Proteomics study reveals that the dysregulation of focal adhesion and ribosome contribute to early pregnancy loss.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26947931", "kind": "science-record", "revision": 6, "content_hash": "sha256:b629530d2884cc630e5e977d471655e7514e1daa0c0db5517ae1ca0e3ed2acfd", "created_at": "2026-11-01T15:40:16Z", "updated_at": "2026-11-01T21:20:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomics study reveals that the dysregulation of focal adhesion and ribosome contribute to early pregnancy loss.", "doi": "10.1002/prca.201500136", "pmid": "26947931", "authors": ["Lingli Xin", "Benhong Xu", "Li Ma", "Qingxiang Hou", "Mei Ye", "Shu Meng", "Xiaoping Ding", "Wei Ge"], "journal": "Proteomics. Clinical applications", "year": 2016, "abstract": "PURPOSE: Early pregnancy loss (EPL) affects 50-70% pregnant women in first trimester. The precise molecular mechanisms underlying EPL are far from being fully understood. Therefore, we aim to identify the molecular signaling pathways relating to EPL.\nEXPERIMENTAL DESIGN: We performed proteomics and bioinformatics analysis of the placental villi in women who have undergone EPL and in normal pregnant women. The proteomics data were validated by Western blot analysis.\nRESULTS: We identified a total of 5952 proteins in placental villi, of which 588 proteins were differentially expressed in the EPL women. Bioinformatics analysis revealed that these differentially expressed proteins participated in a variety of signaling pathways, including the focal adhesion pathway and ribosome pathway. Moreover, results of the Western blot confirmed that Desmin, Lamin A/C, MMP-9, and histone H4 were upregulated in EPL and the Lamin C/ Lamin A ratio decreased obviously in EPL. These proteins could be associated with the pathophysiology of EPL. The data have been deposited to the ProteomeXchange with identifier PXD002391.\nCONCLUSION AND CLINICAL RELEVANCE: Our study demonstrated that the focal adhesion pathway and ribosome pathway are involved in EPL, and these findings might contribute to unveil the pathophysiology of EPL.", "claims": [{"id": "claim-data-access", "statement": "The MS proteomics data have been deposited to the ProteomeXchange Consortium 15 via PRIDE partner repository with the data identifier PXD002391.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26947931", "locator": "sections[9] \"Data analysis\" paragraph 2", "quote": "The MS proteomics data have been deposited to the ProteomeXchange Consortium 15 via PRIDE partner repository with the data identifier PXD002391."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using TMT-labeled quantitative proteomics with pathway enrichment analysis, the study found that the focal adhesion and ribosome pathways are involved in early pregnancy loss; the source data are publicly available through ProteomeXchange/PRIDE under accession PXD002391.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26947931", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Our study demonstrated that the focal adhesion pathway and ribosome pathway are involved in EPL, and these findings might contribute to unveil the pathophysiology of EPL."}, {"asset": "source:pmid:26947931", "locator": "sections[2] \"Introduction\" paragraph 6", "quote": "To comprehensively study the molecular signaling pathways related to EPL, we used TMT labeling‐based proteomics analysis to identify differentially expressed proteins between placental villi from EPL and normal pregnant women."}, {"asset": "source:pmid:26947931", "locator": "sections[9] \"Data analysis\" paragraph 2", "quote": "The thresholds for downregulation and upregulation were set at 0.8 and 1.2, respectively."}, {"asset": "source:pmid:26947931", "locator": "sections[9] \"Data analysis\" paragraph 2", "quote": "The WebGestalt online toolkit was also used to conduct enrichment analysis based on Wikipathways and KEGG analysis databases. The significance level was set at 0.0001."}, {"asset": "source:pmid:26947931", "locator": "sections[9] \"Data analysis\" paragraph 2", "quote": "The MS proteomics data have been deposited to the ProteomeXchange Consortium 15 via PRIDE partner repository with the data identifier PXD002391."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using TMT-labeled quantitative proteomics with pathway enrichment analysis, the study found that the focal adhesion and ribosome pathways are involved in early pregnancy loss; the source data are publicly available through ProteomeXchange/PRIDE under accession PXD002391.", "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:26947931"], "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. 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the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5084743", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD002391", "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=PXD002391", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD002391", "version": null, "note": "The MS proteomics data have been deposited to the ProteomeXchange Consortium 15 via PRIDE partner repository with the data identifier PXD002391.