Different Genome Changes Observed in Cancer Cells

Different Genome Changes Observed in Cancer Cells
(also http://shapiro.bsd.uchicago.edu/Cancer%20Genome%20Changes.pdf)

Genome Change

References

Stress-induced mutagenic activity

(Cisneros, Bussey et al. 2017)

Hypermutability following loss of replication proofreading functions

(Shlien, Campbell et al. 2015)

Massive genome rearrangements (“karyotype chaos”)

(Stephens, Greenman et al. 2011; Nones, Waddell et al. 2014; Rangel, Forero-Castro et al. 2017)

Homology-independent rearrangements (NHEJ)

(Malhotra, Lindberg et al. 2013)

Retrotransposon activation

(Anwar, Wulaningsih et al. 2017)

Non-canonical termination of homologous recombination

(Hartlerode, Willis et al. 2016)

Kataegis ("mutation thunderstorms") and somatic hypermutation

(Hardianti, Tatsumi et al. 2004; Nik-Zainal, Alexandrov et al. 2012; Nik-Zainal, Van Loo et al. 2012; Stephens, Tarpey et al. 2012; Chan, Roberts et al. 2015; Harris 2015; Kazanov, Roberts et al. 2015; Supek and Lehner 2017)

Cytosine deaminase-dependent chromosome translocation

(Robbiani and Nussenzweig 2013; Harris 2015; Kazanov, Roberts et al. 2015)

Chromothripsis ("chromosome shattering")

(Kloosterman, Hoogstraat et al. 2011; Cai, Kumar et al. 2014; Kloosterman, Koster et al. 2014; de Pagter and Kloosterman 2015; Rode, Maass et al. 2016)

Chromothripsis linked to oncogene amplification

(Furgason, Koncar et al. 2015)

Complex insertion-deletion mutations (indels)

(Ye, Wang et al. 2015)

Tandem duplications as well as formation of “amplicons” with rearranged and amplified chromosomal segments, a.k.a. copy number variations (CNVs)

(Beroukhim, Mermel et al. 2010; Inaki, Menghi et al. 2014; Menghi, Inaki et al. 2016)

Formation of amplified circular extrachromosomal DNAs

(Turner, Deshpande et al. 2017)

Processed pseudogene formation

(Cooke, Shlien et al. 2014)

L1 retrotransposition

(Lee, Iskow et al. 2012; Helman, Lawrence et al. 2014; Kemp and Longworth 2015; Scott and Devine 2017)

Extensive L1 retrotransduction of non-repetitive DNA

(Tubio, Li et al. 2014)

Transfer of mitochondrial DNA into nuclear genome

(Ju, Tubio et al. 2015)

RAG transposase/recombinase-mediated chromosome rearrangement in immune system tumors

(Halper-Stromberg, Steranka et al. 2013; Papaemmanuil, Rapado et al. 2014)

Somatic hypermutation involving a reverse transcriptase-based mutator activity

(Steele 2016)

REFERENCES

Anwar, S. L., W. Wulaningsih, et al. (2017). "Transposable Elements in Human Cancer: Causes and Consequences of Deregulation." Int J Mol Sci 18(5). http://www.ncbi.nlm.nih.gov/pubmed/28471386.

Beroukhim, R., C. H. Mermel, et al. (2010). "The landscape of somatic copy-number alteration across human cancers." Nature 463(7283): 899-905. http://www.ncbi.nlm.nih.gov/pubmed/20164920.

Cai, H., N. Kumar, et al. (2014). "Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens." BMC Genomics 15: 82. http://www.ncbi.nlm.nih.gov/pubmed/24476156.

Chan, K., S. A. Roberts, et al. (2015). "An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers." Nat Genet 47(9): 1067-1072. http://www.ncbi.nlm.nih.gov/pubmed/26258849.

Cisneros, L., K. J. Bussey, et al. (2017). "Ancient genes establish stress-induced mutation as a hallmark of cancer." PLoS One 12(4): e0176258. http://www.ncbi.nlm.nih.gov/pubmed/28441401.

Cooke, S. L., A. Shlien, et al. (2014). "Processed pseudogenes acquired somatically during cancer development." Nat Commun 5: 3644. http://www.ncbi.nlm.nih.gov/pubmed/24714652.

de Pagter, M. S. and W. P. Kloosterman (2015). "The Diverse Effects of Complex Chromosome Rearrangements and Chromothripsis in Cancer Development." Recent Results Cancer Res 200: 165-193. http://www.ncbi.nlm.nih.gov/pubmed/26376877.

Furgason, J. M., R. F. Koncar, et al. (2015). "Whole genome sequence analysis links chromothripsis to EGFR, MDM2, MDM4, and CDK4 amplification in glioblastoma." Oncoscience 2(7): 618-628. http://www.ncbi.nlm.nih.gov/pubmed/26328271.

