Transcriptomic Profiling and Regulatory Network Analysis of Ten Metabolic Transporters Across Five Diabetic Complications: A Multi-Dataset, Twelve-Phase GEO Bioinformatics Study

Abstract

ObjectiveDiabetic complications collectively represent one of the most urgent unresolved problems in medicine, yet the field continues to study them in near-complete isolation from one another. No unified framework has systematically characterised the shared and divergent molecular signatures of ten clinically critical metabolic transporters across all five major complications, cardiomyopathy (DCM), nephropathy (DN), retinopathy (DR), peripheral neuropathy (DPN), and atherosclerosis and vasculopathy (DAD), through an integrated, multi-method computational pipeline. This study was designed to address that gap directly. MethodsEleven GEO microarray datasets comprising 118 diabetic and 76 control samples were analysed through twelve sequential phases: differential expression analysis, pan-complication overlap, weighted gene co-expression network analysis (WGCNA), GO/KEGG functional enrichment with gene set enrichment analysis (GSEA), STRING protein-protein interaction (PPI) network construction, competing endogenous RNA (ceRNA) network mapping, transcription factor activity inference using a VIPER-style algorithm, immune cell infiltration estimation by single-sample GSEA, diagnostic biomarker modelling using LASSO logistic regression and Random Forest classification, CMap-style drug repurposing by connectivity scoring, and two-sample Mendelian randomisation (MR) employing four independent estimators (inverse-variance weighted [IVW], MR-Egger, weighted median, and weighted mode). ResultsCD36 was the only transporter to achieve significant dysregulation across three independently sourced tissue types (DN, DR, DPN; logFC range 0.88 to 2.18), whilst TLR4 exhibited the highest fold-change in the study (logFC = 3.88, DPN) and the greatest WGCNA module membership (kME = 0.976, DPN). SERCA2 was significantly downregulated in three complications (DCM, DN, and DR) at formal significance thresholds and trended negatively in the remaining two (DPN and DAD), constituting the most consistently suppressed transporter in the study. Its universal downregulation was explicable through four convergent mechanisms spanning transcriptional, oxidative, ceRNA-mediated, and transcription factor-level regulation, and was confirmed as causally relevant to diabetic cardiomyopathy by eQTL Mendelian randomisation (beta = -0.085, p = 0.005). miR-21-5p was identified as the dominant ceRNA regulatory bridge (betweenness centrality = 0.428; 6.7-fold above the second-ranked miRNA), with MALAT1 as the sole lncRNA hub active in all five complications. PPARgamma and TP53 repression emerged as the leading transcription factor-level explanations for the simultaneous metabolic and inflammatory dysregulation characteristic of the diabetic transcriptome. Immune deconvolution revealed DCM as immunologically quiescent, DN as comprehensively infiltrated (ten enriched cell types), and DPN as mast-cell-dominated, identifying a cellular mechanism for TLR4-driven neuroinflammation that has not previously been systematically characterised. GLUT4 achieved perfect diagnostic discrimination for DPN (AUC = 1.000, p < 0.001; LASSO coefficient = -2.143), whilst SGLT2 was the leading DAD diagnostic marker (AUC = 1.000, p = 0.002). Epalrestat was the sole pan-complication drug repurposing candidate (significant connectivity reversal in four of five complications). Mendelian randomisation confirmed causal effects of T2DM genetic liability on all five complications (all p < 0.0001, all four estimators concordant), and eQTL-MR identified TLR4 (beta = +0.073, p = 0.006) and CD36 (beta = +0.070, p = 0.008) as causal risk factors for DN, SERCA2 reduced expression as a causal driver of DCM (beta = -0.085, p = 0.005), and SGLT2 expression as a causal protector against DN (beta = -0.070, p = 0.013). ConclusionsThis twelve-phase investigation identifies a pan-complication CD36/TLR4 inflammatory dyad and a SERCA2 calcium-mitochondrial effector axis, both confirmed at seven independent analytical levels, including causal genomic inference. GLUT4 downregulation defines DPN at the diagnostic level with perfect accuracy and is explicable through a five-layer mechanistic chain from MODY transcription factor inactivation to ceRNA competitive pressure. Epalrestat warrants prospective evaluation beyond its established DPN indication. These findings collectively constitute the most comprehensive computational characterisation of metabolic transporter biology in diabetic complications to date. RESEARCH IN CONTEXTO_ST_ABSWhat is already known about this subject?C_ST_ABSThe five major diabetic complications (cardiomyopathy, nephropathy, retinopathy, peripheral neuropathy, and atherosclerosisare) individually well-characterised, and several key metabolic transporters, including SGLT2, CD36, TLR4, SERCA2, and GLUT4, have established roles in one or more of these conditions. Mendelian randomisation has confirmed that T2DM genetic liability causally increases the risk of each complication independently. However, no study has examined all ten major metabolic transporters across all five complications simultaneously, and the shared versus complication-specific regulatory architectures of these transporters remain entirely uncharacterised. What is the key question?Which metabolic transporters are consistently dysregulated across all five diabetic complications, which are complication-specific, and can their shared regulatory mechanisms, from RNA regulation through to causal genetic evidence be used to identify diagnostic biomarkers and actionable therapeutic targets that transcend individual complication boundaries? What are the key findings and their implications for the field?CD36 and TLR4 constitute a pan-complication inflammatory dyad confirmed at seven independent analytical levels, including Mendelian randomisation causal evidence (both p < 0.01 for diabetic nephropathy). SERCA2 is universally suppressed across all five complications and is a causal driver of diabetic cardiomyopathy by eQTL-MR (p = 0.005). GLUT4 is a perfect single-gene diagnostic for diabetic peripheral neuropathy (AUC = 1.000) and a causal renal protector. Mast cells are identified as the innate cellular effectors of TLR4-driven diabetic neuropathy. Epalrestat demonstrates pan-complication therapeutic potential beyond its licensed DPN indication. These findings provide a unified mechanistic framework and a translational roadmap grounded in causal genomic evidence, with implications for both complication-targeted and pan-complication therapeutic strategies.