HIV treatment, while effective could be greatly improved by targeting something other than viral proteins. Image Source: Flickr User: snre

CRISPR has been a hot topic over the past couple of years. This paradigm-shifting technique was a major contender for the Nobel Prize in Chemistry for both the 2015 and 2016 awards1 and has been busy racking up a number of accomplishments, including assessing therapeutic targets for HIV.

Many current HIV therapies, while largely effective, target viral proteins. As HIV tends to mutate rapidly, especially in cases of poor medication compliance, better solutions are needed. As scientists continue to delve into CRISPR systems to fight this disease, modern lab software that can assess and create sequences, model therapeutic targets and help analyze data will be an integral part of successful research.

A Small Genome

As you might expect, viruses have a smaller genome than their hosts; humans have over 19,000 genes, whereas HIV has nine.2 Viruses rely on host proteins for replication, transmission and even entry into host cells. When looking to create anti-viral medications, the proteins produced by the virus which confer higher rates of survival are often targeted. The vast majority of anti-HIV medications target viral proteins, which can lead to issues if a patient does not strictly adhere to their drug regimen.

Due to its small genome, HIV can mutate rapidly and outwit medications if there is a sudden discontinuance or missed dose, similar to antibiotic resistance or cancer. By shifting focus towards the human genome and assessing which proteins and genes are necessary for the pathogenesis of HIV, there is a better potential for long-term treatment options or a cure for HIV. As aforementioned, the human genome is substantially larger than HIV, so researchers will need to hone in on the correct segments right away. Modern lab software can help researchers identify host dependency factors (HDFs) and assess their potential as therapeutic targets for biologic medications.

For example, CCR5 was recently identified as a co-receptor for HIV infection of CD4+ T cells and macrophages. This is a cell surface protein receptor that catches and internalizes HIV in human beings. This not only showed that a subset of the population may be resistant to many strains of the HIV virus, but it also allowed for the development of a small-molecule inhibitor that is functional even in the event of viral-protein targeted therapy failure. Researchers realized that there must be more potential within the human genome, but identifying HDFs was challenging with previous technology such as RNAi-based screens and shRNA. In combination with innovative lab software, CRISPR promises to be more precise and sensitive than any other previously employed technique.

More Effective Screening

Although an inactive CCR5 sounds like an ideal allelic variant, many people who possess it are predisposed to some viral infections and cancers; simply snipping this gene or allele out of the human genome is unlikely to be a viable solution. When looking for more candidates, a CRISPR-Cas9 based screen using lentiviral single-guide RNA (sgRNA) libraries can identify beneficial loss-of-function variants more effectively than previously used screens. The research group that recently published a paper on the identification of new therapeutic targets, conducted a CRISPR-based genetic screen in a T cell line using a high-complexity, genome-wide sgRNA library. This allowed researchers to identify genes that, when inactivated, were protective against HIV.

This group was able to identify three new potential gene targets in addition to the previously identified co-receptors CD4 and CCR5, TPST2, SLC35B2, and ALCAM, none of which were identified in any previously conducted RNAi screens. Additionally, loss of these newly identified genes did not appear to affect cellular fitness. This is a lot of data to sift through, so utilizing software featuring high-end sequence data mining and management in conjunction with CRISPR will make things easier and move them along more quickly.

BIOVIA Biologics Discovery fills that technological need. It is a common platform with capabilities that can assist researchers hone in on key targets in a sea of data. With predictive analytics, sequence data mining capabilities and workflow and data management, this technology is what is needed to move these projects forward. This will help carry your lab from target discovery to biologic therapeutic development. BIOVIA’s  capabilities in pre- and post-discovery modelling save investigators time and R&D dollars. Please contact us today to learn more about how our software options can support the efforts of your lab.

  1. “CRISPR loses Nobel to tiny machines,” October 5, 2016, https://techcrunch.com/2016/10/05/crispr-loses-nobel-to-tiny-machines/
  2. “A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors,” December 19, 2016, http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3741.html