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Nikulkova M, Abdrabou W, Carlton JM, Idaghdour Y. Exploiting integrative metabolomics to study host-parasite interactions in Plasmodium infections. Trends Parasitol 2024; 40:313-323. [PMID: 38508901 PMCID: PMC10994734 DOI: 10.1016/j.pt.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 03/22/2024]
Abstract
Despite years of research, malaria remains a significant global health burden, with poor diagnostic tests and increasing antimalarial drug resistance challenging diagnosis and treatment. While 'single-omics'-based approaches have been instrumental in gaining insight into the biology and pathogenicity of the Plasmodium parasite and its interaction with the human host, a more comprehensive understanding of malaria pathogenesis can be achieved through 'multi-omics' approaches. Integrative methods, which combine metabolomics, lipidomics, transcriptomics, and genomics datasets, offer a holistic systems biology approach to studying malaria. This review highlights recent advances, future directions, and challenges involved in using integrative metabolomics approaches to interrogate the interactions between Plasmodium and the human host, paving the way towards targeted antimalaria therapeutics and control intervention methods.
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Affiliation(s)
- Maria Nikulkova
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 11101, USA; Johns Hopkins Malaria Research Institute, Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Wael Abdrabou
- Program in Biology, Division of Science and Mathematics, New York University, Abu Dhabi, United Arab Emirates
| | - Jane M Carlton
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 11101, USA; Johns Hopkins Malaria Research Institute, Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
| | - Youssef Idaghdour
- Program in Biology, Division of Science and Mathematics, New York University, Abu Dhabi, United Arab Emirates
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2
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El Hajj Y, Shahin T, Dieng MM, Alshaikh M, Khair M, Manikandan V, Idaghdour Y. Pregnenolone sulfate induces transcriptional and immunoregulatory effects on T cells. Sci Rep 2024; 14:6782. [PMID: 38514798 PMCID: PMC10958000 DOI: 10.1038/s41598-024-57327-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/18/2024] [Indexed: 03/23/2024] Open
Abstract
Pregnenolone sulfate is a steroid metabolite of the steroidogenesis precursor, pregnenolone, with similar functional properties, including immunosuppression. We recently reported an elevation in serum levels of pregnenolone sulfate in children with malaria, contributing to an immunosuppressed state. Yet, the molecular mechanisms in which this steroid exerts its immunoregulatory functions are lacking. In this study, we examined the effects of pregnenolone sulfate on T cell viability, proliferation and transcriptome. We observed a pregnenolone sulfate dose-dependent induction of T cell death and reduction in proliferation. RNA sequencing analysis of pregnenolone sulfate-treated T cells for 2 and 24 h revealed the downregulation of pro-inflammatory genes and the upregulation of the steroid nuclear receptor superfamily, NR4A, as early-response genes. We also report a strong activation of the integrated stress response mediated by the upregulation of EIF2AK3. These results contribute to the knowledge on transcriptional regulation driving the immunoregulatory effects of pregnenolone sulfate on T cells.
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Affiliation(s)
- Yasmine El Hajj
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Tala Shahin
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Mame Massar Dieng
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Manar Alshaikh
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Mostafa Khair
- Core Technology Platforms, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Vinu Manikandan
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Youssef Idaghdour
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
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3
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Doumatey AP, Shriner D, Zhou J, Lei L, Chen G, Oluwasola-Taiwo O, Nkem S, Ogundeji A, Adebamowo SN, Bentley AR, Gouveia MH, Meeks KAC, Adebamowo CA, Adeyemo AA, Rotimi CN. Untargeted metabolomic profiling reveals molecular signatures associated with type 2 diabetes in Nigerians. Genome Med 2024; 16:38. [PMID: 38444015 PMCID: PMC10913364 DOI: 10.1186/s13073-024-01308-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 02/21/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Type 2 diabetes (T2D) has reached epidemic proportions globally, including in Africa. However, molecular studies to understand the pathophysiology of T2D remain scarce outside Europe and North America. The aims of this study are to use an untargeted metabolomics approach to identify: (a) metabolites that are differentially expressed between individuals with and without T2D and (b) a metabolic signature associated with T2D in a population of Sub-Saharan Africa (SSA). METHODS A total of 580 adult Nigerians from the Africa America Diabetes Mellitus (AADM) study were studied. The discovery study included 310 individuals (210 without T2D, 100 with T2D). Metabolites in plasma were assessed by reverse phase, ultra-performance liquid chromatography and mass spectrometry (RP)/UPLC-MS/MS methods on the Metabolon Platform. Welch's two-sample t-test was used to identify differentially expressed metabolites (DEMs), followed by the construction of a biomarker panel using a random forest (RF) algorithm. The biomarker panel was evaluated in a replication sample of 270 individuals (110 without T2D and 160 with T2D) from the same study. RESULTS Untargeted metabolomic analyses revealed 280 DEMs between individuals with and without T2D. The DEMs predominantly belonged to the lipid (51%, 142/280), amino acid (21%, 59/280), xenobiotics (13%, 35/280), carbohydrate (4%, 10/280) and nucleotide (4%, 10/280) super pathways. At the sub-pathway level, glycolysis, free fatty acid, bile metabolism, and branched chain amino acid catabolism were altered in T2D individuals. A 10-metabolite biomarker panel including glucose, gluconate, mannose, mannonate, 1,5-anhydroglucitol, fructose, fructosyl-lysine, 1-carboxylethylleucine, metformin, and methyl-glucopyranoside predicted T2D with an area under the curve (AUC) of 0.924 (95% CI: 0.845-0.966) and a predicted accuracy of 89.3%. The panel was validated with a similar AUC (0.935, 95% CI 0.906-0.958) in the replication cohort. The 10 metabolites in the biomarker panel correlated significantly with several T2D-related glycemic indices, including Hba1C, insulin resistance (HOMA-IR), and diabetes duration. CONCLUSIONS We demonstrate that metabolomic dysregulation associated with T2D in Nigerians affects multiple processes, including glycolysis, free fatty acid and bile metabolism, and branched chain amino acid catabolism. Our study replicated previous findings in other populations and identified a metabolic signature that could be used as a biomarker panel of T2D risk and glycemic control thus enhancing our knowledge of molecular pathophysiologic changes in T2D. The metabolomics dataset generated in this study represents an invaluable addition to publicly available multi-omics data on understudied African ancestry populations.
