Non-invasive sampling reveals distinct HPV and immune signatures associated with abnormal cytology in people living with HIV

Abstract Persistent high-risk HPV infections drive most anal cancers, disproportionately affecting people with HIV (PLH), for whom cytology-based screening remains essential. However, the biological context of abnormal anal cytology, particular regarding local immune cells, is incompletely understood. In this pilot study, 57 PLH underwent longitudinal non-invasive anal sampling over one year, including cytology, HPV genotyping, and phenotypic characterization of ano-mucosal immune cells. Anal HPV infection and persistence were highly prevalent. Abnormal cytology was associated with more concurrent (high-risk) HPV infections, lower viral loads, and anal immune-microenvironment characterized by increased CD4 and CD8 T cells with upregulated tissue residency, activation, and effector markers. In summary, non-invasive anal sampling revealed that abnormal anal cytology in PLH is characterized by a distinct microenvironmental signature marked by multiple (HR) HPV infections and increased levels of tissue resident, activated and effector ano-mucosal T cells, potentially highlighting the important role of local immune cells.