Profiling the mRNA and miRNA in Peripheral Blood Mononuclear Cells in Subjects with Active Tuberculosis

Figures & data

Table 1 Clinical Characteristics of the Participants

ID	T1	T2	T3	T4	H1	H2	H3	H4
Gender	Female	Male	Female	Female	Male	Female	Female	Female
Age	23	24	56	45	47	34	28	27
Cough for>2 weeks	+	+	+	+	-	-	-	-
Fever for>2 weeks	+	-	-	+	-	-	-	-
T-SPOT	+	+	+	+	-	-	-	-
GeneXpert	+	+	+	+	NA	NA	NA	NA
Radiographic features	+	+	+	+	NA	NA	NA	NA
HIV	-	-	-	-	-	-	-	-
HBV	-	-	-	-	-	-	-	-
Cancer	-	-	-	-	-	-	-	-
ADA	18.8	17.3	11.3	11.4	NA	NA	NA	NA
Alb	40.7	34.2	40.3	40.6	49.1	43.1	75.4	53.3
TP	73.7	55.3	67.9	70.8	73.1	72.6	53.3	75.4
RBC	4.14	4.65	3.94	3.65	5.11	4.71	4.33	4.33
HGB	120	116	116	104	153	125	132	132
WBC	7.4	6.2	2.9	6	4.4	7.9	5.4	5.4

Notes: “+” represent “positive”; “-”represent “negative”.

Abbreviations: HIV, human immunodeficiency virus; HBV, hepatitis B virus; NA, not applicable; ADA, adenosine deaminase; Alb, albumin; TP, total protein; RBC, red blood cell; HGB, hemoglobin; WBC, white blood cell.

Figure 1 Volcano plot of differentially expressed genes (DEGs). Red, significantly up-regulated gene; green, significantly down-regulated gene; gray, non-significantly differently expressed gene.

Figure 2 Bubble diagram of top 20 enriched GO terms and KEGG pathways for significantly differentially expressed genes (DEGs) between ATB and HD. (A) Top 20 ranked GO terms of up-regulated DEGs. (B) Top 20 ranked GO terms of down-regulated DEGs. (C) Top 20 pathways of up-regulated DEGs. (D) Top 20 pathways of down-regulated DEGs. Rich factor: the ratio of genes enriched in the GO term (KEGG) to the number of annotation genes, the enrichment degree was stronger with a bigger Rich factor. The size of dots indicates the number of genes in the GO term (KEGG).

Abbreviations: GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes.

Figure 3 Top 2 modules of PPI sub-network by MCODE in Cytoscape software. (A) module 1; (B) module 2.

Table 2 Differentially Expressed miRNAs (DEM) in ATB Compared with HDs

miRNA	Type	Log2FC(ATB/HD)	P-Adjust	Regulate
hsa-miR-941	Known	1.12891203	0.005289709	Up
hsa-miR-760	Known	1.358401543	0.048009942	Up
hsa-miR-23a-5p	Known	1.21548475	0.002130772	Up
hsa-miR-193a-5p	Known	1.049993343	0.003776702	Up
hsa-miR-183-5p	Known	1.743313601	0.028929263	Up
hsa-miR-12,136	Known	1.751294075	0.009083745	Up
6_14541	Novel	2.11648939	0.023954136	Up
3_8196	Novel	1.005929855	0.048009942	Up
2_6381	Novel	3.26489339	0.03996549	Up
hsa-miR-1277-3p	Known	−2.206447856	8.89431E-05	Down
hsa-miR-33a-5p	Known	−2.328391239	0.002130772	Down
hsa-miR-1277-5p	Known	−2.10788954	0.00253324	Down
hsa-miR-19a-3p	Known	−1.27165401	0.005289709	Down
hsa-miR-1307-5p	Known	−1.998188963	0.005289709	Down
hsa-miR-652-5p	Known	−1.165243492	0.005989237	Down
hsa-miR-19b-3p	Known	−1.223579915	0.007794562	Down
hsa-miR-29c-3p	Known	−1.214234207	0.016080995	Down
hsa-miR-33a-3p	Known	−1.05087557	0.017908658	Down
hsa-miR-590-5p	Known	−1.727717534	0.023835661	Down
hsa-miR-590-3p	Known	−1.01612367	0.023954136	Down
hsa-miR-101-3p	Known	−1.248748508	0.039055415	Down
hsa-miR-16-1-3p	Known	−1.954883466	0.042332706	Down
hsa-miR-1537-3p	Known	−2.892938848	0.042332706	Down
hsa-miR-340-5p	Known	−1.12770789	0.048009942	Down
hsa-miR-545-5p	Known	−1.575959365	0.048009942	Down
1_592	Novel	−2.313761221	0.002236797	Down

Figure 4 Intersection genes between DEGs and target gene of DEMs. DEGs, significantly differentially expressed genes (mRNA) between ATB and HD; DEMs, significantly differentially expressed genes (miRNA) between ATB and HD.

Figure 5 MiRNA-mRNA regulatory network was analyzed using Cytoscape software. Diamond-shaped represents miRNAs, and circular nodes represent target genes. Red, up-regulated miRNA or mRNA; green, down-regulated miRNA or mRNA in active tuberculosis subjects.

Figure 6 We analyzed the expression of five miRNAs (hsa-miR-23a-5p, hsa-miR-183-5p, hsa-miR-193a-5p and hsa-miR-941 and hsa-miR-16-1-3p) in 35 active tuberculosis patients versus 35 healthy donors. U6 was used as reference gene. 2-ΔΔCt method was used to quantify RT-qPCR data. Mann–Whitney test was used to evaluate the differences between groups. P value<0.05 was considered statistically significant.

Abbreviation: RT-qPCR, reverse transcription quantitative real-time PCR.