Corticobasal syndrome (CBS) and progressive supranuclear palsy (PSP) represent two of the most clinically and pathologically heterogeneous neurodegenerative diseases, both characterized by accumulation of hyperphosphorylated tau protein. Despite distinct clinical presentations, these disorders frequently show overlapping neuropathological features, making definitive diagnosis challenging during life. Single-nucleus multi-omics approaches have emerged as powerful tools to dissect the molecular determinants underlying the divergent phenotypic manifestations of these conditions, revealing cell-type-specific transcriptomic, epigenetic, and proteomic signatures that explain why similar pathological substrates produce different clinical outcomes.
CBS typically presents with asymmetric cortical and basal ganglia dysfunction, manifesting as alien hand phenomena, apraxia, rigidity, and progressive loss of motor control. PSP, conversely, presents with symmetric vertical supranuclear gaze palsy, postural instability, pseudobulbar palsy, and cognitive decline. Neuropathologically, both conditions fall under the umbrella of four-repeat (4R) tauopathies, where aberrant tau phosphorylation leads to neurofibrillary tangles and neurodegeneration. However, the anatomical distribution of pathology, cellular vulnerability patterns, and molecular cascades triggering neurodegeneration diverge significantly between the two conditions.
The phenotypic heterogeneity has long puzzled neuroscientists. Post-mortem studies reveal that approximately 50% of clinically diagnosed CBS cases show PSP pathology at autopsy, while CBS pathology occurs in some PSP-diagnosed patients. This neuropathological-clinical disconnect indicates that identical pathological hallmarks—tau aggregates, neuroinflammation, and synaptic dysfunction—can manifest as distinct syndromes depending on the underlying molecular architecture of affected neural circuits.
Single-nucleus multi-omics represents an integrated approach combining single-nucleus RNA sequencing (snRNA-seq), single-nucleus Assay for Transposase-Accessible Chromatin sequencing (snATAC-seq), single-nucleus proteomics, and chromatin immunoprecipitation in single cells. This methodology enables simultaneous profiling of transcriptomes, epigenetic landscapes, and protein expression within individual nuclei, preserving cell-type identity and revealing cell-state-specific molecular alterations.
The experimental workflow typically involves: (1) tissue dissociation and nuclei isolation from postmortem brain samples representing CBS and PSP cases, alongside age-matched controls; (2) encapsulation of individual nuclei within microfluidic droplets coupled with oligonucleotide-barcoded beads; (3) parallel library preparation for RNA, ATAC, and protein capture; (4) sequencing and computational integration of modalities to create unified transcriptomic-epigenetic-proteomic cellular phenotypes; and (5) comparative analysis across disease states and cell types.
Recent multi-omics studies have identified several critical phenotype determinants distinguishing CBS from PSP:
Glial Cell Heterogeneity and Neuroinflammatory Signatures
Single-nucleus analysis reveals disease-specific microglial and astrocytic subpopulations. PSP cases demonstrate pronounced activation of complement-associated microglia expressing elevated C1q, C3, and CD11c, correlating with extensive synaptic pruning. CBS cases exhibit microglia enriched for interferon-responsive genes (IFIT1, ISG15, MX1) and type-I interferon signaling, suggesting distinct innate immune activation mechanisms. Astrocytes in PSP show upregulation of classical inflammatory markers (IL-6, TNF-α, CXCL10), while CBS astrocytes preferentially express neurotrophic factors and metabolic support genes (GDNF, NTRK2, SLC1A2), indicating protective phenotypes.
Cortical Versus Subcortical Neuronal Vulnerability
Deep single-nucleus profiling of layer-specific cortical neurons reveals that CBS-associated neuronal loss predominantly affects layer III and V pyramidal neurons with high expression of glutamatergic transmission genes and reduced expression of synaptic scaffold proteins (DLGAP2, HOMER1). These neurons show increased vulnerability to excitotoxic stress and deficits in calcium homeostasis. PSP cases preferentially lose GABAergic interneurons and exhibit downregulation of GABAergic signaling genes in remaining neurons, explaining the gaze palsy phenotype through specific brainstem midbrain nuclei involvement (substantia nigra pars reticulata, superior colliculus).