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Affiliation(s)
- Ayo P Doumatey
- Center for Research On Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, Building 12 A, Room 1025A, Bethesda, MD, 20892, USA.
| | - Daniel Shriner
- Center for Research On Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, Building 12 A, Room 1025A, Bethesda, MD, 20892, USA
| | - Jie Zhou
- Center for Research On Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, Building 12 A, Room 1025A, Bethesda, MD, 20892, USA
| | - Lin Lei
- Center for Research On Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, Building 12 A, Room 1025A, Bethesda, MD, 20892, USA
| | - Guanjie Chen
- Center for Research On Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, Building 12 A, Room 1025A, Bethesda, MD, 20892, USA
| | | | - Susan Nkem
- Center for Bioethics & Research, Ibadan, Nigeria
| | | | - Sally N Adebamowo
- Department of Epidemiology and Public Health, and the Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Amy R Bentley
- Center for Research On Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, Building 12 A, Room 1025A, Bethesda, MD, 20892, USA
| | - Mateus H Gouveia
- Center for Research On Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, Building 12 A, Room 1025A, Bethesda, MD, 20892, USA
| | - Karlijn A C Meeks
- Center for Research On Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, Building 12 A, Room 1025A, Bethesda, MD, 20892, USA
| | - Clement A Adebamowo
- Department of Epidemiology and Public Health, and the Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Adebowale A Adeyemo
- Center for Research On Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, Building 12 A, Room 1025A, Bethesda, MD, 20892, USA.
| | - Charles N Rotimi
- Center for Research On Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, Building 12 A, Room 1025A, Bethesda, MD, 20892, USA
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4
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Peng C, Jiang X, Jaeger M, van Houten P, van Herwaarden AE, Koeken VACM, Moorlag SJCFM, Mourits VP, Lemmers H, Dijkstra H, Koenen HJPM, Joosten I, van Cranenbroek B, Li Y, Joosten LAB, Netea MG, Netea-Maier RT, Xu CJ. 11-deoxycortisol positively correlates with T cell immune traits in physiological conditions. EBioMedicine 2024; 99:104935. [PMID: 38134621 PMCID: PMC10776925 DOI: 10.1016/j.ebiom.2023.104935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND Endogenous steroid hormones have significant effects on inflammatory and immune processes, but the immunological activities of steroidogenesis precursors remain largely unexplored. METHODS We conducted a systematic approach to examine the association between steroid hormones profile and immune traits in a cohort of 534 healthy volunteers. Serum concentrations of steroid hormones and their precursors (cortisol, progesterone, testosterone, androstenedione, 11-deoxycortisol and 17-OH progesterone) were determined by liquid chromatography-tandem mass spectrometry. Immune traits were evaluated by quantifying cellular composition of the circulating immune system and ex vivo cytokine responses elicited by major human pathogens and microbial ligands. An independent cohort of 321 individuals was used for validation, followed by in vitro validation experiments. FINDINGS We observed a positive association between 11-deoxycortisol and lymphoid cellular subsets numbers and function (especially IL-17 response). The association with lymphoid cellularity was validated in an independent validation cohort. In vitro experiments showed that, as compared to androstenedione and 17-OH progesterone, 11-deoxycortisol promoted T cell proliferation and Candida-induced Th17 polarization at physiologically relevant concentrations. Functionally, 11-deoxycortisol-treated T cells displayed a more activated phenotype (PD-L1high CD25high CD62Llow CD127low) in response to CD3/CD28 co-stimulation, and downregulated expression of T-bet nuclear transcription factor. INTERPRETATION Our findings suggest a positive association between 11-deoxycortisol and T-cell function under physiological conditions. Further investigation is needed to explore the potential mechanisms and clinical implications. FUNDING Found in acknowledgements.
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Affiliation(s)
- Chunying Peng
- Division of Endocrinology, Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Xun Jiang
- Centre for Individualised Infection Medicine (CiiM), A Joint Venture Between the Helmholtz-Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Helmholtz-Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany
| | - Martin Jaeger
- Division of Endocrinology, Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Pepijn van Houten
- Division of Endocrinology, Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Valerie A C M Koeken
- Centre for Individualised Infection Medicine (CiiM), A Joint Venture Between the Helmholtz-Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Helmholtz-Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Research Centre Innovations in Care, Rotterdam University of Applied Science, Rotterdam, the Netherlands
| | - Simone J C F M Moorlag
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Vera P Mourits
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Heidi Lemmers
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Helga Dijkstra
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Hans J P M Koenen
- Laboratory Medical Immunology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Irma Joosten
- Laboratory Medical Immunology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Bram van Cranenbroek
- Laboratory Medical Immunology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Yang Li
- Centre for Individualised Infection Medicine (CiiM), A Joint Venture Between the Helmholtz-Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Helmholtz-Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Romana T Netea-Maier
- Division of Endocrinology, Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Cheng-Jian Xu
- Centre for Individualised Infection Medicine (CiiM), A Joint Venture Between the Helmholtz-Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Helmholtz-Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands.
