Biology:Network of Cancer Genes

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Network of Cancer Genes
Content
DescriptionA web resource on systems-level properties of cancer genes
OrganismsHomo sapiens
Contact
Research centreFrancis Crick Institute
LaboratoryCancer Systems Biology Lab - Ciccarelli Lab
Release dateMay 2023
Access
Websitehttp://www.network-cancer-genes.org/
Miscellaneous
Version7.1

The Network of Cancer Genes (NCG) is a freely accessible web resource of genes that, when altered in their sequence, drive clonal expansion of normal tissues (healthy drivers) or cancer (cancer drivers). The project was launched in 2010 and has reached its 7th release in 2022. In 2023 the additional annotation of cancer drivers that interact with the tumour immune microenvironment (TIME drivers) was added. NCG7.1 reports information on 3,347 cancer drivers and 95 healthy drivers.[1] Of these, 596 are also TIME drivers.[2] NCG7.1 also reports the system-level properties and the associated publications of each driver, as well as a list possible false positives. NCG7.1 enables advanced searches on the primary anatomical site, cancer type, type of sequencing screens and literature supports.

Cancer drivers

A main feature of cancer cells is to acquire an unstable genome leading to genetic alterations that are major drivers of cancer evolution. NCG7.1 collects 591 well-known (canonical) and 2,756 candidate cancer drivers. These lists derive from the manual curation of 313 original publications, including 3 sources of canonical drivers [3][4][5] and 310 cancer sequencing screens. The latter describe whole genome or whole exome sequencing of cancer samples from a total of 41,780 patients from 122 different cancer types.

Healthy drivers

Recent technological advances have enabled detection of genomic instability also in healthy (non cancer) cells driving in situ formation of phenotypically normal clones.[6][7] NCG7.1 collects 95 healthy drivers from 18 sequencing screens of healthy or diseased (non-cancer) tissues from 32,895 donors. Only 8 of these genes are not cancer drivers, suggesting a high overlap between genetic drivers of cancer and non-cancer evolution.[8]

TIME drivers

Cancer evolution occurs in a complex ecosystem formed of cancer and non-cancer cells that compose the tumour microenvironment (TME). An important component of the TME are immune cells, which may hamper or help tumour growth. Cancer cells engage in a dynamic crosstalk with the TIME that often involves cancer drivers. NCG7.1 annotates 596 that may impact on and be impacted by the TIME. Of these, 205 derive from the manual curation of the literature [9][10][11][12][13] and 391 are instead computationally predicted.[2]

Systems level properties

Systems-level properties are properties of genes independent on an individual's gene function[14] Some of these properties can be used to distinguish cancer and healthy drivers from the rest of human genes.[15][16] The systems-level properties reported in NCG are:

  • Duplicability: i.e. the presence of additional genomic sequences matching at least 60% of the gene sequence.[17]
  • Evolutionary appearance: the presence or absence of ortholog genes in seven branches of the tree of life (Prokaryotes, Eukaryotes, Opisthokonts, Metazoans, Vertebrates, Mammals, Primates)
  • Protein-protein interactions: a list of all human proteins interacting with the main protein encoded by the gene of interest and the number of complexes it is part of.
  • microRNA-gene interactions: a list of experimentally verified interactions between the gene of interest and human miRNAs.
  • Functional properties: a list of the functional classes of the gene of interest.
  • Gene expression and protein expression: List of normal tissues and cancer cell lines the gene of interest is expressed in.
  • Essentiality: a list of human cell lines in which the gene was found to be essential.

