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Diray-Arce J, Conti MG, Petrova B, Kanarek N, Angelidou A, Levy O. Integrative Metabolomics to Identify Molecular Signatures of Responses to Vaccines and Infections. Metabolites 2020; 10:E492. [PMID: 33266347 PMCID: PMC7760881 DOI: 10.3390/metabo10120492] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/24/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022] Open
Abstract
Approaches to the identification of metabolites have progressed from early biochemical pathway evaluation to modern high-dimensional metabolomics, a powerful tool to identify and characterize biomarkers of health and disease. In addition to its relevance to classic metabolic diseases, metabolomics has been key to the emergence of immunometabolism, an important area of study, as leukocytes generate and are impacted by key metabolites important to innate and adaptive immunity. Herein, we discuss the metabolomic signatures and pathways perturbed by the activation of the human immune system during infection and vaccination. For example, infection induces changes in lipid (e.g., free fatty acids, sphingolipids, and lysophosphatidylcholines) and amino acid pathways (e.g., tryptophan, serine, and threonine), while vaccination can trigger changes in carbohydrate and bile acid pathways. Amino acid, carbohydrate, lipid, and nucleotide metabolism is relevant to immunity and is perturbed by both infections and vaccinations. Metabolomics holds substantial promise to provide fresh insight into the molecular mechanisms underlying the host immune response. Its integration with other systems biology platforms will enhance studies of human health and disease.
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Affiliation(s)
- Joann Diray-Arce
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA 02115, USA; (M.G.C.); (A.A.)
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; (B.P.); (N.K.)
| | - Maria Giulia Conti
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA 02115, USA; (M.G.C.); (A.A.)
- Department of Maternal and Child Health, Sapienza University of Rome, 5, 00185 Rome, Italy
| | - Boryana Petrova
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; (B.P.); (N.K.)
- Department of Pathology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Naama Kanarek
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; (B.P.); (N.K.)
- Department of Pathology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Asimenia Angelidou
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA 02115, USA; (M.G.C.); (A.A.)
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; (B.P.); (N.K.)
- Department of Neonatology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Ofer Levy
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA 02115, USA; (M.G.C.); (A.A.)
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; (B.P.); (N.K.)
- Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
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Wang X, Shen F, Gao Y, Wang K, Chen R, Luo J, Yang L, Zhang X, Qiu C, Li W, Wu T, Xu X, Wang Y, Cong P, Han Z, Zhang X. Application of genome-wide insertion/deletion markers on genetic structure analysis and identity signature of Malus accessions. BMC PLANT BIOLOGY 2020; 20:540. [PMID: 33256591 PMCID: PMC7708918 DOI: 10.1186/s12870-020-02744-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Apple (Malus ssp.), one of the most important temperate fruit crops, has a long cultivation history and is economically important. To identify the genetic relationships among the apple germplasm accessions, whole-genome structural variants identified between M. domestica cultivars 'Jonathan' and 'Golden Delicious' were used. RESULTS A total of 25,924 insertions and deletions (InDels) were obtained, from which 102 InDel markers were developed. Using the InDel markers, we found that 942 (75.3%) of the 1251 Malus accessions from 35 species exhibited a unique identity signature due to their distinct genotype combinations. The 102 InDel markers could distinguish 16.7-71.4% of the 331 bud sports derived from 'Fuji', 'Red Delicious', 'Gala', 'Golden Delicious', and other cultivars. Five distinct genetic patterns were found in 1002 diploid accessions based on 78 bi-allele InDel markers. Genetic structure analysis indicated that M. domestica showed higher genetic diversity than the other species. Malus underwent a relatively high level of wild-to-crop or crop-to-wild gene flow. M. sieversii was closely related to both M. domestica and cultivated Chinese cultivars. CONCLUSIONS The identity signatures of Malus accessions can be used to determine distinctness, uniformity, and stability. The results of this study may also provide better insight into the genetic relationships among Malus species.
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Affiliation(s)
- Xuan Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Fei Shen
- College of Horticulture, China Agricultural University, Beijing, China
- Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yuan Gao
- Research Institute of Pomology, Chinese Academy of Agricultural Science, Xingcheng, Liaoning, China
| | - Kun Wang
- Research Institute of Pomology, Chinese Academy of Agricultural Science, Xingcheng, Liaoning, China
| | - Ruiting Chen
- College of Horticulture, China Agricultural University, Beijing, China
- Present Address: Shaanxi Haisheng Fruit Industry Development Co., Ltd., Shaanxi, Xian, China
| | - Jun Luo
- College of Information and Electrical Engineering, China Agricultural University, Beijing, China
| | - Lili Yang
- College of Information and Electrical Engineering, China Agricultural University, Beijing, China
| | - Xi Zhang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Changpeng Qiu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Wei Li
- College of Horticulture, China Agricultural University, Beijing, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Peihua Cong
- Research Institute of Pomology, Chinese Academy of Agricultural Science, Xingcheng, Liaoning, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, China.
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Gale TV, Schieffelin JS, Branco LM, Garry RF, Grant DS. Elevated L-threonine is a biomarker for Lassa fever and Ebola. Virol J 2020; 17:188. [PMID: 33243278 PMCID: PMC7690152 DOI: 10.1186/s12985-020-01459-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/23/2020] [Indexed: 11/22/2022] Open
Abstract
Background Lassa fever and Ebola are characterized by non-specific initial presentations that can progress to severe multisystem illnesses with high fatality rates. Samples from additional subjects are examined to extend and corroborate biomarkers with prognostic value for these diseases. Methods Liquid Chromatography Mass Spectrometry metabolomics was used to identify and confirm metabolites disrupted in the blood of Lassa fever and Ebola patients. Authenticated standards are used to confirm the identify of key metabolites. Results We confirm prior results by other investigators that the amino acid l-threonine is elevated during Ebola virus infection. l-Threonine is also elevated during Lassa virus infection. We also confirmed that platelet-activating factor (PAF) and molecules with PAF moiety are reduced in the blood of patients with fatal Lassa fever. Similar changes in PAF and PAF-like molecules were not observed in the blood of Ebola patients. Conclusions Metabolomics may provide tools to identify pathways that are differentially affected during viral hemorrhagic fevers and guide development of diagnostics to monitor and predict outcome.
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Affiliation(s)
- Trevor V Gale
- Department of Microbiology and Immunology, Tulane University, 1430 Tulane Avenue, JBJ568, New Orleans, LA, 70112, USA.,Ansun Biopharma, San Diego, CA, 92121, USA
| | - John S Schieffelin
- Sections of Infectious Disease, Departments of Pediatrics and Internal Medicine, School of Medicine, Tulane University, New Orleans, LA, USA
| | | | - Robert F Garry
- Department of Microbiology and Immunology, Tulane University, 1430 Tulane Avenue, JBJ568, New Orleans, LA, 70112, USA. .,Zalgen Labs, LLC, Germantown, MD, USA.
| | - Donald S Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone. .,Ministry of Health and Sanitation, Freetown, Sierra Leone.
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Integration of metabolomics and transcriptomics reveals novel biomarkers in the blood for tuberculosis diagnosis in children. Sci Rep 2020; 10:19527. [PMID: 33177551 PMCID: PMC7658223 DOI: 10.1038/s41598-020-75513-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/13/2020] [Indexed: 01/11/2023] Open
Abstract
Pediatric tuberculosis (TB) remains a major global health problem. Improved pediatric diagnostics using readily available biosources are urgently needed. We used liquid chromatography-mass spectrometry to analyze plasma metabolite profiles of Indian children with active TB (n = 16) and age- and sex-matched, Mycobacterium tuberculosis-exposed but uninfected household contacts (n = 32). Metabolomic data were integrated with whole blood transcriptomic data for each participant at diagnosis and throughout treatment for drug-susceptible TB. A decision tree algorithm identified 3 metabolites that correctly identified TB status at distinct times during treatment. N-acetylneuraminate achieved an area under the receiver operating characteristic curve (AUC) of 0.66 at diagnosis. Quinolinate achieved an AUC of 0.77 after 1 month of treatment, and pyridoxate achieved an AUC of 0.87 after successful treatment completion. A set of 4 metabolites (gamma-glutamylalanine, gamma-glutamylglycine, glutamine, and pyridoxate) identified treatment response with an AUC of 0.86. Pathway enrichment analyses of these metabolites and corresponding transcriptional data correlated N-acetylneuraminate with immunoregulatory interactions between lymphoid and non-lymphoid cells, and correlated pyridoxate with p53-regulated metabolic genes and mitochondrial translation. Our findings shed new light on metabolic dysregulation in children with TB and pave the way for new diagnostic and treatment response markers in pediatric TB.
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Hackett EE, Sheedy FJ. An Army Marches on Its Stomach: Metabolic Intermediates as Antimicrobial Mediators in Mycobacterium tuberculosis Infection. Front Cell Infect Microbiol 2020; 10:446. [PMID: 32984072 PMCID: PMC7477320 DOI: 10.3389/fcimb.2020.00446] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/21/2020] [Indexed: 12/13/2022] Open
Abstract
The cells of the immune system are reliant on their metabolic state to launch effective responses to combat mycobacterial infections. The bioenergetic profile of the cell determines the molecular fuels and metabolites available to the host, as well as to the bacterial invader. How cells utilize the nutrients in their microenvironment—including glucose, lipids and amino acids—to sustain their functions and produce antimicrobial metabolites, and how mycobacteria exploit this to evade the immune system is of great interest. Changes in flux through metabolic pathways alters the intermediate metabolites present. These intermediates are beginning to be recognized as key modulators of immune signaling as well as direct antimicrobial effectors, and their impact on tuberculosis infection is becoming apparent. A better understanding of how metabolism impacts immunity to Mycobacterium tuberculosis and how it is regulated and thus can be manipulated will open the potential for novel therapeutic interventions and vaccination strategies.
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Affiliation(s)
- Emer E Hackett
- Macrophage Homeostasis, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Frederick J Sheedy
- Macrophage Homeostasis, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
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Adu-Gyamfi CG, Snyman T, Makhathini L, Otwombe K, Darboe F, Penn-Nicholson A, Fisher M, Savulescu D, Hoffmann C, Chaisson R, Martinson N, Scriba TJ, George JA, Suchard MS. Diagnostic accuracy of plasma kynurenine/tryptophan ratio, measured by enzyme-linked immunosorbent assay, for pulmonary tuberculosis. Int J Infect Dis 2020; 99:441-448. [PMID: 32800860 DOI: 10.1016/j.ijid.2020.08.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/05/2020] [Accepted: 08/08/2020] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION The World Health Organization has identified the need for a non-sputum-based test capable of detecting active tuberculosis (TB) as a priority. The plasma kynurenine-to-tryptophan (K/T) ratio, largely mediated by activity of the enzyme indoleamine 2,3-dioxygenase, may have potential as a suitable biomarker for active TB. METHOD We evaluated a commercial enzyme-linked immunosorbent assay (ELISA) in comparison to mass spectrometry for measuring the K/T ratio. We also used ELISA to determine the K/T ratio in plasma from patients with active TB compared to latently infected controls, with and without HIV. RESULTS The two methods showed good agreement, with a mean bias of 0.01 (limit of agreement from -0.06 to 0.10). Using ELISA, it was found that HIV-infected patients with active TB disease had higher K/T ratios than those without TB (median, 0.101 [interquartile range (IQR), 0.091-0.140] versus 0.061 [IQR, 0.034-0.077], P<0.0001). At a cutoff of 0.080, the K/T ratio produced a sensitivity of 90%, a specificity of 80%, a positive predictive value (PPV) of 82%, and a negative predictive value (NPV) of 90%. In a receiver operating characteristics analysis, the K/T ratio had an area under the curve of 0.93. HIV-uninfected patients with active TB also had higher K/T ratios than those with latent TB infections (median, 0.064 [IQR, 0.040-0.088] versus 0.022 [IQR, 0.016-0.027], P<0.0001). A cutoff of 0.040 gave a sensitivity of 85%, a specificity of 92%, a PPV of 91%, and an NPV of 84%. CONCLUSION The plasma K/T ratio is a sensitive biomarker for active TB. The K/T ratio can be measured from blood using ELISA. The K/T ratio should be evaluated as an initial test for TB.
