Abstract Toll like receptor-9 (TLR9) is an innate immunity DNA-receptor, which is widely expressed in various cancers, including breast cancer. Low TLR9 expression in cancer cells was initially associated with poor prognosis among patients with triple negative breast cancer. We have now discovered a similar association also among among other breast cancer subtypes. The mechanism for TLR9-associated poor prognosis is not currently known, but our ongoing studies suggest that it may be due to poor chemotherapy responses. Regulation of TLR9 expression in breast cancer is poorly understood. It has been demonstrated that in cervical cancers, TLR9 expression is suppressed by human papillomavirus (HPV) infections. Although breast cancer is not typically considered HPV-associated, there are reports of HPV in breast cancer. The aim here was to test the hypothesis, that HPV-infections suppress TLR9 expression also in breast cancer. To study this, human breast cancer cells were infected with HPV16 E6-oncoprotein, followed by measurement of TLR9 mRNA and protein in vitro. We also aimed to compare the presence of HPV DNA with TLR9 protein expression in clinical breast cancer specimens. We further studied E6-infection effects on breast cancer proliferation, migration, and invasion. E6-infection decreased TLR9 protein expression in TNBC but not in estrogen receptor expressing (ER+) cells. E6-overexpression significantly altered breast cancer proliferation, but the impact was opposite in TNBC and ER+ cells. No effect on migration and invasion was observed. E6-transfected breast cancer cells were significantly less sensitive in vitro to chemotherapies typically used for the treatment of breast cancer in the adjuvant setting. In vivo studies are pending. HPV DNA was not detected in a pilot cohort of clinical breast cancer specimens (n=37) among Northern Finnish breast cancer specimens. These results indicate that HPV may affect breast cancer TLR9 expression and thereby breast cancer prognosis, through treatment responses. Although HPV was not detected in the small pilot set of our clinical samples, this issue needs to be further studied in larger data sets. Citation Format: Essi Parviainen, Sini Nurmenniemi, Sara Bravaccini, Francesca Pirini, Sara Ravaioli, Arja Jukkola, Katri S. Selander. Human papillomavirus protein E6 regulates Toll like receptor-9 expression in breast cancer cells [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-26-04.