Laboratory Animal and Comparative Medicine ›› 2024, Vol. 44 ›› Issue (5): 531-542.DOI: 10.12300/j.issn.1674-5817.2024.031
• Animal Models of Human Diseases • Previous Articles Next Articles
QI Longju1(), CHEN Shiyuan1,3, LIAO Zehua1,3, SHI Yuanhu1,3, SUN Yuyu1, WANG Qinghua2(
)(
)
Received:
2024-02-27
Revised:
2024-08-06
Online:
2024-10-25
Published:
2024-11-06
Contact:
WANG Qinghua
CLC Number:
QI Longju,CHEN Shiyuan,LIAO Zehua,et al. Transcriptomic Analysis of Menstrual Blood-Derived Stem Cells Transplantation Combined with Exercise Training in Promoting Spinal Cord Injury Recovery in Rats[J]. Laboratory Animal and Comparative Medicine, 2024, 44(5): 531-542. DOI: 10.12300/j.issn.1674-5817.2024.031.
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URL: https://www.slarc.org.cn/dwyx/EN/10.12300/j.issn.1674-5817.2024.031
Figure 1 Distribution of gene expression and principal component analysis of spinal cord tissue samples in the two groups of ratsNote:A showed the distribution of sample expression levels (FPKM, fragments per kilobase of exon model per million mapped fragments); in the figure, the median, interquartile range and extreme values of the samples in SCI (spinal cord injury, as the control, n=3) group and the CTMT (the transplantation of menstrual blood-derived stem cells combined with treadmill training after SCI surgery, n=3) group were relatively close, which indicated that the sequencing results were more homogeneous within the group and the sequencing data quality was high. B showed the principal components analysis (PC1, principal component 1; PC2, principal component 2), and the samples from the same group were clustered together with close proximity, and the differences between samples mainly arose from intergroup differences.
表达上调基因 Up-regulated gene | log2(差异倍数) log2 (FoldChange) | t值 t value | P值 P value | 表达下调基因 Down-regulated gene | log2(差异倍数) log2 (FoldChange) | t值 t value | P值 P value | |
---|---|---|---|---|---|---|---|---|
Psme3 | 2.542 363 895 | 2.672 366 157 | 0.040 381 267 | Ptpdc1 | -0.941 169 616 | -2.823 151 331 | 0.033 418 310 | |
Fgd2 | 1.870 409 798 | 5.277 683 881 | 0.002 476 179 | RT1-N2 | -0.961 937 408 | -3.508 946 559 | 0.014 746 432 | |
Sdc4 | 1.591 559 898 | 2.530 079 050 | 0.048 412 378 | Cd79al | -1.007 349 648 | -3.292 831 274 | 0.018 934 378 | |
Cthrc1 | 1.259 963 833 | 3.177 793 692 | 0.021 693 595 | Six4 | -1.071 889 332 | -15.482 205 520 | 0.000 009 930 | |
RGD1302996 | 1.205 943 515 | 12.811 980 370 | 0.000 027 300 | Matn2 | -1.137 472 728 | -3.927 529 073 | 0.009 277 287 | |
Rabepk | 1.201 118 420 | 2.962 815 910 | 0.028 125 989 | Clec4a3 | -1.273 541 156 | -2.512 270 495 | 0.049 532 946 | |
Bdnf | 1.141 863 432 | 3.525 110 815 | 0.001 447 754 | AABR07051551.2 | -1.308 692 094 | -2.825 531 707 | 0.033 319 465 | |
Pkig | 1.036 827 364 | 6.255 767 217 | 0.001 095 780 | Cmtm3 | -1.324 596 882 | -5.371 453 966 | 0.002 279 345 | |
AABR07065925.1 | 0.970 924 295 | 6.151 591 228 | 0.001 189 396 | Dpy19l3 | -1.623 739 520 | -3.419 084 313 | 0.016 347 174 | |
Ehmt1 | 0.944 670 184 | 6.578 534 619 | 0.000 855 702 | Cd74 | -2.034 312 055 | -2.712 776 259 | 0.038 372 308 | |
AABR07062152.1 | 0.939 321 669 | 6.344 499 009 | 0.001 022 741 | Cxcl13 | -2.697 259 120 | -3.378 916 162 | 0.017 124 825 | |
Ctbp1 | 0.898 198 041 | 5.961 511 123 | 0.001 385 227 | RGD1563231 | -3.151 695 504 | -2.603 665 774 | 0.044 063 014 | |
