Mitochondrial dysfunction, including impaired respiration and increased reactive oxygen species (ROS), is an early feature of Alzheimer’s disease (AD) models. Electron transport chain supercomplexes (mSCs) regulate respiratory efficiency and ROS generation, yet genetic determinants of mSC organization in AD models remain underappreciated. Cox7a2l is known to promote CIII₂/CIV association and CIV incorporation into mSCs. We examined the commonly used mixed-background B6;129S 3xTg-AD mice and B6129SF2/J controls aged 12–15 months, as well as specific rat AD models for changes in mSC organization using blue and clear native-PAGE and DIA-MS. BN and CN-PAGE revealed a marked shift toward larger mSC assemblies in 3xTg-AD mice and a distinct ~650 kDa assembly of complex III absent from controls. Gene sequencing showed that 3xTg-AD mice retained the full-length Cox7a2l variant similar to 129S strains, whereas controls predominantly carried a shortened C57BL/6-associated variant. DIA-MS identified greatly increased Cox7a2l in differential mSC bands. Similar changes were found in 3xTg-AD heart tissue. In contrast, AD rat models and their controls, all expressing full-length Cox7a2l, did not exhibit comparable mSC differences. These findings suggest Cox7a2l genotype as a determinant of mSC organization and highlight the need to account for genetic background when interpreting mSC-dependent mitochondrial phenotypes in mixed-background 3xTg-AD studies. This distinction is essential for accurately separating strain-dependent effects from AD-associated mitochondrial changes.

Cerebral amyloid angiopathy (CAA) is a prevalent cerebral small vessel disease (CSVD) and prominent cause of vascular contributions to cognitive impairments and dementia (VCID). CAA is characterized by progressive accumulation of fibrillar amyloid β in cerebral vessel walls, leading to vascular wall degeneration, thrombotic occlusions, microbleeds, and perivascular inflammation causing cognitive deficits. Underlying mechanisms of CAA progression are poorly understood, and there exist no validated diagnostic biomarkers or therapeutic targets for CAA. Here, we performed proteomic mass spectrometry analysis of whole brain tissue and cerebral microvessel enriched fractions from the rTg-DI rat, a validated and well-characterized preclinical rat model of CAA, to identify potential targets and diagnostic markers related to vasculopathy progression in CAA. There were 92 increased and 104 decreased proteins identified in the rTg-DI whole brain samples, while 29 proteins were identified as increased in the enriched cerebral microvessel fractions. We identified several significant differentially expressed proteins in both sample types with commonly elevated proteins including HTRA1, APOE, APOD, CLU, MDK, and LAP3. This study also confirmed the differential expression of several proteins previously reported in isolated brain regions of rTg-DI rats, including ANXA3, APOD, APOE, CLU, CST3, CTSS, CTSD, CTSZ, GFAP, GSTA3, HTRA1, and ITGB2, with APOE, CLU, HTRA1, and GPC1 all reported in human CAA cases. We thus provide a “high-confidence” list of potential marker candidates from proteomic analysis in the rTg-DI rat model of capillary CAA type-1.