Data supplement
Supplemental Figure S1. Experimental set-up. (A) The kidney of a healthy donor (healthy-K) was transplanted into a recipient with a healthy heart (healthy-H). (B) The kidney of a CKD donor (CKD-K) was transplanted into healthy-H. (C) Healthy-K was transplanted into a recipient with a CKD heart (CKD-H). (D) CKD-K was transplanted into CKD-H.
Supplemental Figure S2. General characteristics of pairwise comparisons concerning log fold change and adjusted P-values in Volcano (upper row) and MA-plots (lower row) for (A) healthy-Kàhealthy-H vs. CKD-Kàhealthy-H, for (B) healthy-KàCKD-H vs. CKD-KàCKD-H, for (C) healthy-KàCKD-H vs.
healthy-Kàhealthy-H and for (D) CKD-KàCKD-H vs. CKD-Kàhealthy-H. K:
kidney; H: heart.
Supplemental Figure S3: Heatmap of the genes associated with the biological process ‘muscle structure development’, showing Log2FC and p- values (A) and top 15 DEGs based on Log2FC values in CKD-Kàhealthy-H vs. healthy-Kàhealthy-H as identified in RNA-sequencing, also showing P- values (B). Green: upregulated gene expression.
Supplemental Figure S4: Heatmap of the top 15 DEGs based on Log2FC values in CKD-KàCKD-H vs. healthy-KàCKD-H as identified in RNA- sequencing, also showing P-values. Green: upregulated gene expression.
Supplemental Figure S5: Heatmap of the top 15 DEGs based on Log2FC values in CKD-Kàhealthy-H vs. healthy-Kàhealthy-H as identified in RNA- sequencing, also showing P-values (A). Heatmap of the genes associated with the molecular function of ‘heparin and haptoglobin binding’, showing Log2FC and p-values (B). Red: downregulated gene expression.
Supplemental Figure S6: Heatmap of the genes associated with the
biological process ‘immune response’, showing Log2FC and p-values (A) and top 15 DEGs based on Log2FC values in CKD-KàCKD-H vs. healthy-
KàCKD-H as identified in RNA-sequencing, also showing P-values (B). Red:
downregulated gene expression.
Supplemental Figure S7. Venn diagrams of exclusive and common DEGs for shared up-regulated molecular functions: Sulfur compound binding (A,C), Glycosaminoglycan binding (B,D), Signaling receptor binding (E,G) and Heparin binding (F,H) for pairwise comparisons healthy-KàCKD-H vs.
healthy-Kàhealthy-H and CKD-KàCKD-H vs. CKD-Kàhealthy-H. Healthy- Kàhealthy-H and CKD-Kàhealthy-H n=6/group and CKD-KàCKD-H and healthy-KàCKD-H n=5/group for RNA-seq. DEG: differentially expressed genes, K: kidney; H: heart.
Supplemental Figure S8: Heatmap of n=25 genes associated with the biological process ‘cellular adhesion’, based on Log2FC, also showing p- values (A) and top 15 DEGs based on Log2FC values in healthy-KàCKD-H
vs. healthy-Kàhealthy-H as identified in RNA-sequencing, also showing P- values (B). Green: upregulated gene expression.
Supplemental Figure S9: Heatmap of n=25 genes associated with the biological process ‘response to cell wounding’, based on Log2FC, also showing p-values (A) and top 15 DEGs based on Log2FC values in CKD- KàCKD-H vs. CKD-Kàhealthy-H as identified in RNA-sequencing, also showing P-values (B). Green: upregulated gene expression.
Supplemental Figure S10. (A) Venn diagram showing the number of DEGs involved in ‘angiogenesis’ and ‘positive regulation of endothelial cell
proliferation’ for pairwise comparisons CKD-Kàhealthy-H vs. healthy- Kàhealthy-H and CKD-KàCKD-H vs. healthy-KàCKD-H. (B) Heat map showing the angiogenesis-associated DEGs, Log2FC changes and P-values.
healthy-Kàhealthy-H and CKD-Kàhealthy-H n=6/group, CKD-KàCKD-H and healthy-KàCKD-H n=5/group for RNA-seq; two-way ANOVA with SNK post-hoc test; *p<0.05. K: kidney; H: heart.
Supplemental Figure S11: Heatmap of the top 15 DEGs based on Log2FC values in healthy-KàCKD-H vs. healthy-Kàhealthy-H as identified in RNA- sequencing, also showing P-values (A) and heatmap of the top 15 DEGs based on Log2FC values in CKD-KàCKD-H vs. CKD-Kàhealthy-H as identified in RNA-sequencing, also showing P-values. Red: downregulated gene expression.