Akr1b10 | 0.859 136 478 | 3.868 507 287 | 0.009 887 528 | Jchain | -3.390 915 739 | -2.827 200 269 | 0.033 250 368 | |
Ssh1 | 0.818 982 469 | 5.813 203 431 | 0.001 564 263 | Ighm | -3.673 986 054 | -3.369 414 954 | 0.017 314 754 | |
Piga | 0.785 438 853 | 3.303 450 635 | 0.018 700 031 | AABR07060872.1 | -5.052 108 514 | -3.355 872 330 | 0.017 589 546 |
Table 1 Significantly up-regulated and down-regulated genes in spinal cord tissues of spinal cord injury rats after transplantation of menstrual blood-derived stem cells combined with exercise training
表达上调基因 Up-regulated gene | log2(差异倍数) log2 (FoldChange) | t值 t value | P值 P value | 表达下调基因 Down-regulated gene | log2(差异倍数) log2 (FoldChange) | t值 t value | P值 P value | |
---|---|---|---|---|---|---|---|---|
Psme3 | 2.542 363 895 | 2.672 366 157 | 0.040 381 267 | Ptpdc1 | -0.941 169 616 | -2.823 151 331 | 0.033 418 310 | |
Fgd2 | 1.870 409 798 | 5.277 683 881 | 0.002 476 179 | RT1-N2 | -0.961 937 408 | -3.508 946 559 | 0.014 746 432 | |
Sdc4 | 1.591 559 898 | 2.530 079 050 | 0.048 412 378 | Cd79al | -1.007 349 648 | -3.292 831 274 | 0.018 934 378 | |
Cthrc1 | 1.259 963 833 | 3.177 793 692 | 0.021 693 595 | Six4 | -1.071 889 332 | -15.482 205 520 | 0.000 009 930 | |
RGD1302996 | 1.205 943 515 | 12.811 980 370 | 0.000 027 300 | Matn2 | -1.137 472 728 | -3.927 529 073 | 0.009 277 287 | |
Rabepk | 1.201 118 420 | 2.962 815 910 | 0.028 125 989 | Clec4a3 | -1.273 541 156 | -2.512 270 495 | 0.049 532 946 | |
Bdnf | 1.141 863 432 | 3.525 110 815 | 0.001 447 754 | AABR07051551.2 | -1.308 692 094 | -2.825 531 707 | 0.033 319 465 | |
Pkig | 1.036 827 364 | 6.255 767 217 | 0.001 095 780 | Cmtm3 | -1.324 596 882 | -5.371 453 966 | 0.002 279 345 | |
AABR07065925.1 | 0.970 924 295 | 6.151 591 228 | 0.001 189 396 | Dpy19l3 | -1.623 739 520 | -3.419 084 313 | 0.016 347 174 | |
Ehmt1 | 0.944 670 184 | 6.578 534 619 | 0.000 855 702 | Cd74 | -2.034 312 055 | -2.712 776 259 | 0.038 372 308 | |
AABR07062152.1 | 0.939 321 669 | 6.344 499 009 | 0.001 022 741 | Cxcl13 | -2.697 259 120 | -3.378 916 162 | 0.017 124 825 | |
Ctbp1 | 0.898 198 041 | 5.961 511 123 | 0.001 385 227 | RGD1563231 | -3.151 695 504 | -2.603 665 774 | 0.044 063 014 | |
Akr1b10 | 0.859 136 478 | 3.868 507 287 | 0.009 887 528 | Jchain | -3.390 915 739 | -2.827 200 269 | 0.033 250 368 | |
Ssh1 | 0.818 982 469 | 5.813 203 431 | 0.001 564 263 | Ighm | -3.673 986 054 | -3.369 414 954 | 0.017 314 754 | |
Piga | 0.785 438 853 | 3.303 450 635 | 0.018 700 031 | AABR07060872.1 | -5.052 108 514 | -3.355 872 330 | 0.017 589 546 |
Figure 2 Volcano plot and clustered heatmap of differentially expressed genes in spinal cord tissues between the two groups of ratsNote: A, in volcano plot, horizontal axis indicated the fold change in the gene expression, the vertical axis indicated the statistical significance of differential gene expression profile, the red and blue dots indicated the upregulated and downregulated genes, respectively, and the gray dots indicated the non-DEGs; B, in clustered heatmap, the horizontal axis indicated the sample names, the vertical axis indicated gene names, the pink indicated highly expressed genes, and the blue indicated low expressed genes. SCI was the control group (spinal cord injury, as the control, n=3), and CTMT was the cell and treadmill training group (the transplantation of menstrual blood-derived stem cells combined with treadmill training after SCI surgery, n=3).