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Affiliation(s)
- Clement Gascua Adu-Gyamfi
- Centre for Vaccines & Immunology, National Institute of Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, South Africa; Department of Chemical Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Tracy Snyman
- Department of Chemical Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lillian Makhathini
- Centre for Vaccines & Immunology, National Institute of Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Kennedy Otwombe
- Perinatal Health Research Unit (PHRU), DST/NRF Centre of Excellence for Biomedical TB Research, and SA MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of The Witwatersrand, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Fatoumatta Darboe
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Adam Penn-Nicholson
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Michelle Fisher
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Dana Savulescu
- Department of Chemical Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Richard Chaisson
- Johns Hopkins University Centre for TB Research, Baltimore, USA; Perinatal Health Research Unit (PHRU), DST/NRF Centre of Excellence for Biomedical TB Research, and SA MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of The Witwatersrand, Johannesburg, South Africa
| | - Neil Martinson
- Johns Hopkins University Centre for TB Research, Baltimore, USA; Perinatal Health Research Unit (PHRU), DST/NRF Centre of Excellence for Biomedical TB Research, and SA MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of The Witwatersrand, Johannesburg, South Africa
| | - Thomas Jens Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Jaya Anna George
- Department of Chemical Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Melinda Shelley Suchard
- Centre for Vaccines & Immunology, National Institute of Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, South Africa; Department of Chemical Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Wildes TJ, Dyson KA, Francis C, Wummer B, Yang C, Yegorov O, Shin D, Grippin A, Dean BD, Abraham R, Pham C, Moore G, Kuizon C, Mitchell DA, Flores CT. Immune Escape After Adoptive T-cell Therapy for Malignant Gliomas. Clin Cancer Res 2020; 26:5689-5700. [PMID: 32788225 DOI: 10.1158/1078-0432.ccr-20-1065] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 06/23/2020] [Accepted: 08/03/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Immunotherapy has been demonstrably effective against multiple cancers, yet tumor escape is common. It remains unclear how brain tumors escape immunotherapy and how to overcome this immune escape. EXPERIMENTAL DESIGN We studied KR158B-luc glioma-bearing mice during treatment with adoptive cellular therapy (ACT) with polyclonal tumor-specific T cells. We tested the immunogenicity of primary and escaped tumors using T-cell restimulation assays. We used flow cytometry and RNA profiling of whole tumors to further define escape mechanisms. To treat immune-escaped tumors, we generated escape variant-specific T cells through the use of escape variant total tumor RNA and administered these cells as ACT. In addition, programmed cell death protein-1 (PD-1) checkpoint blockade was studied in combination with ACT. RESULTS Escape mechanisms included a shift in immunogenic tumor antigens, downregulation of MHC class I, and upregulation of checkpoint molecules. Polyclonal T cells specific for escape variants displayed greater recognition of escaped tumors than primary tumors. When administered as ACT, these T cells prolonged median survival of escape variant-bearing mice by 60%. The rational combination of ACT with PD-1 blockade prolonged median survival of escape variant glioma-bearing mice by 110% and was dependent upon natural killer cells and T cells. CONCLUSIONS These findings suggest that the immune landscape of brain tumors are markedly different postimmunotherapy yet can still be targeted with immunotherapy.
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Affiliation(s)
- Tyler J Wildes
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, Florida
| | - Kyle A Dyson
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, Florida
| | - Connor Francis
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, Florida
| | - Brandon Wummer
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, Florida
| | - Changlin Yang
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, Florida
| | - Oleg Yegorov
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, Florida
| | - David Shin
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, Florida
| | - Adam Grippin
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, Florida
| | - Bayli DiVita Dean
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, Florida
| | - Rebecca Abraham
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, Florida
| | - Christina Pham
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, Florida
| | - Ginger Moore
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, Florida
| | - Carmelle Kuizon
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, Florida
| | - Duane A Mitchell
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, Florida
| | - Catherine T Flores
- University of Florida Brain Tumor Immunotherapy Program, Preston A. Wells, Jr. Center for Brain Tumor Therapy, Lillian S. Wells Department of Neurosurgery, McKnight Brain Institute, University of Florida, Gainesville, Florida.
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Tuberculosis causes highly conserved metabolic changes in human patients, mycobacteria-infected mice and zebrafish larvae. Sci Rep 2020; 10:11635. [PMID: 32669636 PMCID: PMC7363909 DOI: 10.1038/s41598-020-68443-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 06/23/2020] [Indexed: 12/20/2022] Open
Abstract
Tuberculosis is a highly infectious and potentially fatal disease accompanied by wasting symptoms, which cause severe metabolic changes in infected people. In this study we have compared the effect of mycobacteria infection on the level of metabolites in blood of humans and mice and whole zebrafish larvae using one highly standardized mass spectrometry pipeline, ensuring technical comparability of the results. Quantification of a range of circulating small amines showed that the levels of the majority of these compounds were significantly decreased in all three groups of infected organisms. Ten of these metabolites were common between the three different organisms comprising: methionine, asparagine, cysteine, threonine, serine, tryptophan, leucine, citrulline, ethanolamine and phenylalanine. The metabolomic changes of zebrafish larvae after infection were confirmed by nuclear magnetic resonance spectroscopy. Our study identified common biomarkers for tuberculosis disease in humans, mice and zebrafish, showing across species conservation of metabolic reprogramming processes as a result of disease. Apparently, the mechanisms underlying these processes are independent of environmental, developmental and vertebrate evolutionary factors. The zebrafish larval model is highly suited to further investigate the mechanism of metabolic reprogramming and the connection with wasting syndrome due to infection by mycobacteria.
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Ohata PJ, Kerr SJ, Avihingsanon A, Ramautarsing R, Gatechompol S, Ueaphongsukkit T, Phanuphak N, Kroon E, Ubolyam S, Colby D, Phanuphak P. Conference proceedings from the 22nd Bangkok International Symposium on HIV Medicine. Future Virol 2020. [DOI: 10.2217/fvl-2020-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Bangkok International Symposium on HIV Medicine is one of the longest running and largest international conferences in the Asia–Pacific, providing healthcare workers with the most up-to-date information pertaining to HIV and coinfections. In the third week of January 2020, 500 HIV researchers and service providers from over 21 countries worldwide gathered in Bangkok to share data and experiences in the treatment and prevention of HIV, TB and sexually transmitted infections. Highlights of the 2020 symposium included a roundtable discussion of pre-exposure prophylaxis, a 1-day forum on TB, the potential for a HBV cure and, for the first time, oral presentations from four young investigators from the region.
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Affiliation(s)
- Pirapon June Ohata
- HIV-NAT, Thai Red Cross – AIDS Research Centre, 104 Ratchadamri Rd, Pathumwan, Bangkok 10330, Thailand
| | - Stephen J Kerr
- HIV-NAT, Thai Red Cross – AIDS Research Centre, 104 Ratchadamri Rd, Pathumwan, Bangkok 10330, Thailand
- Biostatistics Excellence Centre, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- The Kirby Institute, University of New South Wales, NSW, Sydney 2052, Australia
| | - Anchalee Avihingsanon
- HIV-NAT, Thai Red Cross – AIDS Research Centre, 104 Ratchadamri Rd, Pathumwan, Bangkok 10330, Thailand
- Tuberculosis Research Unit (TB RU), Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Reshmie Ramautarsing
- PREVENTION, Thai Red Cross – AIDS Research Centre, 104 Ratchadamri Rd., Pathumwan, Bangkok 10330, Thailand
| | - Sivaporn Gatechompol
- HIV-NAT, Thai Red Cross – AIDS Research Centre, 104 Ratchadamri Rd, Pathumwan, Bangkok 10330, Thailand
- Tuberculosis Research Unit (TB RU), Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thornthun Ueaphongsukkit
- HIV-NAT, Thai Red Cross – AIDS Research Centre, 104 Ratchadamri Rd, Pathumwan, Bangkok 10330, Thailand
- Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nittaya Phanuphak
- PREVENTION, Thai Red Cross – AIDS Research Centre, 104 Ratchadamri Rd., Pathumwan, Bangkok 10330, Thailand
| | - Eugene Kroon
- SEARCH, Thai Red Cross – AIDS Research Centre, 104 Ratchadamri Rd., Pathumwan, Bangkok 10330, Thailand
| | - Sasiwimol Ubolyam
- HIV-NAT, Thai Red Cross – AIDS Research Centre, 104 Ratchadamri Rd, Pathumwan, Bangkok 10330, Thailand
| | - Donn Colby
- SEARCH, Thai Red Cross – AIDS Research Centre, 104 Ratchadamri Rd., Pathumwan, Bangkok 10330, Thailand
- Henry M Jackson Foundation, Bethesda, MD 20817, USA
- US Military HIV Research Program, Silver Spring, MD 20910, USA
| | - Praphan Phanuphak
- HIV-NAT, Thai Red Cross – AIDS Research Centre, 104 Ratchadamri Rd, Pathumwan, Bangkok 10330, Thailand
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Vaginal metabolome: towards a minimally invasive diagnosis of microbial invasion of the amniotic cavity in women with preterm labor. Sci Rep 2020; 10:5465. [PMID: 32214212 PMCID: PMC7096387 DOI: 10.1038/s41598-020-62542-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/13/2020] [Indexed: 11/25/2022] Open
Abstract
Microbial invasion of the amniotic cavity (MIAC) is only identified by amniocentesis, an invasive procedure that limits its clinical translation. Here, we aimed to evaluate whether the vaginal metabolome discriminates the presence/absence of MIAC in women with preterm labor (PTL) and intact membranes. We conducted a case-control study in women with symptoms of PTL below 34 weeks who underwent amniocentesis to discard MIAC. MIAC was defined as amniotic fluid positive for microorganisms identified by specific culture media. The cohort included 16 women with MIAC and 16 control (no MIAC). Both groups were matched for age and gestational age at admission. Vaginal fluid samples were collected shortly after amniocentesis. Metabolic profiles were analyzed by nuclear magnetic resonance (NMR) spectroscopy and compared using multivariate and univariate statistical analyses to identify significant differences between the two groups. The vaginal metabolomics profile of MIAC showed higher concentrations of hypoxanthine, proline, choline and acetylcholine and decreased concentrations of phenylalanine, glutamine, isoleucine, leucine and glycerophosphocholine. In conclusion, metabolic changes in the NMR-based vaginal metabolic profile are able to discriminate the presence/absence of MIAC in women with PTL and intact membranes. These metabolic changes might be indicative of enhanced glycolysis triggered by hypoxia conditions as a consequence of bacterial infection, thus explaining the utilization of alternative energy sources in an attempt to replenish glucose.
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Identification of serum biomarkers for active pulmonary tuberculosis using a targeted metabolomics approach. Sci Rep 2020; 10:3825. [PMID: 32123207 PMCID: PMC7052258 DOI: 10.1038/s41598-020-60669-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 02/13/2020] [Indexed: 12/13/2022] Open
Abstract
Although tuberculosis (TB) is a severe health problem worldwide, the current diagnostic methods are far from optimal. Metabolomics is increasingly being used in the study of infectious diseases. We performed metabolome profiling to identify potential biomarkers in patients with active TB. Serum samples from 21 patients with active pulmonary TB, 20 subjects with latent TB infection (LTBI), and 28 healthy controls were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) followed by multivariate and univariate analyses. Metabolic profiles indicated higher serum levels of glutamate, sulfoxy methionine, and aspartate and lower serum levels of glutamine, methionine, and asparagine in active TB patients than in LTBI subjects or healthy controls. The ratios between metabolically related partners (glutamate/glutamine, sulfoxy methionine/methionine, and aspartate/asparagine) were also elevated in the active TB group. There was no significant difference in the serum concentration of these metabolites according to the disease extent or risk of relapse in active TB patients. Novel serum biomarkers such as glutamate, sulfoxy methionine, aspartate, glutamine, methionine, and asparagine are potentially useful for adjunctive, rapid, and noninvasive pulmonary TB diagnosis.
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McDonald JT, Stainforth R, Miller J, Cahill T, da Silveira WA, Rathi KS, Hardiman G, Taylor D, Costes SV, Chauhan V, Meller R, Beheshti A. NASA GeneLab Platform Utilized for Biological Response to Space Radiation in Animal Models. Cancers (Basel) 2020; 12:E381. [PMID: 32045996 PMCID: PMC7072278 DOI: 10.3390/cancers12020381] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 02/03/2020] [Accepted: 02/03/2020] [Indexed: 12/12/2022] Open
Abstract
Background: Ionizing radiation from galactic cosmic rays (GCR) is one of the major risk factors that will impact the health of astronauts on extended missions outside the protective effects of the Earth's magnetic field. The NASA GeneLab project has detailed information on radiation exposure using animal models with curated dosimetry information for spaceflight experiments. Methods: We analyzed multiple GeneLab omics datasets associated with both ground-based and spaceflight radiation studies that included in vivo and in vitro approaches. A range of ions from protons to iron particles with doses from 0.1 to 1.0 Gy for ground studies, as well as samples flown in low Earth orbit (LEO) with total doses of 1.0 mGy to 30 mGy, were utilized. Results: From this analysis, we were able to identify distinct biological signatures associating specific ions with specific biological responses due to radiation exposure in space. For example, we discovered changes in mitochondrial function, ribosomal assembly, and immune pathways as a function of dose. Conclusions: We provided a summary of how the GeneLab's rich database of omics experiments with animal models can be used to generate novel hypotheses to better understand human health risks from GCR exposures.
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Affiliation(s)
| | - Robert Stainforth
- Consumer and Clinical Radiation Protection Bureau, Health Canada, Ottawa, ON K1A-1C1, Canada; (R.S.); (V.C.)
| | - Jack Miller
- KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA;
| | - Thomas Cahill
- School of Biological Sciences & Institute for Global Food Security, Queens University Belfast, Belfast BT9 5DL, UK; (T.C.); (W.A.d.S.)
| | - Willian A. da Silveira
- School of Biological Sciences & Institute for Global Food Security, Queens University Belfast, Belfast BT9 5DL, UK; (T.C.); (W.A.d.S.)
| | - Komal S. Rathi
- Department of Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
| | - Gary Hardiman
- School of Biological Sciences & Institute for Global Food Security, Queens University Belfast, Belfast BT9 5DL, UK; (T.C.); (W.A.d.S.)
- Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Deanne Taylor
- Department of Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
- The Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
- The Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sylvain V. Costes
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA 94035, USA;
| | - Vinita Chauhan
- Consumer and Clinical Radiation Protection Bureau, Health Canada, Ottawa, ON K1A-1C1, Canada; (R.S.); (V.C.)
| | - Robert Meller
- Department of Neurobiology and Pharmacology, Morehouse School of Medicine, Atlanta, GA 30310, USA;
| | - Afshin Beheshti
- KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA;
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Rao Muvva J, Parasa VR, Lerm M, Svensson M, Brighenti S. Polarization of Human Monocyte-Derived Cells With Vitamin D Promotes Control of Mycobacterium tuberculosis Infection. Front Immunol 2020; 10:3157. [PMID: 32038652 PMCID: PMC6987394 DOI: 10.3389/fimmu.2019.03157] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 12/31/2019] [Indexed: 12/13/2022] Open
Abstract
Background: Understanding macrophage behavior is key to decipher Mycobacterium tuberculosis (Mtb) pathogenesis. We studied the phenotype and ability of human monocyte-derived cells polarized with active vitamin D [1,25(OH)2D3] to control intracellular Mtb infection compared with polarization of conventional subsets, classical M1 or alternative M2. Methods: Human blood-derived monocytes were treated with active vitamin D or different cytokines to obtain 1,25(OH)2D3-polarized as well as M1- and M2-like cells or fully polarized M1 and M2 subsets. We used an in vitro macrophage Mtb infection model to assess both phenotype and functional markers i.e., inhibitory and scavenger receptors, costimulatory molecules, cytokines, chemokines, and effector molecules using flow cytometry and quantitative mRNA analysis. Intracellular uptake of bacilli and Mtb growth was monitored using flow cytometry and colony forming units. Results: Uninfected M1 subsets typically expressed higher levels of CCR7, TLR2, and CD86, while M2 subsets expressed higher CD163, CD200R, and CD206. Most of the investigated markers were up-regulated in all subsets after Mtb infection, generating a mixed M1/M2 phenotype, while the expression of CD206, HLADR, and CD80 was specifically up-regulated (P < 0.05) on 1,25(OH)2D3-polarized macrophages. Consistent with the pro-inflammatory features of M1 cells, Mtb uptake and intracellular Mtb growth was significantly (P < 0.01–0.001 and P < 0.05–0.01) lower in the M1 (19.3%) compared with the M2 (82.7%) subsets 4 h post-infection. However, infectivity rapidly and gradually increased in M1 cells at 24–72 h. 1,25(OH)2D3-polarized monocyte-derived cells was the most potent subset to inhibit Mtb growth at both 4 and 72 h (P < 0.05–0.01) post-Mtb infection. This ability was associated with high mRNA levels of pro-inflammatory cytokines and the antimicrobial peptide LL-37 but also anti-inflammatory IL-10, while expression of the immunosuppressive enzyme IDO (indoleamine 2,3-dioxygenase) remained low in Mtb-infected 1,25(OH)2D3-polarized cells compared with the other subsets. Conclusions: Mtb infection promoted a mixed M1/M2 macrophage activation, and 1,25(OH)2D3-polarized monocyte-derived cells expressing LL-37 but not IDO, were most effective to control intracellular Mtb growth. Macrophage polarization in the presence of vitamin D may provide the capacity to mount an antimicrobial response against Mtb and simultaneously prevent expression of inhibitory molecules that could accelerate local immunosuppression in the microenvironment of infected tissue.
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Affiliation(s)
- Jagadeeswara Rao Muvva
- Department of Medicine, Center for Infectious Medicine (CIM), ANA Futura, Karolinska Institutet, Stockholm, Sweden
| | | | - Maria Lerm
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Mattias Svensson
- Department of Medicine, Center for Infectious Medicine (CIM), ANA Futura, Karolinska Institutet, Stockholm, Sweden
| | - Susanna Brighenti
- Department of Medicine, Center for Infectious Medicine (CIM), ANA Futura, Karolinska Institutet, Stockholm, Sweden
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64
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Boillat M, Hammoudi PM, Dogga SK, Pagès S, Goubran M, Rodriguez I, Soldati-Favre D. Neuroinflammation-Associated Aspecific Manipulation of Mouse Predator Fear by Toxoplasma gondii. Cell Rep 2020; 30:320-334.e6. [PMID: 31940479 PMCID: PMC6963786 DOI: 10.1016/j.celrep.2019.12.019] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/27/2019] [Accepted: 12/06/2019] [Indexed: 12/13/2022] Open
Abstract
In rodents, the decrease of felid aversion induced by Toxoplasma gondii, a phenomenon termed fatal attraction, is interpreted as an adaptive manipulation by the neurotropic protozoan parasite. With the aim of understanding how the parasite induces such specific behavioral modifications, we performed a multiparametric analysis of T. gondii-induced changes on host behavior, physiology, and brain transcriptome as well as parasite cyst load and distribution. Using a set of complementary behavioral tests, we provide strong evidence that T. gondii lowers general anxiety in infected mice, increases explorative behaviors, and surprisingly alters predator aversion without selectivity toward felids. Furthermore, we show a positive correlation between the severity of the behavioral alterations and the cyst load, which indirectly reflects the level of inflammation during brain colonization. Taken together, these findings refute the myth of a selective loss of cat fear in T. gondii-infected mice and point toward widespread immune-related alterations of behaviors.
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Affiliation(s)
- Madlaina Boillat
- Department of Genetics and Evolution, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Pierre-Mehdi Hammoudi
- Department of Microbiology and Molecular Medicine, Faculty of Medicine-University of Geneva CMU, 1 rue Michel-Servet 1211 Geneva 4, Switzerland
| | - Sunil Kumar Dogga
- Department of Microbiology and Molecular Medicine, Faculty of Medicine-University of Geneva CMU, 1 rue Michel-Servet 1211 Geneva 4, Switzerland
| | - Stéphane Pagès
- Wyss Center for Bio- and Neuroengineering, Geneva, Switzerland; Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland
| | - Maged Goubran
- Hurvitz Brain Sciences Program, Sunnybrook Research Institute, University of Toronto, Toronto, ON, Canada
| | - Ivan Rodriguez
- Department of Genetics and Evolution, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland.
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, Faculty of Medicine-University of Geneva CMU, 1 rue Michel-Servet 1211 Geneva 4, Switzerland.
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65
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Banoei MM, Iupe I, Bazaz RD, Campos M, Vogel HJ, Winston BW, Mirsaeidi M. Metabolomic and metallomic profile differences between Veterans and Civilians with Pulmonary Sarcoidosis. Sci Rep 2019; 9:19584. [PMID: 31863066 PMCID: PMC6925242 DOI: 10.1038/s41598-019-56174-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 12/03/2019] [Indexed: 12/18/2022] Open
Abstract
Sarcoidosis is a disorder characterized by granulomatous inflammation of unclear etiology. In this study we evaluated whether veterans with sarcoidosis exhibited different plasma metabolomic and metallomic profiles compared with civilians with sarcoidosis. A case control study was performed on veteran and civilian patients with confirmed sarcoidosis. Proton nuclear magnetic resonance spectroscopy (1H NMR), hydrophilic interaction liquid chromatography mass spectrometry (HILIC-MS) and inductively coupled plasma mass spectrometry (ICP-MS) were applied to quantify metabolites and metal elements in plasma samples. Our results revealed that the veterans with sarcoidosis significantly differed from civilians, according to metabolic and metallomics profiles. Moreover, the results showed that veterans with sarcoidosis and veterans with COPD were similar to each other in metabolomics and metallomics profiles. This study suggests the important role of environmental risk factors in the development of different molecular phenotypic responses of sarcoidosis. In addition, this study suggests that sarcoidosis in veterans may be an occupational disease.
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Affiliation(s)
| | - Isabella Iupe
- Department of Medicine, University of Miami, Miami, FL, USA
| | - Reza Dowlatabadi Bazaz
- Department of Biological Science, Bio-NMR-metabolomics Research center, University of Calgary, Calgary, Canada
- Departments of Critical Care Medicine, Medicine and Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Michael Campos
- Section of Pulmonary, Miami VA Healthcare System, Miami, FL, USA
- Division of Pulmonary and Critical Care, University of Miami, Miami, FL, USA
| | - Hans J Vogel
- Department of Biological Science, Bio-NMR-metabolomics Research center, University of Calgary, Calgary, Canada
- Departments of Critical Care Medicine, Medicine and Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Brent W Winston
- Department of Biological Science, Bio-NMR-metabolomics Research center, University of Calgary, Calgary, Canada
- Departments of Critical Care Medicine, Medicine and Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Mehdi Mirsaeidi
- Section of Pulmonary, Miami VA Healthcare System, Miami, FL, USA.
- Division of Pulmonary and Critical Care, University of Miami, Miami, FL, USA.
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66
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Yong YK, Tan HY, Saeidi A, Wong WF, Vignesh R, Velu V, Eri R, Larsson M, Shankar EM. Immune Biomarkers for Diagnosis and Treatment Monitoring of Tuberculosis: Current Developments and Future Prospects. Front Microbiol 2019; 10:2789. [PMID: 31921004 PMCID: PMC6930807 DOI: 10.3389/fmicb.2019.02789] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 11/18/2019] [Indexed: 12/22/2022] Open
Abstract
Tuberculosis (TB) treatment monitoring is paramount to clinical decision-making and the host biomarkers appears to play a significant role. The currently available diagnostic technology for TB detection is inadequate. Although GeneXpert detects total DNA present in the sample regardless live or dead bacilli present in clinical samples, all the commercial tests available thus far have low sensitivity. Humoral responses against Mycobacterium tuberculosis (Mtb) antigens are generally low, which precludes the use of serological tests for TB diagnosis, prognosis, and treatment monitoring. Mtb-specific CD4+ T cells correlate with Mtb antigen/bacilli burden and hence might serve as good biomarkers for monitoring treatment progress. Omics-based techniques are capable of providing a more holistic picture for disease mechanisms and are more accurate in predicting TB disease outcomes. The current review aims to discuss some of the recent advances on TB biomarkers, particularly host biomarkers that have the potential to diagnose and differentiate active TB and LTBI as well as their use in disease prognosis and treatment monitoring.
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Affiliation(s)
- Yean K Yong
- Laboratory Center, Xiamen University Malaysia, Sepang, Malaysia
| | - Hong Y Tan
- Laboratory Center, Xiamen University Malaysia, Sepang, Malaysia.,Department of Traditional Chinese Medicine, Xiamen University Malaysia, Sepang, Malaysia
| | - Alireza Saeidi
- Department of Pediatrics, Emory Vaccine Center, Atlanta, GA, United States
| | - Won F Wong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Vijayakumar Velu
- Department of Microbiology and Immunology, Emory Vaccine Center, Atlanta, GA, United States
| | - Rajaraman Eri
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, TAS, Australia
| | - Marie Larsson
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linkoping University, Linkoping, Sweden
| | - Esaki M Shankar
- Division of Infection Biology and Medical Microbiology, Department of Life Sciences, Central University of Tamil Nadu (CUTN), Thiruvarur, India
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Plasma metabolomics in tuberculosis patients with and without concurrent type 2 diabetes at diagnosis and during antibiotic treatment. Sci Rep 2019; 9:18669. [PMID: 31822686 PMCID: PMC6904442 DOI: 10.1038/s41598-019-54983-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 11/19/2019] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis (TB) and type 2 diabetes mellitus (DM), a major TB risk factor, are both accompanied by marked alterations in metabolic processes. Dissecting the specific metabolic changes induced by disease through metabolomics has shown potential to improve our understanding of relevant pathophysiological mechanisms of disease, which could lead to improved treatment. Targeted tandem liquid chromatography–mass spectrometry (LC-MS/MS) was used to compare amine and acylcarnitine levels in plasma samples of patients with TB or TB-DM from Indonesia at time of diagnosis and during antibiotic treatment. Partial least squares discrimination analysis (PLS-DA) showed good separation of patient groups. Amine levels were strongly altered in both disease groups compared to healthy controls, including low concentrations of citrulline and ornithine. Several amino acid ratios discriminated TB from controls (phenylalanine/histidine; citrulline/arginine; kynurenine/tryptophan), possibly reflecting changes in indoleamine-pyrrole 2,3-dioxygenase (IDO) and nitric oxide synthase (NOS) activity. Choline, glycine, serine, threonine and homoserine levels were lower in TB-DM compared to TB, and, in contrast to other analytes, did not normalize to healthy control levels during antibiotic treatment. Our results not only provide important validation of previous studies but also identify novel biomarkers, and significantly enhance our understanding of metabolic changes in human TB and TB-DM.
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68
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Adu-Gyamfi CG, Savulescu D, George JA, Suchard MS. Indoleamine 2, 3-Dioxygenase-Mediated Tryptophan Catabolism: A Leading Star or Supporting Act in the Tuberculosis and HIV Pas-de-Deux? Front Cell Infect Microbiol 2019; 9:372. [PMID: 31737575 PMCID: PMC6828849 DOI: 10.3389/fcimb.2019.00372] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/14/2019] [Indexed: 12/11/2022] Open
Abstract
Progression from latency to active Tuberculosis (TB) disease is mediated by incompletely understood host immune factors. The definitive characteristic of progressive human immunodeficiency virus (HIV) disease is a severe loss in number and function of T lymphocytes. Among the many possible mediators of T lymphocyte loss and ineffective function is the activity of the immune-modulatory enzyme indoleamine 2,3-dioxygenase (IDO). IDO is the rate-limiting enzyme converting tryptophan to kynurenine. IDO activity was initially recognized to mediate tolerance at the foeto-maternal interface. Recently, IDO activity has also been noted to play a critical role in immune tolerance to pathogens. Studies of host immune and metabolic mediators have found IDO activity significantly elevated in HIV and TB disease. In this review, we explore the link between IDO-mediated tryptophan catabolism and the presence of active TB disease in HIV-infected patients. We draw attention to increased IDO activity as a key factor marking the progression from latent to active TB disease in HIV-infected patients.