Previous versions

References

  1. ↑ Dressler, Lisa; Bortolomeazzi, Michele; Keddar, Mohamed Reda; Misetic, Hrvoje; Sartini, Giulia; Acha-Sagredo, Amelia; Montorsi, Lucia; Wijewardhane, Neshika et al. (2022). "Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource" (in en). Genome Biology 23 (1): 35. doi:10.1186/s13059-022-02607-z. ISSN 1474-760X. PMID 35078504. 
  2. ↑ 2.0 2.1 Misetic, Hrvoje; Keddar, Mohamed Reda; Jeannon, Jean-Pierre; Ciccarelli, Francesca D. (2023). "Mechanistic insights into the interactions between cancer drivers and the tumour immune microenvironment". bioRxiv 10.1101/2023.01.24.525325.
  3. ↑ Vogelstein, B.; Papadopoulos, N.; Velculescu, V. E.; Zhou, S.; Diaz, L. A.; Kinzler, K. W. (2013). "Cancer Genome Landscapes" (in en). Science 339 (6127): 1546–1558. doi:10.1126/science.1235122. ISSN 0036-8075. PMID 23539594. Bibcode: 2013Sci...339.1546V. 
  4. ↑ Saito, Yuki; Koya, Junji; Araki, Mitsugu; Kogure, Yasunori; Shingaki, Sumito; Tabata, Mariko; McClure, Marni B.; Yoshifuji, Kota et al. (2020). "Landscape and function of multiple mutations within individual oncogenes" (in en). Nature 582 (7810): 95–99. doi:10.1038/s41586-020-2175-2. ISSN 0028-0836. PMID 32494066. Bibcode: 2020Natur.582...95S. http://www.nature.com/articles/s41586-020-2175-2. 
  5. ↑ Sondka, Zbyslaw; Bamford, Sally; Cole, Charlotte G.; Ward, Sari A.; Dunham, Ian; Forbes, Simon A. (2018). "The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers" (in en). Nature Reviews Cancer 18 (11): 696–705. doi:10.1038/s41568-018-0060-1. ISSN 1474-175X. PMID 30293088. 
  6. ↑ Wijewardhane, Neshika; Dressler, Lisa; Ciccarelli, Francesca D. (2021). "Normal Somatic Mutations in Cancer Transformation" (in en). Cancer Cell 39 (2): 125–129. doi:10.1016/j.ccell.2020.11.002. PMID 33220180. https://linkinghub.elsevier.com/retrieve/pii/S1535610820305948. 
  7. ↑ Kakiuchi, Nobuyuki; Ogawa, Seishi (2021). "Clonal expansion in non-cancer tissues" (in en). Nature Reviews Cancer 21 (4): 239–256. doi:10.1038/s41568-021-00335-3. ISSN 1474-175X. PMID 33627798. http://www.nature.com/articles/s41568-021-00335-3. 
  8. ↑ Acha-Sagredo, A.; Ganguli, P.; Ciccarelli, F.D. (2022). "Somatic variation in normal tissues: friend or foe of cancer early detection?" (in en). Annals of Oncology 33 (12): 1239–1249. doi:10.1016/j.annonc.2022.09.156. PMID 36162751. https://linkinghub.elsevier.com/retrieve/pii/S0923753422041485. 
  9. ↑ Wellenstein, Max D.; de Visser, Karin E. (2018). "Cancer-Cell-Intrinsic Mechanisms Shaping the Tumor Immune Landscape" (in en). Immunity 48 (3): 399–416. doi:10.1016/j.immuni.2018.03.004. PMID 29562192. 
  10. ↑ Martin, Timothy D.; Patel, Rupesh S.; Cook, Danielle R.; Choi, Mei Yuk; Patil, Ajinkya; Liang, Anthony C.; Li, Mamie Z.; Haigis, Kevin M. et al. (2021-09-17). "The adaptive immune system is a major driver of selection for tumor suppressor gene inactivation". Science 373 (6561): 1327–1335. doi:10.1126/science.abg5784. ISSN 0036-8075. PMID 34529489. Bibcode: 2021Sci...373.1327M. http://dx.doi.org/10.1126/science.abg5784. 
