Identification and functional analysis of lncRNAs and mRNAs between tumorigenesis and metastasis in CRC.

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The aim of this study was to identify novel lncRNAs and their functions in CRC progression. Through microarray analysis of paired normal colorectal mucosa (NM), primary tumor (PT), and metastatic lymph node (MLN) tissues, lncRNA and mRNA expression patterns were identified. Further bioinformatic analyses were performed to compare the biological functions of lncRNAs between tumorigenesis and metastasis of CRC, which was further verified by TCGA-COAD and GSE82236. The expression of lncRNA MIR29B2CHG93 in paired CRC tissues was detected in a cohort of CRC patients. The effects of lncRNA MIR29B2CHG93 on proliferation, migration, and invasion were determined by in vitro experiments. We found that tumorigenesis-associated lncRNAs predominantly participated in the regulation of the EMT/P53/PI3K-Akt/KRAS signaling pathway as well as the processes related to cell cycle and cell mitosis, while metastasis-associated lncRNAs mainly regulated blood vessel morphogenesis and immune-related biological processes. Compared to the TCGA and GSE datasets, seven tumorigenesis-associated lncRNAs and eight metastasis-associated lncRNAs were identified. LncRNA MIR29B2CHG93 knockdown remarkably suppressed tumor growth and metastasis in vitro, which acted as a tumor promoter in CRC. The lncRNA MIR29B2CHG93 was significantly upregulated in CRC tissues and was indicator of unfavorable clinical outcome in CRC. These results revealed novel lncRNAs that provide new insights for an in-depth understanding of CRC progression. In particular, this study identified a novel lncRNA MIR29B2CHG93 in CRC progression, which might be a potential biomarker for diagnosis, prognosis and metastasis-prediction in CRC.", "claims": [{"id": "claim-method", "statement": "Significant differences in transcript abundance were determined using the paired t-test method.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34954693", "locator": "sections[5] \"Microarray analyses\" paragraph 2", "quote": "Significant differences in transcript abundance were determined using the paired t-test method."}], "state": "complete"}, {"id": "claim-data-access", "statement": "TCGA-COAD RNA-seq and miRNA data were downloaded from the Genomic Data Commons (GDC) website (https://portal.gdc.cancer.gov/projects/TCGA-COAD).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34954693", "locator": "sections[13] \"Bioinformatics Analysis of TCGA-COAD and GSE82236\" paragraph 2", "quote": "TCGA-COAD RNA-seq and miRNA data were downloaded from the Genomic Data Commons (GDC) website (https://portal.gdc.cancer.gov/projects/TCGA-COAD)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Compared to the TCGA and GSE datasets, seven tumorigenesis-associated lncRNAs and eight metastasis-associated lncRNAs were identified.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34954693", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Compared to the TCGA and GSE datasets, seven tumorigenesis-associated lncRNAs and eight metastasis-associated lncRNAs were identified."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Compared to the TCGA and GSE datasets, seven tumorigenesis-associated lncRNAs and eight metastasis-associated lncRNAs were identified.", "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:34954693"], "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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Through microarray analysis of paired normal colorectal mucosa", "fferential expression analysis of lncRNAs by microarray assay The microarray data showed that a tota", "analysis of lncRNAs by microarray assay The microarray data showed that a total of 461 lncRNA trans", "pared with those in PTs. (G) Verification of microarray data using qRT-PCR (H) Correlation analysis"], "order_basis": "paper_text_order:290", "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": ["lncRNAs were identified. LncRNA MIR29B2CHG93 knockdown remarkably suppressed tumor growth and metas", "ere collected for analysis. Cell culture and transfection The human colorectal cancer cell lines SW480", "105 cells per well, grown for 24 h, and then transfected with shRNA at low multiplicity of infection", "were harvested for analysis three days post-transfection. 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