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Research: Immune signatures correlate with L1 retrotransposition in gastrointestinal cancers
- Hyunchul Jung,
- Jung Kyoon Choi,
- and Eunjung Alice Lee
Genome Res. August 2018 28: 1136-1146; Published in Advance July 3, 2018, doi:10.1101/gr.231837.117
...expression levels of L1 suppressors such as APOBEC3s and SAMHD1. Our results indicate that cancer immunity may contribute to stability by suppressing L1 retrotransposition in gastrointestinal cancers.Somatic retrotransposition of the long interspersed nuclear element-1 (LINE-1 or L1) has been reported...
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Research: L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis
- Stephanie N. Schauer,
- Patricia E. Carreira,
- Ruchi Shukla,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Francisco J. Sanchez-Luque,
- Paola Nicoli,
- Michaela Kindlova,
- Serena Ghisletti,
- Alexandre Dos Santos,
- Delphine Rapoud,
- Didier Samuel,
- Jamila Faivre,
- Adam D. Ewing,
- Sandra R. Richardson,
- and Geoffrey J. Faulkner
Genome Res. May 2018 28: 639-653; Published in Advance April 11, 2018, doi:10.1101/gr.226993.117
....ewing@mater.uq.edu.au, sandra.richardson@mater.uq.edu.au, faulknergj@gmail.comAbstractThe retrotransposon Long Interspersed Element 1 (LINE-1 or L1) is a continuing source of germline and somatic mutagenesis in mammals. Deregulated L1 activity is a hallmark of cancer, and L1 mutagenesis has been described in numerous human...
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Research: Engineered LINE-1 retrotransposition in nondividing human neurons
- Angela Macia,
- Thomas J. Widmann,
- Sara R. Heras,
- Veronica Ayllon,
- Laura Sanchez,
- Meriem Benkaddour-Boumzaouad,
- Martin Muñoz-Lopez,
- Alejandro Rubio,
- Suyapa Amador-Cubero,
- Eva Blanco-Jimenez,
- Javier Garcia-Castro,
- Pablo Menendez,
- Philip Ng,
- Alysson R. Muotri,
- John L. Goodier,
- and Jose L. Garcia-Perez
Genome Res. March 2017 27: 335-348; Published in Advance December 13, 2016, doi:10.1101/gr.206805.116
..., recent data acquired on human tumors suggest that selected somatic tissues may normally tolerate a low level of somatic LINE-1 retrotransposition, as recently described in normal gastrointestinal tissues (Ewing et al. 2015). Indeed, it is also possible that the differential expression of restriction...
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Research: A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancer
- Emma C. Scott,
- Eugene J. Gardner,
- Ashiq Masood,
- Nelson T. Chuang,
- Paula M. Vertino,
- and Scott E. Devine
Genome Res. June 2016 26: 745-755; Published in Advance May 10, 2016, doi:10.1101/gr.201814.115
...@som.umaryland.edu ↵8 Co-first authors ↵9 Present address: Siteman Cancer Center, Washington University School of Medicine, St. Louis, St. Louis, MO 63110, USA AbstractAlthough human LINE-1 (L1) elements are actively mobilized in many cancers, a role for somatic L1 retrotransposition in tumor initiation has not been...
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Research: APOBEC3A drives deaminase mutagenesis in human gastric epithelium
- Yohan An,
- Ji-Hyun Lee,
- Joonoh Lim,
- Jeonghwan Youk,
- Seongyeol Park,
- Ji-Hyung Park,
- Kijong Yi,
- Taewoo Kim,
- Chang Hyun Nam,
- Won Hee Lee,
- Soo A Oh,
- Yoo Jin Bae,
- Thomas M. Klompstra,
- Haeun Lee,
- Jinju Han,
- Junehwak Lee,
- Jung Woo Park,
- Jie-Hyun Kim,
- Hyunki Kim,
- Hugo Snippert,
- Bon-Kyoung Koo,
- and Young Seok Ju
Genome Res. October 2025 35: 2158-2172; Published in Advance August 26, 2025, doi:10.1101/gr.280338.124
...apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC)-associated DNA mutations, suggesting APOBEC enzymes as innate mutagens during cancer initiation and evolution. However, the pure mutagenic impacts of the specific enzymes among this family remain unclear in human normal cell lineages. Here, we...
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Research: Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types
- Akihiro Fujimoto,
- Masashi Fujita,
- Takanori Hasegawa,
- Jing Hao Wong,
- Kazuhiro Maejima,
- Aya Oku-Sasaki,
- Kaoru Nakano,
- Yuichi Shiraishi,
- Satoru Miyano,
- Go Yamamoto,
- Kiwamu Akagi,
- Seiya Imoto,
- and Hidewaki Nakagawa
Genome Res. March 2020 30: 334-346; Published in Advance March 24, 2020, doi:10.1101/gr.255026.119
...sensitivity. Third, we found that replication timing and DNA shape were significantly associated with mutation rates of microsatellites. Last, analysis of mutations in mismatch repair genes showed that somatic SNVs and short indels had larger functional impacts than germline mutations and structural...
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Research: Mutagenesis of human genomes by endogenous mobile elements on a population scale
- Nelson T. Chuang,
- Eugene J. Gardner,
- Diane M. Terry,
- Jonathan Crabtree,
- Anup A. Mahurkar,
- Guillermo L. Rivell,
- Charles C. Hong,
- James A. Perry,
- and Scott E. Devine
Genome Res. December 2021 31: 2225-2235; Published in Advance November 12, 2021, doi:10.1101/gr.275323.121
...for retrotransposition activity. We also compared the germline L1 insertions that we discovered in this study (all sizes) with those discovered in three large studies of somatic L1 insertions in human cancers and found minimal overlap between these data sets (Supplemental Fig. S5). This suggests that there are few...
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Method: The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology
- Eugene J. Gardner,
- Vincent K. Lam,
- Daniel N. Harris,
- Nelson T. Chuang,
- Emma C. Scott,
- W. Stephen Pittard,
- Ryan E. Mills,
- The 1000 Genomes Project Consortium,
- and Scott E. Devine
Genome Res. November 2017 27: 1916-1929; Published in Advance August 30, 2017, doi:10.1101/gr.218032.116
...(Fig. 4) with those that had been measured previously in a cell culture-based assay for L1 retrotransposition (Fig. 4C; Moran et al. 1996; Brouha et al. 2002, 2003; Beck et al. 2010). The LRE3 FL-L1 source element, which is highly active in both the germline and somatic cancer tissues, is also highly...
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Research: Quantitative analysis of Y-Chromosome gene expression across 36 human tissues
- Alexander K. Godfrey,
- Sahin Naqvi,
- Lukáš Chmátal,
- Joel M. Chick,
- Richard N. Mitchell,
- Steven P. Gygi,
- Helen Skaletsky,
- and David C. Page
Genome Res. June 2020 30: 860-873; Published in Advance May 27, 2020, doi:10.1101/gr.261248.120
...to differences between XX and XY individuals. Because the X–Y gene pairs encode regulators of transcription, translation, and protein stability that are highly dosage sensitive (Bellott et al. 2014; Naqvi et al. 2018), small differences in their expression levels could contribute significantly to the widespread...

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