Transcriptional responses of mouse proximal colon and colonoids during early whipworm infection

Trichuriasis, caused by the parasitic nematode Trichuris trichiura, affects429–508 million people worldwide. Although the early phase of whipworm infection is crucial for establishing infection, its underlying molecular mechanisms remain unclear. In this study, we examined and compared host transcriptional responses during early infection of the mouse whipworm, T. muris, using first-stagelarvae (L1) in proximal colons from in vivo models (B6 and STAT6-deficientmice) and in vitro colonoid models. Differentiallyexpressed genes and functional enrichment analysis revealed that while the “neurotransmitter release” pathway was uniquely upregulated in B6 mice, the “lipid metabolism” pathway was commonly modulated in both mice and colonoids, which may have implications for intestinal epithelial function during infection. Enrichment of alternative splicing (AS) events in splicing-related pathways across all models highlighted the need for further investigation into AS regulation mechanisms and its functional roles during early infection. Temporal transcriptomic profilingof L1 T. muris in colonoids identifiedsix clusters representing fundamental molecular pathways associated with parasite development and adaptation. Utilizing dual-RNA sequencing from infected colonoids, we conducted host–parasite co-expression analysis, identifying correlated gene pairs, including a negative correlation between T. muris-secreted serine proteases and mouse genes involved in metabolism and epithelial cell functions. These findings provide valuable insights into the dynamic transcriptional regulation during early L1 T. muris infection in vivo and in vitro, offeringa resource for comparative studies in whipworm infection models. In conclusion, this comparative study serves as a starting point for deeper investigation into molecular mechanisms underlying early whipworm infection and opens up new opportunities for exploring host–parasite interactions. IMPORTANCE Trichuriasis, caused by the parasitic nematode Trichuris trichiura, remains a major public health concern, particularly in resource-limited regions. Current anthelmintics show suboptimal efficacyagainst whipworm infections, highlighting the critical need for novel therapeutic strategies. This study provides a comparative framework by integrating transcriptional profilesfrom in vivo and in vitro models during the early infection phase of T. muris, a mouse model for T. trichiura. Through this approach, we demonstrate the potential of proximal colonoids as a model for investigating key aspects of host–parasite interactions, including epithelial invasion and transcriptional dynamics, during early T. muris infection. By employing dual-RNA sequencing, we not only characterize temporal gene expression dynamics of first-stagelarvae but also identify host–parasite co-expression profiles,thereby shedding light on molecular pathways that may underlie infection establishment and host responses. This work builds upon and solidifiesprevious findingsabout the utility of organoid models for investigating early whipworm infection while providing a foundational resource for exploring intervention strategies targeting the initial stages of infection.