No Genome is an Island Extra References 10


10. Importance of Ecological Transitions in Triggering Genome Change.


·      10.C. Microbial infection and genotoxin activity.


o   Toxin molecule enters the host cell nucleus by mechanisms based on specific membrane interactions and nuclear localization signals (NLSs) (Boesze-Battaglia, Alexander et al. 2016; Frisan 2016; Boesze-Battaglia, Walker et al. 2017).


o   Bacterial outer membrane EVs transport CDT genotoxin (and potentially other genotoxins): the intestinal bacteria Escherichia coli (Bielaszewska, Ruter et al. 2017) and Campylobacter jejuni (Lindmark, Rompikuntal et al. 2009; Elmi, Watson et al. 2012) as well as Aggregatibacter actinomycetemcomitans, which is known to infect the oral cavity (Rompikuntal, Thay et al. 2012).


·      10.D. The complex nature of genome instabilities in cancer cells.


o   Chromosome changes in cancer (Albertson, Collins et al. 2003; Mertens, Johansson et al. 2015; Seki, Mizukami et al. 2015; Ye, Wang et al. 2015; Markowetz 2016; Menghi, Inaki et al. 2016; Steele 2016; Chen, Singh et al. 2017; Kumar, Dillon et al. 2017; Rangel, Forero-Castro et al. 2017; Vargas-Rondon, Villegas et al. 2017; Bloomfield and Duesberg 2018; Grobner, Worst et al. 2018; Nattestad, Goodwin et al. 2018; Viswanathan, Ha et al. 2018; Yi and Ju 2018)


o   Chromothripsis (Kloosterman, Hoogstraat et al. 2011; Magrangeas, Avet-Loiseau et al. 2011; Chen, Ferec et al. 2012; Forment, Kaidi et al. 2012; Jones and Jallepalli 2012; Kloosterman, Tavakoli-Yaraki et al. 2012; Molenaar, Koster et al. 2012; Bassaganyas, Bea et al. 2013; Boeva, Jouannet et al. 2013; Kloosterman and Cuppen 2013; Korbel and Campbell 2013; Zhang, Leibowitz et al. 2013; Cai, Kumar et al. 2014; Kloosterman, Koster et al. 2014; McEvoy, Nagahawatte et al. 2014; Pellestor, Gatinois et al. 2014; Pellestor, Gatinois et al. 2014; de Pagter and Kloosterman 2015; de Pagter, van Roosmalen et al. 2015; Furgason, Koncar et al. 2015; Leibowitz, Zhang et al. 2015; Maciejowski, Li et al. 2015; Terzoudi, Karakosta et al. 2015; Weckselblatt, Hermetz et al. 2015; Zhang, Spektor et al. 2015; Hatch 2016; Nazaryan-Petersen, Bertelsen et al. 2016; Poot 2016; Rode, Maass et al. 2016; Storchova and Kloosterman 2016; Collins, Brand et al. 2017; Ly and Cleveland 2017; Middelkamp, van Heesch et al. 2017; Poot 2017)


o   Chromoplexy. 88% of prostate tumors displayed inter-chromosomal rearrangement chains of 10 or more breakpoints, 63% contained two or more chains, and 39% of all prostate cancer chromosome rearrangements came from chromoplectic chains. (Baca, Prandi et al. 2013)


o   Kataegis. Predominantly C-to-T transitions, as expected for C-to-U deamination products, and are largely fixed on the same DNA strand, a sign of catalytic processivity. (Chan and Gordenin 2015; Chan, Roberts et al. 2015; Kazanov, Roberts et al. 2015; Rebhandl, Huemer et al. 2015; Shlien, Campbell et al. 2015; Swanton, McGranahan et al. 2015; Casellas, Basu et al. 2016)


o   Cell fusions. (Lu and Kang 2009) (Platt, Zhou et al. 2016) ((Rachkovsky, Sodi et al. 1998) (Lu and Kang 2007) (Pawelek and Chakraborty 2008) (Pawelek and Chakraborty 2008) (Pawelek 2014) (Choi 2009) (Lu and Kang 2009) (Lu and Kang 2009) (Gast, Silk et al. 2018) (Rappa, Mercapide et al. 2012) (LaBerge, Duvall et al. 2017) (Chitty, Filipe et al. 2018) )


§  entosis (autophagy) (Overholtzer, Mailleux et al. 2007),

§  DNA exchange (Searles, Santosa et al. 2018),

§  virus-linked fusion (Parris 2005) (Duelli and Lazebnik 2007) (Gao and Zheng 2011),

§  role of Syncytin 1 (Duelli and Lazebnik 2003),

§  MAPK signalling (Dudin, Merlini et al. 2016),

§  tumor evolution (Zhou, Merchak et al. 2015),

§  linked to inflammation (Johansson, Youssef et al. 2008),

§  radiation-induced (Nygren, Liuba et al. 2008),

§  polyploid/WGD/aneuploid oncogenesis (Fujiwara, Bandi et al. 2005) (Fujiwara, Bandi et al. 2005) (Margolis 2005) (Lim and Ganem 2014)


·      Mutational events observed in real-time tumor evolution also found in the germlines of healthy individuals (Goodman 2016) (Abrusan, Szilagyi et al. 2013; Pellestor, Gatinois et al. 2014; Weckselblatt, Hermetz et al. 2015; Fukami, Shima et al. 2017; Middelkamp, van Heesch et al. 2017; Poot 2017)





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