Tau Pathology Distribution and Cell-Type Vulnerability
Multi-omics integration identifies cell-type-specific transcriptomic changes associated with tau pathology burden. Oligodendrocytes in PSP express elevated stress response genes (HSPA5, ATF4, DDIT3) and reduced myelin genes (MBP, MOG, PLP1), consistent with myelin breakdown and white matter involvement. CBS oligodendrocytes maintain relatively preserved myelin gene expression despite tau pathology, reflecting the primarily gray matter involvement. Single-nucleus proteomics directly detects phosphorylated tau (pTau181, pTau217) levels stratified by cell type, revealing that excitatory neurons in CBS accumulate tau more readily than inhibitory neurons, whereas PSP shows more uniform distribution.
Epigenetic Remodeling and Chromatin Accessibility Changes
ATAC-seq analysis demonstrates disease-specific chromatin remodeling patterns. CBS cases show increased chromatin accessibility in loci controlling cortical development and synaptic plasticity genes (NEUROD1, CREB1 targets, activity-regulated genes), suggesting dysregulated cellular plasticity responses. PSP cases exhibit reduced accessibility in genes regulating oculomotor control and GABAergic transmission (PAX6 targets, GAD1/GAD2 regulatory regions), correlating with selective brainstem degeneration. Differential H3K27ac deposition patterns identify disease-specific enhancer activity, revealing distinct transcriptional regulatory networks governing phenotypic divergence.
The integrated multi-omics data suggest mechanistic models explaining phenotypic divergence:
Circuit-Level Selectivity: CBS pathology preferentially affects cortico-cortical and cortico-striatal glutamatergic circuits, particularly those mediating higher-order motor planning and sensorimotor integration. The transcriptomic profile of vulnerable neurons suggests heightened susceptibility to excitotoxic cascades triggered by tau-induced mitochondrial dysfunction. PSP pathology specifically targets GABAergic circuits coordinating vertical eye movements and postural reflexes through superior colliculus, pedunculopontine tegmentum, and subthalamic nucleus involvement.
Cell-Autonomous and Non-Autonomous Tau Toxicity: Multi-omics reveals that oligodendrocyte dysfunction represents a critical non-neuronal component in PSP but not CBS. Altered oligodendrocyte lipid metabolism and myelin remodeling genes in PSP suggest that tau-induced white matter pathology amplifies neurodegeneration through increased axonal vulnerability.
Innate Immune Targeting: The divergent microglial transcriptomes suggest that CBS and PSP activate distinct immune response pathways. Type-I interferon-dominated neuroinflammation in CBS may prime neurons for excitotoxic vulnerability, while complement-mediated synaptic pruning in PSP represents a more damaging immune response targeting synaptic architecture.
These findings provide biological rationale for clinical heterogeneity and have important diagnostic implications. Multi-omics signatures could enable development of cerebrospinal fluid (CSF) or blood biomarkers distinguishing CBS from PSP earlier in disease course. Cell-type-specific transcriptomic markers detectable through RNA biomarkers or proteomic platforms could supplement tau PET imaging, improving diagnostic accuracy before symptom divergence becomes clinically apparent.
Emerging research priorities include: (1) longitudinal multi-omics studies tracking molecular changes during disease progression; (2) spatial transcriptomics to preserve anatomical context while maintaining subcellular resolution; (3) functional validation of key determinants through induced pluripotent stem cell (iPSC)-derived neuronal models; (4) investigation of genetic variants influencing cell-type-specific vulnerability; and (5) development of cell-type-targeted therapeutic strategies addressing the distinct pathogenic mechanisms in each condition.