P-213 Comparative Transcriptomic Analysis of a Reference Adherent-Invasive E. Coli Strain LF82
Bibliographic record
Abstract
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.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".