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Affiliation(s)
- Clement Gascua Adu-Gyamfi
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, Johannesburg, South Africa.,Department of Chemical Pathology, Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Dana Savulescu
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Jaya Anna George
- Department of Chemical Pathology, Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Melinda Shelley Suchard
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, Johannesburg, South Africa.,Department of Chemical Pathology, Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
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69
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Tan VX, Guillemin GJ. Kynurenine Pathway Metabolites as Biomarkers for Amyotrophic Lateral Sclerosis. Front Neurosci 2019; 13:1013. [PMID: 31616242 PMCID: PMC6764462 DOI: 10.3389/fnins.2019.01013] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/06/2019] [Indexed: 12/19/2022] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) currently lacks a robust and well-defined biomarker that can 1) assess the progression of the disease, 2) predict and/or delineate the various clinical subtypes, and 3) evaluate or predict a patient's response to treatments. The kynurenine Pathway (KP) of tryptophan degradation represent a promising candidate as it is involved with several neuropathological features present in ALS including neuroinflammation, excitotoxicity, oxidative stress, immune system activation and dysregulation of energy metabolism. Some of the KP metabolites (KPMs) can cross the blood brain barrier, and many studies have shown their levels are dysregulated in major neurodegenerative diseases including ALS. The KPMs can be easily analyzed in body fluids and tissue and as they are small molecules, and are stable. KPMs have a Janus face action, they can be either or both neurotoxic and/or neuroprotective depending of their levels. This mini review examines and presents evidence supporting the use of KPMs as a relevant set of biomarkers for ALS, and highlights the criteria required to achieve a valid biomarker set for ALS.
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Affiliation(s)
| | - Gilles J. Guillemin
- Macquarie University Centre for MND Research, Department of Biological Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
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70
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Ruiz A, Sarabia C, Torres M, Juárez E. Resolvin D1 (RvD1) and maresin 1 (Mar1) contribute to human macrophage control of M. tuberculosis infection while resolving inflammation. Int Immunopharmacol 2019; 74:105694. [DOI: 10.1016/j.intimp.2019.105694] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 05/26/2019] [Accepted: 06/10/2019] [Indexed: 01/09/2023]
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71
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Silva CAM, Graham B, Webb K, Ashton LV, Harton M, Luetkemeyer AF, Bokatzian S, Almubarak R, Mahapatra S, Hovind L, Kendall MA, Havlir D, Belisle JT, De Groote MA. A pilot metabolomics study of tuberculosis immune reconstitution inflammatory syndrome. Int J Infect Dis 2019; 84:30-38. [PMID: 31009738 PMCID: PMC6613934 DOI: 10.1016/j.ijid.2019.04.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/10/2019] [Accepted: 04/13/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Diagnosis of paradoxical tuberculosis-associated immune reconstitution inflammatory syndrome (TB-IRIS) is challenging and new tools are needed for early diagnosis as well as to understand the biochemical events that underlie the pathology in TB-IRIS. METHODS Plasma samples were obtained from participants from a randomized HIV/TB treatment strategy study (AIDS Clinical Trials Group [ACTG] A5221) with (n = 26) and without TB-IRIS (n = 22) for an untargeted metabolomics pilot study by liquid-chromatography mass spectrometry. The metabolic profile of these participants was compared at the study entry and as close to the diagnosis of TB-IRIS as possible (TB-IRIS window). Molecular features with p < 0.05 and log2 fold change ≥0.58 were submitted for pathway analysis through MetaboAnalyst. We also elucidated potential metabolic signatures for TB-IRIS using a LASSO regression model. RESULTS At the study entry, we showed that the arachidonic acid and glycerophospholipid metabolism were altered in the TB-IRIS group. Sphingolipid and linoleic acid metabolism were the most affected pathways during the TB-IRIS window. LASSO modeling selected a set of 8 and 7 molecular features with the potential to predict TB-IRIS at study entry and during the TB-IRIS window, respectively. CONCLUSION This study suggests that the use of plasma metabolites may distinguish HIV-TB patients with and without TB-IRIS.
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Affiliation(s)
- Carlos A M Silva
- Mycobacterial Research Laboratories, Fort Collins, CO, USA; Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Barbara Graham
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Kristofor Webb
- Mycobacterial Research Laboratories, Fort Collins, CO, USA
| | | | - Marisa Harton
- Mycobacterial Research Laboratories, Fort Collins, CO, USA
| | | | | | | | | | - Laura Hovind
- Frontier Science & Technology Research Foundation, Inc., Amherst, NY, USA
| | - Michelle A Kendall
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health Boston, MA, USA
| | - Diane Havlir
- University of California San Francisco, San Francisco, CA, USA
| | - John T Belisle
- Mycobacterial Research Laboratories, Fort Collins, CO, USA
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López-Hernández Y, Lara-Ramírez EE, Salgado-Bustamante M, López JA, Oropeza-Valdez JJ, Jaime-Sánchez E, Castañeda-Delgado JE, Magaña-Aquino M, Murgu M, Enciso-Moreno JA. Glycerophospholipid Metabolism Alterations in Patients with Type 2 Diabetes Mellitus and Tuberculosis Comorbidity. Arch Med Res 2019; 50:71-78. [PMID: 31349956 DOI: 10.1016/j.arcmed.2019.05.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/08/2019] [Accepted: 05/20/2019] [Indexed: 12/18/2022]
Abstract
Type-2 Diabetes (T2D) is a predisposing cause for developing tuberculosis (TB) in low- and middle-income countries. TB-T2D comorbidity worsens clinical control and prognosis of the affected individuals. The underlying metabolic alterations for this infectious-metabolic disease are still largely unknown. Possible mediators of the increased susceptibility to TB in diabetic patients are lipids levels, which are altered in individuals with T2D. To evaluate the modulation of glycerophospholipids in patients with TB-T2D, an untargeted lipidomic approach was developed by means of ultra-performance liquid chromatography (UPLC) coupled to electrospray ionization/quadrupole time-of-flight mass spectrometry (ESI-QToF). In addition, tandem mass spectrometry was performed to determine the identity of the differentially expressed metabolites. We found that TB infected individuals with or without T2D share a common glycerophospholipid profile characterized by a decrease in phosphatidylcholines. A total of 14 glycerophospholipids were differentially deregulated in TB and TB-T2D patients and could potentially be considered biomarkers. It is necessary to further validate these identified lipids as biomarkers, focusing on the anticipate diagnosis for TB development in T2D predisposed individuals.
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Affiliation(s)
- Yamile López-Hernández
- Laboratorio de Metabolómica y Proteómica, CONACyT-Universidad Autónoma de Zacatecas, Zacatecas, Mexico
| | - Edgar E Lara-Ramírez
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano de Seguro Social, Zacatecas, Mexico
| | - Mariana Salgado-Bustamante
- Biochemistry Department, Medicine Faculty, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Jesús Adrián López
- MicroRNAs Laboratory, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Mexico
| | - Juan J Oropeza-Valdez
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano de Seguro Social, Zacatecas, Mexico
| | - Elena Jaime-Sánchez
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano de Seguro Social, Zacatecas, Mexico
| | - Julio E Castañeda-Delgado
- Cátedras-CONACyT, Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano de Seguro Social, Zacatecas, Mexico
| | | | | | - José A Enciso-Moreno
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano de Seguro Social, Zacatecas, Mexico.
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73
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Maura F, Agnelli L, Leongamornlert D, Bolli N, Chan WC, Dodero A, Carniti C, Heavican TB, Pellegrinelli A, Pruneri G, Butler A, Bhosle SG, Chiappella A, Di Rocco A, Zinzani PL, Zaja F, Piva R, Inghirami G, Wang W, Palomero T, Iqbal J, Neri A, Campbell PJ, Corradini P. Integration of transcriptional and mutational data simplifies the stratification of peripheral T-cell lymphoma. Am J Hematol 2019; 94:628-634. [PMID: 30829413 DOI: 10.1002/ajh.25450] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 02/25/2019] [Indexed: 12/21/2022]
Abstract
The histological diagnosis of peripheral T-cell lymphoma (PTCL) can represent a challenge, particularly in the case of closely related entities such as angioimmunoblastic T-lymphoma (AITL), PTCL-not otherwise specified (PTCL-NOS), and ALK-negative anaplastic large-cell lymphoma (ALCL). Although gene expression profiling and next generations sequencing have been proven to define specific features recurrently associated with distinct entities, genomic-based stratifications have not yet led to definitive diagnostic criteria and/or entered into the routine clinical practice. Herein, to improve the current molecular classification between AITL and PTCL-NOS, we analyzed the transcriptional profiles from 503 PTCLs stratified according to their molecular configuration and integrated them with genomic data of recurrently mutated genes (RHOA G17V , TET2, IDH2 R172 , and DNMT3A) in 53 cases (39 AITLs and 14 PTCL-NOSs) included in the series. Our analysis unraveled that the mutational status of RHOA G17V , TET2, and DNMT3A poorly correlated, individually, with peculiar transcriptional fingerprints. Conversely, in IDH2 R172 samples a strong transcriptional signature was identified that could act as a surrogate for mutational status. The integrated analysis of clinical, mutational, and molecular data led to a simplified 19-gene signature that retains high accuracy in differentiating the main nodal PTCL entities. The expression levels of those genes were confirmed in an independent cohort profiled by RNA-sequencing.
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Affiliation(s)
- Francesco Maura
- Myeloma Service, Department of MedicineMemorial Sloan Kettering Cancer Center New York New York
- Cancer, Ageing and Somatic Mutation ProgrammeWellcome Trust Sanger Institute Hinxton United Kingdom
- Department of Oncology and Hemato‐OncologyUniversity of Milan Milan Italy
| | - Luca Agnelli
- Department of Oncology and Hemato‐OncologyUniversity of Milan Milan Italy
- HematologyFoundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico Milan Italy
| | - Daniel Leongamornlert
- Cancer, Ageing and Somatic Mutation ProgrammeWellcome Trust Sanger Institute Hinxton United Kingdom
| | - Niccolò Bolli
- Cancer, Ageing and Somatic Mutation ProgrammeWellcome Trust Sanger Institute Hinxton United Kingdom
- Department of Oncology and Hemato‐OncologyUniversity of Milan Milan Italy
- Division of HematologyFondazione IRCCS Istituto Nazionale dei Tumori Milan Italy
| | - Wing C. Chan
- Department of PathologyCity of Hope National Medical Center Duarte California
| | - Anna Dodero
- Division of HematologyFondazione IRCCS Istituto Nazionale dei Tumori Milan Italy
| | - Cristiana Carniti
- Division of HematologyFondazione IRCCS Istituto Nazionale dei Tumori Milan Italy
| | - Tayla B. Heavican
- Department of Pathology and MicrobiologyUniversity of Nebraska Medical Center Omaha Nebraska
| | - Alessio Pellegrinelli
- Department of Pathology and Laboratory MedicineFondazione IRCCS Istituto Nazionale dei Tumori Milan Italy
| | - Giancarlo Pruneri
- Department of Pathology and Laboratory MedicineFondazione IRCCS Istituto Nazionale dei Tumori Milan Italy
| | - Adam Butler
- Cancer, Ageing and Somatic Mutation ProgrammeWellcome Trust Sanger Institute Hinxton United Kingdom
| | - Shriram G. Bhosle
- Cancer, Ageing and Somatic Mutation ProgrammeWellcome Trust Sanger Institute Hinxton United Kingdom
| | - Annalisa Chiappella
- Department of HematologyAzienda Ospedaliera Città della Salute e della Scienza Torino Italy
| | - Alice Di Rocco
- Department of Cellular Biotechnology and Hematology, Sapienza University of Rome Rome Italy
| | | | - Francesco Zaja
- Clinical Ematologica, DAMEUniversity of Udine Udine Italy
| | - Roberto Piva
- Department of Molecular Biotechnology and Health SciencesCenter for Experimental Research and Medical Studies, University of Torino Torino Italy
| | - Giorgio Inghirami
- Department of Molecular Biotechnology and Health SciencesCenter for Experimental Research and Medical Studies, University of Torino Torino Italy
- Pathology and Laboratory MedicinesWeill Cornell Medical College New York New York
| | - Wenyi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center Houston Texas
| | - Teresa Palomero
- Institute for Cancer Genetics, Columbia University New York New York
| | - Javeed Iqbal
- Department of Pathology and MicrobiologyUniversity of Nebraska Medical Center Omaha Nebraska
| | - Antonino Neri
- Department of Oncology and Hemato‐OncologyUniversity of Milan Milan Italy
- HematologyFoundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico Milan Italy
| | - Peter J. Campbell
- Cancer, Ageing and Somatic Mutation ProgrammeWellcome Trust Sanger Institute Hinxton United Kingdom
| | - Paolo Corradini
- Department of Oncology and Hemato‐OncologyUniversity of Milan Milan Italy
- Division of HematologyFondazione IRCCS Istituto Nazionale dei Tumori Milan Italy
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74
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Silvestre R, Torrado E. Metabolomic-Based Methods in Diagnosis and Monitoring Infection Progression. EXPERIENTIA SUPPLEMENTUM (2012) 2019; 109:283-315. [PMID: 30535603 PMCID: PMC7124096 DOI: 10.1007/978-3-319-74932-7_7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A robust biomarker screening and validation is crucial for overcoming the current limits in the clinical management of infectious diseases. In this chapter, a general workflow for metabolomics is summarized. Subsequently, an overview of the major contributions of this omics science to the field of biomarkers of infectious diseases is discussed. Different approaches using a variety of analytical platforms can be distinguished to unveil the key metabolites for the diagnosis, prognosis, response to treatment and susceptibility for infectious diseases. To allow the implementation of such biomarkers into the clinics, the performance of large-scale studies employing solid validation criteria becomes essential. Focusing on the etiological agents and after an extensive review of the field, we present a comprehensive revision of the main metabolic biomarkers of viral, bacterial, fungal, and parasitic diseases. Finally, we discussed several articles which show the strongest validation criteria. Following these research avenues, precious clinical resources will be revealed, allowing for reduced misdiagnosis, more efficient therapies, and affordable costs, ultimately leading to a better patient management.
