Identification of Hub Genes Associated with Diabetes Mellitus and Tuberculosis Using Bioinformatic Analysis

Figures & data

Table 1 Details of GEO Data

Accession	Platform	Experiment Type	Group	Tissue Type
GSE114192	GPL18573	High throughput sequencing	46 TB, 52DM, 61 TB with DM patients and 36 controls	Whole blood
GSE102677	GPL18573	High throughput sequencing	11 MET+TB treated and 11 TB treated	PBMCs

Abbreviations: DM, diabetes mellitus; GEO, Gene Expression Omnibus; TB, tuberculosis; MET, metformin; PBMCs, peripheral blood mononuclear cells.

Figure 1 Identification of DEGs in TB, DM, and HC samples. (A) 478 significant DEGs detected in TB as compared to HC samples. (B) 126 significant DEGs detected in DM as compared to HC samples. (C) 869 significant DEGs detected in TB+DM as compared to HC samples. Red dots represent selected up-regulated genes and blue dots represent selected down-regulated genes. Black dots represent genes with no significant inter-group expression differences. (D) 350 DEGs shared by both TB and TB+DM groups. (E) 72 DEGs shared by both DM and TB+DM groups.

Abbreviations: DEGs, differentially expressed genes; TB, tuberculosis; DM, diabetes mellitus; HC, healthy control.

Figure 2 Functional enrichment analysis of common DEGs. (A–D) represent results of BP, CC, MF, and KEGG pathway analyses of DEGs, respectively.

Abbreviations: DEGs, differentially expressed genes; BP, biological process; CC, cellular component; MF, molecular function; KEGG, Kyoto Encyclopedia of Genes and Genomes.

Table 2 Top 10 Hub Genes

Rank	Name	Full Name	Pathway Involved
1	STAT1	Signal transducer and activator of transcription 1	Influenza A, Toll-like receptor signaling pathway
2	IFIT3	Interferon induced protein with tetratricopeptide repeats 3	/
3	RSAD2	Radical S-adenosyl methionine domain containing 2	Influenza A
4	IFI44L	Interferon induced protein 44 like	/
5	GBP1	Guanylate binding protein 1	/
6	XAF1	XIAP associated factor 1	/
7	IRF7	Interferon regulatory factor 7	Influenza A, RIG-I-like receptor signaling pathway, Toll-like receptor signaling pathway
8	ISG15	ISG15 ubiquitin like modifier	RIG-I-like receptor signaling pathway
9	IFI44	Interferon induced protein 44	/
10	IFI6	Interferon alpha inducible protein 6	/

Notes: Pathways with P < 0.05 were considered significantly enriched pathways.

Figure 3 PPI network analysis. (A) Ten hub genes were selected using the plug-in cytoHubba of Cytoscape based on MCC scores. (B) Interactions between MET target genes and hub genes. Dots represent genes and edges represent functional connections between genes.

Abbreviations: PPI, protein–protein interaction; MCC, maximal clique centrality; MET, metformin.

Figure 4 Relative expression of hub genes including (A) STAT1, (B) IFIT3, (C) RSAD2, (D) IFI44L, (E) GBP1, (F) XAF1, (G) IRF7, (H) IFI44L, and (I) IFI6 as measured by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). RQ represents relative quantification values; *Represents P-value <0.05.

Table 3 miRNA and Its Target Genes

miRNA	Genes Targeted by miRNA	Gene Count
miR-3680-3p	IFI44L, XAF1	2
miR-3059-5p	IFI44L, RSAD2	2
miR-629-3p	IFI44L, STAT1	2
miR-29b-2-5p	XAF1, RSAD2	2
miR-514b-5p	XAF1, STAT1	2
miR-4755-5p	RSAD2, STAT1	2
miR-4691-3p	RSAD2, STAT1	2

Figure 5 Interaction network between hub genes and their targeted miRNAs. Red dots represent hub genes, orange dots represent miRNAs, and blue dots represent miRNAs targeting two genes simultaneously.

Figure 6 Gene expression changes of ten hub genes after MET treatment of MTB-infected PBMCs. (A) Hierarchical clustering heatmap of hub genes of MET+MTB and MTB groups. Red indicates relatively up-regulated gene expression, blue indicates relatively down-regulated gene expression, and white indicates no significant change in gene expression. (B–K) Representative gene expression profiles of 11 MET+MTB-treated PBMCs and 11 MTB-treated PBMCs. *Represents P-value <0.05.

Abbreviations: MET, metformin; MTB, Mycobacterium tuberculosis; PBMCs, peripheral blood mononuclear cells.