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George SHL, Medina-Rivera A, Idaghdour Y, Lappalainen T, Gallego Romero I. Increasing diversity of functional genetics studies to advance biological discovery and human health. Am J Hum Genet 2023; 110:1996-2002. [PMID: 37995684 PMCID: PMC10716434 DOI: 10.1016/j.ajhg.2023.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023] Open
Abstract
In this perspective we discuss the current lack of genetic and environmental diversity in functional genomics datasets. There is a well-described Eurocentric bias in genetic and functional genomic research that has a clear impact on the benefit this research can bring to underrepresented populations. Current research focused on genetic variant-to-function experiments aims to identify molecular QTLs, but the lack of data from genetically diverse individuals has limited analyses to mostly populations of European ancestry. Although some efforts have been established to increase diversity in functional genomic studies, much remains to be done to consistently generate data for underrepresented populations from now on. We discuss the major barriers for this continuity and suggest actionable insights, aiming to empower research and researchers from underserved populations.
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Affiliation(s)
- Sophia H L George
- Department of Obstetrics, Gynecology and Reproductive Sciences, Miller School of Medicine, University of Miami, Miami, FL, USA; Sylvester Comprehensive Cancer Center, Miami, FL, USA.
| | - Alejandra Medina-Rivera
- Laboratorio Internacional de Investigación Sobre El Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Youssef Idaghdour
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, UAE; Public Health Research Center, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Tuuli Lappalainen
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden; New York Genome Center, New York, NY, USA.
| | - Irene Gallego Romero
- Melbourne Integrative Genomics and School of BioSciences, University of Melbourne, Parkville, VIC, Australia; Center for Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, Tartu, Estonia
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Hadjilaou A, Brandi J, Riehn M, Friese MA, Jacobs T. Pathogenetic mechanisms and treatment targets in cerebral malaria. Nat Rev Neurol 2023; 19:688-709. [PMID: 37857843 DOI: 10.1038/s41582-023-00881-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2023] [Indexed: 10/21/2023]
Abstract
Malaria, the most prevalent mosquito-borne infectious disease worldwide, has accompanied humanity for millennia and remains an important public health issue despite advances in its prevention and treatment. Most infections are asymptomatic, but a small percentage of individuals with a heavy parasite burden develop severe malaria, a group of clinical syndromes attributable to organ dysfunction. Cerebral malaria is an infrequent but life-threatening complication of severe malaria that presents as an acute cerebrovascular encephalopathy characterized by unarousable coma. Despite effective antiparasite drug treatment, 20% of patients with cerebral malaria die from this disease, and many survivors of cerebral malaria have neurocognitive impairment. Thus, an important unmet clinical need is to rapidly identify people with malaria who are at risk of developing cerebral malaria and to develop preventive, adjunctive and neuroprotective treatments for cerebral malaria. This Review describes important advances in the understanding of cerebral malaria over the past two decades and discusses how these mechanistic insights could be translated into new therapies.
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Affiliation(s)
- Alexandros Hadjilaou
- Protozoen Immunologie, Bernhard-Nocht-Institut für Tropenmedizin (BNITM), Hamburg, Germany.
- Institut für Neuroimmunologie und Multiple Sklerose, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany.
| | - Johannes Brandi
- Protozoen Immunologie, Bernhard-Nocht-Institut für Tropenmedizin (BNITM), Hamburg, Germany
| | - Mathias Riehn
- Protozoen Immunologie, Bernhard-Nocht-Institut für Tropenmedizin (BNITM), Hamburg, Germany
| | - Manuel A Friese
- Institut für Neuroimmunologie und Multiple Sklerose, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Jacobs
- Protozoen Immunologie, Bernhard-Nocht-Institut für Tropenmedizin (BNITM), Hamburg, Germany
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Vandermosten L, Prenen F, Fogang B, Dagneau de Richecour P, Knoops S, Donkeu CJ, Nguefack CDP, Taguebue JV, Ndombo PK, Ghesquière B, Ayong L, Van den Steen PE. Glucocorticoid dysfunction in children with severe malaria. Front Immunol 2023; 14:1187196. [PMID: 37492570 PMCID: PMC10364055 DOI: 10.3389/fimmu.2023.1187196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/23/2023] [Indexed: 07/27/2023] Open
Abstract
Introduction Malaria remains a widespread health problem with a huge burden. Severe or complicated malaria is highly lethal and encompasses a variety of pathological processes, including immune activation, inflammation, and dysmetabolism. Previously, we showed that adrenal hormones, in particular glucocorticoids (GCs), play critical roles to maintain disease tolerance during Plasmodium infection in mice. Here, GC responses were studied in Cameroon in children with uncomplicated malaria (UM), severe malaria (SM) and asymptomatic controls (AC). Methods To determine the sensitivity of leukocytes to GC signaling on a transcriptional level, we measured the ex vivo induction of glucocorticoid induced leucine zipper (GILZ) and FK506-binding protein 5 (FKBP5) by GCs in human and murine leukocytes. Targeted tracer metabolomics on peripheral blood mononuclear cells (PBMCs) was performed to detect metabolic changes induced by GCs. Results Total cortisol levels increased in patients with clinical malaria compared to AC and were higher in the SM versus UM group, while cortisol binding globulin levels were unchanged and adrenocorticotropic hormone (ACTH) levels were heterogeneous. Induction of both GILZ and FKBP5 by GCs was significantly reduced in patients with clinical malaria compared to AC and in malaria-infected mice compared to uninfected controls. Increased activity in the pentose phosphate pathway was found in the patients, but this was not affected by ex vivo stimulation with physiological levels of hydrocortisone. Interestingly, hydrocortisone induced increased levels of cAMP in AC, but not in clinical malaria patients. Discussion Altogether, this study shows that patients with SM have increased cortisol levels, but also a decreased sensitivity to GCs, which may clearly contribute to the severity of disease.
