Molecular signatures of neuro-HIV and methamphetamine co-morbidity revealed by Raman spectroscopy in postmortem human brain tissue

HIV infection and comorbid methamphetamine (METH) use contribute significantly to neurocognitive impairment, yet the molecular brain alterations remain poorly defined. We employed confocal Raman micro-spectroscopy on formalin-fixed, paraffin-embedded cortical sections from Control (HIV-METH-), HIV + METH-, and HIV + METH + individuals, analyzing spectra (950–1800 cm⁻¹) via SVD and classification modeling. Key Raman bands were biochemically assigned and correlated with gene expression data from QPCR. Distinct spectral profiles emerged across cohorts. HIV + and HIV + METH + brains showed reduced intensities at 1040–1140 cm⁻¹, indicating loss of carbohydrates, phospholipids, and nucleic acid backbone integrity. Elevated spectral signals were indicative of lipid buildup, DNA damage, and increased CH₂ saturation, with pronounced effects observed in tissues affected by both HIV and METH exposure. METH use exacerbated HIV-associated disruptions, including thiol depletion and nucleic acid fragmentation. SVD clustering and ROC analysis yielded high classification accuracy (F1 > 0.7). We provide evidence of convergence of transcriptomic and spectroscopic data which highlights a coordinated disruption of metabolic, inflammatory and structural pathways in HIV⁺METH⁺ subjects. The observed lipid remodeling, carbohydrate depletion, and nucleic acid damage suggest Raman spectral signatures may serve as diagnostic markers for HIV and METH-associated neuropathology. These findings demonstrate Raman spectroscopy's sensitivity in detecting HIV and METH induced biochemical brain changes.