MME and PTPRC: key renal biomarkers in lupus nephritis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39301055", "kind": "science-record", "revision": 1, "content_hash": "sha256:9ce59604826450aafe4d0e80ed03e0c4c84a1d5df210de0bb79cfccbc496184a", "created_at": "2026-11-01T20:29:28Z", "updated_at": "2026-11-01T20:29:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "MME and PTPRC: key renal biomarkers in lupus nephritis.", "doi": "10.7717/peerj.18070", "pmid": "39301055", "authors": ["Min Wen", "Marady Hun", "Mingyi Zhao", "Qingnan He"], "journal": "PeerJ", "year": 2024, "abstract": "Background: Lupus nephritis (LN) is an autoimmune-related kidney disease with a poor prognosis, however the potential pathogenic mechanism remains unclear and there is a lack of precise biomarkers. Therefore, a thorough screening and identification of renal markers in LN are immensely beneficial to the research on its pathogenic mechanisms and treatment strategies.\nMethods: We utilized bioinformatics to analyze the differentially expressed genes (DEGs) at the transcriptome level of three clusters: total renal, glomeruli, and renal tubulointerstitium in the GEO database to discover potential renal biomarkers of LN. We utilized NephroSeq datasets and measured mRNA and protein levels in the kidneys of MRL/lpr mice to confirm the expression of key DEGs.\nResults: Seven significantly differential genes (EGR1, MME, PTPRC, RORC, MX1, ZBTB16, FKBP5) were revealed from the transcriptome database of GSE200306, which were mostly enriched in the pathway of the hematopoietic cell lineage and T cell differentiation respectively by KEGG and GO analysis. The seven hot differential genes were verified to have consistent change trends using three datasets from NephroSeq database. The receiver operating characteristic (ROC) curve indicated that five DEGs (PTPRC, MX1, EGR1, MME and RORC) exhibited a higher diagnostic ROC value in both the glomerulus and tubulointerstitium group. Validation of core genes using MRL/lpr mice showed that MME and PTPRC exhibit significantly differential mRNA and protein expression patterns in mouse kidneys like the datasets.\nConclusions: This study identified seven key renal biomarkers through bioinformatics analysis using the GEO and NephroSeq databases. It was identified that MME and PTPRC may have a high predictive value as renal biomarkers in the pathogenesis of LN, as confirmed by animal validation.", "claims": [{"id": "claim-data-access", "statement": "The raw measurements are available in the Supplemental File. The data is available at Genbank (GSE200306) and NephroSeq (Tables S2 and S3).ERCB dataset summaries can be found at: ERCB Lupus Glom Dataset Summary. Available at https://nephroseq.org/ resource/ui/component/dataset.html[balance] (requires registration). ERCB Lupus TubInt Dataset Summary. Available at https://nephroseq.org/ resource/ui/component/dataset.html[balance] (requires registration).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39301055", "locator": "sections[20] \"Additional Information and Declarations\" paragraph 5", "quote": "The raw measurements are available in the Supplemental File. The data is available at Genbank (GSE200306) and NephroSeq (Tables S2 and S3).ERCB dataset summaries can be found at: ERCB Lupus Glom Dataset Summary. Available at https://nephroseq.org/ resource/ui/component/dataset.html[balance] (requires registration). ERCB Lupus TubInt Dataset Summary. Available at https://nephroseq.org/ resource/ui/component/dataset.html[balance] (requires registration)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Seven significantly differential genes (EGR1, MME, PTPRC, RORC, MX1, ZBTB16, FKBP5) were revealed from the transcriptome database of GSE200306, which were mostly enriched in the pathway of the hematopoietic cell lineage and T cell differentiation respectively by KEGG and GO analysis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39301055", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Seven significantly differential genes (EGR1, MME, PTPRC, RORC, MX1, ZBTB16, FKBP5) were revealed from the transcriptome database of GSE200306, which were mostly enriched in the pathway of the hematopoietic cell lineage and T cell differentiation respectively by KEGG and GO analysis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Seven significantly differential genes (EGR1, MME, PTPRC, RORC, MX1, ZBTB16, FKBP5) were revealed from the transcriptome database of GSE200306, which were mostly enriched in the pathway of the hematopoietic cell lineage and T cell differentiation respectively by KEGG and GO analysis.", "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:39301055"], "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:GSE200306"], "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:GSE200306"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39301055", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.18070", "sha256": "sha256:9c5ca6fbfb6624fdb36a304dd51c5c22efc7560d7f4c3aebed53a33eec5f2b72", "bytes": 29574, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.18070", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11412223", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE200306", "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=GSE200306", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE200306", "version": null, "note": "The raw measurements are available in the Supplemental File. The data is available at Genbank (GSE200306) and NephroSeq (Tables S2 and S3).ERCB dataset summaries can be found at: ERCB Lupus Glom Dataset Summary. Available at https://nephroseq.org/ resource/ui/component/dataset.html[balance] (requires registration). ERCB Lupus TubInt Dataset Summary. Available at https://nephroseq.org/ resource/ui/component/dataset.html[balance] (requires registration).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw measurements are available in the Supplemental File. The data is available at Genbank (GSE200306) and NephroSeq (Tables S2 and S3).ERCB dataset summaries can be found at: ERCB Lupus Glom Dataset Summary. Available at https://nephroseq.org/ resource/ui/component/dataset.html[balance] (requires registration). ERCB Lupus TubInt Dataset Summary. 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Conclusions: This", "(n = 3) from the SPF Biotechnology Co., Ltd. Mice were fed standard laboratory chow and supplied dr"], "order_basis": "paper_text_order:1537", "id": "assay:1"}]}