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Affiliation(s)
- Leen Vandermosten
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Fran Prenen
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Balotin Fogang
- Malaria Research Unit, Centre Pasteur du Cameroun, Yaoundé, Cameroon
| | - Pauline Dagneau de Richecour
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Sofie Knoops
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | | | | | - Paul Koki Ndombo
- Mother and Child Center, Chantal Biya Foundation, Yaoundé, Cameroon
| | - Bart Ghesquière
- Metabolomics Expertise Center, Center for Cancer Biology, VIB Center for Cancer Biology, Leuven, Belgium
- Metabolomics Expertise Center, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Lawrence Ayong
- Malaria Research Unit, Centre Pasteur du Cameroun, Yaoundé, Cameroon
| | - Philippe E. Van den Steen
- Laboratory of Immunoparasitology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
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8
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Almojil D, Diawara A, Soulama I, Dieng MM, Manikandan V, Sermé SS, Sombié S, Diarra A, Barry A, Coulibaly SA, Sirima SB, Idaghdour Y. Impact of Plasmodium falciparum infection on DNA methylation of circulating immune cells. Front Genet 2023; 14:1197933. [PMID: 37470040 PMCID: PMC10352500 DOI: 10.3389/fgene.2023.1197933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/02/2023] [Indexed: 07/21/2023] Open
Abstract
The regulation of immune cell responses to infection is a complex process that involves various molecular mechanisms, including epigenetic regulation. DNA methylation has been shown to play central roles in regulating gene expression and modulating cell response during infection. However, the nature and extent to which DNA methylation is involved in the host immune response in human malaria remains largely unknown. Here, we present a longitudinal study investigating the temporal dynamics of genome-wide in vivo DNA methylation profiles using 189 MethylationEPIC 850 K profiles from 66 children in Burkina Faso, West Africa, sampled three times: before infection, during symptomatic parasitemia, and after malaria treatment. The results revealed major changes in the DNA methylation profiles of children in response to both Plasmodium falciparum infection and malaria treatment, with widespread hypomethylation of CpGs upon infection (82% of 6.8 K differentially methylated regions). We document a remarkable reversal of CpG methylation profiles upon treatment to pre-infection states. These changes implicate divergence in core immune processes, including the regulation of lymphocyte, neutrophil, and myeloid leukocyte function. Integrative DNA methylation-mRNA analysis of a top differentially methylated region overlapping the pro-inflammatory gene TNF implicates DNA methylation of TNF cis regulatory elements in the molecular mechanisms of TNF regulation in human malaria. Our results highlight a central role of epigenetic regulation in mounting the host immune response to P. falciparum infection and in response to malaria treatment.
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Affiliation(s)
- Dareen Almojil
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Aïssatou Diawara
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Issiaka Soulama
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Mame Massar Dieng
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Vinu Manikandan
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Samuel S. Sermé
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Salif Sombié
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Amidou Diarra
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Aissata Barry
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | | | - Sodiomon B. Sirima
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Youssef Idaghdour
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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9
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Cen Z, Lu B, Ji Y, Chen J, Liu Y, Jiang J, Li X, Li X. Virus-induced breath biomarkers: A new perspective to study the metabolic responses of COVID-19 vaccinees. Talanta 2023; 260:124577. [PMID: 37116359 PMCID: PMC10122548 DOI: 10.1016/j.talanta.2023.124577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 04/30/2023]
Abstract
Coronavirus disease 2019 (COVID-19) vaccines can protect people from the infection; however, the action mechanism of vaccine-mediated metabolism remains unclear. Herein, we performed breath tests in COVID-19 vaccinees that revealed metabolic reprogramming induced by protective immune responses. In total, 204 breath samples were obtained from COVID-19 vaccinees and non-vaccinated controls, wherein numerous volatile organic compounds (VOCs) were detected by comprehensive two-dimensional gas chromatography and time-of-flight mass spectrometry system. Subsequently, 12 VOCs were selected as biomarkers to construct a signature panel using alveolar gradients and machine learning-based procedure. The signature panel could distinguish vaccinees from control group with a high prediction performance (AUC, 0.9953; accuracy, 94.42%). The metabolic pathways of these biomarkers indicated that the host-pathogen interactions enhanced enzymatic activity and microbial metabolism in the liver, lung, and gut, potentially constituting the dominant action mechanism of vaccine-driven metabolic regulation. Thus, our findings of this study highlight the potential of measuring exhaled VOCs as rapid, non-invasive biomarkers of viral infections. Furthermore, breathomics appears as an alternative for safety evaluation of biological agents and disease diagnosis.
