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Magana-Arachchi D, Madegedara D, Bandara U. Whole Blood vs Serum-Derived Exosomes for Host and Pathogen-Specific Tuberculosis Biomarker Identification: RNA-Seq-Based Machine-Learning Approach. Biochem Genet 2024:10.1007/s10528-024-11002-1. [PMID: 39715973 DOI: 10.1007/s10528-024-11002-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 12/10/2024] [Indexed: 12/25/2024]
Abstract
Mycobacterium tuberculosis (Mtb) remains a leading infectious disease responsible for millions of deaths. RNA sequencing is a rapidly growing technique and a powerful approach to understanding host and pathogen cross-talks via transcriptional responses. However, its application is limited due to the high costs involved.This study is a preliminary attempt to understand host-pathogen cross-talk during TB infection in different TB clinical cohorts using two biological fluids: Whole blood and serum exosomes (EXO). We conducted an RNA-sequencing machine-learning approach using 20 active TB (ATB), 11 latent TB (LTB), three healthy control (HC) whole blood datasets, and two ATB, LTB, and HC serum EXO datasets. During the study, host-derived differentially expressed genes (DEGs) were identified in both whole blood and EXOs, while EXOs were successful in identifying pathogen-derived DEGs only in LTB. The majority of the DEGs in whole blood were up-regulated between ATB and HC, and ATB and LTB, while down-regulated between LTB and HC, which was vice versa for the EXOs, indicating different mechanisms in response to different states of TB infection across the two different biological samples. The pathway analysis revealed that whole blood gene signatures were mainly involved in host immune responses, whereas exosomal gene signatures were involved in manipulating the host's cellular responses and supporting Mtb survival. Overall, identifying both host and pathogen-derived gene signatures in different biological samples for intracellular pathogens like Mtb is vital to decipher the complex interplay between the host and the pathogen, ultimately leading to more successful future interventions.
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Affiliation(s)
| | | | - Upeka Bandara
- National Institute of Fundamental Studies, Kandy, Sri Lanka
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Teymouri S, Yousefi MH, Heidari S, Farokhi S, Afkhami H, Kashfi M. Beyond antibiotics: mesenchymal stem cells and bacteriophages-new approaches to combat bacterial resistance in wound infections. Mol Biol Rep 2024; 52:64. [PMID: 39699690 DOI: 10.1007/s11033-024-10163-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Accepted: 12/09/2024] [Indexed: 12/20/2024]
Abstract
Wound management is a major global health problem. With the rising incidence of diabetic wounds, accidents, and other injuries, the demand for prompt wound treatment has become increasingly critical. Millions of people suffer from serious, large wounds resulting from major accidents, surgeries, and wars. These wounds require considerable time to heal and are susceptible to infection. Furthermore, chronic wounds, particularly in elderly and diabetic patients, often require frequent medical interventions to prevent complications. Consequently, wound management imposes a significant economic burden worldwide. The complications arising from wound infections can vary from localized issues to systemic effects. The most severe local complication of wound infection is the non-healing, which results from the disruption of the wound-healing process. This often leads to significant pain, discomfort, and psychological trauma for the patient. Systemic complications may include cellulitis, osteomyelitis, and septicemia. Mesenchymal stem cells are characterized by their high capacity for division, making them suitable candidates for the treatment of tissue damage. Additionally, they produce antimicrobial peptides and various cytokines, which enhance their antimicrobial activity. Evidence shows that phages are effective in treating wound-related infections, and phage therapy has proven to be highly effective for patients when administered correctly. The purpose of this article is to explore the use of bacteriophages and mesenchymal stem cells in wound healing and infection management.
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Affiliation(s)
- Samane Teymouri
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Hasan Yousefi
- Department of Tissue Engineering and Applied Cell Sciences, School of Medicine, Qom University of Medical Sciences, Qom, Iran
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran
| | | | - Simin Farokhi
- Student Research Committee, USERN Office, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Hamed Afkhami
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran.
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran.
- Department of Medical Microbiology, Faculty of Medicine, Shahed University, Tehran, Iran.
| | - Mojtaba Kashfi
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran.
- Fellowship in Clinical Laboratory Sciences, Mashhad University of Medical Sciences, Mashhad, Iran.
