Characterisation of infection associated microRNA and protein cargo in extracellular vesicles of Theileria annulata infected leukocytes.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30370674", "kind": "science-record", "revision": 8, "content_hash": "sha256:92c090637c2364337dcf90faa977b640d8440f30c53591cd136d4f07ffbda74b", "created_at": "2026-11-01T15:40:38Z", "updated_at": "2026-11-01T22:43:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Characterisation of infection associated microRNA and protein cargo in extracellular vesicles of Theileria annulata infected leukocytes.", "doi": "10.1111/cmi.12969", "pmid": "30370674", "authors": ["Victoria Gillan", "Deborah M Simpson", "Jane Kinnaird", "Kirsty Maitland", "Brian Shiels", "Eileen Devaney"], "journal": "Cellular microbiology", "year": 2019, "abstract": "The protozoan parasites Theileria annulata and Theileria parva are unique amongst intracellular eukaryotic pathogens as they induce a transformation-like phenotype in their bovine host cell. T. annulata causes tropical theileriosis, which is frequently fatal, with infected leukocytes becoming metastatic and forming foci in multiple organs resulting in destruction of the lymphoid system. Exosomes, a subset of extracellular vesicles (EV), are critical in metastatic progression in many cancers. Here, we characterised the cargo of EV from a control bovine lymphosarcoma cell line (BL20) and BL20 infected with T. annulata (TBL20) by comparative mass spectrometry and microRNA (miRNA) profiling (data available via ProteomeXchange, identifier PXD010713 and NCBI GEO, accession number GSE118456, respectively). Ingenuity pathway analysis that many infection-associated proteins essential to migration and extracellular matrix digestion were upregulated in EV from TBL20 cells compared with BL20 controls. An altered repertoire of host miRNA, many with known roles in tumour and/or infection biology, was also observed. Focusing on the tumour suppressor miRNA, bta-miR-181a and bta-miR-181b, we identified putative messenger RNA targets and confirmed the interaction of bta-miR181a with ICAM-1. We propose that EV and their miRNA cargo play an important role in the manipulation of the host cell phenotype and the pathobiology of Theileria infection.", "claims": [{"id": "claim-method", "statement": "To increase the confidence of downstream analysis, in addition to statistical significance (ANOVA p ≤ 0.05), only those proteins identified by two or more unique peptides and exhibiting a fold change ≥2 were selected, resulting in a total of 479 significantly differentially expressed proteins.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30370674", "locator": "sections[4] \"BL20‐EV and TBL20‐EV exhibit differences in protein composition/cargo\" paragraph 3", "quote": "To increase the confidence of downstream analysis, in addition to statistical significance (ANOVA p ≤ 0.05), only those proteins identified by two or more unique peptides and exhibiting a fold change ≥2 were selected, resulting in a total of 479 significantly differentially expressed proteins."}], "state": "complete"}, {"id": "claim-data-access", "statement": "data available via ProteomeXchange, identifier PXD010713 and NCBI GEO, accession number GSE118456, respectively", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30370674", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "data available via ProteomeXchange, identifier PXD010713 and NCBI GEO, accession number GSE118456, respectively"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:30370674"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE118456"], "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": ["data:geo:GSE118456"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30370674", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1111/cmi.12969", "sha256": "sha256:ddd4dd755fa35f672195216fd53fa589f613ffb3d4e14c2e352a73eb9673c5a8", "bytes": 63750, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1111/cmi.12969", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6492283", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE118456", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118456", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE118456", "version": null, "note": "data