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从定植到感染阶段肺炎链球菌共表达基因模块的鉴定，以预测新的潜在毒力基因。

The identification of co-expressed gene modules in Streptococcus pneumonia from colonization to infection to predict novel potential virulence genes.

机构信息

Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.

Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.

出版信息

BMC Microbiol. 2020 Dec 17;20(1):376. doi: 10.1186/s12866-020-02059-0.

DOI:10.1186/s12866-020-02059-0
PMID:33334315
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7745498/
Abstract

BACKGROUND

Streptococcus pneumonia (pneumococcus) is a human bacterial pathogen causing a range of mild to severe infections. The complicated transcriptome patterns of pneumococci during the colonization to infection process in the human body are usually determined by measuring the expression of essential virulence genes and the comparison of pathogenic with non-pathogenic bacteria through microarray analyses. As systems biology studies have demonstrated, critical co-expressing modules and genes may serve as key players in biological processes. Generally, Sample Progression Discovery (SPD) is a computational approach traditionally used to decipher biological progression trends and their corresponding gene modules (clusters) in different clinical samples underlying a microarray dataset. The present study aimed to investigate the bacterial gene expression pattern from colonization to severe infection periods (specimens isolated from the nasopharynx, lung, blood, and brain) to find new genes/gene modules associated with the infection progression. This strategy may lead to finding novel gene candidates for vaccines or drug design.

RESULTS

The results included essential genes whose expression patterns varied in different bacterial conditions and have not been investigated in similar studies.

CONCLUSIONS

In conclusion, the SPD algorithm, along with differentially expressed genes detection, can offer new ways of discovering new therapeutic or vaccine targeted gene products.

摘要

背景

肺炎链球菌（肺炎球菌）是一种人类细菌病原体，可引起多种轻度至重度感染。在人体定植到感染过程中，肺炎球菌复杂的转录组模式通常通过测量必需毒力基因的表达，并通过微阵列分析比较致病和非致病细菌来确定。正如系统生物学研究表明的那样，关键的共表达模块和基因可能是生物过程中的关键参与者。通常，样本进展发现（SPD）是一种传统的计算方法，用于破译不同临床样本中微阵列数据集下的生物进展趋势及其相应的基因模块（簇）。本研究旨在调查从定植到严重感染期（从鼻咽、肺、血液和大脑中分离的标本）的细菌基因表达模式，以寻找与感染进展相关的新基因/基因模块。这种策略可能会发现用于疫苗或药物设计的新基因候选物。

结果

结果包括在不同细菌条件下表达模式不同且在类似研究中尚未研究过的必需基因。

结论

总之，SPD 算法与差异表达基因检测相结合，可以为发现新的治疗或疫苗靶向基因产物提供新的途径。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d66/7745498/b542c7bc43cc/12866_2020_2059_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d66/7745498/b3f4edaa6eb7/12866_2020_2059_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d66/7745498/4782fde4284a/12866_2020_2059_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d66/7745498/0c525acaf1d6/12866_2020_2059_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d66/7745498/47f443d0c2ef/12866_2020_2059_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d66/7745498/76f715ddf569/12866_2020_2059_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d66/7745498/53033a4062d0/12866_2020_2059_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d66/7745498/25286701645b/12866_2020_2059_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d66/7745498/b542c7bc43cc/12866_2020_2059_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d66/7745498/b3f4edaa6eb7/12866_2020_2059_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d66/7745498/4782fde4284a/12866_2020_2059_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d66/7745498/0c525acaf1d6/12866_2020_2059_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d66/7745498/47f443d0c2ef/12866_2020_2059_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d66/7745498/76f715ddf569/12866_2020_2059_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d66/7745498/53033a4062d0/12866_2020_2059_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d66/7745498/25286701645b/12866_2020_2059_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5d66/7745498/b542c7bc43cc/12866_2020_2059_Fig8_HTML.jpg

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