Thesis
Determining HIV-1 quasispecies genomic variability to optimize gRNA excision using the CRISPR/Cas9 gene editing system
Master of Science (M.S.), Drexel University
01 May 2015
DOI:
https://doi.org/10.17918/etd-6497
Abstract
In light of the global human immunodeficiency virus type 1 (HIV-1) epidemic, numerous attempts have been made to combat HIV-1 and cure patients of an otherwise deadly infection. While improving survival rates among HIV-1 infected patients, highly active retroviral therapy (HAART) and related therapies are at best a stalling measure due to the inevitable reemergence of escape virus from latently infected cellular reservoirs. Gene editing technologies hold the promise to permanently excise integrated virus from the genome. The general aim of this research was to thoroughly consider the current state of both Next Generation Sequencing (NGS) and the CRISPR/Cas9 gene-editing technologies and propose a method of optimization for their application to excise HIV-1 proviral DNA from infected host cell targets. To do so, a bioinformatic pipeline was designed and implemented that utilized novel NGS sequence data from HIV-1 infected patients to determine all targetable regions of viral DNA in all quasispecies, and quantify the excision probabilities using the known binding affinities of the CRISPR/Cas9 gene-editing system. The exact gRNA guides have been identified that can facilitate optimized cleavage of these sites using the CRISPR/Cas9 system for proviral excision. With this information, the number and sequences of gRNAs required to excise the patient-specific HIV-1 quasispecies has been determined. These results represent a step along the path towards a sterilizing cure that can thoroughly eradicate HIV/AIDS.
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Details
- Title
- Determining HIV-1 quasispecies genomic variability to optimize gRNA excision using the CRISPR/Cas9 gene editing system
- Creators
- Matthew F. DeSimone - DU
- Contributors
- William Nathanial Dampier (Advisor) - Drexel University (1970-)Ahmet Sacan (Advisor) - Drexel University (1970-)
- Awarding Institution
- Drexel University
- Degree Awarded
- Master of Science (M.S.)
- Publisher
- Drexel University; Philadelphia, Pennsylvania
- Number of pages
- viii, 63 pages
- Resource Type
- Thesis
- Language
- English
- Academic Unit
- School of Biomedical Engineering, Science, and Health Systems (1997-2026); Drexel University
- Other Identifier
- 6497; 991014632527204721