Integrative omics reveals subtle molecular perturbations following ischemic conditioning in a porcine kidney transplant model

BACKGROUND: Remote Ischemic Conditioning (RIC) has been proposed as a therapeutic intervention to circumvent the ischemia/reperfusion injury (IRI) that is inherent to organ transplantation. Using a porcine kidney transplant model, we aimed to decipher the subclinical molecular effects of a RIC regime, compared to non-RIC controls. METHODS: Kidney pairs (n = 8 + 8) were extracted from brain dead donor pigs and transplanted in juvenile recipient pigs following a period of cold ischemia. One of the two kidney recipients in each pair was subjected to RIC prior to kidney graft reperfusion, while the other served as non-RIC control. We designed an integrative Omics strategy combining transcriptomics, proteomics, and phosphoproteomics to deduce molecular signatures in kidney tissue that could be attributed to RIC. RESULTS: In kidney grafts taken out 10 h after transplantation we detected minimal molecular perturbations following RIC compared to non-RIC at the transcriptome level, which was mirrored at the proteome level. In particular, we noted that RIC resulted in suppression of tissue inflammatory profiles. Furthermore, an accumulation of muscle extracellular matrix assembly proteins in kidney tissues was detected at the protein level, which may be in response to muscle tissue damage and/or fibrosis. However, the majority of these protein changes did not reach significance (p < 0.05). CONCLUSIONS: Our data identifies subtle molecular phenotypes in porcine kidneys following RIC, and this knowledge could potentially aid optimization of remote ischemic conditioning protocols in renal transplantation. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12014-022-09343-3

Early outcome in renal transplantation from large donors to small and size-matched recipients - a porcine experimental model

Ravlo K, Chhoden T, Sondergaard P, Secher N, Keller AK, Pedersen M, Bibby BM, Moldrup U, Ostraat EO, Birn H, Norregaard R, Marcussen N, Leuvenink HG, Jespersen B. Early outcome in renal transplantation from large donors to small and size-matched recipients A porcine experimental model. Abstract: Kidney transplantation from a large donor to a small recipient, as in pediatric transplantation, is associated with an increased risk of thrombosis and DGF. We established a porcine model for renal transplantation from an adult donor to a small or size-matched recipient with a high risk of DGF and studied GFR, RPP using MRI, and markers of kidney injury within 10 h after transplantation. After induction of BD, kidneys were removed from similar to 63-kg donors and kept in cold storage for similar to 22 h until transplanted into small (similar to 15 kg, n = 8) or size-matched (n = 8) recipients. A reduction in GFR was observed in small recipients within 60 min after reperfusion. Interestingly, this was associated with a significant reduction in medullary RPP, while there was no significant change in the size-matched recipients. No difference was observed in urinary NGAL excretion between the groups. A significant higher level of HO-1 mRNA was observed in small recipients than in donors and size-matched recipients indicating cortical injury. Improvement in early graft perfusion may be a goal to improve short- and long-term GFR and avoid graft thrombosis in pediatric recipients. (c) 2012 John Wiley & Sons A/S

Additional file 2 of Integrative omics reveals subtle molecular perturbations following ischemic conditioning in a porcine kidney transplant model

Additional file 2: Table S1. Transcriptome sequence alignments. An average sequence alignment of 82% was achieved across all samples. Table S2. List of transcripts identified by transcriptomics. A total of 19,220 transcripts were successfully identified across groups. Table S3. Transcripts differentially expressed between RIC and Non-RIC groups. Table S4. qPCR validation on a panel of targets from discovery transcriptomics. IL1B, LTB4R, PDZD3, SLC16A3, and RASL10A were quantified by qPCR. We observed a slight increase in RIC induced SLC16A3 transcripts, but overall, none of the genes quantified reached statistically significance between RIC and non-RIC, with all having a p-value of &gt; 0.2. Table S5. List of proteins identified by proteomics. A total of 7,546 proteins were successfully identified across groups. Table S6. Proteins differentially expressed between RIC and Non-RIC groups. Table S7. List of proteins and phosphosites identified by phosphoproteomics. A total of 3,524 phosphosites were successfully identified across groups

Additional file 1 of Integrative omics reveals subtle molecular perturbations following ischemic conditioning in a porcine kidney transplant model

Additional file 1: Figure S1. Transcriptomic pathway enrichment analysis reveals subtle alteration of tissue inflammation by RIC. All transcripts (n = 33) which were found to be dysregulated in RIC versus non-RIC controls were searched against the Sus scrofa database in STRING. Only interactions of the highest confidence (scores &gt; 0.90) were included in the analysis. Genes associated with immune regulation are highlighted, with those linked to interleukin biology coloured red, while cytokines are coloured purple. Figure S2. Proteomic pathway enrichment analysis uncovers RIC induced tissue leakage and altered inflammation. Proteins (n = 252) which were found to have the greatest dysregulation in RIC versus non-RIC controls were searched against the Sus scrofa database in STRING. Only interactions of the highest confidence (scores &gt; 0.90) were included in the analysis. Proteins/genes of interest are highlighted, with proteins associated with muscle and ECM coloured in blue, blood coagulation in green, and factors associated with innate immunity coloured red. Figure S3. Kidney tissue phosphoproteomics unaffected by RIC. A) Abundance plots indicate no significant difference in the phosphoproteome between RIC and control groups. B) A Christmas tree plot, with Significance B thresholds colour coded. Minor changes were observed between groups