Halper-Stromberg, E., J. Steranka, et al. (2013). "Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies." BMC Genomics 14: 565. http://www.ncbi.nlm.nih.gov/pubmed/23957733.

Hardianti, M. S., E. Tatsumi, et al. (2004). "Activation-induced cytidine deaminase expression in follicular lymphoma: association between AID expression and ongoing mutation in FL." Leukemia 18(4): 826-831. http://www.ncbi.nlm.nih.gov/pubmed/14990977.

Harris, R. S. (2015). "Molecular mechanism and clinical impact of APOBEC3B-catalyzed mutagenesis in breast cancer." Breast Cancer Res 17: 8. http://www.ncbi.nlm.nih.gov/pubmed/25848704.

Hartlerode, A. J., N. A. Willis, et al. (2016). "Complex Breakpoints and Template Switching Associated with Non-canonical Termination of Homologous Recombination in Mammalian Cells." PLoS Genet 12(11): e1006410. http://www.ncbi.nlm.nih.gov/pubmed/27832076.

Helman, E., M. S. Lawrence, et al. (2014). "Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing." Genome Res 24(7): 1053-1063. http://www.ncbi.nlm.nih.gov/pubmed/24823667.

Inaki, K., F. Menghi, et al. (2014). "Systems consequences of amplicon formation in human breast cancer." Genome Res 24(10): 1559-1571. http://www.ncbi.nlm.nih.gov/pubmed/25186909.

Ju, Y. S., J. M. Tubio, et al. (2015). "Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells." Genome Res 25(6): 814-824. http://www.ncbi.nlm.nih.gov/pubmed/25963125.

Kazanov, M. D., S. A. Roberts, et al. (2015). "APOBEC-Induced Cancer Mutations Are Uniquely Enriched in Early-Replicating, Gene-Dense, and Active Chromatin Regions." Cell Rep 13(6): 1103-1109. http://www.ncbi.nlm.nih.gov/pubmed/26527001.

Kemp, J. R. and M. S. Longworth (2015). "Crossing the LINE Toward Genomic Instability: LINE-1 Retrotransposition in Cancer." Front Chem 3: 68. http://www.ncbi.nlm.nih.gov/pubmed/26734601.

Kloosterman, W. P., M. Hoogstraat, et al. (2011). "Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer." Genome Biol 12(10): R103. http://www.ncbi.nlm.nih.gov/pubmed/22014273.

Kloosterman, W. P., J. Koster, et al. (2014). "Prevalence and clinical implications of chromothripsis in cancer genomes." Curr Opin Oncol 26(1): 64-72. http://www.ncbi.nlm.nih.gov/pubmed/24305569.

Lee, E., R. Iskow, et al. (2012). "Landscape of somatic retrotransposition in human cancers." Science 337(6097): 967-971. http://www.ncbi.nlm.nih.gov/pubmed/22745252.

Malhotra, A., M. Lindberg, et al. (2013). "Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms." Genome Res 23(5): 762-776. http://www.ncbi.nlm.nih.gov/pubmed/23410887.

Menghi, F., K. Inaki, et al. (2016). "The tandem duplicator phenotype as a distinct genomic configuration in cancer." Proc Natl Acad Sci U S A 113(17): E2373-2382. http://www.ncbi.nlm.nih.gov/pubmed/27071093.

Nik-Zainal, S., L. B. Alexandrov, et al. (2012). "Mutational processes molding the genomes of 21 breast cancers." Cell 149(5): 979-993. http://www.ncbi.nlm.nih.gov/pubmed/22608084.

Nik-Zainal, S., P. Van Loo, et al. (2012). "The life history of 21 breast cancers." Cell 149(5): 994-1007. http://www.ncbi.nlm.nih.gov/pubmed/22608083.

Nones, K., N. Waddell, et al. (2014). "Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis." Nat Commun 5: 5224. http://www.ncbi.nlm.nih.gov/pubmed/25351503.

Papaemmanuil, E., I. Rapado, et al. (2014). "RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia." Nat Genet 46(2): 116-125. http://www.ncbi.nlm.nih.gov/pubmed/24413735.

Rangel, N., M. Forero-Castro, et al. (2017). "New Insights in the Cytogenetic Practice: Karyotypic Chaos, Non-Clonal Chromosomal Alterations and Chromosomal Instability in Human Cancer and Therapy Response." Genes (Basel) 8(6). http://www.ncbi.nlm.nih.gov/pubmed/28587191.

Robbiani, D. F. and M. C. Nussenzweig (2013). "Chromosome translocation, B cell lymphoma, and activation-induced cytidine deaminase." Annu Rev Pathol 8: 79-103. http://www.ncbi.nlm.nih.gov/pubmed/22974238.

Rode, A., K. K. Maass, et al. (2016). "Chromothripsis in cancer cells: An update." Int J Cancer 138(10): 2322-2333. http://www.ncbi.nlm.nih.gov/pubmed/26455580.

