Transcriptome Changes In Dorsal Spinal Cord Of Rats With Neuropathic Pain

Figures & data

Figure 1 CCI of sciatic nerve induces mechanical and thermal hypersensitivity. Paw mechanical withdrawal thresholds (A) and thermal withdrawal latency (B) were assessed with electronic Von Frey and plantar test analgesia meter, respectively, on ipsilateral hind paws of CCI and sham-operated rats. n = 6 in both groups. All data were represented as mean ± SD. Statistical analyses consisted of repeated measures two-way ANOVA tests followed by Sidak’s multiple comparisons tests. ^****P < 0.0001 between Sham and CCI groups.

Table 1 Differentially Expressed microRNAs Between Sham-Operated And CCI Rats

microRNA	Fold Change	Intensity (CCI)	Intensity (Sham)
Upregulated in CCI
rno-miR-1b	18.7	2282	113
rno-miR-98-5p	3.7	784	195
rno-miR-31a-3p	2.6	281	101
rno-miR-376b-5p	2.2	529	218
rno-miR-1-3p	2.2	57	24
rno-miR-214-3p	2.1	37	16
Downregulated in CCI
rno-miR-329-5p	−3.7	226	781
rno-miR-675-5p	−2.9	60	163
rno-miR-342-5p	−2.7	34	84
rno-miR-203a-3p	−2.6	28	66
rno-let-7d-5p	−2.5	121	279
rno-miR-542-5p	−2.4	19	41
rno-miR-672-5p	−2.2	16	32

Table 2 Differentially Expressed lncRNAs Between Sham-Operated And CCI Rats

lncRNA (Seq Name)	Gene Symbol	Fold Change	Raw Intensity (CCI)	Raw Intensity (Sham)
Top 20 upregulated in CCI
XR_356687	LOC102552325	52.5	19,188	364
XR_592109	LOC102546410	22.3	107	5
XR_598798	LOC102549116	15.2	73	5
XR_347276	Fancm	13.9	67	5
XR_347276	Fancm	13.9	67	5
XR_592810	LOC102551503	13.0	63	5
XR_593301	LOC100912242	12.7	61	5
XR_347392	Lin52	8.8	58	7
XR_593865	LOC102550632	8.3	40	5
XR_601438	LOC103692636	7.8	40	5
XR_595336	LOC103693645	6.7	32	5
XR_346855	LOC102548844	5.9	57	10
XR_357290	LOC102553550	5.6	38	7
XR_590881	LOC103691449	5.6	27	5
XR_340868	LOC102550064	5.6	95	18
XR_591045	LOC103691528	5.5	27	5
XR_592900	LOC103692568	5.4	76	15
XR_339110	LOC102548550	5.4	27	5
XR_594520	LOC103693250	5.3	37	7
XR_340350	LOC102553293	5.2	30	6
Top 20 downregulated in CCI
ENSRNOT00000034363	AABR06081233.1	−19.4	183	3600
XR_338868	LOC102546527	−10.9	5	57
NR_046246	Rn28s	−10.9	11,145	113,335
NR_046246	Rn28s	−10.9	11,145	113,335
NR_046246	Rn28s	−10.9	11,145	113,335
NR_046246	Rn28s	−10.9	11,145	113,335
XR_342867	LOC102555707	−10.7	5	55
XR_593141	LOC102550062	−10.4	5	54
XR_591024	LOC102556203	−10.3	5	53
XR_338470	LOC102553477	−9.9	6	60
XR_590615	LOC102552001	−9.8	6	56
XR_590615	LOC102552001	−9.8	6	56
XR_601117	LOC103695264	−9.6	660	6129
XR_352792	LOC102551164	−8.5	5	44
XR_342721	LOC102550786	−8.4	5	44
ENSRNOT00000041435	LOC367333	−8.1	5	42
XR_601956	LOC103695347	−7.8	5	40
XR_589758	LOC103690882	−7.4	5	38
ENSRNOT00000075140	AABR06019245.1	−7.1	5	37
ENSRNOT00000075140	AABR06019245.1	−7.1	5	57

