Longitudinal Follow-Up of microRNA Expression During Hepatitis E Virus Infection in Immunocompromised Hosts

Hepatitis E virus (HEV) is a zoonotic cause of acute viral hepatitis that can become chronic in immunocompromised patients. Recently, host microRNAs (miRNAs) miR-122-5p, miR-125b-5p, miR-99a-5p, and miR-192-5p have been associated with acute HEV infection and with chronic HEV infection. Yet, the expression levels of miRNAs during the early phase of HEV infection remained unexplored. In this context, we aimed to identify changes in miRNA profiles occurring between the diagnosis of HEV infection and HEV cure in immunocompromised patients and in a pig model. We retrospectively included 9 immunocompromised patients with HEV infection (5 chronic and 4 resolutive) and 10 immunocompromised pigs (6 HEV-infected and 4 controls). RNAseq was retrospectively performed on pig samples. MiRNA expression was quantified by qPCR on pig and human samples.: Small RNA sequencing and targeted qPCR analyses revealed a pronounced, stage-dependent remodeling of miRNA expression during HEV infection. In patients, viral clearance was associated with early upregulation of miR-99a-5p, miR-122-5p, miR-125b-5p, and miR-194-5p, whereas progression to chronic infection was characterized by sustained downregulation of miR-23a-3p, miR-27a-3p, miR-106a-5p, miR-221-3p, and miR-223-3p. Likewise, a correlation was observed between the dysregulation of miR-181a-5p, miR-425-5p, and let-7b-5p with viral load (HEV RNA), while miR-27a-3p and miR-106a-5p were associated with ALT levels. In pigs, miR-122-5p was upregulated 10 weeks p.i., while 10 miRNAs (miR-16, miR-20a-5p, miR-23a-3p, miR-27a, miR-29a-3p, miR-140-5p, miR-181a, miR-191, miR-423-5p, and miR-99a-5p) were downregulated 11 weeks p.i. MiR-23a-3p, miR-27a, miR-99a-5p, miR-181a, and miR-425-5p were associated with HEV infection in both humans and pigs. Persistent HEV infection in immunocompromised patients and in a pig model showed partial overlap in miRNA responses. Our findings identified circulating miRNAs as stage-specific molecular markers of HEV infection in immunocompromised hosts. MiRNAs could contribute to early stratification of high-risk patients, improving outcomes for vulnerable patients facing this emerging viral disease.