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Kidney_tumour_DNA

This is a bulk DNA and RNA sequencing study of human renal tumours

Type: Cancer Genomics
Archiver: European Genome-Phenome Archive (EGA)

7 Datasets 10 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001004346	This is a bulk DNA and RNA sequencing study of human renal tumours . This dataset contains all the data available for this study on 2018-09-19.	HiSeq X Ten	37
EGAD00001004774	We investigated the somatic genetic basis of Wilms’ tumour and found complex phylogenetic relations between tumours.	HiSeq X Ten	203
EGAD00001005134	We investigated the somatic genetic basis of Wilms' tumour and found complex phylogenetic relations between tumours	HiSeq X Ten	20
EGAD00001006296	Like many childhood cancers, malignant rhabdoid tumours (MRT) are thought to arise from aberrant foetal development. Although MRT predominantly exhibit a mesenchymal phenotype, it has been suggested that the foetal root of MRT lies in neural crest development. Here, we combine phylogenetic analyses of MRT, single cell mRNA assays, and functional experiments in patient-derived MRT organoids, to define the embryological origin of MRT and explore therapeutic avenues that may drive MRT differentiation. Phylogenetic analyses from the distribution of somatic mutations revealed that MRT were related to neural crest-derived, but not to mesodermal tissues, providing direct evidence of the neural crest origin of MRT in humans. In MRT organoids, reversal of the principal driver event underpinning MRT, SMARCB1 loss, induced differentiation along mesenchymal pathways. Together, these findings placed MRT cells on a developmental trajectory of neural crest to mesenchyme conversion, and defined the transcriptional changes underpinning MRT differentiation. Searching perturbation databases for agents that mimic these mRNA changes, we identified HDAC and mTOR inhibition as potential differentiation agents. Treatment of MRT organoids with this drug combination induced proliferation arrest with transcriptional changes akin to SMARCB1 re-expression. Our study defines the embryological root of MRT and proposes a differentiation treatment for this often fatal childhood cancer.	HiSeq X Ten Illumina HiSeq 4000 Illumina NovaSeq 6000 NextSeq 500	30
EGAD00001006423	Leukaemia and related blood cancers occur due to genetic changes that typically accumulate over many years. This study will employ targeted next-generation sequencing to retrace the preclinical evolution of several types of haematological malignancy. Investigating the progression of the earliest pre-malignant ancestral clones promises to offer valuable insights into early leukaemia evolution and therapeutic vulnerabilities of leukaemia stem cells.	HiSeq X Ten Illumina NovaSeq 6000	137
EGAD00001006641	During the course of a lifetime normal human cells accumulate mutations. Here, using multiple samples from the same individuals we compared the mutational landscape in 29 anatomical structures from soma and the germline. Two ubiquitous mutational signatures, SBS1 and SBS5/40, accounted for the majority of acquired mutations in most cell types but their absolute and relative contributions varied substantially. SBS18, potentially reflecting oxidative damage, and several additional signatures attributed to exogenous and endogenous exposures contributed mutations to subsets of cell types. The mutation rate was lowest in spermatogonia, the stem cell from which sperm are generated and from which most genetic variation in the human population is thought to originate. This was due to low rates of ubiquitous mutation processes and may be partially attributable to a low cell division rate of basal spermatogonia. The results provide important insights into how mutational processes affect the soma and germline.	HiSeq X Ten Illumina NovaSeq 6000	1
EGAD00001009005	Single cell transcriptomes, generated using chromium 10X 3' sequencing, for two tumour types (AT/RT, and Ewing's sarcoma). For each individual, tumour and normal whole genome sequencing was also obtained using Illumina short read sequencing to an average depth of 30X. These data were used to validate the accuracy of a method for identifying cancer cell transcriptomes based on the allelic shift produced by copy number changes.	HiSeq X Ten Illumina HiSeq 2500 Illumina HiSeq 4000 Illumina NovaSeq 6000	15

