Pathway and network analysis of more than 2500 whole cancer genomes
| Autor: | Reyna M. A., Haan D., Paczkowska M., Verbeke L. P. C., Vazquez M., Kahraman A., Pulido-Tamayo S., Barenboim J., Wadi L., Dhingra P., Shrestha R., Getz G., Lawrence M. S., Pedersen J. S., Rubin M. A., Wheeler D. A., Brunak S., Izarzugaza J. M. G., Khurana E., Marchal K., von Mering C., Sahinalp S. C., Valencia A., Abascal F., Amin S. B., Bader G. D., Bandopadhayay P., Beroukhim R., Bertl J., Boroevich K. A., Busanovich J., Campbell P. J., Carlevaro-Fita J., Chakravarty D., Chan C. W. Y., Chen K., Choi J. K., Deu-Pons J., Diamanti K., Feuerbach L., Fink J. L., Fonseca N. A., Frigola J., Gambacorti Passerini C., Garsed D. W., Gerstein M., Guo Q., Gut I. G., Hamilton M. P., Haradhvala N. J., Harmanci A. O., Helmy M., Herrmann C., Hess J. M., Hobolth A., Hodzic E., Hong C., Hornshoj H., Isaev K., Johnson R., Johnson T. A., Juul M., Juul R. I., Kahles A., Kellis M., Kim J., Kim J. K., Kim Y., Komorowski J., Korbel J. O., Kumar S., Lanzos A., Larsson E., Lee D., Lehmann K. -V., Li S., Li X., Lin Z., Liu E. M., Lochovsky L., Lou S., Madsen T., Martincorena I., Martinez-Fundichely A., Maruvka Y. E., McGillivray P. D., Meyerson W., Muinos F., Mularoni L., Nakagawa H., Nielsen M. M., Park K., Pons T., Reyes-Salazar I., Rheinbay E., Rubio-Perez C., Saksena G., Salichos L., Sander C., Schumacher S. E., Shackleton M., Shapira O., Shen C., Shuai S., Sidiropoulos N., Sieverling L., Sinnott-Armstrong N., Stein L. D., Tamborero D., Tiao G., Tsunoda T., Umer H. M., Uuskula-Reimand L., Wadelius C., Wang J., Warrell J., Waszak S. M., Weischenfeldt J., Wu G., Yu J., Zhang J., Zhang X., Zhang Y., Zhao Z., Zou L., Reimand J., Stuart J. M., Raphael B. J. |
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| Přispěvatelé: | Reyna, M, Haan, D, Paczkowska, M, Verbeke, L, Vazquez, M, Kahraman, A, Pulido-Tamayo, S, Barenboim, J, Wadi, L, Dhingra, P, Shrestha, R, Getz, G, Lawrence, M, Pedersen, J, Rubin, M, Wheeler, D, Brunak, S, Izarzugaza, J, Khurana, E, Marchal, K, von Mering, C, Sahinalp, S, Valencia, A, Abascal, F, Amin, S, Bader, G, Bandopadhayay, P, Beroukhim, R, Bertl, J, Boroevich, K, Busanovich, J, Campbell, P, Carlevaro-Fita, J, Chakravarty, D, Chan, C, Chen, K, Choi, J, Deu-Pons, J, Diamanti, K, Feuerbach, L, Fink, J, Fonseca, N, Frigola, J, Gambacorti Passerini, C, Garsed, D, Gerstein, M, Guo, Q, Gut, I, Hamilton, M, Haradhvala, N, Harmanci, A, Helmy, M, Herrmann, C, Hess, J, Hobolth, A, Hodzic, E, Hong, C, Hornshoj, H, Isaev, K, Johnson, R, Johnson, T, Juul, M, Juul, R, Kahles, A, Kellis, M, Kim, J, Kim, Y, Komorowski, J, Korbel, J, Kumar, S, Lanzos, A, Larsson, E, Lee, D, Lehmann, K, Li, S, Li, X, Lin, Z, Liu, E, Lochovsky, L, Lou, S, Madsen, T, Martincorena, I, Martinez-Fundichely, A, Maruvka, Y, Mcgillivray, P, Meyerson, W, Muinos, F, Mularoni, L, Nakagawa, H, Nielsen, M, Park, K, Pons, T, Reyes-Salazar, I, Rheinbay, E, Rubio-Perez, C, Saksena, G, Salichos, L, Sander, C, Schumacher, S, Shackleton, M, Shapira, O, Shen, C, Shuai, S, Sidiropoulos, N, Sieverling, L, Sinnott-Armstrong, N, Stein, L, Tamborero, D, Tiao, G, Tsunoda, T, Umer, H, Uuskula-Reimand, L, Wadelius, C, Wang, J, Warrell, J, Waszak, S, Weischenfeldt, J, Wu, G, Yu, J, Zhang, J, Zhang, X, Zhang, Y, Zhao, Z, Zou, L, Reimand, J, Stuart, J, Raphael, B, Reyna, Matthew