A landscape of driver mutations in melanoma
Open accessAbstract
SUMMARY Despite recent insights into melanoma genetics, systematic surveys for driver mutations are challenged by an abundance of passenger mutations caused by carcinogenic ultraviolet (UV) light exposure. We developed a permutation-based framework to address this challenge, employing mutation data from intronic sequences to control for passenger mutational load on a per gene basis. Analysis of large-scale melanoma exome data by this approach discovered six novel melanoma genes (PPP6C, RAC1, SNX31, TACC1, STK19 and ARID2), three of which - RAC1, PPP6C and STK19 - harbored recurrent and potentially targetable mutations. Integration with chromosomal copy number data contextualized the landscape of driver mutations, providing oncogenic insights in BRAF- and NRAS-driven melanoma as well as those without known NRAS/BRAF mutations. The landscape also clarified a mutational basis for RB and p53 pathway deregulation in this malignancy. Finally, the spectrum of driver mutations provided unequivocal genomic evidence for a direct mutagenic role of UV light in melanoma pathogenesis.
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Multiple genome-wide sequencing studies have revealed a paucity of NER gene defects in sporadic malignant melanoma within the general population.
“In view of this, it may be surprising that multiple genome-wide sequencing studies have revealed a paucity of NER gene defects in sporadic MM within the general population (2, 6, 7).”
From A genome-wide screen reveals that Dyrk1A kinase promotes nucleotide excision repair by preventing aberrant overexpression of cyclin D1 and p21 (2023) · cites this paper as [2]
The Results section reports whole-exome sequencing of melanoma samples and identifies driver genes, but it does not assess how often nucleotide excision repair (NER) genes are defective. Searches for NER, nucleotide excision repair, and DNA repair defects found no passage establishing the claimed paucity in sporadic melanoma. (LLM, conf=0.73)
Experimental — accuracy not yet measuredOne study linked UV-induced DNA damage signatures to about 46% of driver mutations.
“One study linked UV-induced DNA damage signatures to approximately 46% of driver mutations30.”
From Mechanisms and prevention of <scp>UV</scp>‐induced melanoma (2018) · cites this paper as [30]
Similar UV-induced p53 mutations are found in approximately 20% of human BRAFV600E mutant melanomas.
“Similar UV-induced p53 mutations are seen in approximately 20% of human BRAFV600E mutant melanomas25–27.”
From Mechanisms and prevention of <scp>UV</scp>‐induced melanoma (2018) · cites this paper as [26]
UV generates mutagenic DNA photolesions that, if unrepaired, lead to UV-signature mutations that cause melanoma.
“UV generates mutagenic DNA photolesions which if unrepaired lead to characteristic “UV-signature mutations” which are causative for melanoma”
From RETRACTED: PKA-Mediated Phosphorylation of ATR Promotes Recruitment of XPA to UV-Induced DNA Damage (2014) · cites this paper as Hodis et al., 2012
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Loss of NF1 in cutaneous melanoma is associated with RAS activation and MEK dependence
Nissan, M. H., Pratilas, C., Jones, A. M., Ramirez, R., Won, H., Liu, C.-L., Tiwari, S., Kong, L., Hanrahan, A. J., Yao, Z., et al. (2014) · Cancer Research · doi:10.1158/0008-5472.can-13-2625 · Cited by 297 · see citing works
SWI/SNF Chromatin Remodeling and Human Malignancies
Masliah‐Planchon, J., Bièche, I., Guinebretière, J., Bourdeaut, F., & Delattre, O. (2014) · Annual Review of Pathology Mechanisms of Disease · doi:10.1146/annurev-pathol-012414-040445 · Cited by 313 · see citing works
Targeting ERK1/2 protein-serine/threonine kinases in human cancers
Roskoski, R. J. (2019) · Pharmacological Research · doi:10.1016/j.phrs.2019.01.039 · Cited by 309 · see citing works
- Authors
- Hodis, E., Watson, I. R., Kryukov, G. V., Arold, S. T., Imielinski, M., Theurillat, J.-P., Nickerson, E., Auclair, D., Li, L., Place, C., DiCara, D., Ramos, A. H., Lawrence, M. S., Cibulskis, K., Sivachenko, A., Voet, D., Saksena, G., Stransky, N., Onofrio, R. C., Winckler, W., Ardlie, K., Wagle, N., Wargo, J., Chong, K., Morton, D. L., Stemke-Hale, K., Chen, G., Noble, M., Meyerson, M., Ladbury, J. E., Davies, M. A., Gershenwald, J. E., Wagner, S. N., Hoon, D. S. B., Schadendorf, D., Lander, E. S., Gabriel, S. B., Getz, G., Garraway, L. A., & Chin, L.
- Affiliations
- Broad Institute (US)
- The University of Texas MD Anderson Cancer Center (US)
- Dana-Farber Cancer Institute (US)
- Massachusetts General Hospital (US)
- Austrian Academy of Sciences (AT)
- Essen University Hospital (DE)
- Corresponding author
- Garraway, Levi A.
- Chin, Lynda
- ORCID
- Hodis, Eran
- Watson, Ian R.
- Kryukov, Gregory V.
- Arold, Stefan T.
- Imielinski, Marcin
- Theurillat, Jean-Philippe
- Auclair, Daniel
- Lawrence, Michael S.
- Cibulskis, Kristian
- Sivachenko, Andrey
- Saksena, Gordon
- Stransky, Nicolas
- Winckler, Wendy
- Ardlie, Kristin
- Wagle, Nikhil
- Wargo, Jennifer
- Noble, Michael
- Meyerson, Matthew
- Ladbury, John E.
- Davies, Michael A.
- Gershenwald, Jeffrey E.
- Wagner, Stephan N.
- Hoon, Dave S.B.
- Schadendorf, Dirk
- Lander, Eric S.
- Gabriel, Stacey B.
- Getz, Gad
- Garraway, Levi A.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2012-07
- Volume
- 150
- Issue
- 2
- Pages
- 251-263
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3600117
- OpenAlex
- W2134471382
- Semantic Scholar
- bd7104f269c2680f45f7cb31d86a7c39acb65f51
- Cited by
- 2,610
- References
- 65
- Citations by year
- 2026: 77 · 2025: 103 · 2024: 107 · 2023: 140 · 2022: 179 · 2021: 192 · 2020: 208 · 2019: 208 · 2018: 233 · 2017: 235 · 2016: 239 · 2015: 232 · 2014: 230 · 2013: 190 · 2012: 33
- FWCI
- 88.13
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 384 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- Funders
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (134379)
- National Institutes of Health (DP2OD002750)
- Canadian Institutes of Health Research
- National Human Genome Research Institute (U54HG003067)
- National Cancer Institute (R01CA093947, U24CA143845, R33CA126674, T32CA009172, P30CA016672, P50CA093459)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Melanoma and MAPK Pathways
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- melanoma, driver mutations, passenger mutations, UV mutagenesis, PPP6C, Rac1, chromosomal copy number, BRAF, NRAS, Rb pathway, p53 pathway, melanoma pathogenesis
- MeSH terms
- Amino Acid Sequence, Cells, Cultured, Humans, Melanocytes, Melanoma, Models, Molecular, Molecular Sequence Data, Ultraviolet Rays, Mutagenesis, Sequence Alignment, rac1 GTP-Binding Protein, Proto-Oncogene Proteins B-raf, Genome-Wide Association Study, Exome
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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