Multi-Omics Database Analysis of Aminoacyl-tRNA Synthetases in Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33266490", "kind": "science-record", "revision": 4, "content_hash": "sha256:ff55eb72e01a613843326893b8bc326fee67608c21070397d97c03bc796fd225", "created_at": "2026-11-01T15:41:17Z", "updated_at": "2026-11-01T21:24:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Multi-Omics Database Analysis of Aminoacyl-tRNA Synthetases in Cancer.", "doi": "10.3390/genes11111384", "pmid": "33266490", "authors": ["Justin Wang", "Ingrid Vallee", "Aditi Dutta", "Yu Wang", "Zhongying Mo", "Ze Liu", "Haissi Cui", "Andrew I Su", "Xiang-Lei Yang"], "journal": "Genes", "year": 2020, "abstract": "Aminoacyl-tRNA synthetases (aaRSs) are key enzymes in the mRNA translation machinery, yet they possess numerous non-canonical functions developed during the evolution of complex organisms. The aaRSs and aaRS-interacting multi-functional proteins (AIMPs) are continually being implicated in tumorigenesis, but these connections are often limited in scope, focusing on specific aaRSs in distinct cancer subtypes. Here, we analyze publicly available genomic and transcriptomic data on human cytoplasmic and mitochondrial aaRSs across many cancer types. As high-throughput technologies have improved exponentially, large-scale projects have systematically quantified genetic alteration and expression from thousands of cancer patient samples. One such project is the Cancer Genome Atlas (TCGA), which processed over 20,000 primary cancer and matched normal samples from 33 cancer types. The wealth of knowledge provided from this undertaking has streamlined the identification of cancer drivers and suppressors. We examined aaRS expression data produced by the TCGA project and combined this with patient survival data to recognize trends in aaRSs' impact on cancer both molecularly and prognostically. We further compared these trends to an established tumor suppressor and a proto-oncogene. We observed apparent upregulation of many tRNA synthetase genes with aggressive cancer types, yet, at the individual gene level, some aaRSs resemble a tumor suppressor while others show similarities to an oncogene. This study provides an unbiased, overarching perspective on the relationship of aaRSs with cancers and identifies certain aaRS family members as promising therapeutic targets or potential leads for developing biological therapy for cancer.", "claims": [{"id": "claim-method", "statement": "However, this apparent correlation did not yield statistical significance based on a Pearson correlation coefficients analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33266490", "locator": "sections[7] \"3.4. Survival Analysis with mRNA Expression\" paragraph 6", "quote": "However, this apparent correlation did not yield statistical significance based on a Pearson correlation coefficients analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We utilized cBioPortal, GEPIA2, and KMPlotter to access and analyze the public database on cancer tissues generated by the TCGA project (https://www.cancer.gov/tcga) and normal tissues from the Genotype-Tissue Expression (GTEx) Project.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33266490", "locator": "sections[2] \"2. 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33266490", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/genes11111384", "sha256": "sha256:70dc8ff484867437c73b241a4f91c317751abc73a4d0ba28fcca44bc96ecce9b", "bytes": 60702, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/genes11111384", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7700366", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:33266490:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d76c16990038be1a2e76622fbb38d38c786c3db80c4e709742a6bbd613ca9429", "bytes": 1766, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#genes-11-01384-t001", "version": null, "note": "Description of cancer type abbreviations used by the Cancer Genome Atlas (TCGA).", "structure": {"pmcid": "PMC7700366", "section_index": 4, "section_title": "3.1. Genomic Variations (DNA)", "row_count": 34, "column_count": 3}, "table": {"label": "Table 1", "caption": "Description of cancer type abbreviations used by the Cancer Genome Atlas (TCGA).", "rows": [["Abbreviation", "Cancer Type", "OS Median Time to Event (Months) [24]"], ["ACC", "Adrenocortical carcinoma", "18.1"], ["BLCA", "Bladder Urothelial Carcinoma", "13.5"], ["BRCA", "Breast invasive carcinoma", "41.8"], ["CESC", "Cervical squamous cell carcinoma and endocervical adenocarcinoma", "19.9"], ["CHOL", "Cholangio carcinoma", "18"], ["COAD", "Colon adenocarcinoma", "13.3"], ["DLBC", "Lymphoid Neoplasm Diffuse Large B-cell Lymphoma", "19.5"], ["ESCA", "Esophageal carcinoma", "11.5"], ["GBM", "Glioblastoma multiforme", "12.6"], ["HNSC", "Head and Neck squamous cell carcinoma", "14.1"], ["KICH", "Kidney Chromophobe", "24.3"], ["KIRC", "Kidney renal clear cell carcinoma", "26.9"], ["KIRP", "Kidney renal papillary cell carcinoma", "21.1"], ["LAML", "Acute Myeloid Leukemia", "9"], ["LGG", "Brain Lower Grade Glioma", "26.7"], ["LIHC", "Liver hepatocellular carcinoma", "13.7"], ["LUAD", "Lung adenocarcinoma", "20.3"], ["LUSC", "Lung squamous cell carcinoma", "18.1"], ["MESO", "Mesothelioma", "15"], ["OV", "Ovarian serous cystadenocarcinoma", "35.3"], ["PAAD", "Pancreatic adenocarcinoma", "12.9"], ["PCPG", "Pheochromocytoma and Paraganglioma", "14.9"], ["PRAD", "Prostate adenocarcinoma", "36.2"], ["READ", "Rectum adenocarcinoma", "22"], ["SARC", "Sarcoma", "21.3"], ["SKCM", "Skin Cutaneous Melanoma", "35.3"], ["STAD", "Stomach adenocarcinoma", "11.3"], ["TGCT", "Testicular Germ Cell Tumors", "18.6"], ["THCA", "Thyroid carcinoma", "33.5"], ["THYM", "Thymoma", "28"], ["UCEC", "Uterine Corpus Endometrial Carcinoma", "23.3"], ["UCS", "Uterine Carcinosarcoma", "17.1"], ["UVM", "Uveal Melanoma", "19.9"]], "row_count": 34, "column_count": 3, "numeric_cells": 34, "header_rows": 1, "locator": "section[4]/table-wrap[1]#genes-11-01384-t001"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "However, this apparent correlation did not yield statistical significance based on a Pearson correlation coefficients analysis."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "KM"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["pearson_r"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pearson."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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