Supplemental Figure S12. (A) Gene network showing significant pathways associated with overlapping genes from the multiple comparison CKD- KàCKD-H vs. CKD-Kàhealthy-H and the rat inflammatory profile
(GO:0006953). (B) Pie chart showing the specific gene clusters associated with the overlapping genes from (A).
Healthy kidney into healthy heart (healthy-K healthy-H)
Healthy kidney into CKD heart (Healthy-K CKD-H)
CKD kidney into healthy heart (CKD-K healthy-H)
CKD kidney into CKD heart (CKD-K CKD-H)
Supplemental Figure S1
A B
C D
A healthy-K healthy-H vs. C
CKD-K healthy-H healthy-K CKD-H vs.
healthy-K healthy-H D CKD-K CKD-H vs.
CKD-K healthy-H
B healthy-K CKD-H vs.
CKD-K CKD-H
Supplemental Figure S2
9.4100×10-7
5.1200×10-9
0.00020.00030.00050.00031.5400×10-9
0.00090.00110.00103.4000×10-9
0.00060.00170.00030.0019
CKD-K è healthy-H vs. healthy-K è healthy-H PenkTfrcAdamtsl2Hspb3Atp6v1g2Prss23Myl9S100a4Xirp2FapHsp90aa1PfkpPtgdsYipf7Csrp2P-value 0.00230.00830.00190.00440.00190.00430.00230.00086.5200×10-8
0.00510.00160.00220.00700.00220.0011 CKD-K è healthy-H vs. healthy-K è healthy-H
Alpk3Ankrd1Casq1Col3a1Csrp2Csrp3Ddit3FlncHacd1HbegfHopxNcam1Nupr1Rcan1Xirp2P-value
Supplemental Figur e S3
AB
0.40700.40740.44500.43190.49570.42390.43370.47810.48560.44660.43220.42620.42950.47940.5213
CKD-K è healthy-H vs. healthy-K è healthy-H Alpk3Ankrd1Casq1Col3a1Csrp2Csrp3Ddit3FlncHacd1HbegfHopxNcam1Nupr1Rcan1Xirp20Log2FC 0.2 0.4 0.60.77150.63560.58600.56210.55970.55780.55060.52710.52130.50950.50920.50230.50190.49860.4957
CKD-K è healthy-H vs. healthy-K è healthy-H PenkTfrcAdamtsl2Hspb3Atp6v1g2Prss23Myl9S100a4Xirp2FapHsp90aa1PfkpPtgdsYipf7Csrp20Log2FC 0.2 0.4 0.6 0.8
Supplemental Figure S4
0.5821 0.5816 0.5077 0.4782 0.4639 0.4607 0.4444 0.4354 0.4297 0.4273 0.4243 0.4148 0.4112 0.4056 0.4012
CKD-Kè CKD-H vs. healthy-Kè CKD-H
AY172581.2 Alas2 Hba1 RGD1306941 Hba2 Gpihbp1 Reln Hcn4 Ptgfr Hbb-b1 Acer2 Ric8b Myo5b Nkx2-5 LOC287167
0 Log2FC
0.2 0.4
0.6 0.0002
0.0002 0.0003 0.0046 0.0008 0.0034 0.0038 0.0026 0.0066 0.0049 0.0073 0.0046 0.0030 0.0049 0.0101
CKD-Kè CKD-H vs. healthy-Kè CKD-H
AY172581.2 Alas2 Hba1 RGD1306941 Hba2 Gpihbp1 Reln Hcn4 Ptgfr Hbb-b1 Acer2 Ric8b Myo5b Nkx2-5 LOC287167
P-value
A
-0.5948 -0.5868 -0.5819 -0.5668 -0.5642 -0.5437 -0.5411 -0.5344 -0.5269 -0.5264 -0.5216 -0.5133 -0.5126 -0.5039 -0.5006
CKD-Kè healthy-H vs. healthy-Kè healthy-H