Figure 3 GO enrichment and KEGG pathway enrichment analyses of differentially expressed genes in spinal cord tissues of the two groups of ratsNote:A-C indicated the 3 analysis ontologies for Gene Ontology (GO) enrichment analysis, including molecular function (A), cellular components (B) and biological processes (C), respectively. D represented the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The X-axis represented the fold enrichment, the Y-axis represented the enrichment items, and the bubble size indicated the number of genes enriched on each item. The larger the bubble, the greater the number of enriched genes. The color corresponded to P-value. The darker the red color, the more significant the difference.
信号通路名 Term of signal pathway | 计数 Count | 富集系数 Gene ratio | P值 P value | 基因名 Genes |
---|---|---|---|---|
Rap1 signaling pathway | 10 | 2.506 265 664 | 0.010 546 665 | Angpt1, Rassf5、Vegfb、Lpar1、Rapgef6、Efna4、Met、Bcar1、Rap1gap、Adcy6 |
Fluid shear stress and atherosclerosis | 8 | 2.005 012 531 | 0.014 625 259 | Prkaa1、Mef2c、Sdc4、Gsta4、Il1r2、Gstt3、Hmox1 |
PI3K-Akt signaling pathway | 13 | 3.258 145 363 | 0.014 714 234 | Prkaa1、Itga4、Angpt1、Bdnf、 Lama4、Lpar1、Vegfb、Ppp2r3b、Efna4、Gng7、Spp1、Col9a3、Met |
ECM-receptor interaction | 6 | 1.503 759 398 | 0.016 252 600 | Sdc4、Itga4、Rgd1565355、Lama4、Spp1、Col9a3 |
Cytokine-cytokine receptor interaction | 11 | 2.756 892 231 | 0.016 582 561 | Cxcl10、Cntf、Il25、Tnfsf15、Tnfrsf9、Il1r2、Il21r、Ccr7、Ltb、Cxcl13、Ccl17 |
IL-17 signaling pathway | 6 | 1.503 759 398 | 0.020 227 194 | Cxcl10、Il25、Traf3、Mmp3、Lcn2、Ccl17 |
Pathways in cancer | 17 | 4.260 651 629 | 0.020 758 687 | Ctbp1、Lama4、Lpar1、Vegfb、Gstt3、Adcy6、Dll4、Gsta4、Peg12、Traf3、Gng7、Rassf5、Ccdc6、Hmox1、E2f3、Met |
Chemical carcinogenesis- DNA adducts | 5 | 1.253 132 832 | 0.040 451 734 | Cyp3a9、Hpgds、Gsta4、Gstt3 |
Cholesterol metabolism | 4 | 1.002 506 266 | 0.053 168 933 | Rgd1565355、Apoh、Apoc1、Apoc3 |
Focal adhesion | 8 | 2.005 012 531 | 0.054 767 437 | Itga4、Lama4、Vegfb、Spp1、Col9a3、 Pip5k1c、Met、Bcar1 |
Metabolic pathway | 36 | 9.022 556 391 | 0.068 256 357 | Mtmr2、Gldc、Mtmr14、Pde3b、Gstt3、Hexd、Ehmt1、Adcy6、Abo、Selenbp1、Cyp3a9、Hpgds、Neu4、Spp1、Hmox1、St3gal6、Ca8、Pip5k1c、Csgalnact1、Car1、Uros、Qrsl1、 Coq7、Sirt3、Nt5c3b、Akr1b10、 Cyp2u1、Gsta4、Akr1c15、P4ha3、Piga、Cat、Acot1、Idnk |
Mineral absorption | 4 | 1.002 506 266 | 0.072 932 376 | Atp7b、Slc40a1、Hmox1、Slc39a4 |
Toll-like receptor signaling pathway | 5 | 1.253 132 832 | 0.074 076 217 | Cxcl10、Irf3、Traf3、Spp1、Tlr3 |
Human papillomavirus infection | 11 | 2.756 892 231 | 0.079 092 324 | Irf3、Itga4、Traf3、Rt1-N2、Lama4、Spp1、Col9a3、Ppp2r3b、Rt1-T24-1、Tlr3、Llgl1 |
Glycosphingolipid biosynthesis | 3 | 0.751 879 699 | 0.081 761 102 | St3gal6、Abo |
Table 2 Results of KEGG pathway enrichment analysis of differentially expressed genes in spinal cord tissues of the two groups of rats
信号通路名 Term of signal pathway | 计数 Count | 富集系数 Gene ratio | P值 P value | 基因名 Genes |
---|---|---|---|---|
Rap1 signaling pathway | 10 | 2.506 265 664 | 0.010 546 665 | Angpt1, Rassf5、Vegfb、Lpar1、Rapgef6、Efna4、Met、Bcar1、Rap1gap、Adcy6 |
