alzheimer-rorb-ec-vulnerability-r1

Direction d1 from the Alzheimer's-mechanism IDEATE run.

What cell-intrinsic transcriptional programs — specifically excitability regulation, calcium handling, proteostasis capacity, and mitochondrial gene expression — distinguish selectively vulnerable RORB+ entorhinal cortex (EC) layer II excitatory neurons from resilient neurons in the same region, and can these molecular features predict inter-individual variation in tau accumulation rate across Braak stages using existing OPEN snRNA-seq atlases?

EC layer II neurons are the first to accumulate phospho-tau and die, defining Braak stage I–II. Leng et al. (2021, Nat Neurosci) showed RORB expression marks these vulnerable neurons with ~50% abundance loss at early stages. WHY RORB+ neurons are vulnerable — high intrinsic excitability, low mitochondrial capacity, limited proteostasis reserve, or a combination — remains unresolved. This OmiCairn run re-analyses open EC snRNA-seq atlases to test candidate cell-intrinsic vulnerability mechanisms by contrasting RORB+ vs. RORB- excitatory neurons within region and across Braak stage.

Hypotheses (pre-registered, lifted from d1):

H1 (primary — calcium-handling / excitability signature): RORB+ EC layer II excitatory neurons express significantly higher levels of voltage-gated calcium-channel subunits (CACNA1C, CACNA1D) and lower levels of calcium-buffering genes (CALB1, PVALB) relative to resilient RORB- EC excitatory neurons, consistent with a calcium-/excitability-driven basis for their selective tau vulnerability. Decision rule: per-donor pseudobulk DE within EC excitatory neurons, RORB+ vs RORB-; report log2FC + Benjamini–Hochberg FDR + 95% bootstrap CI for each gene. H1 passes if CACNA1C and/or CACNA1D are up (log2FC > 0, FDR < 0.05) AND CALB1 and/or PVALB are down (log2FC < 0, FDR < 0.05) in the primary atlas, with the directional sign reproduced in the Braak-staged secondary atlas.

H2 (secondary — integrated stress response / SASP precursor trajectory): Across Braak stages I–IV in EC snRNA-seq data, RORB+ neurons show a progressive shift toward an integrated stress response (ATF4-high; phospho-eIF2α surrogate genes — e.g. ATF4, DDIT3/CHOP, PPP1R15A, ATF3, TRIB3 — upregulated) and a senescence-associated secretory (SASP) precursor state, detectable before frank neuronal loss. Decision rule: ISR/SASP module score per RORB+ cell regressed on Braak stage (ordinal); report slope + p-value + 95% CI. H2 passes if the ISR module score increases monotonically with Braak stage in RORB+ neurons (positive slope, p < 0.05) and the increase precedes the inflection point of RORB+ abundance loss. Report the RORB+ abundance-vs-Braak curve alongside.

A negative or partial result is fully informative. If the calcium / excitability contrast does not separate RORB+ from RORB- neurons, or if the ISR shift is absent, that finding must be reported as the headline rather than re-tuning clustering or gene panels until H1/H2 pass. Report which decomposition (excitability vs proteostasis vs mitochondrial) carries the signal.

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