Hpd Bhlhe41 Sod3 Slc7a4 Wnt5b Ptpru Hba1 Cyp2e1 Cxcl13 Ano5 Ephx1 Rtn4rl2 Agap2 Vtn
Cds1 -0.8
Log2FC
-0.6 -0.4 -0.2 0
Supplemental Figure S5
B
-0.4710 -0.5269 -0.4648 -0.5819 -0.4231 -0.5039
-0.5411 -0.4377
CKD-Kè healthy-H vs. healthy-Kè healthy-H
Ccl7 Cxcl13 Pla2g2d Sod3 Thbs1 Vtn
Hba1 Hba2
-0.4
Log2FC
-0.2 Heparin binding 0
Haptoglobin binding
0.0008 0.0009 0.0004 7.9098×10-9
0.0069 0.0016
0.0006 0.0056
CKD-Kè healthy-H vs. healthy-Kè healthy-H
Ccl7 Cxcl13 Pla2g2d Sod3 Thbs1 Vtn
Hba1 Hba2
P-value
0.0002 0.0002 7.9100×10-11
0.0004 0.0004 0.0006 0.0006 0.0007 0.0009 0.0010 0.0008 0.0007 0.0009 0.0016 0.0017
CKD-Kè healthy-H vs. healthy-Kè healthy-H
Hpd Bhlhe41 Sod3 Slc7a4 Wnt5b Ptpru Hba1 Cyp2e1 Cxcl13 Ano5 Ephx1 Rtn4rl2 Agap2 Vtn Cds1
P-value
A
Supplemental Figure S6
B
0.0001 0.0002 0.0003 0.0005 0.0014 0.0017 0.0026 0.0030 0.0006 0.0026 0.0002 0.0030 0.0004 0.0030 0.0096
CKD-Kè CKD-H vs. healthy-Kè CKD-H
S100a9 Ass1 S100a8 Ccl9 Vtn Rpl26-ps1 Cox6b1 AC136661.1 AC103024.1 Rplp1 Apoa2 Hrsp12 AABR07033020.1 Retnlg Hck
P-value -0.5281
-0.6962 -0.8652 -0.5339 -0.4837 -0.4547 -0.5316 -0.4682 -0.5337 -0.4305 -0.4400 -0.4631 -0.4134 -0.4780 -0.4053 -0.4783 -0.4783 -0.5963 -0.5041 -0.4033 -0.4194 -0.5470 -0.4276 -0.4419 -0.4780 -0.8333 -0.9062 -0.4047 -0.5145 -0.4442 -0.7694
CKD-Kè CKD-H vs. healthy-Kè CKD-H
Apcs Apoa2 Ass1 Batf Bcl2a1 C3 C4bpa C4bpb Cd14 Ceacam1 Coro1a Cxcl13 Cxcl9 Fgr Fyb Hc Hck Ighm Il1rn Lcp1 Lilrb4 Ltb Ncf4 Nlrp3 Olfm4 S100a8 S100a9 Samsn1 Slpi Tlr2 Vtn
-0.8 -0.6 -0.4 -0.2 0
Log2FC
-0.9062 -0.8652 -0.8333 -0.7734 -0.7694 -0.7510 -0.7437 -0.7059 -0.7033 -0.7018 -0.6962 -0.6909 -0.6755 -0.6748 -0.6636
CKD-Kè CKD-H vs. healthy-Kè CKD-H
S100a9 Ass1 S100a8 Ccl9 Vtn Rpl26-ps1 Cox6b1 AC136661.1 AC103024.1 Rplp1 Apoa2 Hrsp12 AABR07033020.1 Retnlg
Hck -1.0
-0.8 -0.6 -0.4 -0.2 0
Log2FC 3.5880×10-8
3.0223×10-8 3.8749×10-8
0.0004 0.0019 0.0001 1.4444×10-5
0.0009 0.0001 0.0048 0.0040 0.0029 0.0065 0.0024 0.0081 2.8094×10-5 1.7209×10-5
0.0001 0.0008 0.0009 0.0074 0.0005 0.0067 0.0051 0.0012 9.1517×10-8 9.9480×10-9
0.0069 0.0010 0.0039 6.7617×10-7
CKD-Kè CKD-H vs. healthy-Kè CKD-H
Apcs Apoa2 Ass1 Batf Bcl2a1 C3 C4bpa C4bpb Cd14 Ceacam1 Coro1a Cxcl13 Cxcl9 Fgr Fyb Hc Hck Ighm Il1rn Lcp1 Lilrb4 Ltb Ncf4 Nlrp3 Olfm4 S100a8 S100a9 Samsn1 Slpi Tlr2 Vtn
P-value
Sulfur compound binding Glycosaminoglycan binding
healthy-K CKD-H vs.
healthy-K healthy-H CKD-K CKD-H vs.
