Protein promise? Application of mass spectrometry-based proteomics techniques to identify cerebrospinal fluid biomarkers for diagnosing suspected central nervous system infections - a focus on Japanese encephalitis virus infection
<p>Neurological infections account for considerable death and disability worldwide. Even in the best-resourced settings, existing diagnostic tests are inadequate and adversely affect patient outcomes. In this thesis, I propose that the identification of host biomarkers of neurological infectio...
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| Format: | Thesis |
| Idioma: | English |
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2022
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| _version_ | 1826315820319375360 |
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| author | Bharucha, TM |
| author2 | Zitzmann, N |
| author_facet | Zitzmann, N Bharucha, TM |
| author_sort | Bharucha, TM |
| collection | OXFORD |
| description | <p>Neurological infections account for considerable death and disability worldwide. Even in the best-resourced settings, existing diagnostic tests are inadequate and adversely affect patient outcomes. In this thesis, I propose that the identification of host biomarkers of neurological infection could fill the gap in case ascertainment.</p>
<p>In Laos, as is the case in other countries in Asia, the leading cause of neurological infection is Japanese encephalitis virus (JEV). Specifically for Japanese encephalitis (JE), the pathogen is present at very low levels such that it is rarely detected in any body fluid, and the mainstay of diagnosis is anti-JEV IgM antibody capture enzyme-linked immunosorbent assay. This has poor specificity. Furthermore, there is no rapid diagnostic test to be used in the rural areas that JEV exists. JE represents an important neurological infection to illustrate the potential role of host protein biomarkers for diagnosis.</p>
<p>I retrospectively tested a cohort of 163 patients recruited as part of the Laos central nervous system (CNS) infection study. Application of liquid chromatography and tandem mass spectrometry (LC-MS/MS), using extensive offline fractionation and tandem mass tag labelling, enabled a comparison of the CSF proteome in 68 JE patient vs 95 non-JE neurological infections. 5,069 proteins were identified, including 4,805 human proteins and 265 pathogen proteins. I incorporated univariate analysis of differential protein expression, network analysis and machine learning techniques to build a ten-protein diagnostic signature of JE.</p>
<p>Pathways related to JE infection included neuronal damage, anti-apoptosis, heat shock and unfolded protein responses, cell adhesion, macrophage and dendritic cell activation as well as a reduced acute inflammatory response, hepatotoxicity, activation of coagulation, extracellular matrix and actin regulation. I verified the results by performing DIA LC-MS/MS in 16 (10%) of the samples, demonstrating 82% accuracy using the same model. Ultimately, antibody-based validation will be required, in a larger group of patients, in different locations and in field settings, to refine the list to 2-3 proteins that could be harnessed in a rapid diagnostic test.</p> |
| first_indexed | 2024-03-07T08:10:37Z |
| format | Thesis |
| id | oxford-uuid:1c4938cb-f86d-43c7-8988-f131ee03460a |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-12-09T03:33:12Z |
| publishDate | 2022 |
| record_format | dspace |
| spelling | oxford-uuid:1c4938cb-f86d-43c7-8988-f131ee03460a2024-12-01T16:22:34ZProtein promise? Application of mass spectrometry-based proteomics techniques to identify cerebrospinal fluid biomarkers for diagnosing suspected central nervous system infections - a focus on Japanese encephalitis virus infectionThesishttp://purl.org/coar/resource_type/c_db06uuid:1c4938cb-f86d-43c7-8988-f131ee03460aEnglishHyrax Deposit2022Bharucha, TMZitzmann, NNewton, PDubot-Pérès, A<p>Neurological infections account for considerable death and disability worldwide. Even in the best-resourced settings, existing diagnostic tests are inadequate and adversely affect patient outcomes. In this thesis, I propose that the identification of host biomarkers of neurological infection could fill the gap in case ascertainment.</p> <p>In Laos, as is the case in other countries in Asia, the leading cause of neurological infection is Japanese encephalitis virus (JEV). Specifically for Japanese encephalitis (JE), the pathogen is present at very low levels such that it is rarely detected in any body fluid, and the mainstay of diagnosis is anti-JEV IgM antibody capture enzyme-linked immunosorbent assay. This has poor specificity. Furthermore, there is no rapid diagnostic test to be used in the rural areas that JEV exists. JE represents an important neurological infection to illustrate the potential role of host protein biomarkers for diagnosis.</p> <p>I retrospectively tested a cohort of 163 patients recruited as part of the Laos central nervous system (CNS) infection study. Application of liquid chromatography and tandem mass spectrometry (LC-MS/MS), using extensive offline fractionation and tandem mass tag labelling, enabled a comparison of the CSF proteome in 68 JE patient vs 95 non-JE neurological infections. 5,069 proteins were identified, including 4,805 human proteins and 265 pathogen proteins. I incorporated univariate analysis of differential protein expression, network analysis and machine learning techniques to build a ten-protein diagnostic signature of JE.</p> <p>Pathways related to JE infection included neuronal damage, anti-apoptosis, heat shock and unfolded protein responses, cell adhesion, macrophage and dendritic cell activation as well as a reduced acute inflammatory response, hepatotoxicity, activation of coagulation, extracellular matrix and actin regulation. I verified the results by performing DIA LC-MS/MS in 16 (10%) of the samples, demonstrating 82% accuracy using the same model. Ultimately, antibody-based validation will be required, in a larger group of patients, in different locations and in field settings, to refine the list to 2-3 proteins that could be harnessed in a rapid diagnostic test.</p> |
| spellingShingle | Bharucha, TM Protein promise? Application of mass spectrometry-based proteomics techniques to identify cerebrospinal fluid biomarkers for diagnosing suspected central nervous system infections - a focus on Japanese encephalitis virus infection |
| title | Protein promise? Application of mass spectrometry-based proteomics techniques to identify cerebrospinal fluid biomarkers for diagnosing suspected central nervous system infections - a focus on Japanese encephalitis virus infection |
| title_full | Protein promise? Application of mass spectrometry-based proteomics techniques to identify cerebrospinal fluid biomarkers for diagnosing suspected central nervous system infections - a focus on Japanese encephalitis virus infection |
| title_fullStr | Protein promise? Application of mass spectrometry-based proteomics techniques to identify cerebrospinal fluid biomarkers for diagnosing suspected central nervous system infections - a focus on Japanese encephalitis virus infection |
| title_full_unstemmed | Protein promise? Application of mass spectrometry-based proteomics techniques to identify cerebrospinal fluid biomarkers for diagnosing suspected central nervous system infections - a focus on Japanese encephalitis virus infection |
| title_short | Protein promise? Application of mass spectrometry-based proteomics techniques to identify cerebrospinal fluid biomarkers for diagnosing suspected central nervous system infections - a focus on Japanese encephalitis virus infection |
| title_sort | protein promise application of mass spectrometry based proteomics techniques to identify cerebrospinal fluid biomarkers for diagnosing suspected central nervous system infections a focus on japanese encephalitis virus infection |
| work_keys_str_mv | AT bharuchatm proteinpromiseapplicationofmassspectrometrybasedproteomicstechniquestoidentifycerebrospinalfluidbiomarkersfordiagnosingsuspectedcentralnervoussysteminfectionsafocusonjapaneseencephalitisvirusinfection |