PCNA-associated factor KIAA0101 transcriptionally induced by ELK1 controls cell proliferation and apoptosis in nasopharyngeal carcinoma: an integrated bioinformatics and experimental study.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32275642", "kind": "science-record", "revision": 7, "content_hash": "sha256:357624cd40c4213a8073e7f0b0b5ddf9b7eecdb79f12c822c83a7cd03418c99e", "created_at": "2026-11-01T15:40:59Z", "updated_at": "2026-11-01T21:23:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "PCNA-associated factor KIAA0101 transcriptionally induced by ELK1 controls cell proliferation and apoptosis in nasopharyngeal carcinoma: an integrated bioinformatics and experimental study.", "doi": "10.18632/aging.102991", "pmid": "32275642", "authors": ["Hu Zhao", "Miaosheng Chen", "Jie Wang", "Gang Cao", "Wei Chen", "Jinke Xu"], "journal": "Aging", "year": 2020, "abstract": "KIAA0101, previously identified as PCNA-associated factor, is overexpressed among almost majority of human cancers and has emerged as an important regulator of cancer progression; however, its function in human nasopharyngeal carcinoma (NPC) remain unknown. Integrated bioinformatics approaches were employed to determine the KIAA0101 expressions in the NPC samples. Lentiviral vectors carrying KIAA0101 shRNA were constructed and stable transfected cells were validated by qRT-PCR and western blot. Cellular functions were then evaluated by MTT, colony formation, Brdu staining, and flow cytometry. Mechanistic studies were systematically investigated by UCSC Genome Browser, GEO, UALCAN, QIAGEN, PROMO and JASPAR, ChIP, and the cBioPortal, et al. The results showed that KIAA0101 ranked top overexpressed gene lists in GSE6631 dataset. KIAA0101 was highly expressed in NPC tissues and cell lines. Furthermore, knockdown of KIAA0101 significantly inhibited cell proliferation and DNA replication, promoted apoptosis and cell cycle arrest in vitro. Meanwhile, the mechanistic study revealed that MAP kinase phosphorylation-dependent activation of ELK1 may enhance neighbor gene expressions of KIAA0101 and TRIP4 by binding both promotor regions in the NPC cells. Taken together, our findings indicate that overexpression of KIAA0101 activated by MAP kinase phosphorylation-dependent activation of ELK1 may play an important role in NPC progression.", "claims": [{"id": "claim-method", "statement": "Student’s t-test was used for statistical comparison and differences among the groups due to lentivirus mediated KIAA0101 knockdown were considered significant at p value < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32275642", "locator": "sections[20] \"Statistical analysis\" paragraph 2", "quote": "Student’s t-test was used for statistical comparison and differences among the groups due to lentivirus mediated KIAA0101 knockdown were considered significant at p value < 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "In order to discover the critical genes involved in NPC progression, GDS3610 dataset containing 25 undifferentiated NPC samples and 3 normal controls were downloaded and analyzed by GeoDiver [24].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32275642", "locator": "sections[3] \"Top ranked and highly expressed KIAA0101 in NPC samples\" paragraph 2", "quote": "In order to discover the critical genes involved in NPC progression, GDS3610 dataset containing 25 undifferentiated NPC samples and 3 normal controls were downloaded and analyzed by GeoDiver [24]."}], "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:32275642"], "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:GSE6631"], "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:GSE6631"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32275642", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/aging.102991", "sha256": "sha256:cfbd84f20b7c7ae53ef08565ee90c81d4cab4d1d3d01af1dd4c9274e734ea5df", "bytes": 44247, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/aging.102991", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7185143", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE6631", "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=GSE6631", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE6631", "version": null, "note": "In order to discover the critical genes involved in NPC progression, GDS3610 dataset containing 25 undifferentiated NPC samples and 3 normal controls were downloaded and analyzed by GeoDiver [24].