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Affiliation(s)
- Ricardo Silvestre
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal
| | - Egídio Torrado
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal
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75
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Duffy FJ, Weiner J, Hansen S, Tabb DL, Suliman S, Thompson E, Maertzdorf J, Shankar S, Tromp G, Parida S, Dover D, Axthelm MK, Sutherland JS, Dockrell HM, Ottenhoff THM, Scriba TJ, Picker LJ, Walzl G, Kaufmann SHE, Zak DE. Immunometabolic Signatures Predict Risk of Progression to Active Tuberculosis and Disease Outcome. Front Immunol 2019; 10:527. [PMID: 30967866 PMCID: PMC6440524 DOI: 10.3389/fimmu.2019.00527] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/27/2019] [Indexed: 12/24/2022] Open
Abstract
There remains a pressing need for biomarkers that can predict who will progress to active tuberculosis (TB) after exposure to Mycobacterium tuberculosis (MTB) bacterium. By analyzing cohorts of household contacts of TB index cases (HHCs) and a stringent non-human primate (NHP) challenge model, we evaluated whether integration of blood transcriptional profiling with serum metabolomic profiling can provide new understanding of disease processes and enable improved prediction of TB progression. Compared to either alone, the combined application of pre-existing transcriptome- and metabolome-based signatures more accurately predicted TB progression in the HHC cohorts and more accurately predicted disease severity in the NHPs. Pathway and data-driven correlation analyses of the integrated transcriptional and metabolomic datasets further identified novel immunometabolomic signatures significantly associated with TB progression in HHCs and NHPs, implicating cortisol, tryptophan, glutathione, and tRNA acylation networks. These results demonstrate the power of multi-omics analysis to provide new insights into complex disease processes.
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Affiliation(s)
- Fergal J Duffy
- Center for Global Infectious Disease Research, Seattle Childrens Research Institute, Seattle, WA, United States
| | - January Weiner
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Scott Hansen
- Oregon Health and Science University, Portland, OR, United States
| | - David L Tabb
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, SAMRC-SHIP South African Tuberculosis Bioinformatics Initiative (SATBBI), Center for Bioinformatics and Computational Biology, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
| | - Sara Suliman
- Department of Pathology, South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Ethan Thompson
- Center for Infectious Disease Research, Seattle, WA, United States
| | | | - Smitha Shankar
- Center for Infectious Disease Research, Seattle, WA, United States
| | - Gerard Tromp
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, SAMRC-SHIP South African Tuberculosis Bioinformatics Initiative (SATBBI), Center for Bioinformatics and Computational Biology, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
| | - Shreemanta Parida
- Max Planck Institute for Infection Biology, Berlin, Germany.,Translational Medicine & Global Health Consulting, Berlin, Germany
| | - Drew Dover
- Center for Global Infectious Disease Research, Seattle Childrens Research Institute, Seattle, WA, United States
| | | | - Jayne S Sutherland
- Vaccines & Immunity Theme, Medical Research Council Unit, Fajara, Gambia
| | - Hazel M Dockrell
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Thomas J Scriba
- Department of Pathology, South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Louis J Picker
- Oregon Health and Science University, Portland, OR, United States
| | - Gerhard Walzl
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, SAMRC-SHIP South African Tuberculosis Bioinformatics Initiative (SATBBI), Center for Bioinformatics and Computational Biology, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
| | | | - Daniel E Zak
- Center for Infectious Disease Research, Seattle, WA, United States
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76
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Fitzgerald BL, Islam MN, Graham B, Mahapatra S, Webb K, Boom WH, Malherbe ST, Joloba ML, Johnson JL, Winter J, Walzl G, Belisle JT. Elucidation of a Human Urine Metabolite as a Seryl-Leucine Glycopeptide and as a Biomarker of Effective Anti-Tuberculosis Therapy. ACS Infect Dis 2019; 5:353-364. [PMID: 30585483 PMCID: PMC6412501 DOI: 10.1021/acsinfecdis.8b00241] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
The
evaluation of new tuberculosis (TB) therapies is limited by the paucity
of biomarkers to monitor treatment response. Previous work detected
an uncharacterized urine metabolite with a molecular mass of 874.3547
Da that showed promise as a biomarker for successful TB treatment.
Using mass spectrometry combined with enzymatic digestions, the metabolite
was structurally characterized as a seryl-leucine core 1 O-glycosylated peptide (SLC1G) of human origin. Examination of SLC1G
in urine revealed a significant abundance increase in individuals
with active TB versus their household contacts and healthy controls.
Moreover, differential decreases in SLC1G levels were observed by
week one in TB patients during successful treatment versus those that
failed treatment. The SLC1G levels were also associated with clinical
parameters used to measure bacterial burden (GeneXpert) and inflammation
(positron emission tomography-computed tomography (PET-CT)). These
results demonstrate the importance of metabolite identification and
provide strong evidence for applying SLC1G as a biomarker of TB treatment
response.
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Affiliation(s)
- Bryna L. Fitzgerald
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 200 West Lake Street, 0922 Campus Delivery, Fort Collins, Colorado 80523, United States
| | - M. Nurul Islam
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 200 West Lake Street, 0922 Campus Delivery, Fort Collins, Colorado 80523, United States
| | - Barbara Graham
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 200 West Lake Street, 0922 Campus Delivery, Fort Collins, Colorado 80523, United States
| | - Sebabrata Mahapatra
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 200 West Lake Street, 0922 Campus Delivery, Fort Collins, Colorado 80523, United States
| | - Kristofor Webb
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 200 West Lake Street, 0922 Campus Delivery, Fort Collins, Colorado 80523, United States
| | - W. Henry Boom
- Department of Medicine, Tuberculosis Research Unit (TBRU), Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Uganda-Case Western Reserve University Research Collaboration, 28A Upper Kololo Terrace, Kampala, Uganda
| | - Stephanus T. Malherbe
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research and MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 241, Francie van Zijl Drive, Cape Town 8000, South Africa
| | - Moses L. Joloba
- School for Biomedical Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - John L. Johnson
- Department of Medicine, Tuberculosis Research Unit (TBRU), Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Uganda-Case Western Reserve University Research Collaboration, 28A Upper Kololo Terrace, Kampala, Uganda
| | - Jill Winter
- Catalysis Foundation for Health, 2100 Addison Street, Berkeley, California 94704, United States
| | - Gerhard Walzl
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research and MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 241, Francie van Zijl Drive, Cape Town 8000, South Africa
| | - John T. Belisle
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, 200 West Lake Street, 0922 Campus Delivery, Fort Collins, Colorado 80523, United States
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77
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Poeta P, Silva V, Guedes A, Eduardo Pereira J, Cláudia Coelho A, Igrejas G. Tuberculosis in the 21th century: Current status of diagnostic methods. Exp Lung Res 2019; 44:352-360. [PMID: 30663432 DOI: 10.1080/01902148.2018.1545880] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Tuberculosis is an infectious bacterial disease with a high mortality rate worldwide constituting a serious public health problem. The diagnostic methods commonly used by health professionals are slow and expensive and the results may take about sixty days which will cause a delay in administrating the most proper treatment to the patient, as well as increase health care costs and infection transmission possibility. Patients infected simultaneously with human immunodeficiency virus and Mycobacterium tuberculosis are a constant and worrying challenge for the scientific community which will research and develop new methods of diagnosis, new drugs and new therapies. Nowadays there are new tuberculosis diagnosis methods and some of which are already in clinical trial phases. These methods have high sensitivity, but do not replace the microbiological examination for isolation and culture of Mycobacterium spp. However, in clinical practice, microbiological, imaging, clinical and epidemiological data integration provide the best diagnosis and treatment possible. Consequently, throughout this paper, the different methods of diagnosis of human tuberculosis with its advantages and disadvantages will be covered, describing new omics and ultra-fast methods to increase knowledge and obtain a rapid diagnosis of tuberculosis.
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Affiliation(s)
- Patrícia Poeta
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,b Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro , Vila Real , Portugal
| | - Vanessa Silva
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,b Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,c Functional Genomics and Proteomics Unit , University of Tras-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,d Associated Laboratory for Green Chemistry (LAQV-REQUIMTE) , University NOVA of Lisboa , Lisboa , Caparica, Portugal
| | - Andreia Guedes
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal
| | - José Eduardo Pereira
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,e CECAV, Centro de Ciência Animal e Veterinária , Universidade de Trás-os-Montes e Alto Douro , Vila Real , Portugal
| | - Ana Cláudia Coelho
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,e CECAV, Centro de Ciência Animal e Veterinária , Universidade de Trás-os-Montes e Alto Douro , Vila Real , Portugal
| | - Gilberto Igrejas
- b Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,c Functional Genomics and Proteomics Unit , University of Tras-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,d Associated Laboratory for Green Chemistry (LAQV-REQUIMTE) , University NOVA of Lisboa , Lisboa , Caparica, Portugal
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78
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Davis AG, Rohlwink UK, Proust A, Figaji AA, Wilkinson RJ. The pathogenesis of tuberculous meningitis. J Leukoc Biol 2019; 105:267-280. [PMID: 30645042 DOI: 10.1002/jlb.mr0318-102r] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/17/2018] [Accepted: 12/05/2018] [Indexed: 01/07/2023] Open
Abstract
Tuberculosis (TB) remains a leading cause of death globally. Dissemination of TB to the brain results in the most severe form of extrapulmonary TB, tuberculous meningitis (TBM), which represents a medical emergency associated with high rates of mortality and disability. Via various mechanisms the Mycobacterium tuberculosis (M.tb) bacillus disseminates from the primary site of infection and overcomes protective barriers to enter the CNS. There it induces an inflammatory response involving both the peripheral and resident immune cells, which initiates a cascade of pathologic mechanisms that may either contain the disease or result in significant brain injury. Here we review the steps from primary infection to cerebral disease, factors that contribute to the virulence of the organism and the vulnerability of the host and discuss the immune response and the clinical manifestations arising. Priorities for future research directions are suggested.
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Affiliation(s)
- Angharad Grace Davis
- The Francis Crick Institute, Midland Road, London, United Kingdom.,Faculty of Life Sciences, University College London, United Kingdom.,Department of Medicine, University of Cape Town, Republic of South Africa
| | - Ursula Karin Rohlwink
- Neuroscience Institute, Division of Neurosurgery, University of Cape Town, Republic of South Africa
| | - Alizé Proust
- The Francis Crick Institute, Midland Road, London, United Kingdom
| | - Anthony A Figaji
- Neuroscience Institute, Division of Neurosurgery, University of Cape Town, Republic of South Africa
| | - Robert J Wilkinson
- The Francis Crick Institute, Midland Road, London, United Kingdom.,Faculty of Life Sciences, University College London, United Kingdom.,Department of Medicine, University of Cape Town, Republic of South Africa.,Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Republic of South Africa.,Department of Medicine, Imperial College, London, United Kingdom
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79
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Metabolite changes in blood predict the onset of tuberculosis. Nat Commun 2018; 9:5208. [PMID: 30523338 PMCID: PMC6283869 DOI: 10.1038/s41467-018-07635-7] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/05/2018] [Indexed: 12/22/2022] Open
Abstract
New biomarkers of tuberculosis (TB) risk and disease are critical for the urgently needed control of the ongoing TB pandemic. In a prospective multisite study across Subsaharan Africa, we analyzed metabolic profiles in serum and plasma from HIV-negative, TB-exposed individuals who either progressed to TB 3–24 months post-exposure (progressors) or remained healthy (controls). We generated a trans-African metabolic biosignature for TB, which identifies future progressors both on blinded test samples and in external data sets and shows a performance of 69% sensitivity at 75% specificity in samples within 5 months of diagnosis. These prognostic metabolic signatures are consistent with development of subclinical disease prior to manifestation of active TB. Metabolic changes associated with pre-symptomatic disease are observed as early as 12 months prior to TB diagnosis, thus enabling timely interventions to prevent disease progression and transmission. The tuberculosis pandemic requires new methods for diagnosing and containing infections prior to active disease. Here, the authors performed a multi-site observational study within sub-Saharan Africa and present serum and plasma metabolic signatures that can predict the onset of active TB with a high degree of sensitivity and specificity.
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80
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Rana A, Thakur S, Kumar G, Akhter Y. Recent Trends in System-Scale Integrative Approaches for Discovering Protective Antigens Against Mycobacterial Pathogens. Front Genet 2018; 9:572. [PMID: 30538722 PMCID: PMC6277634 DOI: 10.3389/fgene.2018.00572] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/06/2018] [Indexed: 11/21/2022] Open
Abstract
Mycobacterial infections are one of the deadliest infectious diseases still posing a major health burden worldwide. The battle against these pathogens needs to focus on novel approaches and key interventions. In recent times, availability of genome scale data has revolutionized the fields of computational biology and immunoproteomics. Here, we summarize the cutting-edge ‘omics’ technologies and innovative system scale strategies exploited to mine the available data. These may be targeted using high-throughput technologies to expedite the identification of novel antigenic candidates for the rational next generation vaccines and serodiagnostic development against mycobacterial pathogens for which traditional methods have been failing.
