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DEVELOPING PLASMA-BASED DIAGNOSTICS: FROM PANCREATIC DUCTAL ADENOCARCINOMA TO HIV

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Date Issued:
2023
Abstract/Description:
Plasma-based diagnostics are ideal for detecting a variety of diseases because they offer a method of detection that is minimally invasive, readily available, and easy to use for monitoring patients as they progress through a disease or respond to treatment. The only serum marker for PDAC is CA19-9 which lacks specificity, has limited sensitivity, and is unreliable for early detection. It is therefore of great importance to develop a diagnostic that is viable for screening and early detection. Exosomal miRNA were determined via bioinformatics analyses and then examined in PDAC cell lines to identify markers with greatest potential. These markers were then examined in plasma from PDAC patients and control groups. Four markers, miR-93-5p, miR-339-3p, miR-425-5p, and miR-425-3p, emerged as the most viable biomarker panel with the ability to detect PDAC in 100% of the early stages (N=5) compared to CA19-9 which showed increased levels in only one patient with early stage PDAC. Additionally, the diagnostic has a specificity of 80% and a sensitivity of 94.7%, making it comparable to CA19-9, and may even be beneficial for use in conjunction with CA19-9. A plasma-based diagnostic was also developed for multi-strain HIV-1 detection utilizing the loop-mediated isothermal amplification (LAMP) method. LAMP primers were developed against the integrase and vpr regions of the HIV-1 genome. They were tested first in cultured HIV samples and then examined for their ability to amplify HIV-1 subtypes A-G. The integrase primer set provided a reliable means of diagnosing all 55 strains and isolates in under 30 minutes, whereas vpr was inconsistent and exhibited high variability in detecting the HIV subtypes. Our limit of detection for B-subtype with integrase was 30 viral copies/reaction. This could provide the basis for a novel, point-of-care diagnostic for use in underdeveloped regions.
Title: DEVELOPING PLASMA-BASED DIAGNOSTICS: FROM PANCREATIC DUCTAL ADENOCARCINOMA TO HIV.
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Name(s): Makler, Amy, author
Asghar, Waseem, Thesis advisor
Florida Atlantic University, Degree grantor
Department of Biological Sciences
Type of Resource: text
Genre: Electronic Thesis Or Dissertation
Date Created: 2023
Date Issued: 2023
Publisher: Florida Atlantic University
Place of Publication: Boca Raton, Fla.
Physical Form: application/pdf
Extent: 94 p.
Language(s): English
Abstract/Description: Plasma-based diagnostics are ideal for detecting a variety of diseases because they offer a method of detection that is minimally invasive, readily available, and easy to use for monitoring patients as they progress through a disease or respond to treatment. The only serum marker for PDAC is CA19-9 which lacks specificity, has limited sensitivity, and is unreliable for early detection. It is therefore of great importance to develop a diagnostic that is viable for screening and early detection. Exosomal miRNA were determined via bioinformatics analyses and then examined in PDAC cell lines to identify markers with greatest potential. These markers were then examined in plasma from PDAC patients and control groups. Four markers, miR-93-5p, miR-339-3p, miR-425-5p, and miR-425-3p, emerged as the most viable biomarker panel with the ability to detect PDAC in 100% of the early stages (N=5) compared to CA19-9 which showed increased levels in only one patient with early stage PDAC. Additionally, the diagnostic has a specificity of 80% and a sensitivity of 94.7%, making it comparable to CA19-9, and may even be beneficial for use in conjunction with CA19-9. A plasma-based diagnostic was also developed for multi-strain HIV-1 detection utilizing the loop-mediated isothermal amplification (LAMP) method. LAMP primers were developed against the integrase and vpr regions of the HIV-1 genome. They were tested first in cultured HIV samples and then examined for their ability to amplify HIV-1 subtypes A-G. The integrase primer set provided a reliable means of diagnosing all 55 strains and isolates in under 30 minutes, whereas vpr was inconsistent and exhibited high variability in detecting the HIV subtypes. Our limit of detection for B-subtype with integrase was 30 viral copies/reaction. This could provide the basis for a novel, point-of-care diagnostic for use in underdeveloped regions.
Identifier: FA00014141 (IID)
Degree granted: Dissertation (PhD)--Florida Atlantic University, 2023.
Collection: FAU Electronic Theses and Dissertations Collection
Note(s): Includes bibliography.
Subject(s): Plasma
Biomarkers
Carcinoma, Pancreatic Ductal
HIV-1
Diagnosis
Persistent Link to This Record: http://purl.flvc.org/fau/fd/FA00014141
Use and Reproduction: Copyright © is held by the author with permission granted to Florida Atlantic University to digitize, archive and distribute this item for non-profit research and educational purposes. Any reuse of this item in excess of fair use or other copyright exemptions requires permission of the copyright holder.
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Host Institution: FAU
Is Part of Series: Florida Atlantic University Digital Library Collections.