Differentially expressed genes.
The analysis of DE genes between the 100μg DNA IM group and 50μg DNA EP
group was shown in Figure 3. The concordance rates of down-regulated and
up-regulated DE genes between the two groups were 56.9% and 53.2%,
respectively. First, we screened out the top 20 up-regulated DE genes
and down-regulated DE genes in the 100μg DNA IM group, and then counted
the differential expression levels of these DE genes in the TB model
group and 50μg DNA EP group (Supplementary Table 1, 2). Second, we
screened out the top 20 up-regulated DE genes and down-regulated DE
genes in the 50μg EP group, and then collected the differential
expression levels of these DE genes in the TB model group and 100μg DNA
IM group (Supplementary Table 3, 4). Finally, we compared the
consistency of DE genes in four tables to analyze the commonality of the
action targets of the two vaccination methods (IM and EP) in the mouse
TB model. The results showed that: (1) Of the top 20 down-regulated and
the top 20 up-regulated DE genes in the 100μg DNA IM group and 50μg DNA
EP group, 18 (81.8%) down-regulated DE genes and 13 (48.1%)
up-regulated DE genes between the two groups were the same. (2) Most of
the DE genes significantly down-regulated in the 100μg DNA IM group and
50μg DNA EP group were related to the digestion and absorption of
nutrients or neuroendocrine, for example, dysfunction of the pancreatic
island (Iapp, Scg2, Chga, Chgb), metabolism of carbohydrate and glycogen
(Amy2a5, Gcg, Ins1), protein hydrolysis (Try5, Cpa1, Gm13011, Try4,
Cpb1), lipid metabolism (Ins1, Pnlip), neuroendocrine (Vstm2l, Resp18),
etc. Most of the significantly up-regulated DE genes were related to the
cellular structural proteins and cellular functional proteins, in which
alveolar cell structure and function proteins account for a large
proportion, for example, Sftpc, Sftpc, Sftpb, Sftpd, Sftpa1, Wfdc2,
Sec14l3, Postn, Cldn5, Aqp5, Emp2, and Foxf1, etc. (3) The expressions
of the top 20 DE genes in 100μg DNA IM group and 50μg DNA EP group,
whether up-regulated or down-regulated, were opposite to those in the TB
model group.