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Affiliation(s)
- Aarti Rana
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, India
| | - Shweta Thakur
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, India
| | - Girish Kumar
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
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81
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Abstract
Tuberculosis kills more people worldwide than any other single infectious disease agent, a threat made more dire by the spread of drug-resistant strains of Mycobacterium tuberculosis (Mtb). Development of new vaccines capable of preventing TB disease and new Mtb infection are an essential component of the strategy to combat the TB epidemic. Accordingly, the WHO considers the development of new TB vaccines a major public health priority. In October 2017, the WHO convened a consultation with global leaders in the TB vaccine development field to emphasize the WHO commitment to this effort and to facilitate creative approaches to the discovery and development of TB vaccine candidates. This review summarizes the presentations at this consultation, updated with scientific literature references, and includes discussions of the public health need for a TB vaccine; the status of efforts to develop vaccines to replace or potentiate BCG in infants and develop new TB vaccines for adolescents and adults; strategies being employed to diversify vaccine platforms; and new animal models being developed to facilitate TB vaccine development. A perspective on the status of these efforts from the major funders and organizational contributors also is included. This presentation highlights the extraordinary progress being made to develop new TB vaccines and provided a clear picture of the exciting development pathways that are being explored.
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Affiliation(s)
| | | | - Johan Vekemans
- Initiative for Vaccine Research, World Health Organization, Geneva, Switzerland
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82
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Hertz D, Schneider B. Sex differences in tuberculosis. Semin Immunopathol 2018; 41:225-237. [PMID: 30361803 DOI: 10.1007/s00281-018-0725-6] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 10/10/2018] [Indexed: 12/11/2022]
Abstract
Tuberculosis is the most prevalent bacterial infectious disease in humans and the leading cause of death from a single infectious agent, ranking above HIV/AIDS. The causative agent, Mycobacterium tuberculosis, is carried by an estimated two billion people globally and claims more than 1.5 million lives each year. Tuberculosis rates are significantly higher in men than in women, reflected by a male-to-female ratio for worldwide case notifications of 1.7. This phenomenon is not new and has been reported in various countries and settings over the last century. However, the reasons for the observed gender bias are not clear, potentially highly complex and discussed controversially in the literature. Both gender- (referring to sociocultural roles and behavior) and sex-related factors (referring to biological aspects) likely contribute to higher tuberculosis rates in men and will be discussed.
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Affiliation(s)
- David Hertz
- Coinfection Unit, Priority Research Area Infections, Research Center Borstel, Parkallee 1-40, 23847, Borstel, Germany
| | - Bianca Schneider
- Coinfection Unit, Priority Research Area Infections, Research Center Borstel, Parkallee 1-40, 23847, Borstel, Germany.
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83
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Salgado-Bustamante M, Rocha-Viggiano AK, Rivas-Santiago C, Magaña-Aquino M, López JA, López-Hernández Y. Metabolomics applied to the discovery of tuberculosis and diabetes mellitus biomarkers. Biomark Med 2018; 12:1001-1013. [PMID: 30043640 DOI: 10.2217/bmm-2018-0050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Tuberculosis (TB) and diabetes mellitus Type 2 (DM2) are two diseases as ancient as they are harmful to human health. The outcome for both diseases in part depends on immune and metabolic individual responses. DM2 is increasing yearly, mainly due to environmental, genetic and lifestyle habits. There are multiple evidence that DM2 is one of the most important risk factor of becoming infected with TB or reactivating latent TB. Mass spectrometry-based metabolomics is an important tool for elucidating the metabolites and metabolic pathways that influence the immune responses to M. tuberculosis infection during diabetes. We provide an up-to-date review highlighting the importance and benefit of metabolomics for identifying biomarkers as candidate molecules for diagnosis, disease activity or prognosis.
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Affiliation(s)
- Mariana Salgado-Bustamante
- Biochemistry Department, Medicine Faculty, Universidad Autonoma de San Luis Potosi, San Luis Potosi, Mexico
| | - Ana K Rocha-Viggiano
- Biochemistry Department, Medicine Faculty, Universidad Autonoma de San Luis Potosi, San Luis Potosi, Mexico
| | - César Rivas-Santiago
- CONACyT, Unidad Academica de Ciencias Biologicas, Universidad Autonoma de Zacatecas, Zacatecas, Mexico
| | - Martín Magaña-Aquino
- Infectology Department, Hospital Central Ignacio Morones Prieto, San Luis Potosi, Mexico
| | - Jesús A López
- MicroRNAs Laboratory, Unidad Academica de Ciencias Biologicas, Universidad Autonoma de Zacatecas, Zacatecas, Mexico
| | - Yamilé López-Hernández
- CONACyT, Unidad Academica de Ciencias Biologicas, Universidad Autonoma de Zacatecas, Zacatecas, Mexico
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Abstract
Recent technological advances have provided deeper insights into the role of small molecules in biological processes. Metabolic profiling has thus entered the arena of -omics studies and rapidly proven its value both as stand-alone and as complement to other more advanced approaches, notably transcriptomics. Here we describe the potential of metabolic profiling for vaccinology embedded in the context of infection and immunity. This discussion is preceded by a description of the relevant technical and analytical tools for biological interpretation of metabolic data. Although not as widely applied as other -omics technologies, we believe that metabolic profiling can make important contributions to the better understanding of mechanisms underlying vaccine-induced responses and their effects on the prevention of infection or disease.
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85
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Incipient and Subclinical Tuberculosis: a Clinical Review of Early Stages and Progression of Infection. Clin Microbiol Rev 2018; 31:31/4/e00021-18. [PMID: 30021818 DOI: 10.1128/cmr.00021-18] [Citation(s) in RCA: 303] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Tuberculosis (TB) is the leading infectious cause of mortality worldwide, due in part to a limited understanding of its clinical pathogenic spectrum of infection and disease. Historically, scientific research, diagnostic testing, and drug treatment have focused on addressing one of two disease states: latent TB infection or active TB disease. Recent research has clearly demonstrated that human TB infection, from latent infection to active disease, exists within a continuous spectrum of metabolic bacterial activity and antagonistic immunological responses. This revised understanding leads us to propose two additional clinical states: incipient and subclinical TB. The recognition of incipient and subclinical TB, which helps divide latent and active TB along the clinical disease spectrum, provides opportunities for the development of diagnostic and therapeutic interventions to prevent progression to active TB disease and transmission of TB bacilli. In this report, we review the current understanding of the pathogenesis, immunology, clinical epidemiology, diagnosis, treatment, and prevention of both incipient and subclinical TB, two emerging clinical states of an ancient bacterium.
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86
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Vrieling F, Ronacher K, Kleynhans L, van den Akker E, Walzl G, Ottenhoff THM, Joosten SA. Patients with Concurrent Tuberculosis and Diabetes Have a Pro-Atherogenic Plasma Lipid Profile. EBioMedicine 2018; 32:192-200. [PMID: 29779698 PMCID: PMC6020709 DOI: 10.1016/j.ebiom.2018.05.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/08/2018] [Accepted: 05/08/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Type 2 diabetes mellitus (DM) is a major risk factor for development of tuberculosis (TB), however the underlying molecular foundations are unclear. Since lipids play a central role in the development of both DM and TB, lipid metabolism may be important for TB-DM pathophysiology. METHODS A 1H NMR spectroscopy-based platform was used to determine 225 lipid and other metabolic intermediates in plasma samples of healthy controls (n = 50) and patients with TB (n = 50), DM (n = 50) or TB-DM (n = 27). RESULTS TB patients presented with wasting disease, represented by decreased amino acid levels including histidine and alanine. Conversely, DM patients were dyslipidemic as evidenced by high levels of very low-density lipoprotein triglycerides and low high-density lipoprotein cholesterol. TB-DM patients displayed metabolic characteristics of both wasting and dyslipidemia combined with disease interaction-specific increases in phospholipid metabolites (e.g. sphingomyelins) and atherogenic remnant-like lipoprotein particles. Biomarker analysis identified the ratios of phenylalanine/histidine and esterified cholesterol/sphingomyelin as markers for TB classification regardless of DM-status. CONCLUSIONS TB-DM patients possess a distinctive plasma lipid profile with pro-atherogenic properties. These findings support further research on the benefits of improved blood lipid control in the treatment of TB-DM.
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Affiliation(s)
- Frank Vrieling
- Department of Infectious Diseases, Leiden University Medical Centre, Leiden, The Netherlands
| | - Katharina Ronacher
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SA MRC Centre for TB Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences Stellenbosch University, Cape Town, South Africa; Mater Research Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Léanie Kleynhans
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SA MRC Centre for TB Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences Stellenbosch University, Cape Town, South Africa
| | - Erik van den Akker
- Department of Biomedical Data Sciences, Leiden University Medical Centre, Leiden, The Netherlands; Pattern Recognition & Bioinformatics, Delft University of Technology, Delft, The Netherlands
| | - Gerhard Walzl
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SA MRC Centre for TB Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences Stellenbosch University, Cape Town, South Africa
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Centre, Leiden, The Netherlands
| | - Simone A Joosten
- Department of Infectious Diseases, Leiden University Medical Centre, Leiden, The Netherlands.
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87
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Adu-Gyamfi CG, Snyman T, Hoffmann CJ, Martinson NA, Chaisson RE, George JA, Suchard MS. Plasma Indoleamine 2, 3-Dioxygenase, a Biomarker for Tuberculosis in Human Immunodeficiency Virus-Infected Patients. Clin Infect Dis 2018; 65:1356-1358. [PMID: 29017244 PMCID: PMC5848309 DOI: 10.1093/cid/cix550] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 06/12/2017] [Indexed: 12/31/2022] Open
Abstract
Background There is no biomarker for diagnosing active tuberculosis in patients with human immunodeficiency virus (HIV) infection. Indoleamine 2, 3-dioxygenase (IDO) is an immunoregulatory enzyme that breaks down tryptophan (Trp) to metabolites known as kynurenines (Kyns). We investigated whether IDO activity, as measured by the ratio of Kyn to Trp, could be used to diagnose or predict active tuberculosis disease in HIV-infected adults. Methods Kyn and Trp concentrations were measured using ultraperformance liquid chromatography mass spectrometry in plasma samples from 32 HIV-infected patients in whom active tuberculosis developed and who were followed up prospectively. We compared to 70 HIV-infected control subjects from the same cohort in whom tuberculosis did not develop, matched by age, sex, and CD4 cell count, and 37 unmatched HIV-infected patients with a diagnosis of pneumonia. Clinical parameters, including body mass index, CD4 cell count, HIV load, and C-reactive protein levels were analyzed. Results At the time of tuberculosis diagnosis, IDO activity was significantly higher in patients with tuberculosis than in controls (P < .001). Six months before tuberculosis diagnosis, IDO activity was significantly higher in all patients who later developed tuberculosis (P < .001) than controls. After 6 months of tuberculosis treatment, IDO activity in patients with tuberculosis declined to levels similar to those in controls. IDO activity was 4-fold higher in patients with tuberculosis than in those with pneumonia, and could be used to distinguish them. With a receiver operating characteristic curve, IDO activity had a sensitivity of 97%, a specificity of 99%, and positive and negative predictive values of 89% and 100% for detecting active tuberculosis disease. Conclusion Plasma IDO activity is suitable as a biomarker of active tuberculosis in HIV-positive patients.
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Affiliation(s)
- Clement G Adu-Gyamfi
- Centre for Vaccines & Immunology, National Institute for Communicable Diseases, Division of the National Health Laboratory Service.,Department of Chemical Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand & National Health Laboratory Service, Johannesburg, South Africa
| | - Tracy Snyman
- Department of Chemical Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand & National Health Laboratory Service, Johannesburg,South Africa
| | | | - Neil A Martinson
- Perinatal Health Research Unit, DST/NRF Centre of Excellence for Biomedical TB Research, and Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Jaya A George
- Department of Chemical Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand & National Health Laboratory Service, Johannesburg,South Africa
| | - Melinda S Suchard
- Centre for Vaccines & Immunology, National Institute for Communicable Diseases, Division of the National Health Laboratory Service.,Department of Chemical Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand & National Health Laboratory Service, Johannesburg, South Africa
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88
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Verma S, Du P, Nakanjako D, Hermans S, Briggs J, Nakiyingi L, Ellner JJ, Manabe YC, Salgame P. "Tuberculosis in advanced HIV infection is associated with increased expression of IFNγ and its downstream targets". BMC Infect Dis 2018; 18:220. [PMID: 29764370 PMCID: PMC5952419 DOI: 10.1186/s12879-018-3127-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 05/02/2018] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is the major cause of death in Human Immunodeficiency Virus (HIV)-infected individuals. However, diagnosis of TB in HIV remains challenging particularly when HIV infection is advanced. Several gene signatures and serum protein biomarkers have been identified that distinguish active TB from latent infection. Our study was designed to assess if gene expression signatures and cytokine levels would distinguish active TB in advanced HIV. METHODS We conducted a case-control study of whole blood RNA-Seq and plasma cytokine/chemokine analysis in HIV-infected with CD4+ T cell count of ≤ 100 cells/μl, with and without active TB. Next, the overlap of the differentially expressed genes (DEG) with the published signatures was performed and then receiver operator characteristic (ROC) analysis was done on small gene discriminators to determine their performance in distinguishing TB in advanced HIV. ELISA was performed on plasma to evaluate cytokine and chemokine levels. RESULTS Hierarchical clustering of the transcriptional profiles showed that, in general, HIV-infected individuals with TB (TB-HIV) clustered separately from those without TB. IPA indicated that the TB-HIV signature was characterized by an increase in inflammatory signaling pathways. Analysis of overlaps between DEG in our data set with published TB signatures revealed that significant overlap was seen with one TB signature and one TB-IRIS signature. ROC analysis revealed that transcript levels of FcGR1A (AUC = 0.85) and BATF2 (AUC = 0.82), previously reported as consistent single gene classifiers of active TB irrespective of HIV status, performed successfully even in advanced HIV. Plasma protein levels of IFNγ, a stimulator of FcGR1A and BATF2, and CXCL10, also up-regulated by IFNγ, accurately classified active TB (AUC = 0.98 and 0.91, respectively) in advanced HIV. Neither of these genes nor proteins distinguished between TB and TB-IRIS. CONCLUSIONS Gene expression of FcGR1A and BATF2, and plasma protein levels of IFNγ and CXCL10 have the potential to independently detect TB in advanced HIV. However, since other lung diseases were not included in this study, these final candidates need to be validated as specific to TB in the advanced HIV population with TB.