CKD-K healthy-H
healthy-K CKD-H vs.
healthy-K healthy-H CKD-K CKD-H vs.
CKD-K healthy-H
A B
C D
Supplemental Figure S7
Signaling receptor binding Heparin binding
healthy-K CKD-H vs.
healthy-K healthy-H CKD-K CKD-H vs.
CKD-K healthy-H
healthy-K CKD-H vs.
healthy-K healthy-H CKD-K CKD-H vs.
CKD-K healthy-H
E F
G H
Supplemental Figure S7 continued
Supplemental Figure S8
1.8839 1.5450 1.4116 1.3825 1.3801 1.3491 1.3377 1.3313 1.3066 1.3005 1.2713 1.1948 1.1885 1.1563 1.1489
healthy-Kè CKD-H vs. healthy-Kè healthy-H
Gdf15 LOC100912195 Ctgf Ncam1 Postn Ltbp2 Tgfb2 Spp1 Cdhr1 Reg3b Akip1 Tceal7 Thbs4 Ankrd23
C4b 0
Log2FC
0.5 1.0 1.5
2.0 5.4676×10-20
8.6899×10-14 1.2376×10-11 2.7959×10-14 1.1287×10-12 1.0890×10-10 1.0685×10-12 2.6843×10-10 5.7257×10-10 4.6945×10-10 5.4311×10-12 1.1185×10-8 1.2583×10-8 3.5553×10-8 9.1301×10-9
healthy-Kè CKD-H vs. healthy-Kè healthy-H
Gdf15 LOC100912195 Ctgf Ncam1 Postn Ltbp2 Tgfb2 Spp1 Cdhr1 Reg3b Akip1 Tceal7 Thbs4 Ankrd23 C4b
P-value 1.4116
1.3825 1.3801 1.3377 1.3313 1.3066 1.3005 1.2713 1.1885 1.1377 1.1370 1.0650 0.9824 0.8898 0.8360 0.7912 0.7784 0.7611 0.7397 0.7380 0.7253 0.7080 0.7058 0.6956 0.6917
healthy-Kè CKD-H vs. healthy-Kè healthy-H
Ctgf Ncam1 Postn Tgfb2 Spp1 Cdhr1 Reg3b Akip1 Thbs4 Tnfrsf12a Sfrp2 Gpnmb Mybpc2 S100a8 Cyfip2 Nfasc S100a9 Apba1 Fbln1 Ptk2b Olfm4 Lrrc16a Selplg Itgb2 Prkcz
0 0.5 1.0 1.5
Log2FC
A B
1.2376×10-11 2.7959×10-14 1.1287×10-12 1.0685×10-12 2.6843×10-10 5.7257×10-10 4.6945×10-10 5.4311×10-12 1.2583×10-8 7.3345×10-11
6.9045×10-8 3.8613×10-12
2.6374×10-6 3.2540×10-6 2.2251×10-5
0.0002 4.6146×10-5
0.0003 1.5829×10-9
0.0001 0.0003 7.0914×10-6
0.0005 0.0001 0.0010
healthy-Kè CKD-H vs. healthy-Kè healthy-H
Ctgf Ncam1 Postn Tgfb2 Spp1 Cdhr1 Reg3b Akip1 Thbs4 Tnfrsf12a Sfrp2 Gpnmb Mybpc2 S100a8 Cyfip2 Nfasc S100a9 Apba1 Fbln1 Ptk2b Olfm4 Lrrc16a Selplg Itgb2 Prkcz
P-value
Supplemental Figure S9
A B
2.5601×10-36 5.4047×10-19 2.4591×10-15 1.4043×10-11 6.0239×10-12 1.0242×10-10 3.7641×10-9 3.5817×10-9 1.7641×10-9 5.9074×10-11 1.3555×10-10 5.8788×10-8 3.0342×10-7 4.9994×10-10 5.6169×10-10
CKD-Kè CKD-H vs. CKD-Kè healthy-H
Cnpy1 Tgfa Chrna1 LOC100910559 Gsta1 Hamp LOC300308 Mpz Cpeb1 Hba1 Alas2 Cdh22 Crtac1 Cytl1 Hbb-b1
P-value 2.7081
2.0714 1.8966 1.5803 1.4387 1.4156 1.4114 1.3859 1.3809 1.3276 1.2990 1.2364 1.2214 1.1913 1.1893
CKD-Kè CKD-H vs. CKD-Kè healthy-H
