Campaign run · Parkinson's disease

parkinson-cellchat-immune-axis-r2

PDStopped before planningAttempt 2 of 3 at this topic

Do LIANA-py (CellChat-equivalent consensus) inferred ligand-receptor (L-R) communications between Hong 2025 peripheral-blood CD8+ T cells (GEO GSE223138) and Fullard brain microglia mirror — at the L-R pair level — the brain-internal CD8+T → microglia communications inferred by Ma 2025 (PMC12322057), thus identifying a "blood-as-foreshadow-of-brain" set of peripheral biomarker ligands?

Status

How far it got: Stopped before planning
Stopped before writing any hypotheses: a dry-run test, a launch superseded by an immediate relaunch, a usage limit or a process failure.
Why it stopped: This run stopped before the planning stage for an operational reason, not a scientific one. Runs in this group are dry-run tests, launches superseded by an immediate relaunch, runs that hit a usage limit, or one process failure. The released data do not say which of these applies to an individual run. No run in the campaign stopped before planning because data were unavailable.
Recorded status: Stopped without a final status. The run stopped without recording a final status.
Census class: Partial. Census class is a label from an earlier, process-level census of the campaign. It does not map one-to-one onto the stages above. How the classes compare.

Research question

The sentence under the run id is quoted from this brief.

Full research brief given to the run

Hong 2025 (npj Parkinson's 11) reported 28 immune-cell-specific PD risk genes from OneK1K + IPDGC + GSE223138 multi-omic integration. Ma 2025 (Nat Commun 16) characterised brain-side CD8+ T-cell × microglia communications via SN scRNA + scTCR-seq. The two cell-type-communication signatures have not been compared at the L-R pair level. If peripheral L-Rs echo brain L-Rs, the peripheral signal could be used as a foreshadow blood biomarker; if they diverge, peripheral-blood-as-PD-biomarker biology is decoupled from the brain-immune axis. Either outcome is informative with strong biomarker implications.

Hypotheses (pre-registered):

H1 (primary — L-R pair concordance): ≥ 5 ligand-receptor pairs are inferred as PD-up-regulated in BOTH the peripheral CD8+T → blood-monocyte direction (Hong 2025) AND the brain CD8+T → microglia direction (Ma 2025), with concordant sign of dysregulation. Permutation null p < 0.01 (10,000 random L-R subsets).

H2 (secondary — Hong-MR-gene enrichment): The shared L-R pairs are enriched (q < 0.05 hypergeometric) for ligands or receptors whose genes appear on the Hong 2025 MR-implicated immune-gene list (FDFT1, CTSB, ARSA, HLA-DQA1, and 24 others reported in Hong 2025 Table 2).

H3 (secondary — peripheral-foreshadow correlation): A "peripheral CD8+T signature score" computed from Hong 2025 PBMC data using the 28 MR-implicated immune genes rank-correlates (Spearman ρ > 0.3, nominal p < 0.05) with the v1 parkinson-tcell-foothold per-donor brain T-cell-module score at the disease-stage level (early vs. late PD).

H4 (secondary — direction-specific dropout): Inferring CD8+T → monocyte (PBMC) and microglia → CD8+T (brain) — the reverse-direction pairs — should NOT show the same H1 enrichment (control: PD signals are in the CD8+T → myeloid direction, not the reverse).

H5 (secondary — method-consensus robustness): Repeat the L-R inference with three methods (CellPhoneDB, NATMI, scTalk) and confirm the H1 shared-pair count is within ±2 of the LIANA consensus result. (LIANA-py provides this consensus natively.)

Null payoff. If peripheral and brain L-R signatures diverge (H1: 0-3 shared pairs), peripheral-blood-as-PD-biomarker biology is decoupled from the brain-immune axis — informative, with strong implications for blood-test development.

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.