1
|
Abhimanyu, Longlax SC, Nishiguchi T, Ladki M, Sheikh D, Martinez AL, Mace EM, Grimm SL, Caldwell T, Portillo Varela A, Sekhar RV, Mandalakas AM, Mlotshwa M, Ginidza S, Cirillo JD, Wallis RS, Netea MG, van Crevel R, Coarfa C, DiNardo AR. TCA metabolism regulates DNA hypermethylation in LPS and Mycobacterium tuberculosis-induced immune tolerance. Proc Natl Acad Sci U S A 2024; 121:e2404841121. [PMID: 39348545 DOI: 10.1073/pnas.2404841121] [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: 03/20/2024] [Accepted: 08/28/2024] [Indexed: 10/02/2024] Open
Abstract
Severe and chronic infections, including pneumonia, sepsis, and tuberculosis (TB), induce long-lasting epigenetic changes that are associated with an increase in all-cause postinfectious morbidity and mortality. Oncology studies identified metabolic drivers of the epigenetic landscape, with the tricarboxylic acid (TCA) cycle acting as a central hub. It is unknown if the TCA cycle also regulates epigenetics, specifically DNA methylation, after infection-induced immune tolerance. The following studies demonstrate that lipopolysaccharide and Mycobacterium tuberculosis induce changes in DNA methylation that are mediated by the TCA cycle. Infection-induced DNA hypermethylation is mitigated by inhibitors of cellular metabolism (rapamycin, everolimus, metformin) and the TCA cycle (isocitrate dehydrogenase inhibitors). Conversely, exogenous supplementation with TCA metabolites (succinate and itaconate) induces DNA hypermethylation and immune tolerance. Finally, TB patients who received everolimus have less DNA hypermethylation demonstrating proof of concept that metabolic manipulation can mitigate epigenetic scars.
Collapse
Affiliation(s)
- Abhimanyu
- Department of Pediatrics, The Global TB Program, William T Shearer Center for Immunobiology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030
| | - Santiago Carrero Longlax
- Department of Pediatrics, The Global TB Program, William T Shearer Center for Immunobiology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030
| | - Tomoki Nishiguchi
- Department of Pediatrics, The Global TB Program, William T Shearer Center for Immunobiology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030
| | - Malik Ladki
- Department of Pediatrics, The Global TB Program, William T Shearer Center for Immunobiology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030
| | - Daanish Sheikh
- Department of Pediatrics, The Global TB Program, William T Shearer Center for Immunobiology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030
| | - Amera L Martinez
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030
| | - Emily M Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032
| | - Sandra L Grimm
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Thaleia Caldwell
- Department of Pediatrics, The Global TB Program, William T Shearer Center for Immunobiology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030
| | - Alexandra Portillo Varela
- Department of Pediatrics, The Global TB Program, William T Shearer Center for Immunobiology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030
| | - Rajagopal V Sekhar
- Translational Metabolism Unit, Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Baylor College of Medicine, Houston, TX 77030
| | - Anna M Mandalakas
- Department of Pediatrics, The Global TB Program, William T Shearer Center for Immunobiology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030
- Epidemiology, Human Genetics & Environmental Sciences, University of Texas-UTHealth School of Public Health, Houston, TX 77030
- Clinical Infectious Disease Group, German Center for Infectious Research (DZIF), Clinical tuberculosis (TB) Unit, Research Center Borstel, Borstel 27246, Germany
| | - Mandla Mlotshwa
- The Aurum institute, Johannesburg 2006, South Africa
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Johannesburg, Johannesburg 2006, South Africa
- Department of Medicine, Vanderbilt University, Nashville, TN 37232
| | | | - Jeffrey D Cirillo
- Center for Airborne Pathogen Research and Imaging, Texas A&M College of Medicine, Bryan, TX 77843
| | - Robert S Wallis
- The Aurum institute, Johannesburg 2006, South Africa
- Department of Medicine, Case Western Reserve University, Cleveland, OH 44106
