The cancer stem cells characteristics analysis of LGR5 + cells that influence lung cancer risk by using single cell RNA-seq analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40341189", "kind": "science-record", "revision": 4, "content_hash": "sha256:f1c269debf8603b75139dfde730b96fee73c9c5f8f5235ff5b288f5b774ecaad", "created_at": "2026-11-01T20:30:30Z", "updated_at": "2026-11-01T22:56:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The cancer stem cells characteristics analysis of LGR5 + cells that influence lung cancer risk by using single cell RNA-seq analysis.", "doi": "10.1038/s41598-025-00585-3", "pmid": "40341189", "authors": ["Ge Wen", "Shaoqing Niu", "Shiqi Mei", "Senming Wang"], "journal": "Scientific reports", "year": 2025, "abstract": "Lung adenocarcinoma (LUAD) is the most popular lung cancer type with highly mortality. We performed a single cell RNA-seq analysis to explore characteristic of cancer stem cells in LUAD. We downloaded the single cell RNA-seq data (GSE149655) from the GEO database, the scRNA-seq analysis was performed by using the \"Seurat\" and \"harmony\" R package. The FindMarkers function and \"ClusterProlifer\" package was used for differentially expressed genes (DEGs) and function enrichment analysis. The protein-protein interaction and transcriptional regulatory network were performed by STRING and ChIPBase database. Immunohistochemistry tests to be used to observe differences in the expression of specific genes in LUAD and paracancerous tissue samples. BEAS-2B and A549 cells was used for vitro assay and the qRT-PCR, western blotting, wound healing, trans-well assays, EdU tests, and flow cytometry were performed. A total of 9 cell clusters were obtained after scRNA-seq analysis, in which the cancer stem cells had higher proportion in LUAD samples. Subsequently, function enrichment analysis revealed that the amino sugar and nucleotide sugar metabolism and DNA replication pathways were activated in cancer stem cells (CSCs), which were further sub-divided into 3 subtypes, the LGR5 + stem cell is a major contributor to cancer progression, its hub genes, such as HLA-DPB1, CD74, CTSH and HLA-DRB5 mediated the unique transcriptional state. In addition, the marker genes of three CSCs were also overexpressed in LUAD cells and the CXCL3 played an important role in mediating cell proliferation, apoptosis, migration and invasion of tumor. We performed a scRNA-seq analysis and identified the LGR5 + stem cell as a major contributor in LUAD progression, our findings are expected to provide new insights into the pathogenesis of LUAD.", "claims": [{"id": "claim-method", "statement": "We used the FindAllMarkers function to calculate the differentially expressed genes (DEGs) of each cell clusters among various samples by using the Wilcoxon-Mann-Whitney tests26.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40341189", "locator": "sections[5] \"Gene set enrichment analysis (GSEA)\" paragraph 2", "quote": "We used the FindAllMarkers function to calculate the differentially expressed genes (DEGs) of each cell clusters among various samples by using the Wilcoxon-Mann-Whitney tests26."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and/or analyzed during the current study are available in the [GSE149655] repository, [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149655].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40341189", "locator": "sections[31] \"notes\" paragraph 1", "quote": "The datasets generated and/or analyzed during the current study are available in the [GSE149655] repository, [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149655]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We performed a scRNA-seq analysis and identified the LGR5 + stem cell as a major contributor in LUAD progression, our findings are expected to provide new insights into the pathogenesis of LUAD.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40341189", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We performed a scRNA-seq analysis and identified the LGR5 + stem cell as a major contributor in LUAD progression, our findings are expected to provide new insights into the pathogenesis of LUAD."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "We performed a scRNA-seq analysis and identified the LGR5 + stem cell as a major contributor in LUAD progression, our findings are expected to provide new insights into the pathogenesis of LUAD.", "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:40341189"], "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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We performed a single cell RNA-seq analysis to explore characteristic of cancer", "d drug sensitivity in patients with LUAD The RNA-seq expression data in transcripts per million (", "cells in LUAD. We downloaded the single cell RNA-seq data (GSE149655) from the GEO database, the"], "order_basis": "paper_text_order:71", "id": "assay:1"}, {"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["data (GSE149655) from the GEO database, the scRNA-seq analysis was performed by using the \"Seurat\"", "ion of lung cancer samples We downloaded the single-cell RNA sequencing (scRNA-seq) data of GSE149655 from GEO datab", "e downloaded the single-cell RNA sequencing (scRNA-seq) data of GSE149655 from GEO database (https:", "total of 9 cell clusters were obtained after scRNA-seq analysis, in which the cancer stem cells had"], "order_basis": "paper_text_order:359", "id": "assay:2"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["e performed by STRING and ChIPBase database. Immunohistochemistry tests to be used to observe differences in t"], "order_basis": "paper_text_order:697", "id": "assay:3"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["nd paracancerous tissue samples. BEAS-2B and A549 cells was used for vitro assay and the qRT-P", "ne BEAS-2B and lung adenocarcinoma cell line A549 were obtained from the American Type Culture", "ican Type Culture Collection (ATCC, USA) and cultured in Dulbecco’s Modified Eagle’s Medium (Gibco) s"], "order_basis": "paper_text_order:848", "id": "assay:4"}, {"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": ["ls was used for vitro assay and the qRT-PCR, western blotting, wound healing, trans-well assays, EdU tests"], "order_basis": "paper_text_order:901", "id": "assay:5"}, {"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": ["d healing, trans-well assays, EdU tests, and flow cytometry were performed. A total of 9 cell clusters w"], "order_basis": "paper_text_order:968", "id": "assay:6"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["ortant role in mediating cell proliferation, apoptosis, migration and invasion of tumor. We perform"], "order_basis": "paper_text_order:1683", "id": "assay:7"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["tissue sample collection, cell culture, and qPCR test Tissues from human specimens of LUAD an", "l Reagent (Invitrogen), and the The ReverTra Qpcr RT Master Mix kit (TOYOBO) was used for the", "to its instructions. Then, we performed the qPCR for target genes detection by using the SYBR", "n (Table 1). Table 1The specific primers for qPCR.NameForward (5’-3’)Reverse (5’-3’)ARSECTTTGA"], "order_basis": "paper_text_order:3416", "id": "assay:8"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We used the FindAllMarkers function to calculate the differentially expressed genes (DEGs) of each cell clusters among various samples by using the Wilcoxon-Mann-Whitney tests26."], "order_basis": "consumes_earlier_output", "id": "assay:9"}]}