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Affiliation(s)
- Zhengnan Cen
- Department of Environmental Science & Engineering, Fudan University, Shanghai, 200438, PR China
| | - Bingqing Lu
- Department of Environmental Science & Engineering, Fudan University, Shanghai, 200438, PR China
| | - Yongyan Ji
- Department of Environmental Science & Engineering, Fudan University, Shanghai, 200438, PR China
| | - Jian Chen
- Department of Environmental Science & Engineering, Fudan University, Shanghai, 200438, PR China
| | - Yongqian Liu
- Department of Environmental Science & Engineering, Fudan University, Shanghai, 200438, PR China
| | - Jiakui Jiang
- Department of Environmental Science & Engineering, Fudan University, Shanghai, 200438, PR China
| | - Xue Li
- Institute of Mass Spectrometry and Atmospheric Environment, Jinan University, Guangzhou, 510632, PR China
| | - Xiang Li
- Department of Environmental Science & Engineering, Fudan University, Shanghai, 200438, PR China.
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10
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Fu J, Zhu F, Xu CJ, Li Y. Metabolomics meets systems immunology. EMBO Rep 2023; 24:e55747. [PMID: 36916532 PMCID: PMC10074123 DOI: 10.15252/embr.202255747] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/24/2022] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
Metabolic processes play a critical role in immune regulation. Metabolomics is the systematic analysis of small molecules (metabolites) in organisms or biological samples, providing an opportunity to comprehensively study interactions between metabolism and immunity in physiology and disease. Integrating metabolomics into systems immunology allows the exploration of the interactions of multilayered features in the biological system and the molecular regulatory mechanism of these features. Here, we provide an overview on recent technological developments of metabolomic applications in immunological research. To begin, two widely used metabolomics approaches are compared: targeted and untargeted metabolomics. Then, we provide a comprehensive overview of the analysis workflow and the computational tools available, including sample preparation, raw spectra data preprocessing, data processing, statistical analysis, and interpretation. Third, we describe how to integrate metabolomics with other omics approaches in immunological studies using available tools. Finally, we discuss new developments in metabolomics and its prospects for immunology research. This review provides guidance to researchers using metabolomics and multiomics in immunity research, thus facilitating the application of systems immunology to disease research.
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Affiliation(s)
- Jianbo Fu
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany.,College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Cheng-Jian Xu
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yang Li
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and Hannover Medical School (MHH), Hannover, Germany.,TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
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11
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Hu X, Zhao J, Zhao J, Yang E, Jia M. Genome-wide liver transcriptomic profiling of a malaria mouse model reveals disturbed immune and metabolic responses. Parasit Vectors 2023; 16:40. [PMID: 36717945 PMCID: PMC9885691 DOI: 10.1186/s13071-023-05672-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/16/2023] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND The liver is responsible for a range of functions in vertebrates, such as metabolism and immunity. In malaria, the liver plays a crucial role in the interaction between the parasite and host. Although malarial hepatitis is a common clinical complication of severe malaria, other malaria-related liver changes have been overlooked during the blood stage of the parasite life-cycle, in contrast to the many studies that have focused on parasite invasion of and replication in the liver during the hepatic stage of the parasite. METHODS A rodent model of malaria was established using Plasmodium yoelii strain 17XL, a lethal strain of rodent malaria, for liver transcriptomic profiling. RESULTS Differentially expressed messenger RNAs were associated with innate and adaptive immune responses, while differentially expressed long noncoding RNAs were enriched in the regulation of metabolism-related pathways, such as lipid metabolism. The coexpression network showed that host genes were related to cellular transport and tissue remodeling. Hub gene analysis of P. yoelii indicated that ubiquitination genes that were coexpressed with the host were evolutionarily conserved. CONCLUSIONS Our analysis yielded evidence of activated immune responses, aberrant metabolic processes and tissue remodeling changes in the livers of mice with malaria during the blood stage of the parasite, which provided a systematic outline of liver responses during Plasmodium infection.
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Affiliation(s)
- Xueyan Hu
- grid.11135.370000 0001 2256 9319Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191 China
| | - Jie Zhao
- grid.11135.370000 0001 2256 9319Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191 China
| | - Junhui Zhao
- grid.11135.370000 0001 2256 9319Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191 China
| | - Ence Yang
- grid.11135.370000 0001 2256 9319Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191 China ,grid.11135.370000 0001 2256 9319Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191 China
| | - Mozhi Jia
- grid.11135.370000 0001 2256 9319Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191 China
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12
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Wang H, Jia H, Gao Y, Zhang H, Fan J, Zhang L, Ren F, Yin Y, Cai Y, Zhu J, Zhu ZJ. Serum metabolic traits reveal therapeutic toxicities and responses of neoadjuvant chemoradiotherapy in patients with rectal cancer. Nat Commun 2022; 13:7802. [PMID: 36528604 PMCID: PMC9759530 DOI: 10.1038/s41467-022-35511-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Neoadjuvant chemoradiotherapy (nCRT) has become the standard treatment for patients with locally advanced rectal cancer (LARC). Therapeutic efficacy of nCRT is significantly affected by treatment-induced diarrhea and hematologic toxicities. Metabolic alternations in cancer therapy are key determinants to therapeutic toxicities and responses, but exploration in large-scale clinical studies remains limited. Here, we analyze 743 serum samples from 165 LARC patients recruited in a phase III clinical study using untargeted metabolomics and identify responsive metabolic traits over the course of nCRT. Pre-therapeutic serum metabolites successfully predict the chances of diarrhea and hematologic toxicities during nCRT. Particularly, levels of acyl carnitines are linked to sex disparity in nCRT-induced diarrhea. Finally, we show that differences in phenylalanine metabolism and essential amino acid metabolism may underlie distinct therapeutic responses of nCRT. This study illustrates the metabolic dynamics over the course of nCRT and provides potential to guide personalized nCRT treatment using responsive metabolic traits.