- Vanderbilt Institute for Global Health, Vanderbilt University, Nashville, TN 37232
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen 6525, Netherlands
- Department of Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, Bonn 53113, Germany
| | - Reinout van Crevel
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen 6525, Netherlands
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford OX1 4BH, United Kingdom
| | - Cristian Coarfa
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Andrew R DiNardo
- Department of Pediatrics, The Global TB Program, William T Shearer Center for Immunobiology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen 6525, Netherlands
| |
Collapse
|
2
|
Auld SC, Sheshadri A, Alexander-Brett J, Aschner Y, Barczak AK, Basil MC, Cohen KA, Dela Cruz C, McGroder C, Restrepo MI, Ridge KM, Schnapp LM, Traber K, Wunderink RG, Zhang D, Ziady A, Attia EF, Carter J, Chalmers JD, Crothers K, Feldman C, Jones BE, Kaminski N, Keane J, Lewinsohn D, Metersky M, Mizgerd JP, Morris A, Ramirez J, Samarasinghe AE, Staitieh BS, Stek C, Sun J, Evans SE. Postinfectious Pulmonary Complications: Establishing Research Priorities to Advance the Field: An Official American Thoracic Society Workshop Report. Ann Am Thorac Soc 2024; 21:1219-1237. [PMID: 39051991 DOI: 10.1513/annalsats.202406-651st] [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: 06/25/2024] [Indexed: 07/27/2024] Open
Abstract
Continued improvements in the treatment of pulmonary infections have paradoxically resulted in a growing challenge of individuals with postinfectious pulmonary complications (PIPCs). PIPCs have been long recognized after tuberculosis, but recent experiences such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have underscored the importance of PIPCs following other lower respiratory tract infections. Independent of the causative pathogen, most available studies of pulmonary infections focus on short-term outcomes rather than long-term morbidity among survivors. In this document, we establish a conceptual scope for PIPCs with discussion of globally significant pulmonary pathogens and an examination of how these pathogens can damage different components of the lung, resulting in a spectrum of PIPCs. We also review potential mechanisms for the transition from acute infection to PIPC, including the interplay between pathogen-mediated injury and aberrant host responses, which together result in PIPCs. Finally, we identify cross-cutting research priorities for the field to facilitate future studies to establish the incidence of PIPCs, define common mechanisms, identify therapeutic strategies, and ultimately reduce the burden of morbidity in survivors of pulmonary infections.
Collapse
|
3
|
Czajka N, Northrup JM, Jones MJ, Shafer ABA. Epigenetic clocks, sex markers and age-class diagnostics in three harvested large mammals. Mol Ecol Resour 2024; 24:e13956. [PMID: 38553977 DOI: 10.1111/1755-0998.13956] [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: 11/23/2023] [Revised: 02/05/2024] [Accepted: 03/14/2024] [Indexed: 06/04/2024]
Abstract
The development of epigenetic clocks, or the DNA methylation-based inference of age, is an emerging tool for ageing in free ranging populations. In this study, we developed epigenetic clocks for three species of large mammals that are the focus of extensive management throughout their range in North America: white-tailed deer, black bear and mountain goat. We quantified differential DNA methylation patterns at over 30,000 cytosine-guanine sites (CpGs) from tissue samples of all three species (black bear n = 49; white-tailed deer n = 47; mountain goat n = 45). We used a penalized regression model (elastic net) to build explanatory (black bear r = .95; white-tailed deer r = .99; mountain goat r = .97) and robust (black bear Median Absolute Error or MAE = 1.33; white-tailed deer MAE = 0.29; mountain goat MAE = 0.61) models of age or clocks. We also characterized individual CpG sites within each species that demonstrated clear differences in methylation levels between age classes and sex, which can be used to develop a suite of accessible diagnostic markers. This tool has the potential to contribute to wildlife monitoring by providing easily obtainable representations of age structure in managed populations.
