Objective: The rectal mucosa is highly susceptible to HIV infection. Mucosal fluid contains soluble immune proteins that influence HIV infection, and previous studies have shown unique mucosal protein expression in HIV-exposed seronegative (HESN) populations, which may contribute to reduced HIV susceptibility. However, the key correlates of susceptibility at the rectal mucosa have not been well defined, which is a critical knowledge gap for our understanding of HIV pathogenesis. Methods: Rectal lavage from low risk men was screened for HIV-neutralizing activity in a TZM-bl reporter cell line against an R5-tropic HIV virus. Label-free tandem mass spectrometry was used to characterize soluble proteins within rectal lavage samples from a low-risk cohort of men (n=15), and HESN men who have sex with men (MSM; n=25). Protein expression between populations was compared using adjusted t tests (p<0.05), and was interpreted using hierarchical clustering and DAVID biofunctional analysis. Protein expression was further analyzed using survey data on sexual behaviours. Proteins associated with the HESN population were screened for antiviral activity in TZM-bl and PBMC culture against an R5- and X4-tropic virus. Major Results: Rectal mucosal fluid was able to inhibit HIV infection in vitro by 40% (p<0.05). Mass spectrometry identified 30/341 (9%) proteins deferentially expressed (DE) in HESN MSM. DE proteins held functions in immunity (p=6.68x10-6, p=0.001) and epithelial barrier development (p=1.81x10-4; p=0.01); notably, specific antiproteases were elevated in HESN secretions, two of which were screened for antiviral activity. Serpin B4 (+2.52 L2FD; p=1.09x10-5), showed significant inhibition of HIV in TZM-bl (45% BaL, 34% IIIB; p<0.05) and PBMC culture (37% BaL, 49% IIIB; p<0.05); cystatin A (+1.52 L2FD; p=1.40x10-3) showed no inhibitory effects. Serpin B4 expression was not associated with frequency of oral intercourse (p=0.32), partner viral load (r=0.16; p=0.29) or presence of HIV neutralizing IgA in secretions (p=0.52). Conclusions: This thesis reports the use of proteomics to understand HIV-susceptibility at the rectal mucosa, and identified serpin B4 as a novel antiviral immune correlate in a population of HESN MSM. These results may help guide future studies of prevention technologies, such as microbicides or vaccines, which would ultimately help limit the spread of HIV. / February 2016