Fluid shear stress and atherosclerosis | 8 | 2.005 012 531 | 0.014 625 259 | Prkaa1、Mef2c、Sdc4、Gsta4、Il1r2、Gstt3、Hmox1 |
PI3K-Akt signaling pathway | 13 | 3.258 145 363 | 0.014 714 234 | Prkaa1、Itga4、Angpt1、Bdnf、 Lama4、Lpar1、Vegfb、Ppp2r3b、Efna4、Gng7、Spp1、Col9a3、Met |
ECM-receptor interaction | 6 | 1.503 759 398 | 0.016 252 600 | Sdc4、Itga4、Rgd1565355、Lama4、Spp1、Col9a3 |
Cytokine-cytokine receptor interaction | 11 | 2.756 892 231 | 0.016 582 561 | Cxcl10、Cntf、Il25、Tnfsf15、Tnfrsf9、Il1r2、Il21r、Ccr7、Ltb、Cxcl13、Ccl17 |
IL-17 signaling pathway | 6 | 1.503 759 398 | 0.020 227 194 | Cxcl10、Il25、Traf3、Mmp3、Lcn2、Ccl17 |
Pathways in cancer | 17 | 4.260 651 629 | 0.020 758 687 | Ctbp1、Lama4、Lpar1、Vegfb、Gstt3、Adcy6、Dll4、Gsta4、Peg12、Traf3、Gng7、Rassf5、Ccdc6、Hmox1、E2f3、Met |
Chemical carcinogenesis- DNA adducts | 5 | 1.253 132 832 | 0.040 451 734 | Cyp3a9、Hpgds、Gsta4、Gstt3 |
Cholesterol metabolism | 4 | 1.002 506 266 | 0.053 168 933 | Rgd1565355、Apoh、Apoc1、Apoc3 |
Focal adhesion | 8 | 2.005 012 531 | 0.054 767 437 | Itga4、Lama4、Vegfb、Spp1、Col9a3、 Pip5k1c、Met、Bcar1 |
Metabolic pathway | 36 | 9.022 556 391 | 0.068 256 357 | Mtmr2、Gldc、Mtmr14、Pde3b、Gstt3、Hexd、Ehmt1、Adcy6、Abo、Selenbp1、Cyp3a9、Hpgds、Neu4、Spp1、Hmox1、St3gal6、Ca8、Pip5k1c、Csgalnact1、Car1、Uros、Qrsl1、 Coq7、Sirt3、Nt5c3b、Akr1b10、 Cyp2u1、Gsta4、Akr1c15、P4ha3、Piga、Cat、Acot1、Idnk |
Mineral absorption | 4 | 1.002 506 266 | 0.072 932 376 | Atp7b、Slc40a1、Hmox1、Slc39a4 |
Toll-like receptor signaling pathway | 5 | 1.253 132 832 | 0.074 076 217 | Cxcl10、Irf3、Traf3、Spp1、Tlr3 |
Human papillomavirus infection | 11 | 2.756 892 231 | 0.079 092 324 | Irf3、Itga4、Traf3、Rt1-N2、Lama4、Spp1、Col9a3、Ppp2r3b、Rt1-T24-1、Tlr3、Llgl1 |
Glycosphingolipid biosynthesis | 3 | 0.751 879 699 | 0.081 761 102 | St3gal6、Abo |
Figure 4 Protein-protein interaction network of differentially expressed genes in spinal cord tissues of the two groups of ratsNote:The size of the dots represented the node and degree, the node with more connections had a larger size; the red color in the dots represented the up-regulation of gene expression in this node, and the blue color represented the down-regulation of gene expression.
Figure 5 Menstrual blood-derived stem cells transplantation combined with treadmill training promotes motor function recovery and BDNF expression in spinal cord injury ratsNote:A showed the local structural pathological changes of the spinal cord injury in the SCI group (spinal cord injury, as the control, n=3) and the CTMT group (the transplantation of menstrual blood-derived stem cells combined with treadmill training after SCI surgery, n=3), observed by hematoxylin-eosin staining (magnified 40 times). B, statistical results of the lesion area in Figure A (***P<0.001, n=3). C, BBB motor score, a higher score indicated a better recovery of motor function. D, Real-time fluorescence quantitative PCR was performed to detect the changes in the transcriptional level of Bdnf gene in the injured spinal cord in rats of SCI and CTMT groups (***P<0.001, n=5). E, Western blotting analysis was performed to detect the changes in the protein level of BDNF in SCI and CTMT groups (***P<0.001, n=5).
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