parkinson-da-vulnerability-r4

Kamath, Macosko et al. (Nat Neurosci 25:588, 2022; DOI 10.1038/s41593-022-01061-1) reported that a single AGTR1+ ventral-tier substantia-nigra pars compacta (SNpc) dopaminergic (DA) neuronal subtype is selectively lost in Parkinson's disease (PD), and that residual AGTR1+ DA cells upregulate TP53 and NR2F2 target programs. The finding was derived from 10 PD/LBD + 8 control donors (387,483 nuclei; 22,048 DA-restricted nuclei) and spatially anchored by Slide-seqV2 to the ventral tier of SNpc. It is the most-cited cellular finding in PD single-cell biology, but has never been formally replicated against three subsequent independent SNpc snRNA-seq atlases under a single re-analysis pipeline.

This OmiCairn run formally tests whether the AGTR1+ vulnerable DA subtype is recoverable, and whether it shows the same PD-specific depletion + TP53/NR2F2 upregulation, in:

• Wang et al. (Sci Adv 10:eadi8287, 2024; GEO GSE184950) — 23 idiopathic PD + 9 control / 315,867 SNpc nuclei.

• Adams L., Song M.K. et al. (Nat Aging 4:364, 2024; GEO GSE193688 + dbGaP phs002819.v1.p1) — 9 young + 8 aged + 14 PD / 69,289 SN nuclei, 10x Multiome.

• Fullard / N M et al. (Sci Data 11:1274, 2024; CELLxGENE collection d5d0df8f-4eee-49d8-a221-a288f50a1590) — 100 donors (75 PD + 25 ctrl), 2,096,155 nuclei across 5 regions; this proposal uses the SNpc slab only.

• Martirosyan et al. (Mol Neurodegen 19:7, 2024; GEO GSE243639) — 15 PD + 14 ctrl / ~84,000 SNpc nuclei; held out for blind external validation in H3.

Hypotheses (pre-registered):

H1 (primary — vulnerable-subtype depletion replicates): The Kamath AGTR1+ DA subtype (defined by the published Kamath top-30 marker panel — AGTR1, SLC6A3, TH, KCNJ6, etc.; full list lifted from GSE178265 supplementary table) recovers as a contiguous cluster in each of Wang (A3), Adams (A4), and Fullard SNpc (A8) atlases at our chosen clustering resolution. The log-fold-change of (AGTR1+ DA cells / total DA cells) PD vs. matched-age control is negative (depletion) in all 3 replication atlases, with FDR < 0.05 (Benjamini–Hochberg). Effect-size requirement: the magnitude of depletion is within ±50% of the Kamath reference (≈3-fold loss → our log2FC ∈ [-2.6, -0.95]).

H2 (secondary — TP53 / NR2F2 program upregulation): Within retained AGTR1+ DA cells, the TP53 target module and NR2F2 target module (lifted directly from Hallmark TP53 signaling + the Kamath-cited NR2F2 ChIP-seq targets) show positive PD-vs-control fold-change at FDR < 0.05 in ≥ 2 of 3 replication atlases.

H3 (secondary — blind-replication out-of-cohort): A "consensus AGTR1+ marker panel" (intersection of the marker-gene sets across Kamath + Wang + Adams + Fullard SNpc, re-derived from our own DE analysis) scored as a per-donor pseudobulk signature stratifies the Martirosyan A5 PD vs. control donors with ROC AUC ≥ 0.75 (95% bootstrap CI excluding 0.5).

H4 (secondary — cluster-resolution sensitivity): We report the sensitivity of H1 to clustering resolution (Leiden / Louvain γ ∈ {0.3, 0.5, 0.8, 1.0, 1.5, 2.0}). H1's sign and FDR pass are stable across at least 4 of the 6 resolutions. (A finding that AGTR1+ depletion is observed only at γ ≈ Kamath's published resolution would itself be biologically informative and must be reported.)

H5 (secondary — spatial vs. proportional vs. expression decomposition): We decompose PD-vs-control DA loss into: (a) total nuclei recovered per donor (sequencing depth / dissection artifact) (b) DA-cluster fraction within total nuclei (c) AGTR1+ subcluster fraction within DA (d) per-cell AGTR1 expression within AGTR1+ DA and report each of (a)–(d) separately. Honest replication of Kamath requires the effect to be predominantly in (c), not in (a) or (b). A dominant (a) effect would indicate the original finding is partly a dissection or doublet artifact.

A negative or partial-replication result is fully informative. This OmiCairn run must report cluster-merging, marker-gene-loss, or resolution-instability findings as the headline rather than tune clustering until H1 passes.

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.