Sams, K. | bioRxiv Science

bioRxiv2025

TICKHUNTER: A Targeted Hybridization-Capture Sequencing Approach for the Detection and Characterization of Tick-borne Pathogens and Blood Meals

As weather systems quickly change, vector communities and their pathogens evolve faster than assay panels can be redesigned. Additionally, PCRs narrow target range makes it structurally unable to catch divergent or reassorted agents. We developed a hybrid capture next-generation sequencing enrichment platform that provides comprehensive detection and characterization of tick-borne agents alongside ecological vertebrate host identification with low-pass sequencing. Analytical validation demonstrated performance comparable to qPCR with superior variant tolerance and multiplexing capacity. Field deployment in subtropical, metropolitan New York detected Anaplasma phagocytophilum strains (n=3) linked to human granulocytic anaplasmosis and a Babesia microti-like species in urban raccoon (Procyon lotor) populations. Tick vector screening revealed a putatively novel chimeric Flavi-like virus in invasive Haemaphysalis longicornis ticks combining segmented and unsegmented genomic features, with codon adaptation analysis indicating strong human compatibility. Serology revealed high Flavivirus seropositivity in NYC raccoons, suggesting an unrecognized urban reservoir role. Blood meal analysis simultaneously revealed complex ecological pathogen transmission networks spanning multiple vertebrate hosts. This integrated surveillance system enables comprehensive pathogen discovery, real-time evolutionary monitoring, and ecological risk assessment, transforming our capacity to detect emerging tick-borne threats in rapidly changing environments and prevent spillovers.

microbiology↗

bioRxiv2022

CRISPRa screen identifies a role for c-KIT signaling in tamoxifen resistance, potentially through upregulation of ABC transporters

Resistance to endocrine therapy is a common problem in patients with estrogen receptor alpha (ER) positive breast cancer. In this study, we took a non-biased genome-wide approach to identify novel mechanisms of endocrine resistance using a clustered regularly interspaced short palindromic repeats (CRISPR) activating (CRISPRa) screen. Results from the screen identified 109 candidate resistance-associated genes, with several of these genes, such as EGFR and SRC, having been previously associated with endocrine resistance. One candidate gene that has not been previously associated with endocrine resistance is the tyrosine kinase receptor, c-KIT. We further tested for associations between c-KIT and endocrine resistance and found that c-KIT overexpressing cells proliferate more rapidly in the presence of tamoxifen compared to control cell lines. To gain deeper insight into the potential role of c-KIT signaling in tamoxifen resistance, we next performed precision nuclear run-on and sequencing (PRO-seq) analysis of c-KIT overexpressing cells to identify downstream factors that may mediate the c-KIT response. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the overexpressed genes found that the only class of factors that was significantly induced by c-KIT was the ATP-binding cassette (ABC) transporters; specifically, ABCA1, ABCA4, and ABCG1. Interestingly, overexpression of two of these ABC transporters, ABCA1 and ABCG1, significantly correlated with worse prognosis in ER+ breast cancer patients following endocrine therapy. We then tested for potential therapeutic effects of c-KIT inhibition on endocrine resistance and found that the c-KIT inhibitor Gleevec appears to synergize with tamoxifen to suppress MCF-7-S cell growth. Together, our findings support the hypothesis that c-KIT signaling promotes endocrine resistance via the induction of ABC transporter activity. Additionally, our studies suggest that inhibition of c-KIT signaling may represent a novel strategy for preventing or overcoming endocrine resistance in ER+ patients.

cancer biology↗