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Affiliation(s)
- Hongmiao Wang
- grid.9227.e0000000119573309Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Huixun Jia
- grid.16821.3c0000 0004 0368 8293Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080 China ,grid.452404.30000 0004 1808 0942Department of Biostatistics, Fudan University Shanghai Cancer Center, Shanghai, 200032 China
| | - Yang Gao
- grid.9227.e0000000119573309Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Haosong Zhang
- grid.9227.e0000000119573309Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jin Fan
- grid.452404.30000 0004 1808 0942Department of Biostatistics, Fudan University Shanghai Cancer Center, Shanghai, 200032 China
| | - Lijie Zhang
- grid.452404.30000 0004 1808 0942Department of Biostatistics, Fudan University Shanghai Cancer Center, Shanghai, 200032 China
| | - Fandong Ren
- grid.9227.e0000000119573309Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Yandong Yin
- grid.9227.e0000000119573309Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Yuping Cai
- grid.9227.e0000000119573309Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Ji Zhu
- grid.417397.f0000 0004 1808 0985Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, 310005 China ,grid.9227.e0000000119573309Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou, 310000 China ,Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, 310000 China ,grid.452404.30000 0004 1808 0942Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200031 China ,grid.513063.2Shanghai Key Laboratory of Radiation Oncology, Shanghai, 200032 China
| | - Zheng-Jiang Zhu
- grid.9227.e0000000119573309Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032 China ,Shanghai Key Laboratory of Aging Studies, Shanghai, 201210 China
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13
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Urinary Metabolic Profiling in Volunteers Undergoing Malaria Challenge in Gabon. Metabolites 2022; 12:metabo12121224. [PMID: 36557262 PMCID: PMC9783708 DOI: 10.3390/metabo12121224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/21/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
The interaction of malaria parasites with their human host is extensively studied, yet only few studies reported how P. falciparum infection affects urinary metabolite profiles and how this is associated with immunity. We present a longitudinal study of the urinary metabolic profiles of twenty healthy Africans with lifelong exposure to malaria and five malaria-naïve Europeans, who were all challenged with direct venous inoculation of live P. falciparum sporozoïtes (PfSPZ) and followed up until they developed symptoms or became thick blood smear positive (TBS). Urine samples were collected before and at 2, 5, 9 and 11 days post challenge and were analysed. Upon infection, all Europeans became TBS positive, while Africans showed either a delay in time to parasitaemia or controlled infection. Our metabolic data showed that Europeans and Africans had distinct alterations in metabolite patterns, with changes mostly seen on days 5 and 9 post PfSPZ infection, and more prominently in Europeans. Within the African group, the levels of formate, urea, trimethylamine, threonine, choline, myo-inositol and acetate were significantly higher in TBS positive whereas the levels of pyruvate, 3-methylhistidine and dimethylglycine were significantly lower in individuals who remained TBS negative. Notably, before inoculation with PfSPZ, a group of metabolites including phenylacetylglutamine can potentially be used to predict parasitaemia control among Africans. Taken together, this study highlights the difference in urinary metabolic changes in response to malaria infection as a consequence of lifelong exposure to malaria and that change detectable before challenge might predict the control of parasitaemia in malaria-endemic areas.
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14
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Zhang Y, Yue Q, Zhu H, Song J, Li D, Liu W, Jiang S, Jiang N, Qiu C, Ai J, Zhang Y, Zhang W. Serum Metabolic Correlates of the Antibody Response in Subjects Receiving the Inactivated COVID-19 Vaccine. Vaccines (Basel) 2022; 10:1890. [PMID: 36366398 PMCID: PMC9699138 DOI: 10.3390/vaccines10111890] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Metabolites are involved in biological process that govern the immune response to infection and vaccination. Knowledge of how metabolites interact with the immune system during immunization with the COVID-19 vaccine is limited. Here, we report that the serum metabolites are correlated with the magnitude of the antibody response in recipients receiving the inactivated COVID-19 vaccine, which provides critical information for studying metabolism regarding the human immune response to vaccination. METHODS 106 healthy volunteers without history of SARS-CoV-2 infection or vaccination were prospectively enrolled to receive the primary series of two doses of inactivated whole-virion SARS-CoV-2 vaccine. The serum samples were collected 2-4 weeks after the second dose. The magnitude of the anti-RBD antibody was quantified using surrogate virus neutralization tests. The profile of metabolites in serum was identified using untargeted metabolomics analysis. RESULTS The level of anti-RBD antibody 14-28 days after the second dose was significantly elevated and its interpersonal variability was diverse in a wide range. Thirty-two samples at extremes of the anti-RBD antibody titer were selected to discover the metabolic correlates. Two hundred and fifteen differential metabolites associated with antibody response independent of body mass index were identified. Pregnenolone and sphingolipid metabolism might be involved in the modulation of the human antibody response to the inactivated COVID-19 vaccine. CONCLUSION We discovered key metabolites as well as those with a related functional significance that might modulate the human immune response to vaccination.
