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HIV-1 infection induced microRNA expression profile and its downstream effects on cellular transcriptome

Duskova, Karolina (2012) HIV-1 infection induced microRNA expression profile and its downstream effects on cellular transcriptome. Master's Thesis, University of Pittsburgh. (Unpublished)

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Abstract

HIV-1 infected individuals show a remarkable variation in virus replication and disease progression. Host cellular gene expression as a response to virus infection is directly correlated with disease patterns. Here, we examine the role of microRNAs on mRNA regulation and its effect in HIV-1 disease progression by performing a comparative microRNA and mRNA profiling.
Total RNA was extracted from subjects with high viral load (HVL)(>45,000 copies/ml), low viral load (LVL) (~<40 copies/ml), and uninfected controls. RNA was quality tested and then reverse transcribed and tested using a Megaplex Real-time PCR for the quantification of expression of 754 miRNAs, in addition to controls, using a high throughput array. Transcriptome profiling was carried out using Illumina HT-12 array, which targets more than 28,688 annotated genes with more than 47,231 probes. Computational analysis to find the mRNA targets of significantly differentially regulated miRNAs was performed with the expression values of both miRNA and mRNA, supplemented with a GenMir++.
HIV-1 infection with high viral load significantly dysregulated the miRNA profile in the infected individuals compared to uninfected or LVL group, whereas infection with low viral load produced a less distinctive profile compared to the controls. These differences are independent of age within these populations. Independent validations confirmed the high throughput results in 65-85% in independent donors. GO enrichment analysis further showed 34 significant terms
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of biological processes in the high viral load compared to controls. A less distinctive profile was seen in the low viral load samples compared to controls on both the miRNA and mRNA levels. Biological validation studies also confirmed the expression of HIV induced host cellular factors in in vitro infected samples. Together, these results indicate that HIV-1 infection differentially regulates host cellular transcriptome through miRNA expression.
Public health relevance: Viral load significantly upregulates miRNA expression, which translates to an altered expression on the mRNA level. The discovery of microRNAs that play a role in HIV infection could lead to the development of new biomarkers that could be used to identify disease progression within the infected individuals as well as the infected individuals’ ability to respond to antiviral treatment.


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Details

Item Type: University of Pittsburgh ETD
Status: Unpublished
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Duskova, Karolinaduskova.karolina@gmail.com
ETD Committee:
TitleMemberEmail AddressPitt UsernameORCID
Thesis AdvisorAyyavoo, Velpandivelpandi@pitt.eduVELPANDI
Committee MemberMartinson, Jeremyjmartins@pitt.eduJMARTINS
Committee MemberBarchowsky, Aaronaab20@pitt.eduAAB20
Date: 29 June 2012
Date Type: Publication
Defense Date: 24 April 2012
Approval Date: 29 June 2012
Submission Date: 4 April 2012
Access Restriction: 5 year -- Restrict access to University of Pittsburgh for a period of 5 years.
Number of Pages: 135
Institution: University of Pittsburgh
Schools and Programs: Graduate School of Public Health > Infectious Diseases and Microbiology
Degree: MS - Master of Science
Thesis Type: Master's Thesis
Refereed: Yes
Uncontrolled Keywords: miRNA, mRNA, profiling, HIV-1 viral load
Date Deposited: 29 Jun 2012 20:12
Last Modified: 29 Jun 2017 05:15
URI: http://d-scholarship.pitt.edu/id/eprint/12011

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