parkinson-lamda-multiregion-r3

Goralski, T.M., Henderson, M.X. et al. (Nat Commun 15:2642, 2024; DOI 10.1038/s41467-024-47027-8; PMC10966039) defined the "Lewy- Associated Molecular Dysfunction from Aggregates" (LAMDA) spatial-transcriptomic signature in PD/PDD/DLB cingulate cortex — 8 donors, NanoString GeoMx DSP whole-transcriptome + CosMx single-cell-resolved spatial profiling — and replicated the program in α-synuclein PFF-injected mouse cortex. They showed that pSyn-positive excitatory cortical neurons converge on a conserved dysfunction program (synaptic loss, mitochondrial dysfunction, proteostasis collapse, vesicle-trafficking failure).

Goralski explicitly framed the result as cortically defined. It has never been tested whether LAMDA is detectable, in the same cell types or in different cell types, in non-cortical Lewy-pathology regions of Parkinson's brain — i.e., across the Braak progression from peripheral (DMNX), through midbrain (SNpc, GPi) to cortical (M1, V1) regions in the same donors.

The Fullard / N M et al. multi-region snRNA-seq atlas (Sci Data 11:1274, 2024; CELLxGENE collection d5d0df8f-4eee-49d8-a221- a288f50a1590) is the ideal test substrate: 100 donors (75 PD + 25 control), 5 regions in 71 of those donors (DMNX, GPi, SNpc, M1, V1), 2.1M nuclei total. Cingulate cortex is NOT part of the Fullard atlas — meaning the Goralski signature can be tested on fully independent tissue (positive-control cross-tissue spec test) and on regions with different Braak progression stages.

Hypotheses (pre-registered):

H1 (primary — LAMDA generalises to non-cortical regions): Score the published Goralski LAMDA gene module (extracted from Goralski Supplementary Data 1 — top-200 upregulated genes in cortical pSyn+ neurons; Zenodo 10.5281/zenodo.10729767) as a per-cell module score across all 5 regions × all ~10 major cell types of the Fullard atlas. Per-(region × cell-type) PD-vs-control mean score difference is tested with linear mixed-effects model (donor as random intercept; sex + age fixed). After BH correction over the 50 tests, at least 3 NON-CORTICAL (region × cell-type) combinations show positive differential LAMDA enrichment at FDR < 0.05, with effect-size > 0.25 SD (Cohen's d).

H2 (secondary — Braak-stage tracking): The LAMDA-enrichment gradient across regions in PD follows Braak progression: DMNX (Braak 1) > SNpc (Braak 3) > GPi (Braak 4) > M1 (Braak 5/6) > V1 (Braak 6), with monotonic ranking test (Spearman ρ on region-ordered mean LAMDA scores) significant at p < 0.05. (NB: this direction is the opposite of cortical-Lewy gradients; we test it explicitly because Goralski's LAMDA is derived from cortex, where it is presumed late. The null hypothesis is no monotonic gradient.)

H3 (secondary — excitatory-neuron specificity replicates): Within each region's neuronal compartment, the LAMDA module score is significantly higher in excitatory neurons than inhibitory neurons (in cortical regions M1, V1), AND in glutamatergic projection neurons compared to local interneurons in subcortical regions (DMNX, SNpc, GPi). Wilcoxon test, BH-corrected per region.

H4 (secondary — gene-program decomposition): Goralski LAMDA is a coarse 200-gene composite. We decompose into 5 functional sub-programs (synaptic / mitochondrial / proteostasis / vesicle / immune) per the Goralski-published functional clustering. We test whether the sub-programs dissociate across regions: do all 5 move together in cortex, but only some sub-programs activate in DMNX or SNpc? This dissociation pattern is the biological discovery target.

H5 (secondary — direction-specific validation in cingulate held-out donor subset): Goralski has a subset of donors with both cingulate (their derivation tissue) and orbitofrontal data not used in the original LAMDA derivation. We hold out the orbitofrontal subset from Goralski's deposited CosMx data as a positive control: LAMDA should re-replicate at p < 0.001 in that tissue, providing a same-modality / same-cohort sanity bar.

A non-generalisation of LAMDA outside cortex would itself be a major scientific finding — it would mean the program is cortex-restricted, contradicting common assumptions that Lewy-pathology gene programs are tissue-agnostic. OmiCairn must report any null finding with the same emphasis as a positive one.

The research question comes from the topic's current research brief. All attempts at a topic share it; earlier attempts may have started from an earlier wording.