoy, Iran.
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Bobak CA, Botha M, Workman L, Hill JE, Nicol MP, Holloway JW, Stein DJ, Martinez L, Zar HJ. Gene Expression in Cord Blood and Tuberculosis in Early Childhood: A Nested Case-Control Study in a South African Birth Cohort. Clin Infect Dis 2023; 77:438-449. [PMID: 37144357 PMCID: PMC10425199 DOI: 10.1093/cid/ciad268] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/21/2023] [Accepted: 04/29/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Transcriptomic profiling of adults with tuberculosis (TB) has become increasingly common, predominantly for diagnostic and risk prediction purposes. However, few studies have evaluated signatures in children, particularly in identifying those at risk for developing TB disease. We investigated the relationship between gene expression obtained from umbilical cord blood and both tuberculin skin test conversion and incident TB disease through the first 5 years of life. METHODS We conducted a nested case-control study in the Drakenstein Child Health Study, a longitudinal, population-based birth cohort in South Africa. We applied transcriptome-wide screens to umbilical cord blood samples from neonates born to a subset of selected mothers (N = 131). Signatures identifying tuberculin conversion and risk of subsequent TB disease were identified from genome-wide analysis of RNA expression. RESULTS Gene expression signatures revealed clear differences predictive of tuberculin conversion (n = 26) and TB disease (n = 10); 114 genes were associated with tuberculin conversion and 30 genes were associated with the progression to TB disease among children with early infection. Coexpression network analysis revealed 6 modules associated with risk of TB infection or disease, including a module associated with neutrophil activation in immune response (P < .0001) and defense response to bacterium (P < .0001). CONCLUSIONS These findings suggest multiple detectable differences in gene expression at birth that were associated with risk of TB infection or disease throughout early childhood. Such measures may provide novel insights into TB pathogenesis and susceptibility.
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Affiliation(s)
- Carly A Bobak
- Department of Biomedical Data Science, Dartmouth College, Hanover, New Hampshire
| | - Maresa Botha
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and South African Medical Research Council Unit on Child and Adolescent Health, Cape Town, South Africa
| | - Lesley Workman
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and South African Medical Research Council Unit on Child and Adolescent Health, Cape Town, South Africa
| | - Jane E Hill
- School of Biomedical Engineering and the School of Chemical and Biological Engineering, University of British Columbia, Vancouver, Canada
| | - Mark P Nicol
- Marshall Centre, Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia
- Division of Medical Microbiology, University of Cape Town, South Africa
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton
- National Institute for Health and Care Research Southampton Biomedical Research Center, University Hospital Southampton, United Kingdom
| | - Dan J Stein
- Department of Psychiatry and Mental Health, University of Cape Town
- Unit on Risk and Resilience in Mental Disorders, South African Medical Research Council
- Neuroscience Institute, University of Cape Town, South Africa
| | - Leonardo Martinez
- Department of Epidemiology, School of Public Health, Boston University, Massachusetts
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and South African Medical Research Council Unit on Child and Adolescent Health, Cape Town, South Africa
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Hasankhani A, Bahrami A, Mackie S, Maghsoodi S, Alawamleh HSK, Sheybani N, Safarpoor Dehkordi F, Rajabi F, Javanmard G, Khadem H, Barkema HW, De Donato M. In-depth systems biological evaluation of bovine alveolar macrophages suggests novel insights into molecular mechanisms underlying Mycobacterium bovis infection. Front Microbiol 2022; 13:1041314. [PMID: 36532492 PMCID: PMC9748370 DOI: 10.3389/fmicb.2022.1041314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/04/2022] [Indexed: 08/26/2023] Open
Abstract
OBJECTIVE Bovine tuberculosis (bTB) is a chronic respiratory infectious disease of domestic livestock caused by intracellular Mycobacterium bovis infection, which causes ~$3 billion in annual losses to global agriculture. Providing novel tools for bTB managements requires a comprehensive understanding of the molecular regulatory mechanisms underlying the M. bovis infection. Nevertheless, a combination of different bioinformatics and systems biology methods was used in this study in order to clearly understand the molecular regulatory mechanisms of bTB, especially the immunomodulatory mechanisms of M. bovis infection. METHODS RNA-seq data were retrieved and processed from 78 (39 non-infected control vs. 39 M. bovis-infected samples) bovine alveolar macrophages (bAMs). Next, weighted gene co-expression network analysis (WGCNA) was performed to identify the co-expression modules in non-infected control bAMs as reference set. The WGCNA module preservation approach was then used to identify non-preserved modules between non-infected controls and M. bovis-infected samples (test set). Additionally, functional enrichment analysis was used to investigate the biological