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Affiliation(s)
- Sheetal Verma
- Department of Medicine, Center for Emerging Pathogens, Rutgers University New Jersey Medical School, Newark, NJ USA
| | - Peicheng Du
- Office of Advanced Research Computing, Rutgers University New Jersey Medical School, Newark, NJ USA
| | - Damalie Nakanjako
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Sabine Hermans
- Amsterdam Institute of Global Health and Development, Amsterdam Medical Center, Amsterdam, Netherlands
| | - Jessica Briggs
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
- Present address: UCSF, Division of Infectious Diseases, San Francisco, CA USA
| | - Lydia Nakiyingi
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Jerrold J. Ellner
- Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, MA USA
| | - Yukari C. Manabe
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Padmini Salgame
- Department of Medicine, Center for Emerging Pathogens, Rutgers University New Jersey Medical School, Newark, NJ USA
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89
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Hoff FW, Hu CW, Qiu Y, Ligeralde A, Yoo SY, Scheurer ME, de Bont ESJM, Qutub AA, Kornblau SM, Horton TM. Recurrent Patterns of Protein Expression Signatures in Pediatric Acute Lymphoblastic Leukemia: Recognition and Therapeutic Guidance. Mol Cancer Res 2018; 16:1263-1274. [PMID: 29669823 DOI: 10.1158/1541-7786.mcr-17-0730] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/21/2018] [Accepted: 03/30/2018] [Indexed: 12/13/2022]
Abstract
Pediatric acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy, and the second leading cause of pediatric cancer-related death in developed countries. While the cure rate for newly diagnosed ALL is excellent, the genetic heterogeneity and chemoresistance of leukemia cells at relapse makes individualized curative treatment plans difficult. We hypothesize that genetic events would coalesce into a finite number of protein signatures that could guide the design of individualized therapy. Custom reverse-phase protein arrays were produced from pediatric ALL (n = 73) and normal CD34+ (n = 10) samples with 194 validated antibodies. Proteins were allocated into 31 protein functional groups (PFG) to analyze them in the context of other proteins, based on known associations from the literature. The optimal number of protein clusters was determined for each PFG. Protein networks showed distinct transition states, revealing "normal-like" and "leukemia-specific" protein patterns. Block clustering identified strong correlation between various protein clusters that formed 10 protein constellations. Patients that expressed similar recurrent combinations of constellations comprised 7 distinct signatures, correlating with risk stratification, cytogenetics, and laboratory features. Most constellations and signatures were specific for T-cell ALL or pre-B-cell ALL; however, some constellations showed significant overlap. Several signatures were associated with Hispanic ethnicity, suggesting that ethnic pathophysiologic differences likely exist. In addition, some constellations were enriched for "normal-like" protein clusters, whereas others had exclusively "leukemia-specific" patterns.Implications: Recognition of proteins that have universally altered expression, together with proteins that are specific for a given signature, suggests targets for directed combinatorial inhibition or replacement to enable personalized therapy. Mol Cancer Res; 16(8); 1263-74. ©2018 AACRSee related article by Hoff et al., p. 1275.
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Affiliation(s)
- Fieke W Hoff
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, Texas.,Department of Pediatric Oncology/Hematology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Chenyue W Hu
- Department of Bioengineering, Rice University, Houston, Texas
| | - Yihua Qiu
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | | | - Suk-Young Yoo
- Department of Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Michael E Scheurer
- Department of Pediatrics and Department of Epidemiology, Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston TX
| | - Eveline S J M de Bont
- Department of Pediatric Oncology/Hematology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Amina A Qutub
- Department of Bioengineering, Rice University, Houston, Texas
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, Texas.
| | - Terzah M Horton
- Department of Pediatrics, Baylor College of Medicine/Dan L. Duncan Cancer Center and Texas Children's Cancer Center, Houston, Texas
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90
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Hoff FW, Hu CW, Qiu Y, Ligeralde A, Yoo SY, Mahmud H, de Bont ESJM, Qutub AA, Horton TM, Kornblau SM. Recognition of Recurrent Protein Expression Patterns in Pediatric Acute Myeloid Leukemia Identified New Therapeutic Targets. Mol Cancer Res 2018; 16:1275-1286. [PMID: 29669821 DOI: 10.1158/1541-7786.mcr-17-0731] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/21/2018] [Accepted: 03/30/2018] [Indexed: 11/16/2022]
Abstract
Heterogeneity in the genetic landscape of pediatric acute myeloid leukemia (AML) makes personalized medicine challenging. As genetic events are mediated by the expression and function of proteins, recognition of recurrent protein patterns could enable classification of pediatric AML patients and could reveal crucial protein dependencies. This could help to rationally select combinations of therapeutic targets. To determine whether protein expression levels could be clustered into functionally relevant groups, custom reverse-phase protein arrays were performed on pediatric AML (n = 95) and CD34+ normal bone marrow (n = 10) clinical specimens using 194 validated antibodies. To analyze proteins in the context of other proteins, all proteins were assembled into 31 protein functional groups (PFG). For each PFG, an optimal number of protein clusters was defined that represented distinct transition states. Block clustering analysis revealed strong correlations between various protein clusters and identified the existence of 12 protein constellations stratifying patients into 8 protein signatures. Signatures were correlated with therapeutic outcome, as well as certain laboratory and demographic characteristics. Comparison of acute lymphoblastic leukemia specimens from the same array and AML pediatric patient specimens demonstrated disease-specific signatures, but also identified the existence of shared constellations, suggesting joint protein deregulation between the diseases.Implication: Recognition of altered proteins in particular signatures suggests rational combinations of targets that could facilitate stratified targeted therapy. Mol Cancer Res; 16(8); 1275-86. ©2018 AACRSee related article by Hoff et al., p. 1263.
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Affiliation(s)
- Fieke W Hoff
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Pediatric Oncology/Hematology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Chenyue W Hu
- Department of Bioengineering, Rice University, Houston, Texas
| | - Yihua Qiu
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Suk-Young Yoo
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hasan Mahmud
- Department of Pediatric Oncology/Hematology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Eveline S J M de Bont
- Department of Pediatric Oncology/Hematology, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Amina A Qutub
- Department of Bioengineering, Rice University, Houston, Texas
| | - Terzah M Horton
- Department of Pediatrics, Baylor College of Medicine/Dan L. Duncan Cancer Center and Texas Children's Cancer Center, Houston, Texas
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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91
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Tuberculosis: advances and challenges in development of new diagnostics and biomarkers. THE LANCET. INFECTIOUS DISEASES 2018; 18:e199-e210. [PMID: 29580818 DOI: 10.1016/s1473-3099(18)30111-7] [Citation(s) in RCA: 211] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/18/2017] [Accepted: 01/02/2018] [Indexed: 11/23/2022]
Abstract
Tuberculosis remains the leading cause of death from an infectious disease worldwide. Early and accurate diagnosis and detection of drug-sensitive and drug-resistant tuberculosis is essential for achieving global tuberculosis control. Despite the introduction of the Xpert MTB/RIF assay as the first-line rapid tuberculosis diagnostic test, the gap between global estimates of incidence and new case notifications is 4·1 million people. More accurate, rapid, and cost-effective screening tests are needed to improve case detection. Diagnosis of extrapulmonary tuberculosis and tuberculosis in children, people living with HIV, and pregnant women remains particularly problematic. The diagnostic molecular technology landscape has continued to expand, including the development of tests for resistance to several antituberculosis drugs. Biomarkers are urgently needed to indicate progression from latent infection to clinical disease, to predict risk of reactivation after cure, and to provide accurate endpoints for drug and vaccine trials. Sophisticated bioinformatic computational tools and systems biology approaches are being applied to the discovery and validation of biomarkers, with substantial progress taking place. New data have been generated from the study of T-cell responses and T-cell function, serological studies, flow cytometric-based assays, and protein and gene expression studies. Alternative diagnostic strategies under investigation as potential screening and triaging tools include non-sputum-based detection with breath-based tests and automated digital radiography. We review developments and key achievements in the search for new tuberculosis diagnostics and biomarkers. We highlight gaps and challenges in evaluation and rollout of new diagnostics and biomarkers, and prioritise areas needing further investment, including impact assessment and cost-benefit studies.
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92
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Goletti D, Lee MR, Wang JY, Walter N, Ottenhoff THM. Update on tuberculosis biomarkers: From correlates of risk, to correlates of active disease and of cure from disease. Respirology 2018; 23:455-466. [PMID: 29457312 DOI: 10.1111/resp.13272] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 12/18/2017] [Accepted: 01/22/2018] [Indexed: 12/23/2022]
Abstract
Tuberculosis (TB) remains a devastating disease, yet despite its enormous toll on global health, tools to control TB are insufficient and often outdated. TB Biomarkers (TB-BM) would constitute extremely useful tools to measure infection status and predict outcome of infection, vaccination or therapy. There are several types of TB-BM: Correlate of Infection; Correlate of TB Disease; Correlate of Increased Risk of Developing Active TB Disease; Correlate of the Curative Response to Therapy; and Correlate of Protection (CoP). Most TB-BM currently studied are host-derived BM, and consist of transcriptomic, proteomic, metabolomic, cellular markers or marker combinations ('signatures'). In particular, vaccine-inducible CoP are expected to be transformative in developing new TB vaccines as they will de-risk vaccine research and development (R&D) as well as human testing at an early stage. In addition, CoP could also help minimizing the need for preclinical studies in experimental animals. Of key importance is that TB-BM are tested and validated in different well-characterized human TB cohorts, preferably with complementary profiles and geographically diverse populations: genetic and environmental factors such as (viral) coinfections, exposure to non-tuberculous mycobacteria, nutritional status, metabolic status, age (infants vs children vs adolescents vs adults) and other factors impact host immune set points and host responses across different populations. In this study, we review the most recent advances in research into TB-BM for the diagnosis of active TB, risk of TB development and treatment-induced TB cure.
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Affiliation(s)
- Delia Goletti
- Translational Research Unit, Department of Epidemiology and Preclinical Research, National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Meng-Rui Lee
- Department of Internal Medicine, National Taiwan University Hospital, Hsinchu, Taiwan
| | - Jann-Yuan Wang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Nicholas Walter
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
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93
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Considine EC, Thomas G, Boulesteix AL, Khashan AS, Kenny LC. Critical review of reporting of the data analysis step in metabolomics. Metabolomics 2017; 14:7. [PMID: 30830321 DOI: 10.1007/s11306-017-1299-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 11/13/2017] [Indexed: 12/29/2022]
Abstract
INTRODUCTION We present the first study to critically appraise the quality of reporting of the data analysis step in metabolomics studies since the publication of minimum reporting guidelines in 2007. OBJECTIVES The aim of this study was to assess the standard of reporting of the data analysis step in metabolomics biomarker discovery studies and to investigate whether the level of detail supplied allows basic understanding of the steps employed and/or reuse of the protocol. For the purposes of this review we define the data analysis step to include the data pretreatment step and the actual data analysis step, which covers algorithm selection, univariate analysis and multivariate analysis. METHOD We reviewed the literature to identify metabolomic studies of biomarker discovery that were published between January 2008 and December 2014. Studies were examined for completeness in reporting the various steps of the data pretreatment phase and data analysis phase and also for clarity of the workflow of these sections. RESULTS We analysed 27 papers, published anytime in 2008 until the end of 2014 in the area or biomarker discovery in serum metabolomics. The results of this review showed that the data analysis step in metabolomics biomarker discovery studies is plagued by unclear and incomplete reporting. Major omissions and lack of logical flow render the data analysis' workflows in these studies impossible to follow and therefore replicate or even imitate. CONCLUSIONS While we await the holy grail of computational reproducibility in data analysis to become standard, we propose that, at a minimum, the data analysis section of metabolomics studies should be readable and interpretable without omissions such that a data analysis workflow diagram could be extrapolated from the study and therefore the data analysis protocol could be reused by the reader. That inconsistent and patchy reporting obfuscates reproducibility is a given. However even basic understanding and reuses of protocols are hampered by the low level of detail supplied in the data analysis sections of the studies that we reviewed.