Publications	Citations
Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors. Young MD, Mitchell TJ, Vieira Braga FA, Tran MGB, Stewart BJ, Ferdinand JR, Collord G, Botting RA, Popescu DM, Loudon KW, Vento-Tormo R, Stephenson E, Cagan A, Farndon SJ, Del Castillo Velasco-Herrera M, Guzzo C, Richoz N, Mamanova L, Aho T, Armitage JN, Riddick ACP, Mushtaq I, Farrell S, Rampling D, Nicholson J, Filby A, Burge J, Lisgo S, Maxwell PH, Lindsay S, Warren AY, Stewart GD, Sebire N, Coleman N, Haniffa M, Teichmann SA, Clatworthy M, Behjati S. Science 361: 2018 594-599	377
Single cell census of human kidney organoids shows reproducibility and diminished off-target cells after transplantation. Subramanian A, Sidhom EH, Emani M, Vernon K, Sahakian N, Zhou Y, Kost-Alimova M, Slyper M, Waldman J, Dionne D, Nguyen LT, Weins A, Marshall JL, Rosenblatt-Rosen O, Regev A, Greka A. Nat Commun 10: 2019 5462	99
Somatic mutations and single-cell transcriptomes reveal the root of malignant rhabdoid tumours. Custers L, Khabirova E, Coorens THH, Oliver TRW, Calandrini C, Young MD, Vieira Braga FA, Ellis P, Mamanova L, Segers H, Maat A, Kool M, Hoving EW, van den Heuvel-Eibrink MM, Nicholson J, Straathof K, Hook L, de Krijger RR, Trayers C, Allinson K, Behjati S, Drost J. Nat Commun 12: 2021 1407	37
Single cell derived mRNA signals across human kidney tumors. Young MD, Mitchell TJ, Custers L, Margaritis T, Morales-Rodriguez F, Kwakwa K, Khabirova E, Kildisiute G, Oliver TRW, de Krijger RR, van den Heuvel-Eibrink MM, Comitani F, Piapi A, Bugallo-Blanco E, Thevanesan C, Burke C, Prigmore E, Ambridge K, Roberts K, Braga FAV, Coorens THH, Del Valle I, Wilbrey-Clark A, Mamanova L, Stewart GD, Gnanapragasam VJ, Rampling D, Sebire N, Coleman N, Hook L, Warren A, Haniffa M, Kool M, Pfister SM, Achermann JC, He X, Barker RA, Shlien A, Bayraktar OA, Teichmann SA, Holstege FC, Meyer KB, Drost J, Straathof K, Behjati S. Nat Commun 12: 2021 3896	21
The Extracellular Matrix Environment of Clear Cell Renal Cell Carcinoma Determines Cancer Associated Fibroblast Growth. Bond KH, Chiba T, Wynne KPH, Vary CPH, Sims-Lucas S, Coburn JM, Oxburgh L. Cancers (Basel) 13: 2021 5873	18
Genetic association and single-cell transcriptome analyses reveal distinct features connecting autoimmunity with cancers. Li S, Lu C, Zhang Y, Zhao X, Lin K, Kong X, Fox D, Xue L, Sun L, Liu Y, Mao F. iScience 25: 2022 104631	2
A transcriptional metastatic signature predicts survival in clear cell renal cell carcinoma. Alchahin AM, Mei S, Tsea I, Hirz T, Kfoury Y, Dahl D, Wu CL, Subtelny AO, Wu S, Scadden DT, Shin JH, Saylor PJ, Sykes DB, Kharchenko PV, Baryawno N. Nat Commun 13: 2022 5747	18
New insights into fibrotic signaling in renal cell carcinoma. Chen JY, Yiu WH, Tang PM, Tang SC. Front Cell Dev Biol 11: 2023 1056964	2
The GPCR-Gα<sub>s</sub>-PKA signaling axis promotes T cell dysfunction and cancer immunotherapy failure. Wu VH, Yung BS, Faraji F, Saddawi-Konefka R, Wang Z, Wenzel AT, Song MJ, Pagadala MS, Clubb LM, Chiou J, Sinha S, Matic M, Raimondi F, Hoang TS, Berdeaux R, Vignali DAA, Iglesias-Bartolome R, Carter H, Ruppin E, Mesirov JP, Gutkind JS. Nat Immunol 24: 2023 1318-1330	12
Targetable NOTCH1 rearrangements in reninoma. Treger TD, Lawrence JEG, Anderson ND, Coorens THH, Letunovska A, Abby E, Lee-Six H, Oliver TRW, Al-Saadi R, Tullus K, Morcrette G, Hutchinson JC, Rampling D, Sebire N, Pritchard-Jones K, Young MD, Mitchell TJ, Jones PH, Tran M, Behjati S, Chowdhury T. Nat Commun 14: 2023 5826	0