Integrative omics reveals subtle molecular perturbations following ischemic conditioning in a porcine kidney transplant model

Abstract Background Remote Ischemic Conditioning (RIC) has been proposed as a therapeutic intervention to circumvent the ischemia/reperfusion injury (IRI) that is inherent to organ transplantation. Using a porcine kidney transplant model, we aimed to decipher the subclinical molecular effects of a RIC regime, compared to non-RIC controls. Methods Kidney pairs (n = 8 + 8) were extracted from brain dead donor pigs and transplanted in juvenile recipient pigs following a period of cold ischemia. One of the two kidney recipients in each pair was subjected to RIC prior to kidney graft reperfusion, while the other served as non-RIC control. We designed an integrative Omics strategy combining transcriptomics, proteomics, and phosphoproteomics to deduce molecular signatures in kidney tissue that could be attributed to RIC. Results In kidney grafts taken out 10 h after transplantation we detected minimal molecular perturbations following RIC compared to non-RIC at the transcriptome level, which was mirrored at the proteome level. In particular, we noted that RIC resulted in suppression of tissue inflammatory profiles. Furthermore, an accumulation of muscle extracellular matrix assembly proteins in kidney tissues was detected at the protein level, which may be in response to muscle tissue damage and/or fibrosis. However, the majority of these protein changes did not reach significance (

Additional file 2 of Integrative omics reveals subtle molecular perturbations following ischemic conditioning in a porcine kidney transplant model

Additional file 2: Table S1. Transcriptome sequence alignments. An average sequence alignment of 82% was achieved across all samples. Table S2. List of transcripts identified by transcriptomics. A total of 19,220 transcripts were successfully identified across groups. Table S3. Transcripts differentially expressed between RIC and Non-RIC groups. Table S4. qPCR validation on a panel of targets from discovery transcriptomics. IL1B, LTB4R, PDZD3, SLC16A3, and RASL10A were quantified by qPCR. We observed a slight increase in RIC induced SLC16A3 transcripts, but overall, none of the genes quantified reached statistically significance between RIC and non-RIC, with all having a p-value of &gt; 0.2. Table S5. List of proteins identified by proteomics. A total of 7,546 proteins were successfully identified across groups. Table S6. Proteins differentially expressed between RIC and Non-RIC groups. Table S7. List of proteins and phosphosites identified by phosphoproteomics. A total of 3,524 phosphosites were successfully identified across groups

Integrative omics reveals subtle molecular perturbations following ischemic conditioning in a porcine kidney transplant model

Abstract Background Remote Ischemic Conditioning (RIC) has been proposed as a therapeutic intervention to circumvent the ischemia/reperfusion injury (IRI) that is inherent to organ transplantation. Using a porcine kidney transplant model, we aimed to decipher the subclinical molecular effects of a RIC regime, compared to non-RIC controls. Methods Kidney pairs (n = 8 + 8) were extracted from brain dead donor pigs and transplanted in juvenile recipient pigs following a period of cold ischemia. One of the two kidney recipients in each pair was subjected to RIC prior to kidney graft reperfusion, while the other served as non-RIC control. We designed an integrative Omics strategy combining transcriptomics, proteomics, and phosphoproteomics to deduce molecular signatures in kidney tissue that could be attributed to RIC. Results In kidney grafts taken out 10 h after transplantation we detected minimal molecular perturbations following RIC compared to non-RIC at the transcriptome level, which was mirrored at the proteome level. In particular, we noted that RIC resulted in suppression of tissue inflammatory profiles. Furthermore, an accumulation of muscle extracellular matrix assembly proteins in kidney tissues was detected at the protein level, which may be in response to muscle tissue damage and/or fibrosis. However, the majority of these protein changes did not reach significance (

Additional file 1 of Integrative omics reveals subtle molecular perturbations following ischemic conditioning in a porcine kidney transplant model

Additional file 1: Figure S1. Transcriptomic pathway enrichment analysis reveals subtle alteration of tissue inflammation by RIC. All transcripts (n = 33) which were found to be dysregulated in RIC versus non-RIC controls were searched against the Sus scrofa database in STRING. Only interactions of the highest confidence (scores &gt; 0.90) were included in the analysis. Genes associated with immune regulation are highlighted, with those linked to interleukin biology coloured red, while cytokines are coloured purple. Figure S2. Proteomic pathway enrichment analysis uncovers RIC induced tissue leakage and altered inflammation. Proteins (n = 252) which were found to have the greatest dysregulation in RIC versus non-RIC controls were searched against the Sus scrofa database in STRING. Only interactions of the highest confidence (scores &gt; 0.90) were included in the analysis. Proteins/genes of interest are highlighted, with proteins associated with muscle and ECM coloured in blue, blood coagulation in green, and factors associated with innate immunity coloured red. Figure S3. Kidney tissue phosphoproteomics unaffected by RIC. A) Abundance plots indicate no significant difference in the phosphoproteome between RIC and control groups. B) A Christmas tree plot, with Significance B thresholds colour coded. Minor changes were observed between groups