The TLR9 agonist MGN1703 triggers a potent type I interferon response in the sigmoid colon

Background & Aims: TLR9 agonists (e.g. MGN1703) are used to treat colorectal and other cancers in clinical trials, yet the impacts of these drugs in human intestines remain unknown. This, together with the fact that there are more potential indications for TLR9 agonist therapy (e.g. ulcerative colitis and HIV), led us to investigate the impact of MGN1703 on intestinal homeostasis and HIV persistence in HIV positive subjects.Methods: Colonic sigmoid mucosal biopsies were collected (baseline and week four) from 11 outpatient subjects in a single-arm, phase 1b/2a study, where HIV positive subjects, on antiretroviral therapy received MGN1703 (60 mg s.c.) twice weekly for four weeks. In fixed tissue sections, we quantitated cell profiles positive for interferon-stimulated and inflammatory proteins. Remaining sigmoid tissue was digested and percoll-enriched intestinal mononuclear cells were obtained for virological and immunological analyses. We also assessed colonic fecal microbiota compositions (baseline and <2 weeks after last dose) using high-throughput 16S ribosomal RNA gene amplicon sequencing.Results: Within sigmoid mucosa, RNASeq revealed 248 significantly regulated genes (FDR<0.05), including many type I interferon-stimulated genes. MGN1703 dosing increased the number of cell-profiles positive for MX1 (p=0.001, mfc=8.8) and ISG15 (p=0.014, mfc=5.6). No cohort-wide changes were observed in neutrophil infiltration (MPO; p=0.97). We observed a significant negative correlation between mucosal baseline gene expression levels of TLR9 and the fold-change in integrated HIV-1 DNA copies (p=0.020). Intestinal homeostasis was maintained with a diversified microbiota composition (Family: Shannon index; p=0.008) in HIV feces.Conclusions: MGN1703 induced a potent type I interferon response in the intestines without a concomitant inflammatory response. Furthermore, higher baseline TLR9 expression was associated with fewer integrated HIV-1 DNA copies. (ClinicalTrials.gov: NCT02443935)