Team:GunnVistaPingry US/Implementation
It’s difficult to downplay the significance of CRISPR technology. With Jennifer Doudna recently winning the Nobel Prize for her CRISPR work, we interviewed Prof. Vijai Singh, author of “Genome Engineering via CRISPR-Cas9 System”, states that “More patents have been granted and more technologies have been developed for diagnostic, therapy, and chemical production”. As we have emphasized, our research on CRISPRi will reveal much about CRISPR and CRISPRa sgRNAs, only requiring minor changes. Therefore, better sgRNA predictions can drastically improve CRISPR research, especially in regards to time and expenses.
Our team will work on future user-friendly implementation:
- We will host the software as an interactive service in the cloud
- We will also provide a feedback mechanism so that end users can report back the quality of guides we suggested. This information again will be used to train the model better
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Build a database for good quality guides for known genes for CRISPR and its variations, as well as different hosts
- Takes care of off-target stringency as well as negative controls
End Users
Future iGEMers and Bioengineers
Bioengineers work on deadlines, and one of the most difficult parts of a less efficient sgRNA is the time loss. PhD students, especially since they need to complete their PhD in a set time, would especially benefit from a more streamlined sgRNA selection system. We interviewed Sai Chiti, a PhD student at the cancer biology lab at La Trobe Institute For Molecular Science in Melbourne, Australia. He stated, “Since I’m working on CRISPR and cancer related studies, it’s really important to get a knockout or a knockin with CRISPR. Our PhD project depends entirely on what we do with the guide RNA. If that fails, then the entire PhD can fail.” He proceeded to list the timely process of designing, inserting, and screening CRISPR. I think guide RNA designing is very crucial because that is an initial first basic step. It’s a very costly process because you use a lot of reagents and a lot of screenings.A better guide RNA will save lots of time and money. More than money, it’s time. We hardly have three and a half years to finish up our PhDs. The entire guide RNA selection, screening, and other processes takes around two to three months. And again, if you make any mistake at a level, especially in the initial guide RNA level, you lose those three months and again you go back and start from scratch. And our deadlines are very important, as we need to cross milestones to get into the next years of our PhDs. Our lab needs to progress, so it’s very essential to have a good guide RNA which has less off-target effects and hits our gene of interest.” It is clear that selecting a less effective guide RNA can significantly hurt research. Our algorithm lays the ground for better guide RNA selection and increased focus in it. Although it is one of the initial steps, it can affect much of the later steps.Covid-19
COVID-19 has impacted all of our lives. But CRISPRia has shown to be effective during this time, as Danilosky’s “Identification of required host factors for SARS-CoV-2 infection in human cells” has shown through genome-wide screens. A genome-wide CRISPR knockout screen identifies host factors for SARS-CoV-2 infection. Knowing which knockdown was going to make COVID-19 less effective allowed the lab. They did that with the CRISPRi screen. Genome-wide screens: library designs. There are 18,000 human genes, and in the future, computer scientists and biologists can combine to use software to build a genome-wide screen library.Stem Cell Research
Stem cells are critical for figuring out protein function, differentiation, and even possess therapeutic application. Our local area, California, is voting on Proposition 14, which authorizes $5.5 billion state bonds for stem cell and related research. CRISPR technology is at the forefront of much of stem cell research. Problems exist with off-target and mutations exist in iPSCs. Professor Shinya Yamanaka pioneered an iPSC derived retinal therapy. He collaborated with a surgeon to show iPSCs could be used for therapy, and they did iPSC culture, but when they found new mutations, and therefore they abandoned clinical trials. With genome editing, one can imagine even more mutations with a poorly selected guide RNA. Professor Tomoda, who worked in CiRA (the premier iPSC-application development center in the world where the developed the retinal therapy) said good guide RNA and off-target stringency are crucial for the possibility of CRISPR implementation in therapeutics and will better help stem cell research.Biopharma and Therapeutics
I originally thought that CRISPR was a long way from being used in therapeutics. However, CRISPR therapeutics, a company by Jennifer Doudna, works on somatic gene editing for its patience. Moreover, Mammoth Biosciences uses CRISPR proteins to detect bacterial viral genes, they are not editing genomes but are building diagnostics. The main concern about CRISPR in therapeutics is about off-targets and guide RNA efficacy, both which our algorithm takes into account. CRISPR may be closer to entering the therapeutics field than originally expected. Although there is much controversy and risk in medical applications of CRISPR, Prof Vijai Singh states that “Risk for disease treatment will always exist. In a treatment for the muscular dystrophy, they corrected the muscular dystrophy gene although risk was 30%-40%. Many are willing to take risks in the medical field, and as CRISPR grows, it has great potential in therapeutics”. It’s all probabilities, and a well-selected sgRNA will increase the probability of a successfully silencing and lower the probability of CRISPR editing.“CiRA | Center for IPS Cell Research and Application,
Kyoto University.” CiRA | Center for IPS Cell Research and Application, Kyoto University, www.cira.kyoto-u.ac.jp/e/. Accessed 28 Oct. 2020.
Cyranoski, David. “Japanese Woman Is First Recipient of Next-Generation Stem Cells.” Nature News, 12 Sept. 2014, www.nature.com/news/japanese-woman-is-first-recipient-of-next-generation-stem-cells-1.15915, 10.1038/nature.2014.15915.
Daniloski, Zharko, et al. “Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells.” Cell, vol. 0, no. 0, 24 Oct. 2020, www.cell.com/cell/fulltext/S0092-8674(20)31394-5?rss=yes, 10.1016/j.cell.2020.10.030. Accessed 28 Oct. 2020.
“INVESTED DIGITAL.” Crisprtx.Com, 2019, www.crisprtx.com/.
Langelier, Julie. “Scientists Comment on Claim of Gene-Edited Babies.” Gladstone.Org, 26 Nov. 2018, gladstone.org/news/scientists-comment-claim-gene-edited-babies. “Mammoth Biosciences.” Mammoth Biosciences, mammoth.bio/.
TEXT OF PROPOSED BOND PROPOSITION 14.