  11. ↑ Mantovani, Alberto; Allavena, Paola; Sica, Antonio; Balkwill, Frances (2008-07-24). "Cancer-related inflammation" (in en). Nature 454 (7203): 436–444. doi:10.1038/nature07205. ISSN 0028-0836. PMID 18650914. Bibcode: 2008Natur.454..436M. https://www.nature.com/articles/nature07205. 
  12. ↑ Lawson, Keith A.; Sousa, Cristovão M.; Zhang, Xiaoyu; Kim, Eiru; Akthar, Rummy; Caumanns, Joseph J.; Yao, Yuxi; Mikolajewicz, Nicholas et al. (2020-10-01). "Functional genomic landscape of cancer-intrinsic evasion of killing by T cells" (in en). Nature 586 (7827): 120–126. doi:10.1038/s41586-020-2746-2. ISSN 0028-0836. PMID 32968282. Bibcode: 2020Natur.586..120L. 
  13. ↑ Dhainaut, Maxime; Rose, Samuel A.; Akturk, Guray; Wroblewska, Aleksandra; Nielsen, Sebastian R.; Park, Eun Sook; Buckup, Mark; Roudko, Vladimir et al. (2022). "Spatial CRISPR genomics identifies regulators of the tumor microenvironment". Cell 185 (7): 1223–1239.e20. doi:10.1016/j.cell.2022.02.015. ISSN 0092-8674. PMID 35290801. PMC 8992964. https://doi.org/10.1016/j.cell.2022.02.015. 
  14. ↑ Ciccarelli, Francesca D. (2010-06-11). "The (r)evolution of cancer genetics". BMC Biology 8 (1): 74. doi:10.1186/1741-7007-8-74. ISSN 1741-7007. PMID 20594288. 
  15. ↑ 15.0 15.1 Repana, Dimitra; Nulsen, Joel; Dressler, Lisa; Bortolomeazzi, Michele; Venkata, Santhilata Kuppili; Tourna, Aikaterini; Yakovleva, Anna; Palmieri, Tommaso et al. (2019). "The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens" (in en). Genome Biology 20 (1): 1. doi:10.1186/s13059-018-1612-0. PMID 30606230. 
  16. ↑ D'Antonio, Matteo; Ciccarelli, Francesca D. (2013-05-29). "Integrated analysis of recurrent properties of cancer genes to identify novel drivers". Genome Biology 14 (5): R52. doi:10.1186/gb-2013-14-5-r52. ISSN 1474-760X. PMID 23718799. 
  17. ↑ Rambaldi, Davide; Giorgi, Federico M.; Capuani, Fabrizio; Ciliberto, Andrea; Ciccarelli, Francesca D. (2008). "Low duplicability and network fragility of cancer genes". Trends in Genetics 24 (9): 427–430. doi:10.1016/j.tig.2008.06.003. ISSN 0168-9525. PMID 18675489. 
  18. ↑ An, Omer; Dall'Olio, Giovanni M.; Mourikis, Thanos P.; Ciccarelli, Francesca D. (2016-01-04). "NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings" (in en). Nucleic Acids Research 44 (D1): D992–D999. doi:10.1093/nar/gkv1123. ISSN 0305-1048. PMID 26516186. 
  19. ↑ An, Omer; Pendino, Vera; D'Antonio, Matteo; Ratti, Emanuele; Gentilini, Marco; Ciccarelli, Francesca D. (2014-01-01). "NCG 4.0: the network of cancer genes in the era of massive mutational screenings of cancer genomes" (in en). Database 2014: bau015. doi:10.1093/database/bau015. PMID 24608173. 
  20. ↑ D'Antonio, Matteo; Pendino, Vera; Sinha, Shruti; Ciccarelli, Francesca D. (2012). "Network of Cancer Genes (NCG 3.0): integration and analysis of genetic and network properties of cancer genes". Nucleic Acids Res. 40 (Database issue): D978–83. doi:10.1093/nar/gkr952. PMID 22080562. 
  21. ↑ Syed, Adnan S.; D'Antonio, Matteo; Ciccarelli, Francesca D. (2010). "Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes". Nucleic Acids Res. 38 (Database issue): D670–5. doi:10.1093/nar/gkp957. PMID 19906700. 

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