behavior of the non-preserved modules and to identify bTB-specific non-preserved modules. Co-expressed hub genes were identified based on module membership (MM) criteria of WGCNA in the non-preserved modules and then integrated with protein-protein interaction (PPI) networks to identify co-expressed hub genes/transcription factors (TFs) with the highest maximal clique centrality (MCC) score (hub-central genes). RESULTS As result, WGCNA analysis led to the identification of 21 modules in the non-infected control bAMs (reference set), among which the topological properties of 14 modules were altered in the M. bovis-infected bAMs (test set). Interestingly, 7 of the 14 non-preserved modules were directly related to the molecular mechanisms underlying the host immune response, immunosuppressive mechanisms of M. bovis, and bTB development. Moreover, among the co-expressed hub genes and TFs of the bTB-specific non-preserved modules, 260 genes/TFs had double centrality in both co-expression and PPI networks and played a crucial role in bAMs-M. bovis interactions. Some of these hub-central genes/TFs, including PSMC4, SRC, BCL2L1, VPS11, MDM2, IRF1, CDKN1A, NLRP3, TLR2, MMP9, ZAP70, LCK, TNF, CCL4, MMP1, CTLA4, ITK, IL6, IL1A, IL1B, CCL20, CD3E, NFKB1, EDN1, STAT1, TIMP1, PTGS2, TNFAIP3, BIRC3, MAPK8, VEGFA, VPS18, ICAM1, TBK1, CTSS, IL10, ACAA1, VPS33B, and HIF1A, had potential targets for inducing immunomodulatory mechanisms by M. bovis to evade the host defense response. CONCLUSION The present study provides an in-depth insight into the molecular regulatory mechanisms behind M. bovis infection through biological investigation of the candidate non-preserved modules directly related to bTB development. Furthermore, several hub-central genes/TFs were identified that were significant in determining the fate of M. bovis infection and could be promising targets for developing novel anti-bTB therapies and diagnosis strategies.
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Affiliation(s)
- Aliakbar Hasankhani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Abolfazl Bahrami
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
- Biomedical Center for Systems Biology Science Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Shayan Mackie
- Faculty of Science, Earth Sciences Building, University of British Columbia, Vancouver, BC, Canada
| | - Sairan Maghsoodi
- Faculty of Paramedical Sciences, Kurdistan University of Medical Sciences, Kurdistan, Iran
| | - Heba Saed Kariem Alawamleh
- Department of Basic Scientific Sciences, AL-Balqa Applied University, AL-Huson University College, AL-Huson, Jordan
| | - Negin Sheybani
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Farhad Safarpoor Dehkordi
- Halal Research Center of IRI, FDA, Tehran, Iran
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Fatemeh Rajabi
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Ghazaleh Javanmard
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Hosein Khadem
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Herman W. Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Marcos De Donato
- Regional Department of Bioengineering, Tecnológico de Monterrey, Monterrey, Mexico
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Leal DFDVB, Santana da Silva MN, Pastana LF, Fernandes MR, de Athayde ADSC, Fernandes Porchera DCR, da Silva CA, Modesto AAC, De Assumpcão PP, dos Santos SEB, dos Santos NPC. Genetic Variants of MicroRNA and DROSHA Genes in Association With the Risk of Tuberculosis in the Amazon Population. Front Genet 2022; 13:850058. [PMID: 35309115 PMCID: PMC8924412 DOI: 10.3389/fgene.2022.850058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 01/28/2022] [Indexed: 11/17/2022] Open
Abstract
Tuberculosis (TB) is a chronic infection caused by Mycobacterium tuberculosis (Mtb) with high incidence and mortality. Studies reported that host genetic variants might be associated with the risk of tuberculosis. The aim of this study was to perform an association study between 26 single nucleotide polymorphisms (SNPs) and tuberculosis and evaluate whether these SNPs may confer risk factors to tuberculosis in the Amazon population. There were 52 males and 126 females, with total of 178 healthy controls. Genotyping was performed using TaqMan Open Array Genotyping. Ancestry-informative markers were used to estimate the ancestral proportions of the individuals in the case and control groups. The results indicated that the SNPs rs10035440 (DROSHA), rs7372209 (miR26-a1), rs1834306 (miR100), rs4919510 (miR608), and rs10739971 (pri-let-7a-1) were significantly associated with high risk and rs3746444 (miR499) and rs6505162 (miR423), with low risk of developing tuberculosis in the Amazon population. Our study concluded that seven miRNA polymorphisms were associated with tuberculosis. Our study contributes to a better understanding of TB pathogenesis and may promote the development of new diagnostic tools against M. tuberculosis infection.
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Affiliation(s)
| | | | | | - Marianne Rodrigues Fernandes
- Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém, Brazil
- *Correspondence: Marianne Rodrigues Fernandes,
| | | | | | | | | | | | - Sidney Emanuel Batista dos Santos
- Núcleo de Pesquisa em Oncologia, Universidade Federal do Pará, Belém, Brazil
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
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