available via ProteomeXchange, identifier PXD010713 and NCBI GEO, accession number GSE118456, respectively", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "data available via ProteomeXchange, identifier PXD010713 and NCBI GEO, accession number GSE118456, respectively", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3330473", "GSM3330474", "GSM3330475", "GSM3330476", "GSM3330477", "GSM3330478", "GSM3330479", "GSM3330480"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "19172", "taxon": "Bos taurus", "title": "miRNA profiling of extracellular vesicles from Theileria annulata infected B cells (TBL20) and their uninfected control counterparts (BL20)", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PXD010713", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD010713", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD010713", "version": null, "note": "data available via ProteomeXchange, identifier PXD010713 and NCBI GEO, accession number GSE118456, respectively", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "data available via ProteomeXchange, identifier PXD010713 and NCBI GEO, accession number GSE118456, respectively", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Bovine extracellular vesicle LC-MSMS C4PR_LIV", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30370674:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0a9eed31f46f16a81544e21736655069c1db077255907c4f564ec3a1a4911b0e", "bytes": 1174, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#cmi12969-tbl-0001", "version": null, "note": "Host miRNA differentially expressed in TBL20‐EV compared with BL20‐EV", "structure": {"pmcid": "PMC6492283", "section_index": 5, "section_title": "BL20‐EV and TBL20‐EV exhibit differences in miRNA cargo", "row_count": 7, "column_count": 3}, "table": {"label": "Table 1", "caption": "Host miRNA differentially expressed in TBL20‐EV compared with BL20‐EV", "rows": [["microRNA", "Log2 (p value)", "Function"], ["bta‐miR‐222", "1.63 (p = 1.5E‐05)", "Oncogene in many human malignancies (Felicetti et al., 2016; Kara et al., 2015; Li et al., 2016; M. Wang et al., 2016)"], ["bta‐miR‐24‐3p", "2.66 (p = 1.5E‐05)", "Promotes cell proliferation and inhibits apoptosis in human breast cancer (Lu et al., 2015)"], ["bta‐miR‐27a‐3p", "3.39 (p = 3.3E‐05)", "Promotes cellular proliferation (Kara et al., 2015; Nakata et al., 2015; Wu et al., 2015)"], ["bta‐miR‐155", "2.94 (p = 9.3E‐04)", "Tumour associated miRNA (Faraoni, Antonetti, Cardone, & Bonmassar, 2009; Jurkovicova et al., 2014; Kara et al., 2015)"], ["bta‐miR‐146a", "2.76 (p = 4.3E‐05)", "Tumour associated miRNA (Petrovic, Davidovic, Bajic, Obradovic, & Isenovic, 2017; Sun et al., 2015)"], ["bta‐miR‐181a/b", "−1.35/−1.05 (p = 8E‐05/2E‐05)", "Tumour suppressors (Shi et al., 2008; H. Wang et al., 2015; Weng et al., 2015)"]], "row_count": 7, "column_count": 3, "numeric_cells": 18, "header_rows": 1, "locator": "section[5]/table-wrap[1]#cmi12969-tbl-0001"}}, {"id": "asset:table:pmid:30370674:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:91bdb033ff6cc8c0e1d6c815a0d915e30b43f46fd6c9dc336804b2d4c18e3b0c", "bytes": 1942, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#cmi12969-tbl-0002", "version": null, "note": "The top 15 upregulated proteins in TBL20‐EV compared with BL20‐EV and predicted bta‐miR‐181a and bta‐miR‐181b binding sites", "structure": {"pmcid": "PMC6492283", "section_index": 6, "section_title": "Computational analysis of bta‐miR‐181a and b mRNA targets", "row_count": 17, "column_count": 5}, "table": {"label": "Table 2", "caption": "The top 15 upregulated proteins in TBL20‐EV compared with BL20‐EV and predicted bta‐miR‐181a and bta‐miR‐181b binding sites", "rows": [["Gene", "Fold change (up in TBL20‐EV)", "q value", "No. of miR‐181a binding sites (combined ddG)", "No. of miR‐181b binding sites (combined ddG)"], ["VTA1_BOVIN Vacuolar protein sorting‐associated proteinb", "16.5", "3.13E‐08", "4(−2.99)", "3 (−5.37)"], ["ICAM‐1_BOVIN Intercellular adhesion molecule 1", "9.6", "4.96E‐08", "2 (−9.01)", "0"], ["NEUM_BOVIN Neuromodulin", "56.2", "7.06E‐08", "1 (2.51)", "1 (−4.86)"], ["TSN6_BOVIN Tetraspanin‐6b", "12.6", "8.72E‐08", "1 (−6)", "1 (−9)"], ["VPS4B_BOVIN Vacuolar protein sorting‐associated protein 4Bb", "9.5", "8.72E‐08", "2 (−4.88)", "2 (−6.32)"], ["MFGM_BOVIN Lactadherin", "6.6", "8.72E‐08", "0", "0"], ["SATT_BOVIN Neutral amino acid transporter A", "7.3", "1.85E‐07", "0", "1 (−6)"], ["ITA5_BOVIN Integrin alpha‐5", "6.1", "2.02E‐07", "0", "1 (0.7)"], ["IST1_BOVIN IST1 homologueb", "10.5", "2.58E‐07", "1 (2)", "3 (−9)"], ["TMEDA_BOVIN Transmembrane emp24 domain‐containing protein 10b", "5.4", "2.58E‐07", "3 (−4.51)", "3 (−4.1)"], ["VPS28_BOVIN Vacuolar protein sorting‐associated protein 28 homologueb", "6.8", "2.91E‐07", "3 (−4.13)", "1 (0.51)"], ["CHM1B_BOVIN Charged multivesicular body protein 1bb", "9", "3.00E‐07", "2 (0.2)", "3 (5.58)"], ["MMP‐9_BOVIN Matrix metalloproteinase‐9", "23.3", "9.12E‐07", "1 (−13.05)", "1 (−11.84)"], ["VAPA_BOVIN Vesicle‐associated membrane protein‐associated protein Ab", "10.4", "9.12E‐07", "2 (−4.76)", "2 (−5.83)"], ["MPP7_BOVIN MAGUK p55 Subfamily Member 7", "7.5", "9.12E‐07", "4 (−5.69)", "2 (−8.05)"], ["aHA1A_BOVIN BOLA‐1 Class I histocompatibility antigen, alpha chain", "3.8", "8.47E‐06", "2 (−11.95)", "2 (−14.5)"]], "row_count": 17, "column_count": 5, "numeric_cells": 77, "header_rows": 1, "locator": "section[6]/table-wrap[1]#cmi12969-tbl-0002"}}], "gaps": ["asset:data:geo:GSE118456 not downloaded", "asset:data:geo:GSE118456 licence not read", "asset:data:geo:PXD010713 not downloaded", "asset:data:geo:PXD010713 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "To increase the confidence of downstream analysis, in addition to statistical significance (ANOVA p ≤ 0.05), only those proteins identified by two or more unique peptides and exhibiting a fold change ≥2 were selected, resulting in a total of 479 significantly differentially expressed proteins."}}], "targets": [], "gaps": []}, "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD010713", "10.6019/PXD010713", "GSE118456"], "resolved_accessions": ["PXD010713", "GSE118456"], "statements": ["data available via ProteomeXchange, identifier PXD010713 and NCBI GEO, accession number GSE118456, respectively"], "basis": "The paper names PXD010713, GSE118456 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:30370674", "data:geo:GSE118456", "asset:table:pmid:30370674:1", "asset:table:pmid:30370674:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE118456"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:12:39Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 54908, "completion_tokens": 1489, "cached_tokens": 776}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:30370674", "type": "paper", "label": "pmid:30370674"}, {"id": "source:pmid:30370674", "type": "manuscript", "label": "PMID 30370674 full text"}, {"id": "data:geo:GSE118456", "type": "dataset", "label": "GEO GSE118456"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30370674", "type": "paper", "label": "pmid:30370674"}, {"id": "source:pmid:30370674", "type": "manuscript", "label": "PMID 30370674 full text"}, {"id": "data:geo:GSE118456", "type": "dataset", "label": "GEO GSE118456"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30370674", "type": "extraction", "used": ["source:pmid:30370674"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE118456", "type": "accession_resolution", "used": ["data:geo:GSE118456"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:30370674", "parent_hash": "sha256:a875500dfb552e266bee5883fe2ee1fb2d99b663a71db28b6da4deaa9feee02c", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE118456 licence not read", "asset:data:geo:GSE118456 not downloaded", "asset:data:geo:PXD010713 licence not read", "asset:data:geo:PXD010713 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["cted with T. annulata (TBL20) by comparative mass spectrometry and microRNA (miRNA) profiling (data availab", "cation was performed using Progenesis QI for Proteomics v.2.0 (Waters Ltd., Newcastle‐upon‐Tyne, Uni", "ween experimental groups. 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