Collapse
Affiliation(s)
- Natalie Czajka
- Department of Environmental Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Joseph M Northrup
- Department of Environmental Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, Ontario, Canada
| | - Meaghan J Jones
- Department of Biochemistry and Medical Genetics, Children's Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Aaron B A Shafer
- Department of Environmental Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- Department of Forensic Science, Trent University, Peterborough, Ontario, Canada
| |
Collapse
|
4
|
Singh M, Patel B, Seo M, Ahn P, Wais N, Shen H, Nakka S, Kishore P, Venketaraman V. TB and HIV induced immunosenescence: where do vaccines play a role? FRONTIERS IN AGING 2024; 5:1385963. [PMID: 38903242 PMCID: PMC11188299 DOI: 10.3389/fragi.2024.1385963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/13/2024] [Indexed: 06/22/2024]
Abstract
This paper tackles the complex interplay between Human Immunodeficiency virus (HIV-1) and Mycobacterium tuberculosis (M. tuberculosis) infections, particularly their contribution to immunosenescence, the age-related decline in immune function. Using the current literature, we discuss the immunological mechanisms behind TB and HIV-induced immunosenescence and critically evaluate the BCG (Bacillus Calmette-Guérin) vaccine's role. Both HIV-1 and M. tuberculosis demonstrably accelerate immunosenescence: M. tuberculosis through DNA modification and heightened inflammation, and HIV-1 through chronic immune activation and T cell production compromise. HIV-1 and M. tuberculosis co-infection further hastens immunosenescence by affecting T cell differentiation, underscoring the need for prevention and treatment. Furthermore, the use of the BCG tuberculosis vaccine is contraindicated in patients who are HIV positive and there is a lack of investigation regarding the use of this vaccine in patients who develop HIV co-infection with possible immunosenescence. As HIV does not currently have a vaccine, we focus our review more so on the BCG vaccine response as a result of immunosenescence. We found that there are overall limitations with the BCG vaccine, one of which is that it cannot necessarily prevent re-occurrence of infection due to effects of immunosenescence or protect the elderly due to this reason. Overall, there is conflicting evidence to show the vaccine's usage due to factors involving its production and administration. Further research into developing a vaccine for HIV and improving the BCG vaccine is warranted to expand scientific understanding for public health and beyond.
Collapse
Affiliation(s)
- Mona Singh
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA, United States
| | - Bhumika Patel
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA, United States
| | - Michael Seo
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA, United States
| | - Phillip Ahn
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA, United States
| | - Nejma Wais
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA, United States
| | - Haley Shen
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA, United States
| | - SriHarsha Nakka
- Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka, India
- Masters of Public Health, Chamberlain University, Addison, IL, United States
| | - Priya Kishore
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA, United States
| | - Vishwanath Venketaraman
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA, United States
| |
Collapse
|
5
|
Qin Y, Li T, An P, Ren Z, Xi J, Tang B. Important role of DNA methylation hints at significant potential in tuberculosis. Arch Microbiol 2024; 206:177. [PMID: 38494532 DOI: 10.1007/s00203-024-03888-7] [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: 12/02/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 03/19/2024]
Abstract
Tuberculosis (TB), an infectious disease caused by Mycobacterium tuberculosis (Mtb) infection, has persisted as a major global public health threat for millennia. Until now, TB continues to challenge efforts aimed at controlling it, with drug resistance and latent infections being the two main factors hindering treatment efficacy. The scientific community is still striving to understand the underlying mechanisms behind Mtb's drug resistance and latent infection. DNA methylation, a critical epigenetic modification occurring throughout an individual's growth and development, has gained attention following advances in high-throughput sequencing technologies. Researchers have observed abnormal DNA methylation patterns in the host genome during Mtb infection. Given the escalating issue of drug-resistant Mtb, delving into the role of DNA methylation in TB's development is crucial. This review article explores DNA methylation's significance in human growth, development and disease, and its role in regulating Mtb's evolution and infection processes. Additionally, it discusses potential applications of DNA methylation research in tuberculosis.
