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Powell SM, Jarsberg LG, Zionce ELM, Anderson LN, Gritsenko MA, Nahid P, Jacobs JM. Longitudinal analysis of host protein serum signatures of treatment and recovery in pulmonary tuberculosis. PLoS One 2024; 19:e0294603. [PMID: 38421964 PMCID: PMC10903915 DOI: 10.1371/journal.pone.0294603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/03/2023] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND A better understanding of treatment progression and recovery in pulmonary tuberculosis (TB) infectious disease is crucial. This study analyzed longitudinal serum samples from pulmonary TB patients undergoing interventional treatment to identify surrogate markers for TB-related outcomes. METHODS Serum that was collected at baseline and 8, 17, 26, and 52 weeks from 30 TB patients experiencing durable cure were evaluated and compared using a sensitive LC-MS/MS proteomic platform for the detection and quantification of differential host protein signatures relative to timepoint. The global proteome signature was analyzed for statistical differences across the time course and between disease severity and treatment groups. RESULTS A total of 676 proteins showed differential expression in the serum over these timepoints relative to baseline. Comparisons to understand serum protein dynamics at 8 weeks, treatment endpoints at 17 and 26 weeks, and post-treatment at 52 weeks were performed. The largest protein abundance changes were observed at 8 weeks as the initial effects of antibiotic treatment strongly impacted inflammatory and immune modulated responses. However, the largest number of proteome changes was observed at the end of treatment time points 17 and 26 weeks respectively. Post-treatment 52-week results showed an abatement of differential proteome signatures from end of treatment, though interestingly those proteins uniquely significant at post-treatment were almost exclusively downregulated. Patients were additionally stratified based upon disease severity and compared across all timepoints, identifying 461 discriminating proteome signatures. These proteome signatures collapsed into discrete expression profiles with distinct pathways across immune activation and signaling, hemostasis, and metabolism annotations. Insulin-like growth factor (IGF) and Integrin signaling maintained a severity signature through 52 weeks, implying an intrinsic disease severity signature well into the post-treatment timeframe. CONCLUSION Previous proteome studies have primarily focused on the 8-week timepoint in relation to culture conversion status. While this study confirms previous observations, it also highlights some differences. The inclusion of additional end of treatment and post-treatment time points offers a more comprehensive assessment of treatment progression within the serum proteome. Examining the expression dynamics at these later time periods will help in the investigation of relapse patients and has provided indicative markers of response and recovery.
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Affiliation(s)
- Samantha M. Powell
- Biologcal Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Leah G. Jarsberg
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Erin L. M. Zionce
- Earth Systems Science Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Lindsey N. Anderson
- Biologcal Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Marina A. Gritsenko
- Biologcal Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Payam Nahid
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Jon M. Jacobs
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
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Gregory DJ, Han F, Li P, Gritsenko M, Kyle J, Riley FE, Chavez D, Yotova V, Sindeaux RH, Hawash MBF, Xu F, Hung LY, Hayden DL, Tompkins RG, Lanford RE, Kobzik L, Hellman J, Jacobs JM, Barreiro LB, Xiao W, Warren HS. Multi-Omic blood analysis reveals differences in innate inflammatory sensitivity between species. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.30.23299243. [PMID: 38076828 PMCID: PMC10705660 DOI: 10.1101/2023.11.30.23299243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Vertebrates differ greatly in responses to pro-inflammatory agonists such as bacterial lipopolysaccharide (LPS), complicating use of animal models to study human sepsis or inflammatory disorders. We compared transcriptomes of resting and LPS-exposed blood from six LPS-sensitive species (rabbit, pig, sheep, cow, chimpanzee, human) and four LPS-resilient species (mice, rats, baboon, rhesus), as well as plasma proteomes and lipidomes. Unexpectedly, at baseline, sensitive species already had enhanced expression of LPS-responsive genes relative to resilient species. After LPS stimulation, maximally different genes in resilient species included genes that detoxify LPS, diminish bacterial growth, discriminate sepsis from SIRS, and play roles in autophagy and apoptosis. The findings reveal the molecular landscape of species differences in inflammation, and may inform better selection of species for pre-clinical models.
