Proteomic profiling of kidney biopsies in nephrotic syndrome.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39991116", "kind": "science-record", "revision": 2, "content_hash": "sha256:940c2c4839ab3148092406736b4df723cc778c7e7a31fa28a1902c2c15356287", "created_at": "2026-11-01T20:30:13Z", "updated_at": "2026-11-01T21:34:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic profiling of kidney biopsies in nephrotic syndrome.", "doi": "10.12688/wellcomeopenres.22633.1", "pmid": "39991116", "authors": ["Emily Williams", "Maryline Fresquet", "Anna S Li", "Craig Lawless", "David Knight", "Elizabeth Colby", "Judy Watson", "Gavin I Welsh", "Moin A Saleem", "Rachel Lennon"], "journal": "Wellcome open research", "year": 2024, "abstract": "Background: Minimal change disease (MCD) and focal segmental glomerulosclerosis (FSGS) are patterns of kidney injury observed in the filtering units of the kidney known as glomeruli. These histological patterns are seen in kidney biopsies from individuals with idiopathic nephrotic syndrome (iNS), which occurs in both children and adults. However, there is some indication that MCD and FSGS are within the same phenotypic spectrum.\nMethods: From the NURTuRE cohort of individuals with NS, we performed laser microdissection and mass spectrometry analysis of kidney biopsy samples to identify proteomic patterns of disease. 56 individuals with iNS segregated by histological pattern (37 MCD and 19 FSGS) across three age groups: early childhood (0-6 years), late childhood (6-18 years) and adult (>18 years).\nResults: We found no distinct clustering of proteomic profiles between MCD and FSGS, but identified global differences in glomerular cell and extracellular matrix composition related to both histological pattern and age. The proteomic data are available via ProteomeXchange with identifier PXD053362.\nConclusions: The lack of distinct clustering between MCD and FSGS in our study suggests shared biological processes between these injury patterns of iNS, supporting the hypothesis that they are part of the same disease spectrum. The global differences observed in glomerular cell and extracellular matrix composition suggest involvement of diverse biogeological processes as different patterns of iNS manifests in different age groups. This study also demonstrates the feasibility of pooling bioresources, central processing of heterogeneous tissue samples, and developing laser-microdissection and proteomic analysis methodology.", "claims": [{"id": "claim-method", "statement": "Whilst we observed some variation in the detection of proteins across the samples ( Figure 2A), a principal component analysis (PCA) based on quantitative MS data demonstrated no clear separation between samples grouped according to histological pattern or age.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39991116", "locator": "sections[10] \"Identification of glomerular proteins from patient biopsies\" paragraph 2", "quote": "Whilst we observed some variation in the detection of proteins across the samples ( Figure 2A), a principal component analysis (PCA) based on quantitative MS data demonstrated no clear separation between samples grouped according to histological pattern or age."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data availability\nProteomeXchange PRIDE database: Proteomic profiling of kidney biopsies in nephrotic syndrome. Accession number PXD053362;\nhttps://www.ebi.ac.uk/pride/archive/projects/PXD053362 21 .", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39991116", "locator": "sections[18] \"Data availability\" paragraphs 1-3", "quote": "Data availability\nProteomeXchange PRIDE database: Proteomic profiling of kidney biopsies in nephrotic syndrome. Accession number PXD053362;\nhttps://www.ebi.ac.uk/pride/archive/projects/PXD053362 21 ."}], "state": "complete"}, {"id": "claim-target-result", "statement": "There was no distinct clustering of glomerular proteomic profiles between MCD and FSGS, while global differences in glomerular cell and extracellular matrix composition were associated with histological pattern and age.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39991116", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We found no distinct clustering of proteomic profiles between MCD and FSGS, but identified global differences in glomerular cell and extracellular matrix composition related to both histological pattern and age."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "There was no distinct clustering of glomerular proteomic profiles between MCD and FSGS, while global differences in glomerular cell and extracellular matrix composition were associated with histological pattern and age.", "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:39991116"], "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:PXD053362"], "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:PXD053362"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39991116", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12688/wellcomeopenres.22633.1", "sha256": "sha256:7d17ceaf5fb308b46f9fbc0c88c8941ae46ceebc9992006b515ebf21c784f17c", "bytes": 30102, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.12688/wellcomeopenres.22633.1", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11845903", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD053362", "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=PXD053362", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD053362", "version": null, "note": "Data availability\nProteomeXchange PRIDE database: Proteomic profiling of kidney biopsies in nephrotic syndrome. 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