Cnpy1 Tgfa Chrna1 LOC100910559 Gsta1 Hamp LOC300308 Mpz Cpeb1 Hba1 Alas2 Cdh22 Crtac1 Cytl1 Hbb-b1
0 Log2FC
1 2 1.0574
0.9242 0.8664 0.7798 0.7582 0.7305 0.7005 0.6920 0.6907 0.6858 0.6758 0.6739 0.6664 0.6531 0.6451 0.6395 0.6368 0.6268 0.6185 0.6074 0.6072 0.6026 0.5951 0.5844 0.5804
CKD-Kè CKD-H vs. CKD-Kè healthy-H
Dgkg Nrg1 Bloc1s3 Pllp Adm Serpine2 Ajuba Cfb Lrrc16a Il18 Foxc2 Gp1bb Mmrn1 Lbp Lyve1 Hopx Vwf Cfh Serping1 Procr Ptger4 P2rx1 Ahnak2 C4b
Thbd 0
Log2FC
0.5
1.0 9.5687×10
-6
0.0001 0.0002 0.0004 3.7977×10-7
0.0008 0.0005 1.5448×10-5
0.0009 0.0032 0.0045 0.0019 0.0055 0.0066 0.0056 0.0004 0.0017 0.0092 0.0095 0.0008 0.0013 0.0100 0.0134 0.0072 0.0009
CKD-Kè CKD-H vs. CKD-Kè healthy-H
Dgkg Nrg1 Bloc1s3 Pllp Adm Serpine2 Ajuba Cfb Lrrc16a Il18 Foxc2 Gp1bb Mmrn1 Lbp Lyve1 Hopx Vwf Cfh Serping1 Procr Ptger4 P2rx1 Ahnak2 C4b Thbd
P-value
Nuclear division Organelle fission Cell cycle process
healthy-K CKD-H vs.
healthy-K healthy-H CKD-K CKD-H vs.
CKD-K healthy-H healthy-K CKD-H vs.
healthy-K healthy-H CKD-K CKD-H vs.
CKD-K healthy-H CKD-K CKD-H vs.
CKD-K healthy-H healthy-K CKD-H vs.
healthy-K healthy-H
A B C
D E F
Supplemental Figure S10
Supplemental Figure S11
A
-1.0633 -0.9838 -0.9750 -0.9567 -0.9458 -0.8954 -0.8737 -0.8634 -0.8491 -0.8454 -0.8289 -0.8152 -0.8053 -0.8026 -0.7825
healthy-Kè CKD-H vs. healthy-Kè healthy-H
Mki67 Epha7 Klhl33 Phkg1 Prc1 LOC100360726 AY172581.24 Baalc AY172581.9 Ky AABR07052585.1 Mum1l1 Stc2 Frem2
Myh6 -1.0
Log2FC
-0.5 0
3.8167×10-7 2.9506×10-6 7.7839×10-8 1.8808×10-7 7.2126×10-6 8.9961×10-7 1.6668×10-5 3.9292×10-5 4.9480×10-5 3.4847×10-6 3.6569×10-10
0.0001 4.2167×10-6
0.0001 4.9115×10-11
healthy-Kè CKD-H vs. healthy-Kè healthy-H
Mki67 Epha7 Klhl33 Phkg1 Prc1 LOC100360726 AY172581.24 Baalc AY172581.9 Ky AABR07052585.1 Mum1l1 Stc2 Frem2 Myh6
P-value
Supplemental Figure S11
continued
B
-1.0785 -0.9951 -0.9454 -0.9351 -0.9241 -0.9164 -0.9112 -0.9046 -0.9005 -0.8842 -0.8803 -0.8763 -0.8644 -0.8457 -0.8384
CKD-Kè CKD-H vs. CKD-Kè healthy-H
Mki67 Tfrc Irf6 Npas2 RGD1307100 Lcor AABR07052585.1 Ccna2 Kdm5a S100a8 Prnd Fam111a N4bp2 Lpp
Psd3 -1.0
Log2FC
-0.5 0
4.4608×10-6 5.4053×10-7 2.8171×10-5
0.0001 9.0097×10-6
0.0001 3.5158×10-5
0.0002 1.4043×10-5
0.0001 0.0002 0.0002 2.4961×10-5
0.0002 2.7766×10-5
CKD-Kè CKD-H vs. CKD-Kè healthy-H
Mki67 Tfrc Irf6 Npas2 RGD1307100 Lcor AABR07052585.1 Ccna2 Kdm5a S100a8 Prnd Fam111a N4bp2 Lpp Psd3
P-value