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Affiliation(s)
- E C Considine
- The Irish Centre for Fetal and Neonatal Translational Research (INFANT), Department of Obstetrics and Gynaecology, University College Cork, Cork, Ireland.
| | - G Thomas
- SQU4RE, Sint-Alfonsusstraat 17, 8800, Roeselare, Belgium
| | - A L Boulesteix
- Department of Medical Informatics, Biometry and Epidemiology, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - A S Khashan
- The Irish Centre for Fetal and Neonatal Translational Research (INFANT), Department of Obstetrics and Gynaecology, University College Cork, Cork, Ireland
- Department of Epidemiology and Public Health, University College Cork, Cork, Ireland
| | - L C Kenny
- The Irish Centre for Fetal and Neonatal Translational Research (INFANT), Department of Obstetrics and Gynaecology, University College Cork, Cork, Ireland
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Ottas A, Fishman D, Okas TL, Püssa T, Toomik P, Märtson A, Kingo K, Soomets U. Blood serum metabolome of atopic dermatitis: Altered energy cycle and the markers of systemic inflammation. PLoS One 2017; 12:e0188580. [PMID: 29176763 PMCID: PMC5703555 DOI: 10.1371/journal.pone.0188580] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 11/09/2017] [Indexed: 12/19/2022] Open
Abstract
Atopic dermatitis is a chronic inflammatory disease which usually starts in the early childhood and ends before adulthood. However up to 3% of adults remain affected by the disease. The onset and course of the disease is influenced by various genetic and environmental factors. Although the immune system has a great effect on the outcome of the disease, metabolic markers can also try to explain the background of atopic dermatitis. In this study we analyzed the serum of patients with atopic dermatitis using both targeted and untargeted metabolomics approaches. We found the most significant changes to be related to phosphatidylcholines, acylcarnitines and their ratios and a cleavage peptide of Fibrinogen A-α. These findings that have not been reported before will further help to understand this complex disease.
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Affiliation(s)
- Aigar Ottas
- Department of Biochemistry, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- * E-mail:
| | - Dmytro Fishman
- Faculty of Science and Technology, Institute of Computer Science, University of Tartu, Tartu, Estonia
- Quretec OÜ, Tartu, Estonia
| | | | - Tõnu Püssa
- Department of Food Hygiene, Estonian University of Life Sciences, Tartu, Estonia
| | - Peeter Toomik
- Department of Food Hygiene, Estonian University of Life Sciences, Tartu, Estonia
| | - Aare Märtson
- Clinic of Traumatology and Orthopedics, Tartu University Hospital, Tartu, Estonia
| | - Külli Kingo
- Department of Dermatology, University of Tartu; Clinic of Dermatology, Tartu University Hospital, Tartu, Estonia
| | - Ursel Soomets
- Department of Biochemistry, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
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95
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Zeng G, Zhang G, Chen X. Th1 cytokines, true functional signatures for protective immunity against TB? Cell Mol Immunol 2017; 15:206-215. [PMID: 29151578 DOI: 10.1038/cmi.2017.113] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 09/15/2017] [Accepted: 09/19/2017] [Indexed: 12/12/2022] Open
Abstract
The lack of an effective preventative vaccine against tuberculosis (TB) presents a great challenge to TB control. Since it takes an extremely long time to accurately determine the protective efficacy of TB vaccines, there is a great need to identify the surrogate signatures of protection to facilitate vaccine development. Unfortunately, antigen-specific Th1 cytokines that are currently used to evaluate the protective efficacy of the TB vaccine, do not align with the protection and failure of TB vaccine candidates in clinical trials. In this review, we discuss the limitation of current Th1 cytokines as surrogates of protection and address the potential elements that should be considered to finalize the true functional signatures of protective immunity against TB.
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Affiliation(s)
- Gucheng Zeng
- Department of Microbiology, Key Laboratory for Tropical Diseases Control of the Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Guoliang Zhang
- Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Guangdong Medical University, Shenzhen, Guangdong 518112, China
| | - Xinchun Chen
- Department of Pathogen Biology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
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96
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Plasma lipidomics of tuberculosis patients: altered phosphatidylcholine remodeling. Future Sci OA 2017; 4:FSO255. [PMID: 29255627 PMCID: PMC5729594 DOI: 10.4155/fsoa-2017-0011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/02/2017] [Indexed: 11/17/2022] Open
Abstract
Aim: Decreased circulating levels of lysophosphatidylcholines have been monitored in the serum of tuberculosis (TB) patients. However, the etiology of these findings has not been explored and other critical lung surfactant lipids have not been examined. Materials & methods: We undertook a lipidomics analysis of 30 controls and 30 TB patients, utilizing a high-resolution mass spectrometric analytical platform that assays over 1800 lipids. Findings: As previously reported, we found decrements in the plasma levels of lysophosphatidylcholines in TB patients. In addition, we report for the first time that there are increases in the plasma levels of phosphatidylcholines and phosphatidylglycerols in TB patients. Conclusion: These data suggest that TB results in altered glycerophosphocholine remodeling involving deacylation–reacylation reactions at sn-2 of the glycerol backbone. Such alterations in lipid remodeling have the potential to exert negative effects on the function of lung surfactant, on signal transduction mechanisms and membrane structural lipid architecture in TB patients. On investigating tuberculosis patients, we found altered metabolism of structural lipids that are essential to lung function. These new biomarkers may be useful to monitor the efficacy of current and new patient treatment strategies in the future.
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97
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Hoffman JD, Parikh I, Green SJ, Chlipala G, Mohney RP, Keaton M, Bauer B, Hartz AMS, Lin AL. Age Drives Distortion of Brain Metabolic, Vascular and Cognitive Functions, and the Gut Microbiome. Front Aging Neurosci 2017; 9:298. [PMID: 28993728 PMCID: PMC5622159 DOI: 10.3389/fnagi.2017.00298] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 08/30/2017] [Indexed: 12/15/2022] Open
Abstract
Advancing age is the top risk factor for the development of neurodegenerative disorders, including Alzheimer's disease (AD). However, the contribution of aging processes to AD etiology remains unclear. Emerging evidence shows that reduced brain metabolic and vascular functions occur decades before the onset of cognitive impairments, and these reductions are highly associated with low-grade, chronic inflammation developed in the brain over time. Interestingly, recent findings suggest that the gut microbiota may also play a critical role in modulating immune responses in the brain via the brain-gut axis. In this study, our goal was to identify associations between deleterious changes in brain metabolism, cerebral blood flow (CBF), gut microbiome and cognition in aging, and potential implications for AD development. We conducted our study with a group of young mice (5-6 months of age) and compared those to old mice (18-20 months of age) by utilizing metabolic profiling, neuroimaging, gut microbiome analysis, behavioral assessments and biochemical assays. We found that compared to young mice, old mice had significantly increased levels of numerous amino acids and fatty acids that are highly associated with inflammation and AD biomarkers. In the gut microbiome analyses, we found that old mice had increased Firmicutes/Bacteroidetes ratio and alpha diversity. We also found impaired blood-brain barrier (BBB) function and reduced CBF as well as compromised learning and memory and increased anxiety, clinical symptoms often seen in AD patients, in old mice. Our study suggests that the aging process involves deleterious changes in brain metabolic, vascular and cognitive functions, and gut microbiome structure and diversity, all which may lead to inflammation and thus increase the risk for AD. Future studies conducting comprehensive and integrative characterization of brain aging, including crosstalk with peripheral systems and factors, will be necessary to define the mechanisms underlying the shift from normal aging to pathological processes in the etiology of AD.
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Affiliation(s)
- Jared D Hoffman
- Sanders-Brown Center on Aging, University of KentuckyLexington, KY, United States.,Depatment of Pharmacology and Nutritional Science, University of KentuckyLexington, KY, United States
| | - Ishita Parikh
- Sanders-Brown Center on Aging, University of KentuckyLexington, KY, United States
| | - Stefan J Green
- Research Resources Center, University of Illinois at ChicagoChicago, IL, United States
| | - George Chlipala
- Research Resources Center, University of Illinois at ChicagoChicago, IL, United States
| | | | | | - Bjoern Bauer
- Department of Pharmaceutical Sciences, University of KentuckyLexington, KY, United States
| | - Anika M S Hartz
- Sanders-Brown Center on Aging, University of KentuckyLexington, KY, United States.,Depatment of Pharmacology and Nutritional Science, University of KentuckyLexington, KY, United States
| | - Ai-Ling Lin
- Sanders-Brown Center on Aging, University of KentuckyLexington, KY, United States.,Depatment of Pharmacology and Nutritional Science, University of KentuckyLexington, KY, United States.,Department of Engineering, University of KentuckyLexington, KY, United States
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98
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Lustgarten MS, Fielding RA. Metabolites Associated With Circulating Interleukin-6 in Older Adults. J Gerontol A Biol Sci Med Sci 2017; 72:1277-1283. [PMID: 26975982 DOI: 10.1093/gerona/glw039] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 02/15/2016] [Indexed: 12/23/2022] Open
Abstract
Background Circulating levels of the pro-inflammatory cytokine interleukin-6 (IL-6) levels are elevated in older adults, but mechanisms are unclear. In the current study, we used an untargeted metabolomic approach to develop an improved understanding about mechanisms related to circulating IL-6 in older adults. Methods Serum IL-6 values were log-transformed to normalize its distribution. Multivariable-adjusted linear regression was used to examine the association between 324 serum metabolites with log IL-6. Backward elimination linear regression was used to develop a metabolite predictor set representative of log IL-6. Results Thirty-six metabolites were significantly associated (p < 0.05 and q < 0.30) with log IL-6 in 73 older adults (average age, 78 years). Metabolites related to tryptophan metabolism (kynurenine, 3-indoxyl sulfate, indoleacetate, indolepropionate, C-glycosyltryptophan), infectious burden (C-glycosyltryptophan, N6-carbamoylthreonyladenosine, 1-methylurate, N-formylmethionine, N1-methyladenosine, 3-indoxyl sulfate, bilirubin (E,E), indoleacetate, γ-CEHC, N-acetylneuraminate), aryl hydrocarbon receptor activation and cytochrome P450 (CYP) 1A expression (kynurenine, 3-indoxyl sulfate, indoleacetate, N6-carbamoylthreonyladenosine, bilirubin, 1-methylurate) were positively associated, whereas metabolites related to CYP-mediated ω-oxidation (adipate, 8-hydroxyoctanoate, azelate, sebacate, undecanedioate, γ-CEHC), and peroxisome proliferator activated receptor-alpha (PPAR-α) activation (13 + 9-HODE, bilirubin, 5-oxoproline, cholesterol, glycerate, uridine) were negatively associated with log IL-6. The use of backward elimination regression identified tyrosine, cysteine, uridine, bilirubin, N-formylmethionine, indoleacetate, and 3-indoxyl sulfate to collectively explain 51% of the variance inherent in log IL-6. Conclusions These data suggest roles for tryptophan metabolism, infectious burden, activation of host defense, and detoxification through CYP1A-mediated pathways in mechanisms related to elevated inflammation, whereas CYP-mediated ω-oxidation and PPAR-α activation may be related to decreased inflammation in older adults.
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Affiliation(s)
- Michael S Lustgarten
- Nutrition, Exercise Physiology, and Sarcopenia Laboratory, Jean Mayer USDA Human Nutrition Research Center, Tufts University, Boston, Massachusetts
| | - Roger A Fielding
- Nutrition, Exercise Physiology, and Sarcopenia Laboratory, Jean Mayer USDA Human Nutrition Research Center, Tufts University, Boston, Massachusetts
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99
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Kaufmann SH, Weiner J, Maertzdorf J. Accelerating tuberculosis vaccine trials with diagnostic and prognostic biomarkers. Expert Rev Vaccines 2017; 16:845-853. [DOI: 10.1080/14760584.2017.1341316] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Stefan H.E. Kaufmann
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - January Weiner
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Jeroen Maertzdorf
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
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100
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Is spaceflight-induced immune dysfunction linked to systemic changes in metabolism? PLoS One 2017; 12:e0174174. [PMID: 28542224 PMCID: PMC5443495 DOI: 10.1371/journal.pone.0174174] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 03/04/2017] [Indexed: 12/22/2022] Open
Abstract
The Space Shuttle Atlantis launched on its final mission (STS-135) on July 8, 2011. After just under 13 days, the shuttle landed safely at Kennedy Space Center (KSC) for the last time. Female C57BL/6J mice flew as part of the Commercial Biomedical Testing Module-3 (CBTM-3) payload. Ground controls were maintained at the KSC facility. Subsets of these mice were made available to investigators as part of NASA’s Bio-specimen Sharing Program (BSP). Our group characterized cell phenotype distributions and phagocytic function in the spleen, catecholamine and corticosterone levels in the adrenal glands, and transcriptomics/metabolomics in the liver. Despite decreases in most splenic leukocyte subsets, there were increases in reactive oxygen species (ROS)-related activity. Although there were increases noted in corticosterone levels in both the adrenals and liver, there were no significant changes in catecholamine levels. Furthermore, functional analysis of gene expression and metabolomic profiles suggest that the functional changes are not due to oxidative or psychological stress. Despite changes in gene expression patterns indicative of increases in phagocytic activity (e.g. endocytosis and formation of peroxisomes), there was no corresponding increase in genes related to ROS metabolism. In contrast, there were increases in expression profiles related to fatty acid oxidation with decreases in glycolysis-related profiles. Given the clear link between immune function and metabolism in many ground-based diseases, we propose a similar link may be involved in spaceflight-induced decrements in immune and metabolic function.
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