Collapse
Affiliation(s)
- Yuexuan Qin
- School of Life Science, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical University, Bengbu, 233030, Anhui Province, China
| | - Tianyue Li
- School of Life Science, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical University, Bengbu, 233030, Anhui Province, China
| | - Peiyan An
- School of Life Science, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical University, Bengbu, 233030, Anhui Province, China
| | - Zhi Ren
- First Affiliated Hospital of Bengbu Medical University, Bengbu, 233030, Anhui Province, China
| | - Jun Xi
- School of Life Science, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical University, Bengbu, 233030, Anhui Province, China.
| | - Bikui Tang
- School of Life Science, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical University, Bengbu, 233030, Anhui Province, China.
| |
Collapse
|
6
|
Li LS, Yang L, Zhuang L, Ye ZY, Zhao WG, Gong WP. From immunology to artificial intelligence: revolutionizing latent tuberculosis infection diagnosis with machine learning. Mil Med Res 2023; 10:58. [PMID: 38017571 PMCID: PMC10685516 DOI: 10.1186/s40779-023-00490-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/06/2023] [Indexed: 11/30/2023] Open
Abstract
Latent tuberculosis infection (LTBI) has become a major source of active tuberculosis (ATB). Although the tuberculin skin test and interferon-gamma release assay can be used to diagnose LTBI, these methods can only differentiate infected individuals from healthy ones but cannot discriminate between LTBI and ATB. Thus, the diagnosis of LTBI faces many challenges, such as the lack of effective biomarkers from Mycobacterium tuberculosis (MTB) for distinguishing LTBI, the low diagnostic efficacy of biomarkers derived from the human host, and the absence of a gold standard to differentiate between LTBI and ATB. Sputum culture, as the gold standard for diagnosing tuberculosis, is time-consuming and cannot distinguish between ATB and LTBI. In this article, we review the pathogenesis of MTB and the immune mechanisms of the host in LTBI, including the innate and adaptive immune responses, multiple immune evasion mechanisms of MTB, and epigenetic regulation. Based on this knowledge, we summarize the current status and challenges in diagnosing LTBI and present the application of machine learning (ML) in LTBI diagnosis, as well as the advantages and limitations of ML in this context. Finally, we discuss the future development directions of ML applied to LTBI diagnosis.
Collapse
Affiliation(s)
- Lin-Sheng Li
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, the Eighth Medical Center of PLA General Hospital, Beijing, 100091, China
- Hebei North University, Zhangjiakou, 075000, Hebei, China
- Senior Department of Respiratory and Critical Care Medicine, the Eighth Medical Center of PLA General Hospital, Beijing, 100091, China
| | - Ling Yang
- Hebei North University, Zhangjiakou, 075000, Hebei, China
| | - Li Zhuang
- Hebei North University, Zhangjiakou, 075000, Hebei, China
| | - Zhao-Yang Ye
- Hebei North University, Zhangjiakou, 075000, Hebei, China
| | - Wei-Guo Zhao
- Senior Department of Respiratory and Critical Care Medicine, the Eighth Medical Center of PLA General Hospital, Beijing, 100091, China.
| | - Wen-Ping Gong
- Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, the Eighth Medical Center of PLA General Hospital, Beijing, 100091, China.