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Affiliation(s)
- Yi Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Qiaoyan Yue
- Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing 210006, China
| | - Haojing Zhu
- Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing 210006, China
| | - Jieyu Song
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Dingding Li
- Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing 210006, China
| | - Wen Liu
- Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing 210006, China
| | - Shujun Jiang
- Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing 210006, China
- Nanjing Research Center for Infectious Diseases of Integrated Traditional Chinese and Western Medicine, Nanjing 210006, China
| | - Ning Jiang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Chao Qiu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Jingwen Ai
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Yanliang Zhang
- Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing 210006, China
- Nanjing Research Center for Infectious Diseases of Integrated Traditional Chinese and Western Medicine, Nanjing 210006, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai 200040, China
- Shanghai Huashen Institute of Microbes and Infections, No. 6 Lane 1220 Huashan Rd., Shanghai 200031, China
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15
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Das A, Sahu W, Ojha DK, Reddy KS, Suar M. Comparative Analysis of Host Metabolic Alterations in Murine Malaria Models with Uncomplicated or Severe Malaria. J Proteome Res 2022; 21:2261-2276. [PMID: 36169658 DOI: 10.1021/acs.jproteome.2c00123] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Malaria varies in severity, with complications ranging from uncomplicated to severe malaria. Severe malaria could be attributed to peripheral hyperparasitemia or cerebral malaria. The metabolic interactions between the host and Plasmodium species are yet to be understood during these infections of varied pathology and severity. An untargeted metabolomics approach utilizing the liquid chromatography-mass spectrometry platform has been used to identify the affected host metabolic pathways and associated metabolites in the serum of murine malaria models with uncomplicated malaria, hyperparasitemia, and experimental cerebral malaria. We report that mice with malaria share similar metabolic attributes like higher levels of bile acids, bile pigments, and steroid hormones that have been reported for human malaria infections. Moreover, in severe malaria, upregulated levels of metabolites like phenylalanine, histidine, valine, pipecolate, ornithine, and pantothenate, with decreased levels of arginine and hippurate, were observed. Metabolites of sphingolipid metabolism were upregulated in experimental cerebral malaria. Higher levels of 20-hydroxy-leukotriene B4 and epoxyoctadecamonoenoic acids were found in uncomplicated malaria, with lower levels observed for experimental cerebral malaria. Our study provides insights into host biology during different pathological stages of malaria disease and would be useful for the selection of animal models for evaluating diagnostic and therapeutic interventions against malaria. The raw data files are available via MetaboLights with the identifier MTBLS4387.
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Affiliation(s)
- Aleena Das
- School of Biotechnology, Kalinga Institute of Industrial Technology (Deemed University), Bhubaneswar751024, India.,Technology Business Incubator, Kalinga Institute of Industrial Technology (Deemed University), Bhubaneswar751024, India
| | - Welka Sahu
- School of Biotechnology, Kalinga Institute of Industrial Technology (Deemed University), Bhubaneswar751024, India
| | - Deepak Kumar Ojha
- School of Biotechnology, Kalinga Institute of Industrial Technology (Deemed University), Bhubaneswar751024, India
| | - K Sony Reddy
- School of Biotechnology, Kalinga Institute of Industrial Technology (Deemed University), Bhubaneswar751024, India
| | - Mrutyunjay Suar
- School of Biotechnology, Kalinga Institute of Industrial Technology (Deemed University), Bhubaneswar751024, India.,Technology Business Incubator, Kalinga Institute of Industrial Technology (Deemed University), Bhubaneswar751024, India
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16
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Tian H, Ni Z, Lam SM, Jiang W, Li F, Du J, Wang Y, Shui G. Precise Metabolomics Reveals a Diversity of Aging-Associated Metabolic Features. SMALL METHODS 2022; 6:e2200130. [PMID: 35527334 DOI: 10.1002/smtd.202200130] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/24/2022] [Indexed: 06/14/2023]
Abstract
Mass spectrometry-based metabolomics has emerged as a powerful technique for biomedical research, although technical issues with its analytical precision and structural characterization remain. Herein, a robust non-targeted strategy for accurate quantitation and precise profiling of metabolomes is developed and applied to investigate plasma metabolic features associated with human aging. A comprehensive set of isotope-labeled standards (ISs) covering major metabolic pathways is incorporated to quantify polar metabolites. Matching rules to select ISs for calibration follow a primary criterion of minimal coefficients of variations (COVs). If minimal COVs between specific ISs for a particular metabolite fall within 5% window, a further selection of ISs is conducted based on structural similarities and proximity in retention time. The introduction and refined selection of appropriate ISs for quantitation reduces the COVs of 480 identified metabolites in quality control samples from 14.3% to 9.8% and facilitates identification of additional metabolite. Finally, the precise metabolomics approach reveals perturbations in a diverse array of metabolic pathways across aging that principally implicate steroid metabolism, amino acid metabolism, lipid metabolism, and purine metabolism, which allows the authors to draw correlates to the pathology of various age-related diseases. These findings provide clues for the prevention and treatment of these age-related diseases.
