Abstract
BackgroundThe human body is colonized by a vast number of microbes. Microbiota can benefit many normal life processes, but can also cause many diseases by interfering the regular metabolism and immune system. Recent studies have demonstrated that the microbial community is closely associated with various types of cell carcinoma. The search for key factors, which also refer to cancer causing agents, can provide an important clue in understanding the regulatory mechanism of microbiota in uterine cervix cancer.ResultsIn this paper, we investigated microbiota composition and gene expression data for 58 squamous and adenosquamous cell carcinoma. A host-microbial covariance network was constructed based on the 16s rRNA and gene expression data of the samples, which consists of 259 abundant microbes and 738 differentially expressed genes (DEGs). To search for risk factors from host-microbial networks, the method of bi-partite betweenness centrality (BpBC) was used to measure the risk of a given node to a certain biological process in hosts. A web-based tool KF-finder was developed, which can efficiently query and visualize the knowledge of microbiota and differentially expressed genes (DEGs) in the network.ConclusionsOur results suggest that prevotellaceade, tissierellaceae and fusobacteriaceae are the most abundant microbes in cervical carcinoma, and the microbial community in cervical cancer is less diverse than that of any other boy sites in health. A set of key risk factors anaerococcus, hydrogenophilaceae, eubacterium, PSMB10, KCNIP1 and KRT13 have been identified, which are thought to be involved in the regulation of viral response, cell cycle and epithelial cell differentiation in cervical cancer. It can be concluded that permanent changes of microbiota composition could be a major force for chromosomal instability, which subsequently enables the effect of key risk factors in cancer. All our results described in this paper can be freely accessed from our website at http://www.nwpu-bioinformatics.com/KF-finder/.
Highlights
The human body is colonized by a vast number of microbes
Composition of the microbiota To study the microbial community in cervical cancer, we examined the 16s raw data of cancer cases and assigned taxonomy to each sequence
The main contributions of this paper can be concluded in three aspects: (1) microbial community distributed in cervical carcinoma cells is less diverse than that of other body sites; (2) a web-based tool MiteFinder was developed which enables users to query and visualize host-microbial networks, microbes and differentially expressed genes in a fast-and-easy way; (3) a set of key risk factors have been identified, which have proven to have association with cancers in several previous publications
Summary
The human body is colonized by a vast number of microbes. Microbiota can benefit many normal life processes, but can cause many diseases by interfering the regular metabolism and immune system. Genome-wide association studies and subsequent meta-analyses showed that differentially expressed genes (DEGs) in cervical cancer are more likely to locate in the region of frequent chromosomal aberration [9,10,11,12]. Compared to the microbial community in NCL-HPV negative ones, these in cervical cancer samples have higher variation within groups. All these findings implicate that cervical microbiota is an important clue in the research of the cervical cancer pathology. In order to understand how the microbial community interplay with host genes and cause cell carcinoma in the molecular level, more and more research groups make efforts of identify key factors, known as cancercausing agents, which can drive the progress of cervical carcinogenesis
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