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Affiliation(s)
- David J. Gregory
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Feifei Han
- Harvard Medical School, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Peng Li
- Harvard Medical School, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Marina Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA, USA
| | - Jennifer Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA, USA
| | - Frank E. Riley
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA, USA
| | - Deborah Chavez
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio TX, USA
| | - Vania Yotova
- Centre Hospitalier Universitaire Sainte-Justine, Montréal, Québec, Canada
| | | | - Mohamed B. F. Hawash
- Centre Hospitalier Universitaire Sainte-Justine, Montréal, Québec, Canada
- Department of Biochemistry, University of Montréal, Montréal, Québec, Canada
| | - Fengyun Xu
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, USA
| | - Li-Yuan Hung
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Douglas L. Hayden
- Harvard Medical School, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ron G. Tompkins
- Harvard Medical School, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Robert E. Lanford
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio TX, USA
| | - Lester Kobzik
- Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Judith Hellman
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan M. Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA, USA
| | - Luis B. Barreiro
- Centre Hospitalier Universitaire Sainte-Justine, Montréal, Québec, Canada
- Department of Biochemistry, University of Montréal, Montréal, Québec, Canada
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
- Committee on Immunology, University of Chicago, Chicago, IL, USA
| | - Wenzhong Xiao
- Harvard Medical School, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - H. Shaw Warren
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA
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Kaur B, Dixit R, Bakshi S, Konar M, Sinha SK, Duseja AK, Sharma S. Proteomic-based identification of APCS as candidate protein for diagnosis of patients exhibiting anti-tubercular drug induced liver injury. Sci Rep 2023; 13:10135. [PMID: 37349331 PMCID: PMC10287637 DOI: 10.1038/s41598-023-35930-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: 12/17/2022] [Accepted: 05/25/2023] [Indexed: 06/24/2023] Open
Abstract
Traditional markers evaluate anti-tubercular drug-induced liver injury (AT-DILI). However, these markers have certain limitations and studies are in progress to characterize AT-DILI at an early stage. In the present study, 40 patients were categorized and equally distributed into healthy controls, newly diagnosed tuberculosis (TB), TB without hepatotoxicity and TB with hepatotoxicity groups based on their conventional liver function tests. Relative protein quantification was performed on depleted pooled serum samples of each representative group by LC-MS/MS, and validation of shortlisted protein was done by ELISA. Levels of all analysed biochemical parameters showed a statistical increment in the hepatotoxicity group compared to the other three groups, representing AT-DILI. Comparative proteomic analysis between TB with hepatotoxicity versus TB without hepatotoxicity groups highlighted 24 significant differentially expressed proteins, including PROS1, KNG1, CFH, LCAT, APCS and ADIPOQ. Identified proteins were involved in complement activation, triglyceride-rich lipoprotein particle remodelling and pathways comprising complement, coagulation cascades and cholesterol metabolism. Based on functional relevance, the serum amyloid P component (APCS) was shortlisted for validation, and it showed a similar trend as observed in the discovery phase with 100% sensitivity and 87% specificity; however, findings need exploration in larger cohorts.
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Affiliation(s)
- Bhavneet Kaur
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Ravi Dixit
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Shikha Bakshi
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Monidipa Konar
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Saroj K Sinha
- Department of Gastroenterology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Ajay Kumar Duseja
- Department of Hepatology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Sadhna Sharma
- Department of Biochemistry, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India.
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Bahlool AZ, Grant C, Cryan SA, Keane J, O'Sullivan MP. All trans retinoic acid as a host-directed immunotherapy for tuberculosis. CURRENT RESEARCH IN IMMUNOLOGY 2022; 3:54-72. [PMID: 35496824 PMCID: PMC9040133 DOI: 10.1016/j.crimmu.2022.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/11/2022] [Accepted: 03/22/2022] [Indexed: 12/22/2022] Open
Abstract
Tuberculosis (TB) is the top bacterial infectious disease killer and one of the top ten causes of death worldwide. The emergence of strains of multiple drug-resistant tuberculosis (MDR-TB) has pushed our available stock of anti-TB agents to the limit of effectiveness. This has increased the urgent need to develop novel treatment strategies using currently available resources. An adjunctive, host-directed therapy (HDT) designed to act on the host, instead of the bacteria, by boosting the host immune response through activation of intracellular pathways could be the answer. The integration of multidisciplinary approaches of repurposing currently FDA-approved drugs, with a targeted drug-delivery platform is a very promising option to reduce the long timeline associated with the approval of new drugs - time that cannot be afforded given the current levels of morbidity and mortality associated with TB infection. The deficiency of vitamin A has been reported to be highly associated with the increased susceptibility of TB. All trans retinoic acid (ATRA), the active metabolite of vitamin A, has proven to be very efficacious against TB both in vitro and in vivo. In this review, we discuss and summarise the importance of vitamin A metabolites in the fight against TB and what is known regarding the molecular mechanisms of ATRA as a host-directed therapy for TB including its effect on macrophages cytokine profile and cellular pathways. Furthermore, we focus on the issues behind why previous clinical trials with vitamin A supplementation have failed, and how these issues might be overcome.
