Comprehensive Bioinformatics Analysis Reveals PTPN1 (PTP1B) Is a Promising Immunotherapy Target Associated with T Cell Function for Liver Cancer.

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This study aimed to investigate the immunological correlation and function of PTP1B in liver cancer. The expression profiles and corresponding clinical information of liver cancer patients were obtained from the TCGA and ICGC databases. GSE146115 and GSE98638 retrieved from the GEO database were used for the single-cell RNA-seq analysis. The mRNA expression of PTP1B (PTPN1) was increased in patients with most malignancies (all p < 0.05), including liver cancer (p < 0.001). Furthermore, up-regulated PTPN1 was connected to advanced tumor stage (p < 0.05) and worse prognosis (p < 0.01) in liver cancer. Through Cox regression analysis, PTPN1 was considered as an independent prognosis factor of overall survival (p < 0.05) and acted as a high-risk factor (hazard ratio > 1). Gene function and pathway analysis suggested PTPN1 was involved in T cell-related immune responses. Moreover, a close relationship was also found between PTPN1 expression and immune checkpoints as well as immune cells, especially with T cell-related checkpoints (all p < 0.001) and T cells (all p < 0.001). Single-cell RNA-seq analysis further illustrated that the enrichment of PTPN1 in the T cell population may be linked to its exhaustion in the liver cancer microenvironment. Overall, PTPN1 (PTP1B) closely related to T cell may function as an immunotherapy target for liver cancer.", "claims": [{"id": "claim-method", "statement": "To test whether PTPN1 was an independent prognostic factor of OS, univariate and multivariate Cox regression analyses were performed using the R package “survival.”", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36741874", "locator": "sections[6] \"2.4. 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Two GEO datasets (GSE146115 and GSE98638) were obtained from the GEO database (https://www.ncbi.nlm.nih.gov/gds/?term=) for single-cell RNA-seq analysis."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Overall, PTPN1 (PTP1B) closely related to T cell may function as an immunotherapy target for liver cancer.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36741874", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Overall, PTPN1 (PTP1B) closely related to T cell may function as an immunotherapy target for liver cancer."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Overall, PTPN1 (PTP1B) closely related to T cell may function as an immunotherapy target for liver cancer.", "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:36741874"], "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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