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Bharucha T, Gangadharan B, Kumar A, Myall AC, Ayhan N, Pastorino B, Chanthongthip A, Vongsouvath M, Mayxay M, Sengvilaipaseuth O, Phonemixay O, Rattanavong S, O’Brien DP, Vendrell I, Fischer R, Kessler B, Turtle L, de Lamballerie X, Dubot-Pérès A, Newton PN, Zitzmann N, SEAe Consortium. Deep Proteomics Network and Machine Learning Analysis of Human Cerebrospinal Fluid in Japanese Encephalitis Virus Infection. J Proteome Res 2023; 22:1614-1629. [PMID: 37219084 PMCID: PMC10246887 DOI: 10.1021/acs.jproteome.2c00563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Indexed: 05/24/2023]
Abstract
Japanese encephalitis virus is a leading cause of neurological infection in the Asia-Pacific region with no means of detection in more remote areas. We aimed to test the hypothesis of a Japanese encephalitis (JE) protein signature in human cerebrospinal fluid (CSF) that could be harnessed in a rapid diagnostic test (RDT), contribute to understanding the host response and predict outcome during infection. Liquid chromatography and tandem mass spectrometry (LC-MS/MS), using extensive offline fractionation and tandem mass tag labeling (TMT), enabled comparison of the deep CSF proteome in JE vs other confirmed neurological infections (non-JE). Verification was performed using data-independent acquisition (DIA) LC-MS/MS. 5,070 proteins were identified, including 4,805 human proteins and 265 pathogen proteins. Feature selection and predictive modeling using TMT analysis of 147 patient samples enabled the development of a nine-protein JE diagnostic signature. This was tested using DIA analysis of an independent group of 16 patient samples, demonstrating 82% accuracy. Ultimately, validation in a larger group of patients and different locations could help refine the list to 2-3 proteins for an RDT. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD034789 and 10.6019/PXD034789.
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Affiliation(s)
- Tehmina Bharucha
- Department
of Biochemistry, University of Oxford, OX1 3QU, Oxford, U.K.
- Kavli
Institute for Nanoscience Discovery, University
of Oxford, OX1 3QU, Oxford, U.K.
- Lao-Oxford-Mahosot
Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, 0100 Lao PDR
| | - Bevin Gangadharan
- Department
of Biochemistry, University of Oxford, OX1 3QU, Oxford, U.K.
- Kavli
Institute for Nanoscience Discovery, University
of Oxford, OX1 3QU, Oxford, U.K.
| | - Abhinav Kumar
- Department
of Biochemistry, University of Oxford, OX1 3QU, Oxford, U.K.
- Kavli
Institute for Nanoscience Discovery, University
of Oxford, OX1 3QU, Oxford, U.K.
| | - Ashleigh C. Myall
- Department
of Infectious Disease, Imperial College
London, London W12 0NN, U.K.
- Department
of Mathematics, Imperial College London, London W12 0NN, U.K.
| | - Nazli Ayhan
- Unité
Des Virus Emergents UVE, Aix Marseille Univ,
IRD190, INSERM 1207, IHU Méditerranée Infection, Marseille 13005, France
| | - Boris Pastorino
- Unité
Des Virus Emergents UVE, Aix Marseille Univ,
IRD190, INSERM 1207, IHU Méditerranée Infection, Marseille 13005, France
| | - Anisone Chanthongthip
- Lao-Oxford-Mahosot
Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, 0100 Lao PDR
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot
Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, 0100 Lao PDR
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot
Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, 0100 Lao PDR
- Institute
of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane 43130, Lao PDR
- Centre
for Tropical Medicine & Global Health, Nuffield Department of
Medicine, University of Oxford, Oxford OX3 7LG, U.K.
| | - Onanong Sengvilaipaseuth
- Lao-Oxford-Mahosot
Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, 0100 Lao PDR
| | - Ooyanong Phonemixay
- Lao-Oxford-Mahosot
Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, 0100 Lao PDR
| | - Sayaphet Rattanavong
- Lao-Oxford-Mahosot
Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, 0100 Lao PDR
| | - Darragh P. O’Brien
- Target
Discovery Institute, Centre for Medicines Discovery, Nuffield Department
of Medicine, University of Oxford, Oxford OX3 7FZ, U.K.
| | - Iolanda Vendrell
- Target
Discovery Institute, Centre for Medicines Discovery, Nuffield Department
of Medicine, University of Oxford, Oxford OX3 7FZ, U.K.
- Chinese
Academy of Medical Sciences Oxford Institute, Nuffield Department
of Medicine, University of Oxford, Oxford OX3 7BN, U.K.
| | - Roman Fischer
- Target
Discovery Institute, Centre for Medicines Discovery, Nuffield Department
of Medicine, University of Oxford, Oxford OX3 7FZ, U.K.
