A bioinformatics approach to elucidate conserved genes and pathways in C. elegans as an animal model for cardiovascular research

Abstract

Cardiovascular disease (CVD) is a collective term for disorders of the heart and blood vessels. The molecular events and biochemical pathways associated with CVD are difficult to study in clinical settings on patients and in vitro conditions. Animal models play a pivotal and indispensable role in CVD research. Caenorhabditis elegans, a nematode species, has emerged as a prominent experimental organism widely utilized in various biomedical research fields. However, the specific number of CVD-related genes and pathways within the C. elegans genome remains undisclosed to date, limiting its in-depth utilization for investigations. In the present study, we conducted a comprehensive analysis of genes and pathways related to CVD within the genomes of humans and C. elegans through a systematic bioinformatic approach. A total of 1113 genes in C. elegans orthologous to the most significant CVD-related genes in humans were identified, and the GO terms and pathways were compared to study the pathways that are conserved between the two species. In order to infer the functions of CVD-related orthologous genes in C. elegans, a PPI network was constructed. Orthologous gene PPI network analysis results reveal the hubs and important KRs: pmk-1, daf-21, gpb-1, crh-1, enpl-1, eef-1G, acdh-8, hif-1, pmk-2, and aha-1 in C. elegans. Modules were identified for determining the role of the orthologous genes at various levels in the created network. We also identified 9 commonly enriched pathways between humans and C. elegans linked with CVDs that include autophagy (animal), the ErbB signaling pathway, the FoxO signaling pathway, the MAPK signaling pathway, ABC transporters, the biosynthesis of unsaturated fatty acids, fatty acid metabolism, glutathione metabolism, and metabolic pathways. This study provides the first systematic genomic approach to explore the CVD-associated genes and pathways that are present in C. elegans, supporting the use of C. elegans as a prominent animal model organism for cardiovascular diseases.

Keywords: C. elegans; Animal models; Cardiovascular disease; Orthologous genes; PPI network.

Figure 1

Schematic representation of the methodology of study showing the cardiovascular disease proteins were compared and analyzed.

Figure 2

Identification of key regulators using three attributes of CVD PPI Network. (A–C) Topological properties of the top 20 DEGs in terms of centrality measurements of degree, betweenness, and closeness. (D) Intersections among top ten genes having the highest centrality values of closeness, betweenness and degree. 11 common genes among the top 20 genes of each of topological parameter. (E) Bar plot showing the fold change for expression of 11 key regulators in individual healthy control and CVD patients. The red bar shows log2 foldchange of upregulated genes and green bars shows log2 foldchange of downregulated genes.

Figure 3

Relative expression of 11 key regulators normalized (norm) signal values between healthy controls and CVD patients. IL1B: interleukin 1 beta; JUN: Jun proto-oncogene, AP-1 transcription factor subunit; FN1: fibronectin 1; CXCL8: C-X-C motif chemokine ligand 8; TLR4: toll-like receptor 4; PTPRC: protein tyrosine phosphatase, receptor type C; MAPK3: mitogen-activated protein kinase 3; HSP90AA1: heat shock protein 90 alpha family class A member 1; IL6: interleukin 6; STAT3: signal transducer and activator of transcription 3; MYC: v-myc avian myelocytomatosis viral oncogene homolog.

Figure 4

C. elegans orthologous gene PPI regulatory network of the top ten hub genes of CVD. Regulatory network of the top ten (A) Degree genes (B) Betweenness centrality genes (C) Closeness centrality genes (D) Bottleneck genes. (E) Intersections among top 20 genes having the highest degree and centrality values of closeness, betweenness. 10 common genes among the top twenty genes of each of topological parameter.

Figure 5

Top 4 modules of C. elegans orthologous gene PPI Network: (A) Module 1 has 24 nodes and 276 edges with a score of 24.000; (B) Module 2 has 49 nodes and 361 edges with a score of 15.042; (C) Module 3 has 17 nodes and 114 edges with a score of 14.250 and (D) Module 4 has 8 nodes and 25 edges with a score of 7.143.

Figure 6

Functional comparison of the protein associated with CVD in humans and C. elegans. (A) Biological pathways of CVD proteins in humans and C. elegans using KEGG pathways with p-values. (B) Bar plot shows pathways comparison of the protein associated with CVD in humans and C. elegans. Y-axes represent no. of proteins and X-axis represents pathways.

Figure 7

Functional enrichment analysis of C. elegans orthologous genes. (A) The significant enriched biological process of targeted C. elegans orthologous genes. (B) The significantly enriched cellular component, (C) The significant enriched molecular function and (D) KEGG Pathway. Dot size indicate count. The count represents the number of genes associated with each process. The dot colour denotes the p values of process, and the x-axis represents the fold enrichment score. The red colour text represents the similar gene enrichment and Pathways in humans and C. elegans.