Leveraging single-cell and multi-omics approaches to identify MTOR-centered deubiquitination signatures in esophageal cancer therapy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39742278", "kind": "science-record", "revision": 3, "content_hash": "sha256:6c9e9665eb06006d778415fceb4709828058b1dfc29e41081add907e84f1ff2a", "created_at": "2026-11-01T20:30:04Z", "updated_at": "2026-11-01T22:13:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Leveraging single-cell and multi-omics approaches to identify MTOR-centered deubiquitination signatures in esophageal cancer therapy.", "doi": "10.3389/fimmu.2024.1490623", "pmid": "39742278", "authors": ["Kang Tian", "Ziang Yao", "Da Pan"], "journal": "Frontiers in immunology", "year": 2024, "abstract": "Background: Esophageal squamous cell carcinoma (ESCC) remains a significant challenge in oncology due to its aggressive nature and heterogeneity. As one of the deadliest malignancies, ESCC research lags behind other cancer types. The balance between ubiquitination and deubiquitination processes plays a crucial role in cellular functions, with its disruption linked to various diseases, including cancer.\nMethods: Our study utilized diverse analytical approaches, encompassing Cox regression models, single-cell RNA sequencing, intercellular communication analysis, and Gene Ontology enrichment. We also conducted mutation profiling and explored potential immunotherapeutic agents. Furthermore, in vitro cellular experiments and in vivo mouse models were performed to validate findings. These methodologies aimed to establish deubiquitination-related gene signatures (DRGS) for predicting ESCC patient outcomes and response to immunotherapy.\nResults: By integrating datasets from TCGA-ESCC and GSE53624, we developed a DRGS model based on 14 deubiquitination-related genes (DUBGs). This signature effectively forecasts ESCC prognosis, drug responsiveness, and immune cell infiltration patterns. It also influences the mutational landscape of patients. Those classified as high-risk exhibited reduced survival rates, increased genetic alterations, and more complex cellular interactions, potentially explaining their poor outcomes. Notably, in vitro and in vivo experiments identified MTOR, a key component of the signature, as a promising therapeutic target for ESCC treatment.\nConclusion: Our research highlights the significance of 14 DUBGs in ESCC progression. The risk score derived from this gene set enables clinical stratification of patients into distinct prognostic groups. Moreover, MTOR emerges as a potential target for personalized ESCC therapy, offering new avenues for treatment strategies.", "claims": [{"id": "claim-method", "statement": "Deubiquitination-related genes were identified as prognostic factors using univariate Cox regression, Lasso regression, and multivariate Cox regression analyses.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39742278", "locator": "sections[4] \"Establishment of DRGS for ESCC patients’ prognosis\" paragraph 2", "quote": "Deubiquitination-related genes were identified as prognostic factors using univariate Cox regression, Lasso regression, and multivariate Cox regression analyses."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39742278", "locator": "sections[24] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Kaplan-Meier survival analysis revealed that ESCC patients in the high-risk group had significantly shorter survival probabilities, with 1-, 3-, and 5-year AUCs of 0.67, 0.74, and 0.75, respectively, indicating a robust predictive capability of the DRGS for ESCC patients ( Figures 2I–J ).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39742278", "locator": "sections[16] \"Construction and validation of a prognostic model related to deubiquitination\" paragraph 2", "quote": "Kaplan-Meier survival analysis revealed that ESCC patients in the high-risk group had significantly shorter survival probabilities, with 1-, 3-, and 5-year AUCs of 0.67, 0.74, and 0.75, respectively, indicating a robust predictive capability of the DRGS for ESCC patients ( Figures 2I–J )."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Kaplan-Meier survival analysis revealed that ESCC patients in the high-risk group had significantly shorter survival probabilities, with 1-, 3-, and 5-year AUCs of 0.67, 0.74, and 0.75, respectively, indicating a robust predictive capability of the DRGS for ESCC patients ( Figures 2I–J ).", "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:39742278"], "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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Single-cell RNA-seq analysis and risk score evaluation of deubiq"], "order_basis": "paper_text_order:602", "id": "assay:2"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["rthermore, in vitro cellular experiments and in vivo mouse models were performed to validate find", "g their poor outcomes. Notably, in vitro and in vivo experiments identified MTOR, a key component", "e, in vitro cellular experiments and in vivo mouse models were performed to validate findings.", "cells ( Figures 9B, C, E, F ). Additionally, in vivo experiments using a subcutaneous tumor model"], "order_basis": "paper_text_order:819", "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": 0.77, "evidence": ["l Bank (Beijing, China) (31). The cells were cultured in 1640 medium (Gibco, USA)supplemented with 10"], "order_basis": "paper_text_order:2869", "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": ["EC25, using siRNA technology. Five days post-transfection, qRT-PCR was performed to assess MTOR expres", "ollected from mice injected with mEC25 cells transfected with either negative control siRNA (siNC) or", "OR in esophageal cancer, we constructed MTOR knockdown cell lines, KYSE30 and mEC25, using siRNA te", "levels, confirming the effectiveness of MTOR knockdown in the KYSE30 and mEC25 cell lines ( Figures"], "order_basis": "paper_text_order:14466", "id": "assay:5"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["1, **p < 0.01. (E) Cell proliferation assay (CCK-8) in KYSE30 cells showing reduced cell growth", "ontrol (siNC). (F) Cell proliferation assay (CCK-8) in mEC25 cells showing reduced cell growth"], "order_basis": "paper_text_order:16055", "id": "assay:6"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Deubiquitination-related genes were identified as prognostic factors using univariate Cox regression, Lasso regression, and multivariate Cox regression analyses."], "order_basis": "consumes_earlier_output", "id": "assay:7"}]}