TMT-labeling Proteomics of Papillary Thyroid Carcinoma Reveal Invasive Biomarkers.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32922552", "kind": "science-record", "revision": 7, "content_hash": "sha256:4a74db3e5d2c22732d8063c77633dc492051af99e8ec10dbb7621fd74148f015", "created_at": "2026-11-01T15:41:10Z", "updated_at": "2026-11-01T21:23:47Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "TMT-labeling Proteomics of Papillary Thyroid Carcinoma Reveal Invasive Biomarkers.", "doi": "10.7150/jca.47290", "pmid": "32922552", "authors": ["Jiaqi Dai", "Xiaqing Yu", "Yali Han", "Li Chai", "Yina Liao", "Peng Zhong", "Ruting Xie", "Xuechen Sun", "Qingqing Huang", "Jian Wang", "Zhiqiang Yin", "Yun Zhang", "Zhongwei Lv", "Chengyou Jia"], "journal": "Journal of Cancer", "year": 2020, "abstract": "Background and Aim: Invasion and metastasis are critical events in papillary thyroid carcinoma (PTC) progression. Protein markers specific to this process may avoid over-treatment and urgently needed. Methods: TMT-labeled mass spectrometry-based proteomics were carried out on PTC and invasive phenotype (iPTC) (3 pairs per group) and cross validate differentially expressed proteins (DEPs) (FC>1.5 and <0.67 and p<0.05) with GEO and TCGA datasets and the correlation genes of DEPs were also analyzed. Results: We identified and quantified 4607 proteins identical to PTC and iPTC groups. Among which 12 DEPs in PTC and 179 DEPs in iPTCs were found. Cross-validation with GSE60542 and TCGA database revealed 10 DEPs that all significant correlated with metastasis and staging. Upregulated SLC27A6 showed negative correlation with 6 out of 9 downregulated DEPs including HGD, CA4, COL23A1, SLC26A7, FHL1 and TPO. Conclusion: The panel of 7 genes (SLC27A6 and 6 downregulated DEPs) could have ideal prediction value to improve our understanding of invasiveness of PTC.", "claims": [{"id": "claim-method", "statement": "DEPs in pairwise comparisons were identified by two-sided t-test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32922552", "locator": "sections[10] \"Statistical analysis\" paragraph 2", "quote": "DEPs in pairwise comparisons were identified by two-sided t-test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "To validate whether the DEPs were consistent at mRNA level and genomic level, we also analyzed GEO datasets using the GPL570 platform which included 11 PTC samples from N0 (no lymph node metastasis) and 13 from N+ (with lymph node metastasis) patients (GEO dataset: GSE60542) .", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32922552", "locator": "sections[7] \"Validation of DEPs in iPTC by GSE and TCGA sources\" paragraph 2", "quote": "To validate whether the DEPs were consistent at mRNA level and genomic level, we also analyzed GEO datasets using the GPL570 platform which included 11 PTC samples from N0 (no lymph node metastasis) and 13 from N+ (with lymph node metastasis) patients (GEO dataset: GSE60542) ."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:32922552"], "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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"taxon": "Homo sapiens", "title": "Revisiting the transcriptional analysis of primary tumors and associated nodal metastases with enhanced biological and statistical controls: application to thyroid cancer", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE60542 not downloaded", "asset:data:geo:GSE60542 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-2", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], 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Methods: TMT-labeled mass spectrometry-based proteomics were carried out on PTC and", "istical analysis The statistical analysis of LC-MS/MS data was performed by R software 3.4.3. We u"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["is set at 1.5-fold change and p < 0.05. 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