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Khola S, Kumar S, Bhanwala N, Khatik GL. Polyketide Synthase 13 (Pks13) Inhibition: A Potential Target for New Class of Anti-tubercular Agents. Curr Top Med Chem 2024; 24:2362-2376. [PMID: 39297467 DOI: 10.2174/0115680266322983240906055750] [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: 04/14/2024] [Revised: 07/31/2024] [Accepted: 08/15/2024] [Indexed: 10/29/2024]
Abstract
Tuberculosis is one of the deadly infectious diseases that has resurfaced in multiple/ extensively resistant variants (MDR/XDR), threatening humankind. Today's world has a higher prevalence of tuberculosis (TB) than it has ever had throughout human history. Due to severe adverse effects, the marketed medications are not entirely effective in these forms. So, developing new drugs with a promising target is an immense necessity. Pks13 has emerged as a promising target for the mycobacterium. The concluding step of mycolic acid production involved Pks13, a crucial enzyme that helps form the precursor of mycolic acid via the Claisen-condensation reaction. It has five domains at the active site for targeting the enzyme and is used to test chemical entities for their antitubercular activity. Benzofurans, thiophenes, coumestans, N-phenyl indoles, and β lactones are the ligands that inhibit the Pks13 enzyme, showing potential antitubercular properties.
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Affiliation(s)
- Sonia Khola
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, Uttar Pradesh, 226002, India
| | - Sachin Kumar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, Uttar Pradesh, 226002, India
| | - Neeru Bhanwala
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, Uttar Pradesh, 226002, India
| | - Gopal L Khatik
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, Uttar Pradesh, 226002, India
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Kiselinova M, Naesens L, Huis In ’t Veld D, Boelens J, Van Braeckel E, Vande Weygaerde Y, Callens S. Management Challenges of Extrapulmonary Nontuberculous Mycobacterial Infection: A Single-Center Case Series and Literature Review. Pathogens 2023; 13:12. [PMID: 38276158 PMCID: PMC10819148 DOI: 10.3390/pathogens13010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/16/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
Extrapulmonary nontuberculous mycobacterial (NTM) disease remains largely enigmatic, yet these mycobacteria are increasingly acknowledged as important opportunistic pathogens in humans. Traditionally, NTM infections have been identified across various anatomical locations, with the respiratory system being the most affected and best understood. Historically, extrapulmonary NTM infection was predominantly associated with HIV/AIDS, with Mycobacterium avium lymphadenopathy being the most commonly reported. Today, however, because of the expanding utilization of immunosuppressive therapies and the demographic shift towards an aging population, an increasing number of NTM infections are expected and seen. Hence, a heightened index of suspicion is essential, necessitating a multifaceted approach to identification and drug sensitivity testing to improve treatment outcomes. In extrapulmonary NTM management, expert consultation is strongly recommended to determine the most efficacious treatment regimen, as individualized, patient-tailored therapies are often required. Furthermore, the economic burden of NTM disease is considerable, accompanied by high rates of hospitalization. To optimize the management of these intricate infections, there is an urgent need for comprehensive data on incidence, prevalence, and outcomes. This case-based series delves into the intricate nature of extrapulmonary NTM infections, focusing on both rapid and slow-growing NTM species, and explores therapeutic options, resistance mechanisms, and host-related immunological factors.
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Affiliation(s)
- Maja Kiselinova
- Department of General Internal Medicine, Ghent University Hospital, 9000 Ghent, Belgium; (L.N.); (S.C.)
| | - Leslie Naesens
- Department of General Internal Medicine, Ghent University Hospital, 9000 Ghent, Belgium; (L.N.); (S.C.)
| | - Diana Huis In ’t Veld
- Department of General Internal Medicine, Ghent University Hospital, 9000 Ghent, Belgium; (L.N.); (S.C.)
| | - Jerina Boelens
- Department of Microbiology, Ghent University Hospital, 9000 Ghent, Belgium;
| | - Eva Van Braeckel
- Department of Respiratory Medicine, Ghent University Hospital, 9000 Ghent, Belgium (Y.V.W.)
- Department of Internal Medicine and Paediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | | | - Steven Callens
- Department of General Internal Medicine, Ghent University Hospital, 9000 Ghent, Belgium; (L.N.); (S.C.)
- Department of Internal Medicine and Paediatrics, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
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Zhou J, Shi Y. Mesenchymal stem/stromal cells (MSCs): origin, immune regulation, and clinical applications. Cell Mol Immunol 2023; 20:555-557. [PMID: 37225837 PMCID: PMC10229593 DOI: 10.1038/s41423-023-01034-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/26/2023] Open
Affiliation(s)
- Jun Zhou
- The Third Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu, China
| | - Yufang Shi
- The Third Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu, China.
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