- Chinese
Academy of Medical Sciences Oxford Institute, Nuffield Department
of Medicine, University of Oxford, Oxford OX3 7BN, U.K.
| | - Benedikt Kessler
- Target
Discovery Institute, Centre for Medicines Discovery, Nuffield Department
of Medicine, University of Oxford, Oxford OX3 7FZ, U.K.
- Chinese
Academy of Medical Sciences Oxford Institute, Nuffield Department
of Medicine, University of Oxford, Oxford OX3 7BN, U.K.
| | - Lance Turtle
- Institute
of Infection, Veterinary and Ecological Sciences, Faculty of Health
and Life Sciences, University of Liverpool, Liverpool L69 7BE, U.K.
- Tropical
and Infectious Disease Unit, Liverpool University
Hospitals NHS Foundation Trust (Member of Liverpool Health Partners), Liverpool L69 7BE, U.K.
| | - Xavier de Lamballerie
- Unité
Des Virus Emergents UVE, Aix Marseille Univ,
IRD190, INSERM 1207, IHU Méditerranée Infection, Marseille 13005, France
| | - Audrey Dubot-Pérès
- Lao-Oxford-Mahosot
Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, 0100 Lao PDR
- Unité
Des Virus Emergents UVE, Aix Marseille Univ,
IRD190, INSERM 1207, IHU Méditerranée Infection, Marseille 13005, France
- Centre
for Tropical Medicine & Global Health, Nuffield Department of
Medicine, University of Oxford, Oxford OX3 7LG, U.K.
| | - Paul N. Newton
- Lao-Oxford-Mahosot
Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, 0100 Lao PDR
- Centre
for Tropical Medicine & Global Health, Nuffield Department of
Medicine, University of Oxford, Oxford OX3 7LG, U.K.
| | - Nicole Zitzmann
- Department
of Biochemistry, University of Oxford, OX1 3QU, Oxford, U.K.
- Kavli
Institute for Nanoscience Discovery, University
of Oxford, OX1 3QU, Oxford, U.K.
| | - SEAe Consortium
- Biology
of Infection Unit, Institut Pasteur, 75015 Paris France
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Integrative Proteomics and Transcriptomics Profiles of the Oviduct Reveal the Prolificacy-Related Candidate Biomarkers of Goats ( Capra hircus) in Estrous Periods. Int J Mol Sci 2022; 23:ijms232314888. [PMID: 36499219 PMCID: PMC9737051 DOI: 10.3390/ijms232314888] [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: 10/20/2022] [Revised: 11/16/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The oviduct is a dynamic reproductive organ for mammalian reproduction and is required for gamete storage, maturation, fertilization, and early embryonic development, and it directly affects fecundity. However, the molecular regulation of prolificacy occurring in estrous periods remain poorly understood. This study aims to gain a better understanding of the genes involved in regulating goat fecundity in the proteome and transcriptome levels of the oviducts. Twenty female Yunshang black goats (between 2 and 3 years old, weight 52.22 ± 0.43 kg) were divided into high- and low-fecundity groups in the follicular (FH and FL, five individuals per group) and luteal (LH and LL, five individuals per group) phases, respectively. The DIA-based high-resolution mass spectrometry (MS) method was used to quantify proteins in twenty oviducts. A total of 5409 proteins were quantified, and Weighted gene co-expression network analysis (WGCNA) determined that the tan module was highly associated with the high-fecundity trait in the luteal phase, and identified NUP107, ANXA11, COX2, AKP13, and ITF140 as hub proteins. Subsequently, 98 and 167 differentially abundant proteins (DAPs) were identified in the FH vs. FL and LH vs. LL comparison groups, respectively. Parallel reaction monitoring (PRM) was used to validate the results of the proteomics data, and the hub proteins were analyzed with Western blot (WB). In addition, biological adhesion and transporter activity processes were associated with oviductal function, and several proteins that play roles in oviductal communication with gametes or embryos were identified, including CAMSAP3, ITGAM, SYVN1, EMG1, ND5, RING1, CBS, PES1, ELP3, SEC24C, SPP1, and HSPA8. Correlation analysis of proteomics and transcriptomic revealed that the DAPs and differentially expressed genes (DEGs) are commonly involved in the metabolic processes at the follicular phase; they may prepare the oviductal microenvironment for gamete reception; and the MAP kinase activity, estrogen receptor binding, and angiotensin receptor binding terms were enriched in the luteal phase, which may be actively involved in reproductive processes. By generating the proteome data of the oviduct at two critical phases and integrating transcriptome analysis, we uncovered novel aspects of oviductal gene regulation of fecundity and provided a reference for other mammals.
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