P-213 Comparative Transcriptomic Analysis of a Reference Adherent-Invasive E. Coli Strain LF82
Notice bibliographique
Résumé
Adherent-invasive E. coli (AIEC) strains are implicated in the pathogenesis of Crohn's disease. These strains are distinguished from commensal E. coli strains by their ability to adhere and invade intestinal epithelial cells and to survive within macrophages in vitro. Thus far, no molecular signatures that clearly distinguish AIEC strains from commensal strains have been identified. The lack of molecular probes hampers our ability to examine the effect of AIEC colonization with CD clinical outcomes, such as postoperative recurrence of ileal CD. We have taken a comparative genomic approach to identify potential probes by comparing the genomic sequences of a panel of AIEC strains (LF82, MS107-1, MS110-3, MS115-1, MS119-7, MS124-1, MS145-7, MS57-2, MS79-10, MS85-1, NRG857, UM146) with a selection of commensal E. coli strains (HS, IAI1, SE11, ATCC.8739, K12_DH10B, K12_MG1655, K12_W3110, ED1a, MS185-1, MS187-1, MS196-1, MS198-1, MS45-1, MS60-1, MS78-1, MS84-1). Furthermore, we conducted a comparative transcriptomic analysis of the AIEC strain, LF82, with a nonpathogenic strain, HS. Transcriptomic analysis was carried out on RNA extracted from triplicate cultures of LF82 and HS grown for 2h (exponential phase) and 24 h (stationary phase). Illumina 150bp-single end RNA-Sequencing was conducted at the New York Genome Center. The LF82 and HS RNA transcripts were aligned to their respective reference genomes using the BWA aligner, raw hit counts quantified (HTSeq), and data normalized (edgeR) to RPKM. A gene-to-gene comparison via TBLASTN was conducted to construct a mapping between LF82 genes with their counterparts in HS. To identify differences in expression of genes (>2fold, FDR <0.05) between LF82 and HS strains, the 2 h and 24 h RPKM values were analyzed by repeated measures ANOVA (RMANOVA), where the 2 h and 24 h values were treated as repeated measures. The genes present in LF82, but not in HS, were then surveyed in additional E.coli strains to determine their distribution in AIEC and non-invasive E.coli strains. Of the 4376 genes containing CDS in LF82, 3632 were shared with the commensal HS strain. RMANOVA revealed that 329 genes were significantly increased and 606 genes were significantly decreased in LF82 relative to HS. Transcripts related to the siderophores metabolic and biosynthetic pathways were significantly increased in LF82 (FDR <0.05). In contrast, transcripts related to the oxidation-reduction pathway were decreased in LF82. Of the 741 genes present only in the LF82 genome (<85% TBLASTN identity), 736 genes had detectable RNA expression (RPKM >1). Of these 736 genes, 7 genes showed <85% TBLASTN identity in 15 of 16 non-invasive E.coli strains and >85% TBLASTN identity in 6–7 of 12 AIEC strains. Five of the genes were putative CRISPR genes, and 2 encoded hypothetical proteins. Comparative transcriptomic analysis indicates that there is altered expression of iron sensing and oxidation-reduction pathways in the reference AIEC strain, LF82, compared to the nonpathogenic HS strain. Iron acquisition is an essential virulence trait in other extraintestinal pathogenic E. coli associated with urinary tract infections. The analysis has also identified candidate signature transcripts for a subset of AIEC strains.
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,001 | 0,001 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,002 | 0,001 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».