Composing CODAs to cervical cancer screening through an integrated CRISPR and fluorescent nucleic acid approach

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ABSTRACT Challenges. Despite being curable when caught early, cervical cancer remains the second leading cause of death in women living in sub-Saharan Africa. Even with available screening technologies (cytology, visual inspection with acetic acid (VIA), and sometimes high-risk Human Papillomavirus [hrHPV] testing), only 10-20% of eligible women in low-and-middle-income countries (LMIC) are currently screened. Barriers cited include technical expertise, laboratory capacity, cost, and access. Most developed countries have adopted PCR-based HPV screening, furthering the resource divide with LMICs, where 80% of cancer deaths occur. Innovation. In dire response to the diagnostic gaps unveiled by the pandemic, team members within our group developed and validated in human specimens a robust and frugal technology to detect nucleic acid targets. The approach, CRISPR Optical Detection of Anisotropy or CODA, combines CRISPR/Cas (a Nobel Prize- winning technology for highly precise gene editing) with fluorescence anisotropy (differential rotational motion of fluorescent molecules). Automated nucleic acid readouts are generated in < 30 minutes. We have adopted this technology for: a) the detection of DNA and RNA markers of CIN2+; and b) reliable use by clinicians and clinical lab personnel in point-of-care settings. Our plan for this proposal is to operationalize this technology for low resource settings, notably our partner sites in Uganda and Ghana, with close LMIC input. We will then leverage CODA and other parameters to create a panel of tests to optimally detect CIN2+ in a single encounter. Aim 1: Construct a robust CODA platform for comprehensive HPV screening. Aim 2: Further examine CODA performance on human specimens and refine for LMIC operations. Aim 3: Develop a novel and rapid multi-modal algorithm for screen and treat in LMICs. Impact. Given CODA's core strengths in nucleic acid analyses (e.g., DNA or RNA), we envision an approach that yields fully quantitive readouts of high-risk HPV DNA and E6, E7, and p16 mRNA. Since the CODA assay underlies all readouts driving this proposal, a high potential exists for end-user-friendly, practical, and rapid triage of high-risk cervical disease or invasive cancer. These benefits could help decentralize and harmonize screening efforts with those guidelines currently endorsed by resource-rich countries.