Historically, Alzheimer's disease (AD) and Parkinson's disease (PD) have been investigated as two distinct disorders of the brain. However, a few similarities in neuropathology and clinical symptoms have been documented over the years. Traditional single-gene centric studies, such as differential gene expression analyses, have struggled to unravel the molecular basis for the observed pathological links between AD and PD. To address this, we tailor a latent factor framework to analyze synchronous gene co-expression at sub-cell-type resolution. Utilizing large, single-nucleus transcriptomics datasets in AD (70,634 nuclei) and PD (340,902 nuclei) from postmortem human brains, we systematically extract and juxtapose disease-critical molecular signatures in the brain. Our transcriptomic analysis reveals shared molecular programs between AD and PD that systematically localize to specific glial and neuronal cell types. In neurons, convergent gene groups in AD and PD relate to cytoskeletal dynamics and mitochondrial stress mechanisms. Similarly, overlapping gene groups in microglia modules implicate T cell activation mechanisms and synapse pruning pathways. In parallel, AD- and PD-associated genes in astrocytes are involved in heavy metal processing; oligodendrocytes highlight convergent dysregulation in myelin synthesis. In addition, our analysis reveals APOE, an AD GWAS gene, has disease predictive roles in PD-associated gene modules. Conversely, SNCA, a PD GWAS gene, emerges within AD associated gene modules. Our multi-module sub-cell-type approach offers unique insights into the molecular basis of shared neuropathology in AD and PD.