Integrated database towards a global view on Kidney Physiopathology
Integrated database towards a global view on Kidney Physiopathology
This integrated database groups together biological and physiological information from human and mouse kidneys, combining data obtained from various innovative technologies such as next generation sequencing, single-cell RNA sequencing, microarrays, drug screening, with data from histology, blood and urine tests, etc. Biological samples available for each individual are gathered in the biobank.
- Transcriptome in single cell types
Information was obtained from single-cell RNA sequencing data. Libraries were created from freshly harvested cells using the 10X genomics platform.
1-Renal progenitors and papillary RCC scRNAseq dataset.
This dataset combines scRNAseq data obtained from wild-type human renal progenitor cell cultures from our laboratory together with papillary RCC scRNAseq data from Young et al.[1]. The results of this analysis can be found in this article[2]:
Peired AJ et al. Science Translational Medicine, 2020
The dataset is also available in NCBI's Gene Expression Omnibus repository as GSE137620.
2- Renal cells from wild-type, unilateral IRI at 3 and 7 days scRNAseq dataset.
Wild-type C57Bl/6 mice underwent ischemia/reperfusion injury (IRI) at 7 weeks for 30 min as previously described [3]. Mice were sacrificed at 3 days (n = 3) and 7 days (n = 3) after IRI. Healthy mouse kidney (n = 1) was used as control. The results of this analysis can be found in this article [4].
Gnemmi et al. Cells, 2022
3-Panobinostat- and control-treated murine renal progenitor scRNAseq dataset.
Dataset of Pax2+ cells from Pax2.rtTA;TetO.Cre;R26.mT/mG mice (n=2) treated with Panobinostat or vehicle. The results of this analysis can be found in this article [5]:
The dataset is also available in NCBI's Gene Expression Omnibus repository as GSE195785.
4-Panobinostat-, givinostat- and ruxolitinib-treated mouse kidney scRNAseq dataset.
Dataset of mouse kidney cells derived from vehicle (n=2), panobinostat (n=2), givinostat (n=2) and ruxolitinib (n=2) treated mice. The results of this analysis can be found in this article [5]:
The dataset is also available in NCBI's Gene Expression Omnibus repository as GSE195784.
5- Panobinostat- and control-treated parietal epithelial cell scRNAseq dataset.
Dataset of panobinostat- and control-treated parietal epithelial cell cultures obtained from outgrowth of glomeruli of healthy human kidney. The results of this analysis can be found in this article [5]:
The dataset is also available in NCBI's Gene Expression Omnibus repository as GSE195797.
6- Human renal proximal tubule epithelial cell scRNAseq dataset.
Dataset of primary cultures of human proximal tubular cells at passages 6, 7 and 8. The results of this analysis can be found in this article [6 ]
The dataset is also available in NCBI's Gene Expression Omnibus repository as GSE212275 .
7- Renal cells from wild-type mice with unilateral IRI at 2 and 30 days scRNAseq dataset.
Wild-type C57Bl/6 mice underwent ischemia/reperfusion injury (IRI) at 7 weeks for 30 min as previously described [3]. Mice were sacrificed at 2 days and 30 days after IRI. The results of this analysis can be found in this article [6] .
The dataset is also available in NCBI's Gene Expression Omnibus repository as GSE212273.
References:
1. Young, M.D.; Mitchell, T.J.; Vieira Braga, F.A.; Tran, M.G.B.; Stewart, B.J.; Ferdinand, J.R.; Collord, G.; Botting, R.A.; Popescu, D.M.; Loudon, K.W., et al. Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors. Science 2018, 361, 594-599, doi:10.1126/science.aat1699.
2. Peired, A.J.; Antonelli, G.; Angelotti, M.L.; Allinovi, M.; Guzzi, F.; Sisti, A.; Semeraro, R.; Conte, C.; Mazzinghi, B.; Nardi, S., et al. Acute kidney injury promotes development of papillary renal cell adenoma and carcinoma from renal progenitor cells. Sci Transl Med 2020, 12, doi:10.1126/scitranslmed.aaw6003.
3. Lazzeri, E.; Angelotti, M.L.; Peired, A.; Conte, C.; Marschner, J.A.; Maggi, L.; Mazzinghi, B.; Lombardi, D.; Melica, M.E.; Nardi, S., et al. Endocycle-related tubular cell hypertrophy and progenitor proliferation recover renal function after acute kidney injury. Nat Commun 2018, 9, 1344, doi:10.1038/s41467-018-03753-4.
4. Gnemmi, V.; Li, Q.; Ma, Q.; De Chiara, L.; Carangelo, G.; Li, C.; Molina-Van den Bosch, M.; Romagnani, P.; Anders, H.-J.; Steiger, S. Asymptomatic Hyperuricemia Promotes Recovery from Ischemic Organ Injury by Modulating the Phenotype of Macrophages. Cells 2022, 11, 626.
5. Melica, M.E.; Antonelli, G.; Semeraro, R.; Angelotti, M.L.; Lugli, G.; Landini, S.; Ravaglia, F.; Regina, G.; Conte, C.; De Chiara, L., et al. Differentiation of crescent-forming kidney progenitor cells into podocytes attenuates severe glomerulonephritis in mice. Sci Transl Med 2022, 14, eabg3277, doi:10.1126/scitranslmed.abg3277.
6. De Chiara, L.; Conte, C.; Semeraro, R.; Diaz-Bulnes, P.; Angelotti, M.L.; Mazzinghi, B.; Molli, A.; Antonelli, G.; Landini, S.; Melica, M.E., et al. Tubular cell polyploidy protects from lethal acute kidney injury but promotes consequent chronic kidney disease. Nat Commun 2022, 13, 5805, doi:10.1038/s41467-022-33110-5.
Ultimo aggiornamento
10.10.2022