Figure 2 mRNA expression between the CCI and sham-operated rats. (A) Hierarchical clustering shows a differential mRNA expression profiles between two groups. The upregulated mRNAs in the CCI group are shown in red, and the downregulated ones are in green. (B) Box plots show the distribution of mRNAs for the two groups. The distributions (the means, the 25th and 75th percentiles) were nearly the same in the CCI and Sham groups after normalization, indicating that the overall expression of mRNA was uniform between the two groups. (C) Scatter plots assess the mRNA expression differences between CCI and Sham groups. The mRNAs above the top green line (indicated with red dot) and below the bottom green line (indicated with green dot) are differential mRNAs (fold change ≥ 2.0 or ≤ −2.0, respectively), while mRNAs with no expression difference are represented with black dots between the two border lines.

Table 3 Differentially Expressed mRNAs Between Sham-Operated And CCI Rats

mRNA (Seq Name)	Gene Symbol	Fold Change	Raw Intensity (CCI)	Raw Intensity (Sham)
Top 20 upregulated in CCI
NM_212504	Hspa1b	23.9	4098	172
NM_001024740	Ccdc116	16.4	141	9
NM_001025028	Fam35a	15.5	74	5
NM_001017496	Cxcl13	12.8	366	30
ENSRNOT00000008897	Ptprd	11.6	378	35
NM_001113390	Ptprr	11.0	53	5
NM_080694	Cacng6	9.6	134	15
NM_001108873	Tnfrsf10b	9.6	105	11
NM_012912	Atf3	8.9	1452	168
ENSRNOT00000044252	Ascl4	8.6	41	5
NM_001000884	Olr1117	8.5	41	5
ENSRNOT00000026719	Col6a3	8.3	72	9
ENSRNOT00000018645	Zc3hav1l	8.2	162	21
NM_053551	Pdk4	7.7	190	27
NM_001031637	Abca17	7.5	42	6
NM_001145755	Nlrp1a	6.7	93	15
ENSRNOT00000010289	Apold1	6.7	2507	381
ENSRNOT00000049430	Rbbp6	6.4	365	62
NM_019216	Gdf15	6.3	31	5
NM_001145072	Iqcf5	6.2	59	10
Top 20 downregulated in CCI
NM_001108582	Dapl1	−22.0	11	240
ENSRNOT00000032726	Cylc2	−15.2	6	92
NM_133292	Sval1	−13.8	5	72
ENSRNOT00000065875	AABR06030627.1	−13.1	12	163
NM_001108480	Bcl2l12	−9.7	5	50
NM_001305124	Tmem220	−9.4	147	1431
NM_001008931	Vom1r48	−9.0	12	108
ENSRNOT00000046533	LOC287992	−8.3	5	43
NM_001000659	Olr587	−7.8	5	40
ENSRNOT00000038519	Grhl1	−7.6	16	126
NM_001108922	Stk32c	−7.4	424	3119
ENSRNOT00000060162	AABR06088936.1	−7.3	5	38
NM_013030	Slc34a1	−7.1	5	37
NM_001137670	Sept14	−7.1	6	45
NM_019622	Espn	−7.1	266	1939
NM_001277165	Ldb3	−7.0	5	36
NM_001012140	Rab34	−6.7	7	50
NM_001000809	Olr1245	−6.7	5	34
NM_001244797	Cidec	−6.5	9	60
NM_001108926	Cabp4	−6.5	7	49

Figure 3 Gene ontology enrichment analysis. Enriched gene ontology (GO) terms correspond to the 405 differentially upregulated (A-C) mRNAs and 545 downregulated (D-F) mRNAs in CCI group. (A, D) Top 10 significantly (Sig) enriched biological processes (BP) terms for the upregulated and downregulated differentially expressed (DE) mRNAs in CCI group, respectively. (B, E) Top 10 enriched cellular component (CC) terms for the upregulated and downregulated DE mRNAs in CCI group, respectively. (C, F) Top 10 enriched molecular function (MF) terms for the upregulated and downregulated DE mRNAs in CCI group, respectively.

Figure 4 KEGG pathways significantly enriched by differentially expressed mRNAs. (A) Pathways significantly enriched (P < 0.05) by the upregulated mRNAs in CCI group. (B) KEGG pathways significantly enriched (P < 0.05) by the downregulated mRNAs in CCI group.