| |
Collapse
|
7
|
Reyes A, Ortiz G, Duarte LF, Fernández C, Hernández-Armengol R, Palacios PA, Prado Y, Andrade CA, Rodriguez-Guilarte L, Kalergis AM, Simon F, Carreño LJ, Riedel CA, Cáceres M, González PA. Contribution of viral and bacterial infections to senescence and immunosenescence. Front Cell Infect Microbiol 2023; 13:1229098. [PMID: 37753486 PMCID: PMC10518457 DOI: 10.3389/fcimb.2023.1229098] [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: 05/25/2023] [Accepted: 08/24/2023] [Indexed: 09/28/2023] Open
Abstract
Cellular senescence is a key biological process characterized by irreversible cell cycle arrest. The accumulation of senescent cells creates a pro-inflammatory environment that can negatively affect tissue functions and may promote the development of aging-related diseases. Typical biomarkers related to senescence include senescence-associated β-galactosidase activity, histone H2A.X phosphorylation at serine139 (γH2A.X), and senescence-associated heterochromatin foci (SAHF) with heterochromatin protein 1γ (HP-1γ protein) Moreover, immune cells undergoing senescence, which is known as immunosenescence, can affect innate and adaptative immune functions and may elicit detrimental effects over the host's susceptibility to infectious diseases. Although associations between senescence and pathogens have been reported, clear links between both, and the related molecular mechanisms involved remain to be determined. Furthermore, it remains to be determined whether infections effectively induce senescence, the impact of senescence and immunosenescence over infections, or if both events coincidently share common molecular markers, such as γH2A.X and p53. Here, we review and discuss the most recent reports that describe cellular hallmarks and biomarkers related to senescence in immune and non-immune cells in the context of infections, seeking to better understand their relationships. Related literature was searched in Pubmed and Google Scholar databases with search terms related to the sections and subsections of this review.
Collapse
Affiliation(s)
- Antonia Reyes
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gerardo Ortiz
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luisa F. Duarte
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Christian Fernández
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Santiago, Chile
| | - Rosario Hernández-Armengol
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Pablo A. Palacios
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Yolanda Prado
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Catalina A. Andrade
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Linmar Rodriguez-Guilarte
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexis M. Kalergis
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Felipe Simon
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Leandro J. Carreño
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Claudia A. Riedel
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Mónica Cáceres
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Santiago, Chile
| | - Pablo A. González
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Grifoni A, Alonzi T, Alter G, Noonan DM, Landay AL, Albini A, Goletti D. Impact of aging on immunity in the context of COVID-19, HIV, and tuberculosis. Front Immunol 2023; 14:1146704. [PMID: 37292210 PMCID: PMC10246744 DOI: 10.3389/fimmu.2023.1146704] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/11/2023] [Indexed: 06/10/2023] Open
Abstract
Knowledge of aging biology needs to be expanded due to the continuously growing number of elderly people worldwide. Aging induces changes that affect all systems of the body. The risk of cardiovascular disease and cancer increases with age. In particular, the age-induced adaptation of the immune system causes a greater susceptibility to infections and contributes to the inability to control pathogen growth and immune-mediated tissue damage. Since the impact of aging on immune function, is still to be fully elucidated, this review addresses some of the recent understanding of age-related changes affecting key components of immunity. The emphasis is on immunosenescence and inflammaging that are impacted by common infectious diseases that are characterized by a high mortality, and includes COVID-19, HIV and tuberculosis.
Collapse
Affiliation(s)
- Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Tonino Alonzi
- Translational Research Unit, National Institute for Infectious Diseases “Lazzaro Spallanzani”-IRCCS, Rome, Italy
| | - Galit Alter
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
| | - Douglas McClain Noonan
- Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS) MultiMedica, Milan, Italy
- Immunology and General Pathology Laboratory, Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Alan L. Landay
- Department of Internal Medicine, Rush Medical College, Chicago, IL, United States
| | | | - Delia Goletti
- Translational Research Unit, National Institute for Infectious Diseases “Lazzaro Spallanzani”-IRCCS, Rome, Italy
| |
Collapse
|
10
|
Bobak CA, Zhao Y, Levy JJ, O’Malley AJ. GRANDPA: GeneRAtive network sampling using degree and property augmentation applied to the analysis of partially confidential healthcare networks. APPLIED NETWORK SCIENCE 2023; 8:23. [PMID: 37188323 PMCID: PMC10173245 DOI: 10.1007/s41109-023-00548-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/24/2023] [Indexed: 05/17/2023]
Abstract
Protecting medical privacy can create obstacles in the analysis and distribution of healthcare graphs and statistical inferences accompanying them. We pose a graph simulation model which generates networks using degree and property augmentation and provide a flexible R package that allows users to create graphs that preserve vertex attribute relationships and approximating the retention of topological properties observed in the original graph (e.g., community structure). We illustrate our proposed algorithm using a case study based on Zachary's karate network and a patient-sharing graph generated from Medicare claims data in 2019. In both cases, we find that community structure is preserved, and normalized root mean square error between cumulative distributions of the degrees across the generated and the original graphs is low (0.0508 and 0.0514 respectively).
