Decoding Host Gene Expression and Splicing Networks Driven by Quiescent Intracellular UPEC Reservoirs

Uropathogenic Escherichia  coli (UPEC)  cause  recurrent  urinary  tract  infections  by  forming quiescent  intracellular  reservoirs  (QIRs)  within  bladder  epithelial  cells,  enabling  immune evasion  and  antibiotic  tolerance.  However,  how  QIRs  reprogram  host  cellular  processes remains poorly understood. This project aims to  define how  QIR formation alters host  gene expression  and  alternative  splicing  to  promote  bacterial  persistence.  Using fluorescence‑labelled UPEC, infected bladder epithelial cells harbouring QIRs will be isolated by  flow  cytometry  and  analysed  by  long‑read  Oxford  Nanopore  RNA  sequencing  and single‑cell RNA sequencing. QIR‑specific alternative splicing events, including exon skipping and  intron  retention,  will  be  systematically  identified  and  validated  at  transcript  and  protein levels. Changes in key splicing regulators and kinases associated with QIR formation will also be  examined.  Functional  pathway  analyses  will  focus  on  immune  signalling,  ubiquitination,autophagy, and cell survival. This study will provide the first comprehensive insight into host splicing reprogrammed by intracellular bacterial reservoirs, uncovering novel host–pathogen interaction mechanisms underlying persistent and recurrent UPEC infection.