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Affiliation(s)
- Ahmad Z. Bahlool
- School of Pharmacy and Biomolecular Sciences (PBS), Royal College of Surgeons in Ireland (RCSI), 123 St Stephens Green, Dublin 2, Ireland
- Tissue Engineering Research Group (TERG), Royal College of Surgeons in Ireland (RCSI), 123 St Stephens Green, Dublin 2, Ireland
- Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James's Hospital, Trinity College Dublin, The University of Dublin, Dublin 8, Ireland
| | - Conor Grant
- Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James's Hospital, Trinity College Dublin, The University of Dublin, Dublin 8, Ireland
| | - Sally-Ann Cryan
- School of Pharmacy and Biomolecular Sciences (PBS), Royal College of Surgeons in Ireland (RCSI), 123 St Stephens Green, Dublin 2, Ireland
- Tissue Engineering Research Group (TERG), Royal College of Surgeons in Ireland (RCSI), 123 St Stephens Green, Dublin 2, Ireland
- SFI Advanced Materials and Bioengineering Research (AMBER) Centre, RCSI & TCD, Dublin, Ireland
- SFI Centre for Research in Medical Devices (CURAM), RCSI, Dublin and National University of Ireland, Galway, Ireland
| | - Joseph Keane
- Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James's Hospital, Trinity College Dublin, The University of Dublin, Dublin 8, Ireland
| | - Mary P. O'Sullivan
- Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James's Hospital, Trinity College Dublin, The University of Dublin, Dublin 8, Ireland
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Mycobacterium tuberculosis Affects Protein and Lipid Content of Circulating Exosomes in Infected Patients Depending on Tuberculosis Disease State. Biomedicines 2022; 10:biomedicines10040783. [PMID: 35453532 PMCID: PMC9025801 DOI: 10.3390/biomedicines10040783] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/15/2022] [Accepted: 03/23/2022] [Indexed: 11/25/2022] Open
Abstract
Tuberculosis (TB), which is caused by the bacterium Mycobacterium tuberculosis (Mtb), is still one of the deadliest infectious diseases. Understanding how the host and pathogen interact in active TB will have a significant impact on global TB control efforts. Exosomes are increasingly recognized as a means of cell-to-cell contact and exchange of soluble mediators. In the case of TB, exosomes are released from the bacillus and infected cells. In the present study, a comprehensive lipidomics and proteomics analysis of size exclusion chromatography-isolated plasma-derived exosomes from patients with TB lymphadenitis (TBL) and treated as well as untreated pulmonary TB (PTB) was performed to elucidate the possibility to utilize exosomes in diagnostics and knowledge building. According to our findings, exosome-derived lipids and proteins originate from both the host and Mtb in the plasma of active TB patients. Exosomes from all patients are mostly composed of sphingomyelins (SM), phosphatidylcholines, phosphatidylinositols, free fatty acids, triacylglycerols (TAG), and cholesterylesters. Relative proportions of, e.g., SMs and TAGs, vary depending on the disease or treatment state and could be linked to Mtb pathogenesis and dormancy. We identified three proteins of Mtb origin: DNA-directed RNA polymerase subunit beta (RpoC), Diacyglycerol O-acyltransferase (Rv2285), and Formate hydrogenase (HycE), the latter of which was discovered to be differently expressed in TBL patients. Furthermore, we discovered that Mtb infection alters the host protein composition of circulating exosomes, significantly affecting a total of 37 proteins. All TB patients had low levels of apolipoproteins, as well as the antibacterial proteins cathelicidin, Scavenger Receptor Cysteine Rich Family Member (SSC5D), and Ficolin 3 (FCN3). When compared to healthy controls, the protein profiles of PTB and TBL were substantially linked, with 14 proteins being co-regulated. However, adhesion proteins (integrins, Intercellular adhesion molecule 2 (ICAM2), CD151, Proteoglycan 4 (PRG4)) were shown to be more prevalent in PTB patients, while immunoglobulins, Complement component 1r (C1R), and Glutamate receptor-interacting protein 1 (GRIP1) were found to be more abundant in TBL patients, respectively. This study could confirm findings from previous reports and uncover novel molecular profiles not previously in focus of TB research. However, we applied a minimally invasive sampling and analysis of circulating exosomes in TB patients. Based on the findings given here, future studies into host–pathogen interactions could pave the way for the development of new vaccines and therapies.
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