Assessment of helminth-HIV co-infection as a potential risk factor for colorectal cancer in South African adult subpopulation.

Abstract

Background: Colorectal cancer (CRC) incidence is rising in sub-Saharan Africa, where HIV and helminth infections remain endemic. These chronic infections induce profound immune, microvirome, metabolic, and epigenetic perturbations, yet their integrated contribution to CRC susceptibility in African populations is poorly understood. This thesis presents the first comprehensive investigation linking immune checkpoint dysregulation, gut DNA virome driven functional shifts, and stool-based methylation biomarkers in HIV-helminth co-infection, providing a novel, multi-dimensional view of infection-associated cancer risk. Methods: This retrospective observational study analysed stored samples from a peri‑urban community south of Durban, South Africa, collected between March 2020 and May 2021. Multiplex assays were performed on 78 serum samples to profile immunoregulatory markers. Shotgun metagenomic sequencing of 62 stool samples was conducted to characterise the gut virome and assess epigenetic and metabolic signatures. Fecal occult blood testing was also evaluated as a potential non‑invasive CRC screening tool. Results: Multiplex immune assays showed that HIV infection elevated PD-1 (adjusted β = 0.12, p = 0.034) and TIM-3 (β = 23.15, p = 0.052) while reducing CD28 (β = -651.95, p = 0.010). Helminth infection increased TIM-3 (β = 20.98, p = 0.020), and co-infection elevated PD-1 (β = 0.18, p = 0.0046) and PD-L2 (β = 7.95, p = 0.033), with marked CD28 downregulation across all infected groups, indicating a sustained immunosuppressive state conducive to tumor escape. Stool DNA showed strong virome convergence between CRC and HIV-helminth co-infected groups (p < 2.2 × 10⁻¹⁶). Functional enrichment included tRNA modification GTPase (K03650) and adenine-specific DNA methylase (COG2189) as shared viral epigenetic signatures, alongside distinct metabolic reprogramming, particularly butyrate metabolism, oxidative stress response, and polyamine biosynthesis. These pathways were consistently enriched across CRC, helminthonly, and HIV-helminth co-infected groups and are associated with promoting tumor initiation, immune evasion, and disease progression. and progression. Stool-based methylation assays detected vimentin methylation in 90% of CRC cases and at high frequencies in infected groups (HIV: 92.9%, helminth: 93.3%, HIV-helminth co-infected: 77.9%) compared to 10% in uninfected controls, indicating early epigenetic reprogramming before clinical disease onset. Conclusion: By integrating immune, virome, metabolic, and epigenetic datasets, this thesis identifies convergent molecular signatures linking HIV-helminth co-infection to CRC. These findings advance mechanistic understanding of infection-driven oncogenesis and highlight the potential for non-invasive, multi-marker screening to guide precision cancer prevention in high burden African settings. This work establishes a new framework for cancer risk assessment in populations where infectious and oncologic burdens collide.