Spatial modulation of the cervical immune landscape by HIV risk factors

The female genital tract is the first line of defense against any sexually transmitted infections, including viruses, bacteria, or fungi, playing a critical role in maintaining reproductive and overall health. Among these infections, HIV remains a significant global public health concern, particularly in sub-Saharan Africa, where it is one of the leading causes of death. Women and girls in this region account for the majority of new cases, highlighting the need to understand the molecular mechanism that influence HIV susceptibility in the female genital tract, in order to develop effective interventions and preventive strategies.

The overreaching aim of this thesis is to identify modulations in the transcriptional landscape of the cervical mucosa, first by bulk transcriptomics (paper I and III) on the larger cohort, then at higher resolution by spatial transcriptomics (paper II and IV) on a smaller subset of samples. Specifically, in paper I and II we looked at the effect of the contraceptive compound DMPA and in paper III and IV at different compositions of the vaginal microbiome.

The injectable contraceptive compound DMPA has been suggested to induce an increased risk for HIV acquisition. This is concerning as it is a popular contraceptive choice in many HIV endemic areas.

In paper I we found long-term DMPA use associated with a significant disruption of the epithelial barrier and an enhanced immunological profile. These are factors associated with heightened HIV susceptibility, on the other hand there was no link between DMPA use and differences in microbiome profiles at either clinical or molecular level. In paper II we determined the spatial location of processes identified in paper I as well as identifying a mucosal-wide immunoglobulin gene upregulation verified by staining. The heightened resolution revealed that markers of epithelial barrier disruption not only stemmed from the epithelium but also from the submucosa. Specifically, the submucosa exhibited extracellular matrix dysfunction.

In paper III we compared the 16S rRNA taxonomical composition of cervicovaginal samples with paired tissue biopsy samples as well as correlating these with the tissue host-transcriptome. The tissue microbiome profile was similar although distinct from the cervico-vaginal microbiota. We hypothesize that the difference could stem from some bacteria's ability to adhere to the tissue lining and form biofilm, thus showing up at higher abundance in the tissue biopsy compared to the fluid samples. In paper IV we, similarly to paper III, identified that more diverse microbiome profiles associated with increased innate immune responses and epithelial barrier structure remodeling. We found that the microbiota profile defined by high microbial diversity (L4) had the largest shift in host transcriptome compared to the other three groups (L1-L3). This shift in gene expression was dominated by downregulation of genes in the clusters closest to the basal membrane.

In conclusion, this thesis provides novel insights into the transcriptional and spatial dynamics of the cervical mucosa in response to hormonal contraceptive use and variations in vaginal microbiota composition. Additionally, we are the first to extensively characterize the whole-transcriptome landscape across the ectocervical mucosa at high spatial resolution.

Together these results contribute to our understanding of the mechanisms underlying HIV and STI susceptibility. These insights could inform the development of more effective prevention strategies and targeted interventions aimed at improving reproductive health and reducing STI risk, particularly for women in high-risk settings.

List of scientific papers

I. Multi-omics analysis of the cervical epithelial integrity of women using depot medroxyprogesterone acetate. Bradley F, Franzén Boger M, Kaldhusdal V, Åhlberg A, Edfeldt G, Lajoie J, Bergström S, Omollo K, Damdimopoulos A, Czarnewski P, Månberg A, Oyugi J, Kimani J, Nilsson P, Fowke K, Tjernlund A, Broliden K. PLoS Pathogens, 2022, 18(5):e1010494. https://doi.org/10.1371/journal.ppat.1010494

II. Spatial transcriptomics unveils estrogen-modulated immune responses and structural alterations in the ectocervical mucosa of depot medroxyprogesterone acetate users. Kaldhusdal V, Franzen Boger M, Tjernlund A, Burgener A, Bradley F, Lajoie J, Omollo K, Kimani J, Fowke K, Czarnewski P, Broliden K. Scientific Reports 2025 15:1, 15(1), 1-16. https://doi.org/10.1038/s41598-024-83775-9

III. Distinct cervical tissue-adherent and luminal microbiome communities correlate with mucosal host gene expression and protein levels in Kenyan sex workers. Edfeldt G, Kaldhusdal V, Czarnewski P, Bradley F, Bergström S, Lajoie J, Xu J, Månberg A, Kimani J, Oyugi J, Nilsson P, Tjernlund A, Fowke K, Kwon D*, Broliden K *. Microbiome, 2023, 11(1):67. https://doi.org/10.1186/s40168-023-01502-4 * Shared senior authors

IV. Spatially restricted host transcriptional signatures across the human ectocervical mucosa in response to different cervicovaginal microbiome compositions. Kaldhusdal V, Edfeldt G, Franzen Boger M, Burgener A, Lajoie J, Omollo K, Kimani J, Tjernlund A, Fowke K, Kwon D, Broliden K. [Manuscript]