Scott, E. C. and S. E. Devine (2017). "The Role of Somatic L1 Retrotransposition in Human Cancers." Viruses 9(6). http://www.ncbi.nlm.nih.gov/pubmed/28561751.

Shlien, A., B. B. Campbell, et al. (2015). "Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers." Nat Genet. http://www.ncbi.nlm.nih.gov/pubmed/25642631.

Steele, E. J. (2016). "Somatic hypermutation in immunity and cancer: Critical analysis of strand-biased and codon-context mutation signatures." DNA Repair (Amst) 45: 1-24. http://www.ncbi.nlm.nih.gov/pubmed/27449479.

Stephens, P. J., C. D. Greenman, et al. (2011). "Massive genomic rearrangement acquired in a single catastrophic event during cancer development." Cell 144(1): 27-40. http://www.ncbi.nlm.nih.gov/pubmed/21215367.

Stephens, P. J., P. S. Tarpey, et al. (2012). "The landscape of cancer genes and mutational processes in breast cancer." Nature 486(7403): 400-404. http://www.ncbi.nlm.nih.gov/pubmed/22722201.

Supek, F. and B. Lehner (2017). "Clustered Mutation Signatures Reveal that Error-Prone DNA Repair Targets Mutations to Active Genes." Cell 170(3): 534-547 e523. http://www.ncbi.nlm.nih.gov/pubmed/28753428.

Tubio, J. M., Y. Li, et al. (2014). "Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes." Science 345(6196): 1251343. http://www.ncbi.nlm.nih.gov/pubmed/25082706.

Turner, K. M., V. Deshpande, et al. (2017). "Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity." Nature 543(7643): 122-125. http://www.ncbi.nlm.nih.gov/pubmed/28178237.

Ye, K., J. Wang, et al. (2015). "Systematic discovery of complex insertions and deletions in human cancers." Nat Med. http://www.ncbi.nlm.nih.gov/pubmed/26657142.

Different Genome Changes Observed in Cancer Cells (also http://shapiro.bsd.uchicago.edu/Cancer%20Genome%20Changes.pdf)
Genome Change	References
Stress-induced mutagenic activity	(Cisneros, Bussey et al. 2017)
Hypermutability following loss of replication proofreading functions	(Shlien, Campbell et al. 2015)
Massive genome rearrangements (“karyotype chaos”)	(Stephens, Greenman et al. 2011; Nones, Waddell et al. 2014; Rangel, Forero-Castro et al. 2017)
Homology-independent rearrangements (NHEJ)	(Malhotra, Lindberg et al. 2013)
Retrotransposon activation	(Anwar, Wulaningsih et al. 2017)
Non-canonical termination of homologous recombination	(Hartlerode, Willis et al. 2016)
Kataegis ("mutation thunderstorms") and somatic hypermutation	(Hardianti, Tatsumi et al. 2004; Nik-Zainal, Alexandrov et al. 2012; Nik-Zainal, Van Loo et al. 2012; Stephens, Tarpey et al. 2012; Chan, Roberts et al. 2015; Harris 2015; Kazanov, Roberts et al. 2015; Supek and Lehner 2017)
Cytosine deaminase-dependent chromosome translocation	(Robbiani and Nussenzweig 2013; Harris 2015; Kazanov, Roberts et al. 2015)
Chromothripsis ("chromosome shattering")	(Kloosterman, Hoogstraat et al. 2011; Cai, Kumar et al. 2014; Kloosterman, Koster et al. 2014; de Pagter and Kloosterman 2015; Rode, Maass et al. 2016)
Chromothripsis linked to oncogene amplification	(Furgason, Koncar et al. 2015)
Complex insertion-deletion mutations (indels)	(Ye, Wang et al. 2015)
Tandem duplications as well as formation of “amplicons” with rearranged and amplified chromosomal segments, a.k.a. copy number variations (CNVs)	(Beroukhim, Mermel et al. 2010; Inaki, Menghi et al. 2014; Menghi, Inaki et al. 2016)
Formation of amplified circular extrachromosomal DNAs	(Turner, Deshpande et al. 2017)
Processed pseudogene formation	(Cooke, Shlien et al. 2014)
L1 retrotransposition	(Lee, Iskow et al. 2012; Helman, Lawrence et al. 2014; Kemp and Longworth 2015; Scott and Devine 2017)
Extensive L1 retrotransduction of non-repetitive DNA	(Tubio, Li et al. 2014)
Transfer of mitochondrial DNA into nuclear genome	(Ju, Tubio et al. 2015)
RAG transposase/recombinase-mediated chromosome rearrangement in immune system tumors	(Halper-Stromberg, Steranka et al. 2013; Papaemmanuil, Rapado et al. 2014)
Somatic hypermutation involving a reverse transcriptase-based mutator activity	(Steele 2016)