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pmid:39513308
The Risk Genes S1PR5, CMC1, and ASAH1 as Potential Targets for the Diagnosis, Immunotherapy, and Treatment of Colon Adenocarcinoma by Single-Cell and Bulk RNA Sequencing Analysis
Zipeng Xu · Jiantao Gong · Weidong Hu · Chen Ge · Genxi Tong · Fengjun Cai · Zhenghai Zhu · Yihang Yuan · Chaobo Chen
Current medicinal chemistry · 2024 doi:10.2174/0109298673331144241009082052
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Complete file
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In this study, a new special Immune Cell Functions (ICF) risk model was constructed using single-cell and bulk RNA sequencing data to develop a new understanding and clinical applications for COAD.\nMETHODS: The immune function gene sets were downloaded from a literature reference, and the COAD single-cell dataset GSE146771 was downloaded from the Tumour Immune Single Cell Hub database. Using Lasso analysis, a multiple gene signature was made from the enrichment scores of immune function gene sets that were enriched in different ways. Robust validation of the signature was then performed in multiple independent cohorts. After that, we built the model using a 10-fold cross-test and evaluated its independence for clinical usage using a nomogram. We also investigated the connection between signature and immune function, genetic variation, immunotherapy, and the cancer immunological microenvironment. Lastly, we used qPCR and immunohistochemistry to examine the expression of the unreported model genes. To find the regulatory functions of unreported model genes, an EdU assay was employed.\nRESULTS: First, 20 differentially enriched immune function gene sets were identified. Ten genes can be used as a risk profile to assess the prognosis of colon cancer, according to Lasso regression analysis. Signature performance was stable in both the training cohort and two independent GEO external cohorts, and risk scores were confirmed as independent prognostic factors. At the same time, our risk model continued to be highly predictive across various clinical clusters and clinical characteristics, such as immune checkpoints, tumour genome mutations, and chemotherapeutic drug resistance. Patients in the low-risk group have exhibited a higher chance of benefiting from immunotherapy, according to immunotherapy response research. qPCR and immunohistochemistry analysis have revealed S1PR5 expression as high in COAD tissues, while CMC1 and ASAH1 expression has been found to be low. According to the findings of the functional experiment, S1PR5, CMC1, and ASAH1 may control the ability of CRC cells to proliferate.\nCONCLUSION: In this study, using scRNA-seq and bulk RNA-seq data, we created a risk model to predict the prognosis and effectiveness of immunotherapy in patients with COAD. In addition, we have discovered three model genes (S1PR5, CMC1, and ASAH1) that have not been reported before. These genes have the potential to be novel therapeutic targets in Colorectal Cancer (CRC). 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{"state": "partial", "methods": [{"id": "method-1", "family": "regression_modelling", "specific": "ols", "label": "Regression modelling", "dsl_operations": ["ols_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "These signatures were identified after removing redundant genes in the training set using Lasso linear regression with a seed value of 1,110."}}, {"id": "method-2", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": 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Lastly, we used qPCR and immunohistochemistry to examine the expr", "ccording to immunotherapy response research. qPCR and immunohistochemistry analysis have revea", "used quantitative Polymerase Chain Reaction (qPCR) and Immunohistochemistry (IHC) research to", "with Colorectal Adenocarcinoma (COAD). Both qPCR (Figs. 15A-C) and immunohistochemistry (Figs"], "order_basis": "paper_text_order:1163", "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": 0.99, "evidence": ["l microenvironment. Lastly, we used qPCR and immunohistochemistry to examine the expression of the unreported", "to immunotherapy response research. qPCR and immunohistochemistry analysis have revealed S1PR5 expression as h", "itative Polymerase Chain Reaction (qPCR) and Immunohistochemistry (IHC) research to examine the expression of", "arcinoma (COAD). Both qPCR (Figs. 15A-C) and immunohistochemistry (Figs. 15D-F) showed that in COAD tissues, t"], "order_basis": "paper_text_order:1172", "id": "assay:3"}, {"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["roliferate. CONCLUSION: In this study, using scRNA-seq and bulk RNA-seq data, we created a risk mod"], "order_basis": "paper_text_order:2394", "id": "assay:4"}, {"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": ["ts approval for this study. Cell Culture and Transfection The human CRC cell lines SW480 and SW620 wer", "nce group consisted of SW620 cells that were transfected with lentiviral expression vectors (pLVX-IRE", "rol group consisted of SW480 cells that were transfected with the vector. The findings showed that st"], "order_basis": "paper_text_order:3363", "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": ["ates. Cells labelled as SW480 and SW620 were cultured in Leibovitz's L-15 media (Sigma, Beijing, Chin"], "order_basis": "paper_text_order:3514", "id": "assay:6"}, {"role": "analysis", "definition_id": "regression_modelling", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["ols_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["These signatures were identified after removing redundant genes in the training set using Lasso linear regression with a seed value of 1,110."], "order_basis": "consumes_earlier_output", "id": "assay:7"}]}