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "In order to discover the critical genes involved in NPC progression, GDS3610 dataset containing 25 undifferentiated NPC samples and 3 normal controls were downloaded and analyzed by GeoDiver [24].", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM153813", "GSM153814", "GSM153815", "GSM153816", "GSM153817", "GSM153818", "GSM153819", "GSM153820", "GSM153821", "GSM153822", "GSM153823", "GSM153824", "GSM153825", "GSM153826", "GSM153827", "GSM153828", "GSM153829", "GSM153830", "GSM153831", "GSM153832", "GSM153833", "GSM153834", "GSM153835", "GSM153836", "GSM153837", "GSM153838", "GSM153839", "GSM153840", "GSM153841", "GSM153842", "GSM153843", "GSM153844", "GSM153845", "GSM153846", "GSM153847", "GSM153848", "GSM153849", "GSM153850", "GSM153851", "GSM153852", "GSM153853", "GSM153854", "GSM153855", "GSM153856"], "sample_count": 44, "group_sizes": null, "group_sizes_basis": null, "platform": "8300", "taxon": "Homo sapiens", "title": "Expression data from head and neck squamous cell carcinoma", "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:GSE6631 not downloaded", "asset:data:geo:GSE6631 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": null, "specific": null, "label": "Paired t-test (Student’s t-test)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Student’s t-test was used for statistical comparison and differences among the groups due to lentivirus mediated KIAA0101 knockdown were considered significant at p value < 0.05."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE6631"], "resolved_accessions": ["GSE6631"], "statements": ["In order to discover the critical genes involved in NPC progression, GDS3610 dataset containing 25 undifferentiated NPC samples and 3 normal controls were downloaded and analyzed by GeoDiver [24]."], "basis": "The paper names GSE6631 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:32275642", "data:geo:GSE6631"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE6631"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:19:23Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 36392, "completion_tokens": 2325, "cached_tokens": 784}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:32275642", "type": "paper", "label": "pmid:32275642"}, {"id": "source:pmid:32275642", "type": "manuscript", "label": "PMID 32275642 full text"}, {"id": "data:geo:GSE6631", "type": "dataset", "label": "GEO GSE6631"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32275642", "type": "paper", "label": "pmid:32275642"}, {"id": "source:pmid:32275642", "type": "manuscript", "label": "PMID 32275642 full text"}, {"id": "data:geo:GSE6631", "type": "dataset", "label": "GEO GSE6631"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32275642", "type": "extraction", "used": ["source:pmid:32275642"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE6631", "type": "accession_resolution", "used": ["data:geo:GSE6631"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:32275642", "parent_hash": "sha256:240c9d0eeb7b3c3379eb7edb631f0a3c9869a7a3e9a44979c8d6e866dcfee8a0", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE6631 licence not read", "asset:data:geo:GSE6631 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["uced by ELK1 controls cell proliferation and apoptosis in nasopharyngeal carcinoma: an integrated b", "proliferation and DNA replication, promoted apoptosis and cell cycle arrest in vitro. Meanwhile, t", "t. Cellular functions were then evaluated by MTT, colony formation, Brdu staining, and flow c"], "order_basis": "paper_text_order:53", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["g KIAA0101 shRNA were constructed and stable transfected cells were validated by qRT-PCR and western", "in NPC tissues and cell lines. Furthermore, knockdown of KIAA0101 significantly inhibited cell pro", "amples. Lentiviral vectors carrying KIAA0101 shRNA were constructed and stable transfected cell", "ntiviral vector PSCSI-GFP shRNA for KIAA0101 knockdown (shKIAA0101-1 and shKIAA0101-2, more informa"], "order_basis": "paper_text_order:549", "id": "assay:2"}, {"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": ["nsfected cells were validated by qRT-PCR and western blot. Cellular functions were then evaluated by M"], "order_basis": "paper_text_order:631", "id": "assay:3"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["by MTT, colony formation, Brdu staining, and flow cytometry. Mechanistic studies were systematically inv"], "order_basis": "paper_text_order:729", "id": "assay:4"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["After normalization to get rid of biases in microarray data, results of heatmap and volcano plot sh", "mentary Figure 1, gray columns, ***p<0.001). Microarray data further revealed that KIAA0101 was over"], "order_basis": "paper_text_order:1892", "id": "assay:5"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["niversity (Changsha, China). Both cells were cultured in RPMI 1640 medium supplemented with 10% fetal"], "order_basis": "paper_text_order:4272", "id": "assay:6"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Kaplan-Meier"], "order_basis": "consumes_earlier_output", "id": "assay:7"}]}