Investigating potential plasma nephrotoxicity biomarkers associated with first-line antiretroviral therapy regimens in people living with HIV in South Africa

Abstract

Introduction: South Africa contributes to 20% of the global HIV burden and hosts the largest national antiretroviral therapy program worldwide. Antiretroviral drugs (ARVs) used for HIV treatment can cause nephrotoxicity, which can progress into acute kidney injury (AKI) in patients. With early detection, this side-effect is reversible. However, current serum creatinine tests are unreliable for early detection in the South African population. Therefore, identifying potential protein biomarkers in plasma using mass spectrometry-based proteomics, can help with early detection of ARV-associated AKI in people living with HIV (PLHIV) in South Africa. Plasma is a favourable source of novel biomarkers as it is easily accessible, with minimal invasiveness, and is present throughout the body, serving as an indicator of a patient’s health state. Aim: This study aims to identify and quantify differentially abundant plasma proteins that can distinguish PLHIV with and without AKI in the South African population. Methodology: One hundred and thirty-five plasma samples (53 AKI; 82 non-AKI) were compared with an in-house sample preparation protocol, using magnetic microspheres for automated on-bead sample clean-up and protein digestion. The peptides were analysed with an Evosep One LC system coupled to a Sciex TripleTOF® 5600 mass spectrometer, using a SWATH-data acquisition method. Data were processed using SpectronautTM 17. An unpaired t-test was used to determine differentially abundant proteins identified between the AKI and non-AKI groups. Differentially abundant proteins with a fold-change ≥ 1.68, at an FDR of 1% were considered candidate markers. Enrichr was used to identify enriched gene ontology (GO) biological processes (BP), molecular functions (MF), cellular compartments (CC), and enriched pathways associated with the candidate markers (ranked by p-value ≤ 0.05). Results and discussion: Thirty-four candidate protein markers were identified. Three candidate markers showed increased abundance, while 31 candidate markers showed decreased abundance in the AKI group compared to the non-AKI group. The enrichment analysis revealed that the candidate markers participated in enriched biological processes, functions, and pathways of immune response, programmed cell death, cholesterol/lipid metabolism, and regulation of cell survival, repair, and regeneration. Conclusion: Candidate markers participate in enriched biological processes that correspond to known pathophysiological and cellular mechanisms contributing to AKI, suggesting that the candidate marker identified can be further verified for distinguishing the AKI group from the non-AKI group and validated as biomarkers for AKI.