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Affiliation(s)
- He Tian
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhen Ni
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- LipidALL Technologies Company Limited, Changzhou, Jiangsu Province, 213022, China
| | - Wenxi Jiang
- Beijing Institute of Heart, Lung, and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
| | - Fengjuan Li
- Beijing Institute of Heart, Lung, and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
| | - Jie Du
- Beijing Institute of Heart, Lung, and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
| | - Yuan Wang
- Beijing Institute of Heart, Lung, and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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17
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Barupal DK, Mahajan P, Fakouri-Baygi S, Wright RO, Arora M, Teitelbaum SL. CCDB: A database for exploring inter-chemical correlations in metabolomics and exposomics datasets. ENVIRONMENT INTERNATIONAL 2022; 164:107240. [PMID: 35461097 PMCID: PMC9195052 DOI: 10.1016/j.envint.2022.107240] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/01/2022] [Accepted: 04/08/2022] [Indexed: 05/18/2023]
Abstract
Inter-chemical correlations in metabolomics and exposomics datasets provide valuable information for studying relationships among chemicals reported for human specimens. With an increase in the number of compounds for these datasets, a network graph analysis and visualization of the correlation structure is difficult to interpret. We have developed the Chemical Correlation Database (CCDB), as a systematic catalogue of inter-chemical correlation in publicly available metabolomics and exposomics studies. The database has been provided via an online interface to create single compound-centric views. We have demonstrated various applications of the database to explore: 1) the chemicals from a chemical class such as Per- and Polyfluoroalkyl Substances (PFAS), polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), phthalates and tobacco smoke related metabolites; 2) xenobiotic metabolites such as caffeine and acetaminophen; 3) endogenous metabolites (acyl-carnitines); and 4) unannotated peaks for PFAS. The database has a rich collection of 35 human studies, including the National Health and Nutrition Examination Survey (NHANES) and high-quality untargeted metabolomics datasets. CCDB is supported by a simple, interactive and user-friendly web-interface to retrieve and visualize the inter-chemical correlation data. The CCDB has the potential to be a key computational resource in metabolomics and exposomics facilitating the expansion of our understanding about biological and chemical relationships among metabolites and chemical exposures in the human body. The database is available at www.ccdb.idsl.me site.
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Affiliation(s)
- Dinesh Kumar Barupal
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA.
| | - Priyanka Mahajan
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
| | - Sadjad Fakouri-Baygi
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
| | - Robert O Wright
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
| | - Manish Arora
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
| | - Susan L Teitelbaum
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
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18
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Tarkhan AH, Anwardeen NR, Sellami M, Donati F, Botrè F, de la Torre X, Elrayess MA. Comparing metabolic profiles between female endurance athletes and non-athletes reveals differences in androgen and corticosteroid levels. J Steroid Biochem Mol Biol 2022; 219:106081. [PMID: 35182726 DOI: 10.1016/j.jsbmb.2022.106081] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 02/09/2022] [Indexed: 11/24/2022]
Abstract
Endurance training is associated with physiological changes in elite athletes, but little is known about female-specific effects of endurance training. Despite the significant rise in female sports participation, findings from studies performed on male athletes are largely extrapolated to females without taking into consideration sex-specific differences in metabolism. Subsequently, this study aimed to investigate the steroid hormone profiles of elite female endurance athletes in comparison with their non-athletic counterparts. Untargeted metabolomics-based mass spectroscopy combined with ultra-high-performance liquid chromatography was performed on serum samples from 51 elite female endurance athletes and 197 non-athletic females. The results showed that, compared to non-athletic females, certain androgen, pregnenolone, and progestin steroid hormones were reduced in elite female endurance athletes, while corticosteroids were elevated. The most significantly altered steroid hormones were 5alpha-androstan-3alpha,17alpha-diol monosulfate (FDR = 1.90 × 10-05), androstenediol (3alpha, 17alpha) monosulfate (FDR = 2.93 × 10-04), and cortisol (FDR = 2.93 × 10-04). Conclusively, the present study suggests that elite female endurance athletes have a unique steroid hormone profile with implications on their general health and performance.
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Affiliation(s)
| | | | - Maha Sellami
- Physical Education Department (PE), College of Education, Qatar University, Doha, Qatar.
| | - Francesco Donati
- Laboratorio Antidoping, Federazione Medico Sportiva Italiana, Rome, Italy.
| | - Francesco Botrè
- Laboratorio Antidoping, Federazione Medico Sportiva Italiana, Rome, Italy.
| | - Xavier de la Torre
- Laboratorio Antidoping, Federazione Medico Sportiva Italiana, Rome, Italy.
| | - Mohamed A Elrayess
- Biomedical Research Center, Qatar University, Doha, Qatar; Vice President for Medical and Health Sciences Office, QU Health, Qatar University, Doha, Qatar.
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Zhang C, Hansen MEB, Tishkoff SA. Advances in integrative African genomics. Trends Genet 2022; 38:152-168. [PMID: 34740451 PMCID: PMC8752515 DOI: 10.1016/j.tig.2021.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/16/2021] [Accepted: 09/28/2021] [Indexed: 12/16/2022]
Abstract
There has been a rapid increase in human genome sequencing in the past two decades, resulting in the identification of millions of previously unknown genetic variants. However, African populations are under-represented in sequencing efforts. Additional sequencing from diverse African populations and the construction of African-specific reference genomes is needed to better characterize the full spectrum of variation in humans. However, sequencing alone is insufficient to address the molecular and cellular mechanisms underlying variable phenotypes and disease risks. Determining functional consequences of genetic variation using multi-omics approaches is a fundamental post-genomic challenge. We discuss approaches to close the knowledge gaps about African genomic diversity and review advances in African integrative genomic studies and their implications for precision medicine.
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Affiliation(s)
- Chao Zhang
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew E B Hansen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah A Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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20
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Affiliation(s)
- Malcolm J McConville
- Department of Biochemistry and Pharmacology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, Victoria, Australia.
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21
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Steroid response to malaria. Nat Rev Immunol 2021; 21:472-473. [PMID: 34163063 DOI: 10.1038/s41577-021-00581-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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