Identification of the prognostic biomarkers and their correlations with immune infiltration in colorectal cancer through bioinformatics analysis and in vitro experiments.

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The objective was to identify novel hub genes that were helpful for prognosis and targeted therapy in CRC. GSE23878, GSE24514, GSE41657, GSE81582 were filtered from the gene expression omnibus (GEO). Differentially expressed genes (DEGs) were identified through GEO2R, which were enriched in the GO term and KEGG pathway in DAVID. PPI network was constructed and analyzed using STRING and hub genes were screened out. The relationships between hub genes and prognoses in CRC were evaluated in GEPIA based on the cancer genome atlas (TCGA) and genotype-tissue expression (GTEx). The transcription factors and miRNA-mRNA interaction networks for hub genes were performed using miRnet and miRTarBase. The relationship between hub genes and tumor-infiltrating lymphocytes were analyzed in TIMER. The protein levels of hub genes were identified in HPA. The expression levels of hub gene in CRC and its effect on the biological effect of CRC cells were identified in vitro. As hub genes, the mRNA levels of BIRC5, CCNB1, KIF20A, NCAPG, and TPX2 were highly expressed in CRC and had excellent prognostic value. The BIRC5, CCNB1, KIF20A, NCAPG, and TPX2 were closely associated with transcription factors, miRNAs, tumor-infiltrating lymphocytes, suggesting their involvement in the regulation of CRC. BIRC5 highly expressed in CRC tissues and cells, and promoted the proliferation, migration, and invasion of CRC cells. BIRC5, CCNB1, KIF20A, NCAPG, and TPX2 are hub genes that serve as promising prognostic biomarkers in CRC. BIRC5 plays an important role in the development and progression of CRC.", "claims": [{"id": "claim-method", "statement": "The online tool-GEO2R (https://www.ncbi.nlm.nih.gov/gov/geo/geo2r) was used for screening the DEGs from the gene expression profiles (GSE23878, GSE24514, GSE41657, and GSE81582) between the CRC samples and normal samples, respectively. The adjusted P-value (adjust P) < 0.05 and |log2 Fold Change (log2 FC) |> 1 were applied to identify DEGs. The log-rank P < 0.05 and P (HR) < 0.05 were set as the threshold criteria. The t-test was performed on the relevant results (*P < 0.05).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37389063", "locator": "sections[4] \"Data processing\" paragraph 2", "quote": "The online tool-GEO2R (https://www.ncbi.nlm.nih.gov/gov/geo/geo2r) was used for screening the DEGs from the gene expression profiles (GSE23878, GSE24514, GSE41657, and GSE81582) between the CRC samples and normal samples, respectively."}, {"asset": "source:pmid:37389063", "locator": "sections[4] \"Data processing\" paragraph 2", "quote": "The adjusted P-value (adjust P) < 0.05 and |log2 Fold Change (log2 FC) |> 1 were applied to identify DEGs."}, {"asset": "source:pmid:37389063", "locator": "sections[7] \"Survival analysis and validation of hub genes\" paragraph 2", "quote": "The log-rank P < 0.05 and P (HR) < 0.05 were set as the threshold criteria."}, {"asset": "source:pmid:37389063", "locator": "sections[22] \"Survival analysis and validation of hub genes in CRC\" paragraph 2", "quote": "The t-test was performed on the relevant results (*P < 0.05)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The four gene expression profiles (GSE23878, GSE24514, GSE41657, and GSE81582) were acquired from the GEO (https://www.ncbi.nlm.nih.gov/geo). The GSE23878 included 35 CRC samples and 24 normal colorectal samples [10].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37389063", "locator": "sections[3] \"Data extraction\" paragraph 2", "quote": "The four gene expression profiles (GSE23878, GSE24514, GSE41657, and GSE81582) were acquired from the GEO (https://www.ncbi.nlm.nih.gov/geo)."}, {"asset": "source:pmid:37389063", "locator": "sections[3] \"Data extraction\" paragraph 2", "quote": "The GSE23878 included 35 CRC samples and 24 normal colorectal samples [10]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Across four gene-expression datasets, 281 DEGs were consistently identified, and BIRC5, CCNB1, KIF20A, NCAPG, and TPX2 were identified as prognostic hub genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37389063", "locator": "sections[19] \"Identification of DEGs in CRC\" paragraph 2", "quote": "281 DEGs were consistently expressed in the four gene datasets (Fig. 1A and B)."}, {"asset": "source:pmid:37389063", "locator": "sections[22] \"Survival analysis and validation of hub genes in CRC\" paragraph 2", "quote": "In summary, the BIRC5, CCNB1, KIF20A, NCAPG, and TPX2 were considered as the hub genes with good prognostic value."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Across four gene-expression datasets, 281 DEGs were consistently identified, and BIRC5, CCNB1, KIF20A, NCAPG, and TPX2 were identified as prognostic hub genes.", "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:37389063"], "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 transcription factors"], "order_basis": "paper_text_order:3922", "id": "assay:4"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["P < 0.05 was set as the threshold criterion. Immunohistochemical analysis of hub genes The protein levels of", "ps://www.proteinatlas.org/), which contained immunohistochemical expression data for human samples [21]. The", "16.18E-01356The genes were ranked by degree. Immunohistochemical analysis of prognostic hub genes In the HPA,", "IF20A, NCAPG, and TPX2 were identified in an immunohistochemical analysis using the antibodies HPA002830, CAB"], "order_basis": "paper_text_order:4683", "id": "assay:5"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The online tool-GEO2R (https://www.ncbi.nlm.nih.gov/gov/geo/geo2r) was used for screening the DEGs from the gene expression profiles (GSE23878, GSE24514, GSE41657, and GSE81582) between the CRC samples and normal samples, respectively. The adjusted P-value (adjust P) < 0.05 and |log2 Fold Change (log2 FC) |> 1 were applied to identify DEGs. The log-rank P < 0.05 and P (HR) < 0.05 were set as the threshold criteria. The t-test was performed on the relevant results (*P < 0.05)."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}