Integrative Analysis of Regulatory Module Reveals Associations of Microgravity with Dysfunctions of Multi-body Systems and Tumorigenesis

Abstract

Previous studies have demonstrated that microgravity could lead to health risks. The investigation of the molecular mechanisms from the aspect of systems biology has not been performed yet. Here, we integratively analyzed transcriptional and post-transcriptional regulations based on gene and miRNA expression profiles in human peripheral blood lymphocytes cultured in modeled microgravity. Two hundred and thirty dysregulated TF-miRNA (transcription factor and microRNA) feed-forward loops (FFLs) were identified in microgravity. The immune, cardiovascular, endocrine, nervous and skeletal system subnetworks were constructed according to the functions of dysregulated FFLs. Taking the skeletal system as an example, most of genes and miRNAs in the subnetwork were involved in bone loss. In addition, several drugs have been predicted to have potential to reduce bone loss, such as traditional Chinese medicines Emodin and Ginsenoside Rh2. Furthermore, we investigated the relationships between microgravity and 20 cancer types, and found that most of cancers might be promoted by microgravity. For example, rectum adenocarcinoma (READ) might be induced by microgravity through reducing antigen presentation and suppressing IgA-antibody-secreting cells' migration. Collectively, TF-miRNA FFL might provide a novel mechanism to elucidate the changes induced by microgravity, serve as drug targets to relieve microgravity effects, and give new insights to explore the relationships between microgravity and cancers.

Keywords: cancer; drug; feed-forward loop; miRNA; microgravity; regulatory network.

Figure 1

Three types of feed-forward loops (FFLs) and functional analysis of the dysregulated FFLs. (A). TF-FFL: transcription factor (TF) and microRNA (miRNA) regulate gene; TF regulates miRNA. (B). miRNA-FFL: TF and miRNA regulate gene; miRNA regulates TF. (C). FB-FFL (feed-back FFL): TF and miRNA regulate gene; TF and miRNA mutually regulate each other. Pathway enrichment analysis for genes (D) and miRNAs (E) in the dysregulated FFLs, respectively. The length of blue and red bar represents the number of genes (miRNAs) and –log10(p-value), respectively. The pink bar represents p-value = 0.05. (F). Dysregulated hub FFL subnetwork. Red and green represent upregulation and downregulation, respectively. The darker color represents larger |log₂FC| value. The diamond, triangle and circular node represent TF, miRNA and gene, respectively. The blue stars indicate the known cancer genes. (G). Proportion of the known cancer genes in the hub FFL network, dysregulated FFL network and background regulatory network.

Figure 2

System function-related FFLs. (A). System function-related FFLs in five systems including immune, cardiovascular, endocrine, nervous and skeletal systems, which encoded by green, blue, red, yellow and purple, respectively. Edges connect the FFLs with the functions of body systems. (B). Number of dysregulated TF-FFLs (red), miRNA-FFLs (green) and FB-FFLs (purple) in microgravity for five human body systems.

Figure 3

Subnetworks for five human body systems. The red diamond, green triangle and grey circular node represent TF, miRNA and gene, respectively.

Figure 4

Five human body system subnetwork analysis and candidate drugs for bone loss. Venn diagram of nodes (A) and edges (B) in five subnetworks. (C). Modules shared by at least three subnetworks. The diamond, triangle and circular node represent TF, miRNA and gene, respectively. The colors of the circle outside the module represent corresponding systems. (D). Heatmap of genes and miRNAs in skeletal system subnetwork. Purple and blue text represent that the gene or miRNA functions are related to osteoblast and osteoclast, respectively. (E). Skeletal system subnetwork and the potential drugs reversing bone loss. Red and green represent upregulation and downregulation, respectively. The darker color represents larger |log₂FC| value. The diamond, triangle and circular node represent TF, miRNA and gene, respectively.

Figure 5

Relationships between microgravity and cancers. (A). Wilcoxon rank-sum test results. (B). Pathway enrichment analysis for 115 DE genes. The length of blue and red bar represents the number of genes and −log10(p-value), respectively. The pink bar represents p-value = 0.05. (C). Boxplots of the expression of six genes (HLA-DPA1, HLA-DQA1, HLA-DPB1, HLA-DMB, CXCL12 and TNFSF13) in rectum adenocarcinoma (READ) samples and microgravity samples. (D). Intestinal immune network for IgA production pathway. The green box represents the downregulated gene enriched in the pathway.