Microbiology of Intestinal Diseases, Biology Department, Universitat de Girona, Girona, Spain.
Front Cell Infect Microbiol. 2023 Sep 11;13:1228159. doi: 10.3389/fcimb.2023.1228159. eCollection 2023.
Adherent-invasive (AIEC) is strongly associated with the pathogenesis of Crohn's disease (CD). However, no molecular markers currently exist for AIEC identification. This study aimed to identify differentially expressed genes (DEGs) between AIEC and non-AIEC strains that may contribute to AIEC pathogenicity and to evaluate their utility as molecular markers.
Comparative transcriptomics was performed on two closely related AIEC/non-AIEC strain pairs during Intestine-407 cell infection. DEGs were quantified by RT-qPCR in the same RNA extracts, as well as in 14 AIEC and 23 non-AIEC strains to validate the results across a diverse strain collection. Binary logistical regression was performed to identify DEGs whose quantification could be used as AIEC biomarkers.
Comparative transcriptomics revealed 67 differences in expression between the two phenotypes in the strain pairs, 50 of which (81.97%) were corroborated by RT-qPCR. When explored in the whole strain collection, 29 DEGs were differentially expressed between AIEC and non-AIEC phenotypes (p-value < 0.042), and 42 genes between the supernatant fraction of infected cell cultures and the cellular fraction containing adhered and intracellular bacteria (p-value < 0.049). Notably, six DEGs detected in the strain collection were implicated in arginine biosynthesis and five in colanic acid synthesis. Furthermore, two biomarkers based on and gene expression were proposed with an accuracy of ≥ 85% in our strain collection.
This is the first transcriptomic study conducted using AIEC-infected cell cultures. We have identified several genes that may be involved in AIEC pathogenicity, two of which are putative biomarkers for identification.
黏附侵袭性（AIEC）与克罗恩病（CD）的发病机制密切相关。然而，目前尚无用于鉴定 AIEC 的分子标志物。本研究旨在鉴定 AIEC 和非 AIEC 菌株之间差异表达的基因（DEGs），这些基因可能有助于 AIEC 的致病性，并评估它们作为分子标志物的效用。
在 Intestine-407 细胞感染过程中，对两个密切相关的 AIEC/非 AIEC 菌株对进行了比较转录组学研究。通过 RT-qPCR 在相同的 RNA 提取物中定量 DEGs，以及在 14 株 AIEC 和 23 株非 AIEC 菌株中验证结果，以在多样化的菌株集合中验证结果。使用二元逻辑回归鉴定可以用作 AIEC 生物标志物的 DEGs 定量。
比较转录组学揭示了菌株对中两种表型之间的 67 个表达差异，其中 50 个（81.97%）通过 RT-qPCR 得到证实。在整个菌株集合中探索时，AIEC 和非 AIEC 表型之间有 29 个 DEGs 表达差异（p 值<0.042），而在感染细胞培养物的上清液部分和含有黏附和胞内细菌的细胞部分之间有 42 个基因表达差异（p 值<0.049）。值得注意的是，在菌株集合中检测到的 6 个 DEGs 涉及精氨酸生物合成，5 个涉及粘多糖合成。此外，提出了基于 和 基因表达的两个标志物，在我们的菌株集合中准确性≥85%。
这是首次使用 AIEC 感染细胞培养物进行的转录组学研究。我们已经鉴定了几个可能参与 AIEC 致病性的基因，其中两个是鉴定的潜在生物标志物。