Collapse
Affiliation(s)
- Carly A. Bobak
- Department of Biomedical Data Science, Dartmouth College, Hanover, NH USA
- The Dartmouth Institute for Health Policy and Clinical Practice, Dartmouth College, Hanover, NH USA
- Research Computing, Dartmouth College, Hanover, NH USA
| | - Yifan Zhao
- Department of Biomedical Data Science, Dartmouth College, Hanover, NH USA
- The Dartmouth Institute for Health Policy and Clinical Practice, Dartmouth College, Hanover, NH USA
| | - Joshua J. Levy
- Department of Pathology and Laboratory Medicine, Dartmouth College, Hanover, NH USA
- Department of Dermatology, Dartmouth College, Hanover, NH USA
- Department of Epidemiology, Dartmouth College, Hanover, NH USA
| | - A. James O’Malley
- Department of Biomedical Data Science, Dartmouth College, Hanover, NH USA
- The Dartmouth Institute for Health Policy and Clinical Practice, Dartmouth College, Hanover, NH USA
| |
Collapse
|
11
|
Baluku JB, Namiiro S, Namanda B, Katusabe S, Namusoke D, Nkonge R, Okecha T, Nassaazi C, Niyonzima N, Bogere N, Nuwagira E, Nabwana M, Ssekamatte P, Andia-Biraro I, Worodria W, Salata R, Mfinanga S, Gerson S, Kirenga B. Mycobacterium tuberculosis infection and cytogenetic abnormalities among people with HIV. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2023; 888:503640. [PMID: 37188437 DOI: 10.1016/j.mrgentox.2023.503640] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/17/2023]
Abstract
OBJECTIVE To compare cytogenetic abnormalities among people living with HIV (PLWH) with and without previous exposure to Mycobacterium tuberculosis (Mtb) (both latent tuberculosis infection [LTBI] and active tuberculosis [TB]). METHODS Adult PLWH (≥18 years) were randomly selected at three HIV clinics in Uganda. Previous active TB was confirmed in the clinics' TB records. LTBI was defined as a positive QuantiFERON-TB Gold Plus assay. Participants' buccal mucosal exfoliated cells were examined (per 2000 cells) using the buccal micronucleus assay for chromosomal aberrations (micronuclei and/or nuclear buds), cytokinetic defects (binucleated cells), proliferative potential (normal differentiated cells and basal cell frequency) and/or cell death (condensed chromatin, karyorrhexis, pyknotic and karyolytic cells). RESULTS Among 97 PLWH, 42 (43.3%) had exposure to Mtb;16 had previous successfully treated active TB and 26 had LTBI. PLWH with exposure to Mtb had a higher median number of normal differentiated cells (1806.5 [1757.0 - 1842.0] vs. 1784.0 [1732.0 - 1843.0], p = 0.031) and fewer karyorrhectic cells (12.0 [9.0 - 29.0] vs. 18.0 [11.0 - 30.0], p = 0.048) than those without. PLWH with LTBI had fewer karyorrhectic cells than those without (11.5 [8.0 - 29.0] vs. 18.0 [11 - 30], p = 0.006). CONCLUSION We hypothesized that previous exposure to Mtb is associated with cytogenetic damage among PLWH. We found that exposure to Mtb is associated with more normal differentiated cells and less frequent karyorrhexis (a feature of apoptosis). It is unclear whether this increases the propensity for tumorigenesis.
