Protein Isoaspartate Repair in Amyotrophic Lateral Sclerosis: An Integrative Bioinformatic Analysis of the PCMT Gene Family

Abstract Protein homeostasis is a fundamental determinant of neuronal survival, and its disruption contributes to the pathogenesis of amyotrophic lateral sclerosis (ALS). Protein L-isoaspartate O-methyltransferases (PCMTs) are evolutionarily conserved proteins involved in the recognition and processing of damaged proteins through the repair of isoaspartyl residues and protein quality-control pathways; however, their potential involvement in ALS remains largely unexplored. Here, we performed a comprehensive in silico characterization of the PCMT family (PCMT1, PCMTD1, and PCMTD2) by integrating structural, transcriptomic, single-cell, genetic, and protein modeling analyses. Domain analysis demonstrated that all three proteins share a conserved PCMT domain, while predicted S-adenosylmethionine-binding motifs were identified in PCMT1 and PCMTD2 but not PCMTD1, indicating evolutionary conservation with functional divergence. Expression profiling revealed that PCMT family genes are expressed in ALS-relevant tissues and broadly distributed across neuronal, glial, vascular, and immune cell populations in both healthy and ALS-associated brain single-cell data sets. Analysis of multiple independent ALS transcriptomic cohorts identified consistent upregulation of PCMT family members, with PCMTD1 exhibiting the most reproducible disease-associated expression changes across nervous system tissues and peripheral blood. Gene set correlation analyses further revealed distinct relationships between PCMT expression and neuronal pathways, with PCMT1 showing positive associations with axonal transport and synaptic signaling, whereas PCMTD1 and PCMTD2 displayed largely inverse correlation patterns. Rare missense variants identified in ALS patients were predicted to impair protein function and decrease protein stability, while structural modeling suggested that several substitutions may disrupt conserved residues and the local protein architecture. Collectively, these findings identify the PCMT family as previously underexplored candidates associated with ALS and provide a comprehensive framework for future mechanistic studies investigating their roles in neuronal protein homeostasis and neurodegeneration.