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The MS proteomics data have been deposited to the ProteomeXchange Consortium 15 via PRIDE partner repository with the data identifier PXD002391.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Proteomics Study of Molecular Mechanisms Involved in Early Pregnancy Loss", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:26947931:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7129adbaafbd2431b4a60e30a51048f31a983a754795583dff2f055915f85a4a", "bytes": 576, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#prca1742-tbl-0001", "version": null, "note": "Comparison of subject characteristics between the EPL group and normal group", "structure": {"pmcid": "PMC5084743", "section_index": 11, "section_title": "Subjects characteristics", "row_count": 7, "column_count": 4}, "table": {"label": "Table 1", "caption": "Comparison of subject characteristics between the EPL group and normal group", "rows": [["Subject characteristics", "Group", "Mean ± SD (n = 5)", "p‐Value"], ["Age (years)", "EPL", "30.6 ± 2.015", "0.54"], ["", "Control", "29.0 ± 1.517", ""], ["Pregnancy duration (days)", "EPL", "47.0 ± 6.301", "0.57"], ["", "Control", "42.8 ± 3.338", ""], ["Number of previous pregnancies", "EPL", "1.8 ± 0.374", "0.69"], ["", "Control", "2.0 ± 0.316", ""]], "row_count": 7, "column_count": 4, "numeric_cells": 10, "header_rows": 1, "locator": "section[11]/table-wrap[1]#prca1742-tbl-0001"}}, {"id": "asset:table:pmid:26947931:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a01f01e0f71b21bacf49907247bcedd05b2cff8ffc1c3f764bd3b663945a4110", "bytes": 2843, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#prca1742-tbl-0002", "version": null, "note": "Pathways in which differentially expressed proteins are involved, based on Wikipathway database", "structure": {"pmcid": "PMC5084743", "section_index": 14, "section_title": "Pathways involving the differentially expressed proteins", "row_count": 15, "column_count": 4}, "table": {"label": "Table 2", "caption": "Pathways in which differentially expressed proteins are involved, based on Wikipathway database", "rows": [["Pathway name", "Gene no.", "Entrez Gene", "Statistics"], ["Glycolysis and gluconeogenesis", "13", "6515 2597 2806 5230 3939 4190 2805 2821 5315 2023 5223 7167 3945", "C = 50; O = 13; E = 0.66; R = 19.71; rawp = 7.28 × 10−14; adjp = 7.50 × 10−12"], ["Epithelium TarBase", "23", "10105 5236 5270 3915 3035 4677 5725 10061 10971 4691 51809 5315 4144 10797 488 83858 23603 822 396 5878 1021 143888 4907", "C = 340; O = 23; E = 4.49; R = 5.13 rawp = 2.37 × 10−10; adjp = 1.22 × 10−8"], ["Lymphocyte TarBase", "28", "10105 10484 5236 5270 3915 3035 4677 5725 26973 10061 10971 4691 51809 5315 4144 11137 10797 488 83858 23603 822 396 6902 10642 5878 1021 143888 4907", "C = 533; O = 28; E = 7.03; R = 3.98 rawp = 8.98 × 10−10; adjp = 3.08 × 10−8"], ["Focal adhesion", "16", "2335 3915 208 3684 7148 3908 284217 3371 3689 7448 2321 3912 5062 1282 3694 3911", "C = 185; O = 16; E = 2.44; R = 6.56 rawp = 4.07 × 10−9; adjp = 1.05 × 10−7"], ["Statin pathway", "7", "6646 341 336 348 6713 5360 335", "C = 30; O = 7; E = 0.40; R = 17.69 rawp = 1.05 × 10−7; adjp = 2.16 × 10−6"], ["Leukocyte TarBase", "13", "10105 5270 26973 10971 5315 10797 488 23603 822 396 6902 5878 1021", "C = 160; O = 13; E = 2.11; R = 6.16 rawp = 2.40 × 10−7; adjp = 3.61 × 10−6"], ["Vitamin A and carotenoid metabolism", "8", "1382 948 5950 54884 8854 220 216 5947", "C = 49; O = 8; E = 0.65; R = 12.37; rawp = 2.45 × 10−7; adjp = 3.61 × 10−6"], ["Muscle cell TarBase", "21", "10105 10484 5236 3915 26973 10971 4691 51809 5315 11137 10797 488 83858 23603 822 396 6902 10642 1021 143888 4907", "C = 424; O = 21; E = 5.59; R = 3.75 rawp = 3.03 × 10−7; adjp = 3.90 × 10−6"], ["mRNA processing", "11", "3178 3182 5725 3183 22826 10236 27316 3184 3191 4904 3192", "C = 132; O = 11; E = 1.74; R = 6.32 rawp = 1.57 × 10−6; adjp = 1.80 × 10−5"], ["Cytoplasmic ribosomal proteins", "9", "6202 6154 6230 6204 4736 3921 6147 6201 6223", "C = 88; O = 9; E = 1.16; R = 7.75 rawp = 2.58 × 10−6; adjp = 2.66 × 10−5"], ["Complement and coagulation cascades", "7", "718 2 336 5265 5340 2244 717", "C = 51; O = 7; E = 0.67; R = 10.40 rawp = 4.70 × 10−6; adjp = 4.03 × 10−5"], ["Translation factors", "7", "1984 1975 7458 5610 1938 10209 26986", "C = 51; 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The proteomics data were validated by Western blot analysis. RESULTS: We identified a total of", "d ribosome pathway. Moreover, results of the Western blot confirmed that Desmin, Lamin A/C, MMP-9, and", "in −80°C until further proteomics analysis. Western blot analysis of the differentially expressed pro", "results of the proteomics data, we performed Western blot analysis of four relevant proteins in four E"], "order_basis": "paper_text_order:517", "id": "assay:1"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["pathway enrichment"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}