Cell-Cell Communication Alterations via Intercellular Signaling Pathways in Substantia Nigra of Parkinson's Disease.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35283752", "kind": "science-record", "revision": 3, "content_hash": "sha256:6934549a9e4c7f9e9c02db26bfc26cc221d7742e610219c517b637eefbe4f9d8", "created_at": "2026-11-01T18:14:04Z", "updated_at": "2026-11-01T21:27:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Cell-Cell Communication Alterations via Intercellular Signaling Pathways in Substantia Nigra of Parkinson's Disease.", "doi": "10.3389/fnagi.2022.828457", "pmid": "35283752", "authors": ["Maoxin Huang", "Liang Xu", "Jin Liu", "Pei Huang", "Yuyan Tan", "Shengdi Chen"], "journal": "Frontiers in aging neuroscience", "year": 2022, "abstract": "Parkinson's disease (PD) is a neurodegenerative movement disorder characterized with dopaminergic neuron (DaN) loss within the substantia nigra (SN). Despite bulk studies focusing on intracellular mechanisms of PD inside DaNs, few studies have explored the pathogeneses outside DaNs, or between DaNs and other cells. Here, we set out to probe the implication of intercellular communication involving DaNs in the pathogeneses of PD at a systemic level with bioinformatics methods. We harvested three online published single-cell/single-nucleus transcriptomic sequencing (sc/snRNA-seq) datasets of human SN (GSE126838, GSE140231, and GSE157783) from the Gene Expression Omnibus (GEO) database, and integrated them with one of the latest integration algorithms called Harmony. We then applied CellChat, the latest cell-cell communication analytic algorithm, to our integrated dataset. We first found that the overall communication quantity was decreased while the overall communication strength was enhanced in PD sample compared with control sample. We then focused on the intercellular communication where DaNs are involved, and found that the communications between DaNs and other cell types via certain signaling pathways were selectively altered in PD, including some growth factors, neurotrophic factors, chemokines, etc. pathways. Our bioinformatics analysis showed that the alteration in intercellular communications involving DaNs might be a previously underestimated aspect of PD pathogeneses with novel translational potential.", "claims": [{"id": "claim-method", "statement": "Euclidean distance between any pair of the shared signaling pathways was computed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35283752", "locator": "sections[20] \"Analysis of Cell–Cell Communications That Involve Dopaminergic Neuron Mediated by Intercellular Signaling Pathways\" paragraph 2", "quote": "Euclidean distance between any pair of the shared signaling pathways was computed."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126836, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE140231, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157783.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35283752", "locator": "sections[21] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126836, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE140231, and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157783."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:35283752"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE126836"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE126836"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35283752", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fnagi.2022.828457", "sha256": "sha256:4a56d2a5c258456d2c3c482494368e664620c4839d6c238011808f0851ec46d2", "bytes": 107483, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fnagi.2022.828457", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8914319", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE126836", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126836", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE126836", "version": null, "note": "Publicly available datasets were analyzed in this study. 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