{"id":{"repo_id":"mit","oai_identifier":"oai:dspace.mit.edu:1721.1/130803"},"canonical_url":"https://search.dev.ndltd.org/etd/mit/oai:dspace.mit.edu:1721.1/130803","repository":{"repo_id":"mit","name":"MIT","base_url":"https://dspace.mit.edu/oai/request"},"display":{"title":"CRISPRi screens to identify combination therapies for the improved treatment of ovarian cancer","abstract":"Ovarian cancer is the fifth leading cause of cancer death for women in the United States, with only modest improvements in patient survival in the past few decades. Standard-of-care consists of surgical debulking followed by a combination of platinum and taxane agents, but relapse and resistance frequently occur. To identify genes that confer sensitivity or resistance in tumor cells treated with platinum chemotherapeutics, I performed genome-wide screens combining cisplatin or oxaliplatin with CRISPRi pooled gene knockdowns. Screens were analyzed at 9-days to mimic patient care, and at 48-hours to isolate the short-term DNA damage response. Genes whose knockdown caused sensitivity to the platinum chemotherapeutics were identified through a multi-objective optimization approach to account for knockdown efficiencies and variances in sequencing depth.","abstract_html":"Ovarian cancer is the fifth leading cause of cancer death for women in the United States, with only modest improvements in patient survival in the past few decades. Standard-of-care consists of surgical debulking followed by a combination of platinum and taxane agents, but relapse and resistance frequently occur. To identify genes that confer sensitivity or resistance in tumor cells treated with platinum chemotherapeutics, I performed genome-wide screens combining cisplatin or oxaliplatin with CRISPRi pooled gene knockdowns. Screens were analyzed at 9-days to mimic patient care, and at 48-hours to isolate the short-term DNA damage response. Genes whose knockdown caused sensitivity to the platinum chemotherapeutics were identified through a multi-objective optimization approach to account for knockdown efficiencies and variances in sequencing depth.","abstract_has_math":false,"creators":["Handly, Erika Daphne."],"institution":"Massachusetts Institute of Technology","degree_name":"Doctoral","degree_level":null,"degree_discipline":null,"degree_department":"Massachusetts Institute of Technology. Department of Biological Engineering","school":null,"contributors":[],"advisors":["Michael Yaffe."],"committee_chairs":[],"committee_members":[],"year":2021,"date_issued":"2021","date_published":"2021","updated_at":"2026-07-22T22:21:21Z","subjects":["Biological Engineering."],"languages":["eng"],"rights":["MIT theses may be protected by copyright. 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Standard-of-care consists of surgical debulking followed by a combination of platinum and taxane agents, but relapse and resistance frequently occur. To identify genes that confer sensitivity or resistance in tumor cells treated with platinum chemotherapeutics, I performed genome-wide screens combining cisplatin or oxaliplatin with CRISPRi pooled gene knockdowns. Screens were analyzed at 9-days to mimic patient care, and at 48-hours to isolate the short-term DNA damage response. Genes whose knockdown caused sensitivity to the platinum chemotherapeutics were identified through a multi-objective optimization approach to account for knockdown efficiencies and variances in sequencing depth.","To filter the noise in the genome-wide screen and more confidently identify 'hits,' a smaller pooled CRISPRi screen of four hundred targets was designed, and a few 'hits' were validated. Interestingly, knockdown of FAAP24, a component of the FA core complex, was found to sensitize multiple ovarian cancer cells to platinum compounds, and thus may be a promising candidate for a combination treatment with oxaliplatin and cisplatin. Chapter 5 details an implementation of a combination therapy with cisplatin using peptide nanoparticles. Peptide nanoparticles are a promising therapeutic for the delivery of siRNA and allow for targeting of specific proteins that are difficult to inhibit with small molecular inhibitors; specifically, nanoplexes allowed for the targeting of the REV3 protein, the catalytic component of the translesion synthesis polymerase.","Interfering with REV3 expression through siRNA has a synergistic effect with cisplatin treatment in both human and mouse models of lung cancer, indicating that REV3 is an excellent target to combine with cisplatin therapies. This REV3 knock-down sensitivity was also extended to human ovarian cancer cell lines, indicating the potential of the combination treatment for both lung and ovarian cancers."]},{"key":"dc:description.degree","label":"Dc Description Degree","values":["Ph. D."]},{"key":"dc:title","label":"Title","values":["CRISPRi screens to identify combination therapies for the improved treatment of ovarian cancer"]}]}],"canonical_facts":{"dc:contributor.advisor":["Michael Yaffe."],"dc:contributor.department":["Massachusetts Institute of Technology. Department of Biological Engineering","BioEng"],"dc:contributor.other":["Massachusetts Institute of Technology. Department of Biological Engineering."],"dc:creator":["Handly, Erika Daphne."],"dc:date.accessioned":["2021-05-25T18:20:22Z"],"dc:date.available":["2021-05-25T18:20:22Z"],"dc:date.issued":["2021"],"dc:description":["Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, February, 2021","Cataloged from the official PDF version of thesis. \"February 2021.\"","Includes bibliographical references (pages 153-168)."],"dc:description.abstract":["Ovarian cancer is the fifth leading cause of cancer death for women in the United States, with only modest improvements in patient survival in the past few decades. Standard-of-care consists of surgical debulking followed by a combination of platinum and taxane agents, but relapse and resistance frequently occur. To identify genes that confer sensitivity or resistance in tumor cells treated with platinum chemotherapeutics, I performed genome-wide screens combining cisplatin or oxaliplatin with CRISPRi pooled gene knockdowns. Screens were analyzed at 9-days to mimic patient care, and at 48-hours to isolate the short-term DNA damage response. Genes whose knockdown caused sensitivity to the platinum chemotherapeutics were identified through a multi-objective optimization approach to account for knockdown efficiencies and variances in sequencing depth.","To filter the noise in the genome-wide screen and more confidently identify 'hits,' a smaller pooled CRISPRi screen of four hundred targets was designed, and a few 'hits' were validated. Interestingly, knockdown of FAAP24, a component of the FA core complex, was found to sensitize multiple ovarian cancer cells to platinum compounds, and thus may be a promising candidate for a combination treatment with oxaliplatin and cisplatin. Chapter 5 details an implementation of a combination therapy with cisplatin using peptide nanoparticles. Peptide nanoparticles are a promising therapeutic for the delivery of siRNA and allow for targeting of specific proteins that are difficult to inhibit with small molecular inhibitors; specifically, nanoplexes allowed for the targeting of the REV3 protein, the catalytic component of the translesion synthesis polymerase.","Interfering with REV3 expression through siRNA has a synergistic effect with cisplatin treatment in both human and mouse models of lung cancer, indicating that REV3 is an excellent target to combine with cisplatin therapies. This REV3 knock-down sensitivity was also extended to human ovarian cancer cell lines, indicating the potential of the combination treatment for both lung and ovarian cancers."],"dc:description.degree":["Ph. D."],"dc:identifier.uri":["https://hdl.handle.net/1721.1/130803"],"dc:language.iso":["eng"],"dc:publisher":["Massachusetts Institute of Technology"],"dc:rights":["MIT theses may be protected by copyright. Please reuse MIT thesis content according to the MIT Libraries Permissions Policy, which is available through the URL provided."],"dc:rights.uri":["http://dspace.mit.edu/handle/1721.1/7582"],"dc:subject":["Biological Engineering."],"dc:title":["CRISPRi screens to identify combination therapies for the improved treatment of ovarian cancer"],"dc:type":["Thesis"],"thesis:degree_name":["Doctoral"]},"updated_at":"2026-07-22T22:21:21Z"}