Collapse
Affiliation(s)
- Joseph Baruch Baluku
- Makerere University Lung Institute, Kampala, Uganda; Division of pulmonology, Kiruddu National Referral Hospital, Kampala, Uganda.
| | - Sharon Namiiro
- Department of internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Brenda Namanda
- Division of pulmonology, Kiruddu National Referral Hospital, Kampala, Uganda
| | - Shamim Katusabe
- Division of pulmonology, Kiruddu National Referral Hospital, Kampala, Uganda
| | | | - Reagan Nkonge
- Division of pulmonology, Kiruddu National Referral Hospital, Kampala, Uganda
| | | | | | | | | | - Edwin Nuwagira
- Department of Internal Medicine, Mbarara University of Science and Technology, Uganda
| | - Martin Nabwana
- Makerere University-Johns Hopkins University Research Collaboration, Kampala, Uganda
| | - Phillip Ssekamatte
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Irene Andia-Biraro
- Department of internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - William Worodria
- Makerere University Lung Institute, Kampala, Uganda; Department of internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Robert Salata
- Department of Medicine, UH Cleveland Medical Center, USA
| | - Sayoki Mfinanga
- National Institute for Medical Research, Muhimbili Center, Tanzania
| | - Stanton Gerson
- School of Medicine, Case Western Reserve University, USA
| | | |
Collapse
|
12
|
Bonavida V, Frame M, Nguyen KH, Rajurkar S, Venketaraman V. Mycobacterium tuberculosis: Implications of Ageing on Infection and Maintaining Protection in the Elderly. Vaccines (Basel) 2022; 10:1892. [PMID: 36366400 PMCID: PMC9693366 DOI: 10.3390/vaccines10111892] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/05/2022] [Accepted: 11/06/2022] [Indexed: 09/10/2024] Open
Abstract
Several reports have suggested that ageing negatively affects the human body resulting in the alteration of various parameters important for sufficient immune health. Although, the breakdown of innate and adaptive immunity has been hypothesized to increase an individual's susceptibility to infections including Mycobacteria tuberculosis (M. tb), little research has been done to bridge this gap and understand the pathophysiology underlying how ageing increases the pathogenesis of M. tb infection. Our objective was to study research from a plethora of resources to better understand the pathogenesis of ageing and its link to the human immune system. To achieve this goal, this article explores how ageing decreases the collective T-cell immune response, reduces glutathione (GSH) production, over activates the mammalian target of rapamycin (mTORC1) pathway, inhibits autophagy and mitophagy, and alters various protective genes/transcription factors. Specifically highlighting how each of these pathways cripple an individual's immune system and increases their susceptibility from M. tb infection. Furthermore, research summarized in this article gives rise to an additional mechanism of susceptibility to M. tb infection which includes a potential defect in antigen presenting by dendritic cells rather than the T-cells response. Inflammaging has also been shown to play a role in the ageing of the immune system and can also potentially be a driving factor for increased susceptibility to M. tb infection in the elderly. In addition, this article features possible preventative strategies that could decrease infections like M. tb in this population. These strategies would need to be further explored and range from immunomodulators, like Everolimus to antioxidant supplementation through GSH intake. We have also proposed the need to research these therapies in conjunction with the administration of the BCG vaccine, especially in endemic populations, to better understand the risk contracting M. tb infection as well as ways to prevent infection in the first place.
Collapse
Affiliation(s)
- Victor Bonavida
- Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Mitchell Frame
- Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Kevin H. Nguyen
- Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Shlok Rajurkar
- Division of Biological Sciences, University California Berkeley, Berkeley, CA 94720, USA
| | - Vishwanath Venketaraman
- Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| |
Collapse
|
13
|
Olmo-Fontánez AM, Turner J. Tuberculosis in an Aging World. Pathogens 2022; 11:pathogens11101101. [PMID: 36297158 PMCID: PMC9611089 DOI: 10.3390/pathogens11101101] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/18/2022] [Accepted: 09/22/2022] [Indexed: 11/29/2022] Open
Abstract
Tuberculosis (TB) is one of the leading causes of death due to its being an infectious disease, caused by the airborne pathogen Mycobacterium tuberculosis (M.tb). Approximately one-fourth of the world’s population is infected with latent M.tb, and TB is considered a global threat killing over 4000 people every day. The risk of TB susceptibility and mortality is significantly increased in individuals aged 65 and older, confirming that the elderly represent one of the largest reservoirs for M.tb infection. The elderly population faces many challenges that increase their risk of developing respiratory diseases, including TB. The challenges the elderly face in this regard include the following: decreased lung function, immuno-senescence, inflammaging, adverse drug effects, low tolerance to anti-TB drugs, lack of suitable diagnoses/interventions, and age-associated comorbidities. In order to find new therapeutic strategies to maintain lung homeostasis and resistance to respiratory infections as we age, it is necessary to understand the molecular and cellular mechanisms behind natural lung aging. This review focuses primarily on why the elderly are more susceptible to TB disease and death, with a focus on pulmonary function and comorbidities.
