Sulochan Malla ¹ Annie G Bryant ² Rojashree Jayakuma ² Benjamin Woost ² Nina Wolf ² Andrew Li ² Sudeshna Das ¹ Susanne J. Van Veluw ¹ Rachel Bennett ^1*

• ¹ Massachusetts General Hospital, Harvard Medical School, Boston, United States
• ² Department of Neurology, Massachusetts General Hospital, Boston, United States

White matter hyperintensities (WMHs) are commonly detected on T2-weighted magnetic resonance imaging (MRI) scans, occurring in both typical aging and Alzheimer’s disease (AD). Despite their frequent appearance and their association with cognitive decline in AD, the molecular factors contributing to WMHs remain unclear. In this study, we investigated the transcriptomic profiles of two commonly affected brain regions with coincident AD pathology—frontal subcortical white matter (frontal-WM) and occipital subcortical white matter (occipital-WM)—and compared with age-matched cognitively intact controls. Through RNA-sequencing in frontal- and occipital-WM bulk tissues, we identified an upregulation of genes associated with brain vasculature function in AD white matter. To further elucidate vasculature-specific transcriptomic features, we performed RNA-seq analysis on blood vessels isolated from these white matter regions, which revealed an upregulation of genes related to protein folding pathways. Finally, comparing gene expression profiles between AD individuals with high- versus low-WMH burden showed an increased expression of pathways associated with immune function. Taken together, our study characterizes the diverse molecular profiles of white matter changes in AD and provides mechanistic insights into the processes underlying AD-related WMHs.