A [0000-0003-4688-7965], Verbeke, Lieven PC [0000-0003-1909-8119], Vazquez, Miguel [0000-0002-5713-1058], Kahraman, Abdullah [0000-0003-3523-4467], Shrestha, Raunak [0000-0002-1144-1413], Getz, Gad [0000-0002-0936-0753], Pedersen, Jakob Skou [0000-0002-7236-4001], Rubin, Mark A [0000-0002-8321-9950], Khurana, Ekta [0000-0002-4351-7566], Marchal, Kathleen [0000-0002-2169-4588], von Mering, Christian [0000-0001-7734-9102], Reimand, Jüri [0000-0002-2299-2309], Stuart, Joshua M [0000-0002-2171-565X], Raphael, Benjamin J [0000-0003-1274-048X], Apollo - University of Cambridge Repository |
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
Medizin General Physics and Astronomy medicine.disease_cause Genome 0302 clinical medicine PCAWG Drivers and Functional Interpretation Working Group Neoplasms Databases Genetic Cancer genomics Medicine and Health Sciences 2.1 Biological and endogenous factors Aetiology lcsh:Science Càncer Promoter Regions Genetic health care economics and organizations Cancer Genetics Mutation Multidisciplinary Women's cancers Radboud Institute for Molecular Life Sciences [Radboudumc 17] 3. Good health Women's cancers Radboud Institute for Health Sciences [Radboudumc 17] TERT PROMOTER MUTATIONS Gene Expression Regulation Neoplastic 030220 oncology & carcinogenesis RNA splicing Medical Genetics Metabolic Networks and Pathways Human Biotechnology EXPRESSION RNA Splicing Factors Cellular signalling networks GENES PROTEINS Science RNA Splicing 610 Medicine & health Biology Article General Biochemistry Genetics and Molecular Biology Chromatin remodeling Promoter Regions 03 medical and health sciences Databases Rare Diseases SDG 3 - Good Health and Well-being Genetic medicine Humans Gene Medicinsk genetik Whole genome sequencing Neoplastic Genome Human Human Genome Biology and Life Sciences PCAWG Consortium Computational Biology TLE4 SOMATIC MUTATIONS General Chemistry medicine.disease Chromatin Assembly and Disassembly ENCYCLOPEDIA Genòmica 030104 developmental biology Gene Expression Regulation DISCOVERY lcsh:Q Genètica protein-coding genes Mutation genome sequencing RNA splicing cancer genomes |
| Zdroj: | Reyna, Matthew A; Haan, David; Paczkowska, Marta; Verbeke, Lieven P C; Vazquez, Miguel; Kahraman, Abdullah; Pulido-Tamayo, Sergio; Barenboim, Jonathan; Wadi, Lina; Dhingra, Priyanka; Shrestha, Raunak; Getz, Gad; Lawrence, Michael S; Pedersen, Jakob Skou; Rubin, Mark Andrew; Wheeler, David A; Brunak, Søren; Izarzugaza, Jose M G; Khurana, Ekta; Marchal, Kathleen; ... (2020). Pathway and network analysis of more than 2500 whole cancer genomes. Nature communications, 11(1), p. 729. Nature Publishing Group 10.1038/s41467-020-14367-0 Nature Communications, 11, 1 Nature communications, vol 11, iss 1 Reyna, M A, Haan, D, Paczkowska, M, Verbeke, L P C, Vazquez, M, Kahraman, A, Pulido-Tamayo, S, Barenboim, J, Wadi, L, Dhingra, P, Shrestha, R, Getz, G, Lawrence, M S, Pedersen, J S, Rubin, M A, Wheeler, D A, Brunak, S, Izarzugaza, J M G, Khurana, E, Marchal, K, von Mering, C, Sahinalp, S C, Valencia, A, PCAWG Drivers and Functional Interpretation Working Group, Reimand, J, Stewart, J, Raphael, B & PCAWG Consortium 2020, ' Pathway and network analysis of more than 2500 whole cancer genomes ', Nature Communications, vol. 11, no. 1, 729 . https://doi.org/10.1038/s41467-020-14367-0 