Collapse
Affiliation(s)
- Angélica M. Olmo-Fontánez
- Host Pathogen Interactions and Population Health Programs, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
- Integrated Biomedical Sciences Program, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Joanne Turner
- Host Pathogen Interactions and Population Health Programs, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
- Correspondence:
| |
Collapse
|
14
|
Grimm SL, Mendez EF, Stertz L, Meyer TD, Fries GR, Gandhi T, Kanchi R, Selvaraj S, Teixeira AL, Kosten TR, Gunaratne P, Coarfa C, Walss-Bass C. MicroRNA-mRNA networks are dysregulated in opioid use disorder postmortem brain: Further evidence for opioid-induced neurovascular alterations. Front Psychiatry 2022; 13:1025346. [PMID: 36713930 PMCID: PMC9878702 DOI: 10.3389/fpsyt.2022.1025346] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/05/2022] [Indexed: 01/15/2023] Open
Abstract
INTRODUCTION To understand mechanisms and identify potential targets for intervention in the current crisis of opioid use disorder (OUD), postmortem brains represent an under-utilized resource. To refine previously reported gene signatures of neurobiological alterations in OUD from the dorsolateral prefrontal cortex (Brodmann Area 9, BA9), we explored the role of microRNAs (miRNA) as powerful epigenetic regulators of gene function. METHODS Building on the growing appreciation that miRNAs can cross the blood-brain barrier, we carried out miRNA profiling in same-subject postmortem samples from BA9 and blood tissues. RESULTS miRNA-mRNA network analysis showed that even though miRNAs identified in BA9 and blood were fairly distinct, their target genes and corresponding enriched pathways overlapped strongly. Among the dominant enriched biological processes were tissue development and morphogenesis, and MAPK signaling pathways. These findings point to robust, redundant, and systemic opioid-induced miRNA dysregulation with a potential functional impact on transcriptomic changes. Further, using correlation network analysis, we identified cell-type specific miRNA targets, specifically in astrocytes, neurons, and endothelial cells, associated with OUD transcriptomic dysregulation. Finally, leveraging a collection of control brain transcriptomes from the Genotype-Tissue Expression (GTEx) project, we identified a correlation of OUD miRNA targets with TGF beta, hypoxia, angiogenesis, coagulation, immune system, and inflammatory pathways. DISCUSSION These findings support previous reports of neurovascular and immune system alterations as a consequence of opioid abuse and shed new light on miRNA network regulators of cellular response to opioid drugs.
Collapse
Affiliation(s)
- Sandra L Grimm
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, United States.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States.,Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
| | - Emily F Mendez
- Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Laura Stertz
- Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Thomas D Meyer
- Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Gabriel R Fries
- Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Tanmay Gandhi
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, United States.,Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
| | - Rupa Kanchi
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, United States.,Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
| | - Sudhakar Selvaraj
- Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Antonio L Teixeira
- Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Thomas R Kosten
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States.,Department of Psychiatry, Baylor College of Medicine, Houston, TX, United States
| | - Preethi Gunaratne
- Department of Biology and Biochemistry, University of Houston, TX, United States
| | - Cristian Coarfa
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, United States.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States.,Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
| | - Consuelo Walss-Bass
- Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| |
Collapse
|