NATURE COMMUNICATIONS Nature Communications Nature Communications, 11 (1) Nature Communications, Vol 11, Iss 1, Pp 1-17 (2020) Nature Communications, 11 Reyna, M A, Haan, D, Paczkowska, M, Verbeke, L P C, Vazquez, M, Kahraman, A, Pulido-Tamayo, S, Barenboim, J, Wadi, L, Dhingra, P, Shrestha, R, Getz, G, Lawrence, M S, Pedersen, J S, Rubin, M A, Wheeler, D A, Brunak, S, Izarzugaza, J M G, Khurana, E, Marchal, K, von Mering, C, Sahinalp, S C, Valencia, A, Abascal, F, Amin, S B, Bader, G D, Bandopadhayay, P, Beroukhim, R, Bertl, J, Boroevich, K A, Busanovich, J, Campbell, P J, Carlevaro-Fita, J, Chakravarty, D, Chan, C W Y, Chen, K, Choi, J K, Deu-Pons, J, Diamanti, K, Feuerbach, L, Fink, J L, Fonseca, N A, Frigola, J, Gambacorti-Passerini, C, Garsed, D W, Gerstein, M, Larsson, E, Nielsen, M M, Sidiropoulos, N, Weischenfeldt, J, PCAWG Drivers and Functional Interpretation Working Group & PCAWG Consortium 2020, ' Pathway and network analysis of more than 2500 whole cancer genomes ', Nature Communications, vol. 11, no. 1, 729, pp. 1-17 . https://doi.org/10.1038/s41467-020-14367-0 Reyna, M A, Haan, D, Paczkowska, M, Verbeke, L P C, Vazquez, M, Kahraman, A, Pulido-Tamayo, S, Barenboim, J, Wadi, L, Dhingra, P, Shrestha, R, Getz, G, Lawrence, M S, Pedersen, J S, Rubin, M A, Wheeler, D A, Brunak, S, Izarzugaza, J M G, Khurana, E, Marchal, K, von Mering, C, Sahinalp, S C, Valencia, A, Reimand, J, Stuart, J M & Raphael, B J 2020, ' Pathway and network analysis of more than 2500 whole cancer genomes ', Nature Communications, vol. 11, no. 1, 729 . https://doi.org/10.1038/s41467-020-14367-0 |
| ISSN: | 2041-1723 |
| DOI: | 10.1038/s41467-020-14367-0 |
| Popis: | The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding mutations across 2583 whole cancer genomes from 27 tumor types compiled by the ICGC/TCGA PCAWG project that was motivated by the success of pathway and network analyses in prioritizing rare mutations in protein-coding genes. While few non-coding genomic elements are recurrently mutated in this cohort, we identify 93 genes harboring non-coding mutations that cluster into several modules of interacting proteins. Among these are promoter mutations associated with reduced mRNA expression in TP53, TLE4, and TCF4. We find that biological processes had variable proportions of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered primarily by coding mutations, while developmental pathways, including Wnt and Notch, altered by both coding and non-coding mutations. RNA splicing is primarily altered by non-coding mutations in this cohort, and samples containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as samples with coding mutations in these genes. These analyses contribute a new repertoire of possible cancer genes and mechanisms that are altered by non-coding mutations and offer insights into additional cancer vulnerabilities that can be investigated for potential therapeutic treatments. Understanding deregulation of biological pathways in cancer can provide insight into disease etiology and potential therapies. Here, as part of the PanCancer Analysis of Whole Genomes (PCAWG) consortium, the authors present pathway and network analysis of 2583 whole cancer genomes from 27 tumour types. |
| Databáze: | OpenAIRE |
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