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Research: Somatic retrotransposition in the developing rhesus macaque brain
- Victor Billon,
- Francisco J. Sanchez-Luque,
- Jay Rasmussen,
- Gabriela O. Bodea,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Seth W. Cheetham,
- Stephanie N. Schauer,
- Prabha Ajjikuttira,
- Thomas J. Meyer,
- Cora E. Layman,
- Kimberly A. Nevonen,
- Natasha Jansz,
- Jose L. Garcia-Perez,
- Sandra R. Richardson,
- Adam D. Ewing,
- Lucia Carbone,
- and Geoffrey J. Faulkner
Genome Res. July 2022 32: 1298-1314; Published in Advance June 21, 2022, doi:10.1101/gr.276451.121
...retrotransposon subfamily activation in the early embryo, followed by repression in adult tissues. These data highlight endogenous macaque L1 retrotransposition potential, provide prototypical evidence of L1-mediated somatic mosaicism in a nonhuman primate, and allude to L1 mobility in the brain over the past 30...
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Research: Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development
- Patricia Gerdes,
- Dorothy Chan,
- Mischa Lundberg,
- Francisco J. Sanchez-Luque,
- Gabriela O. Bodea,
- Adam D. Ewing,
- Geoffrey J. Faulkner,
- and Sandra R. Richardson
Genome Res. September 2023 33: 1465-1481; Published in Advance October 5, 2023, doi:10.1101/gr.278003.123
...), and assessment of L1 methylation status en masse may mask individual L1s whose methylation dynamics differ from those of their subfamily. Indeed, studies of human L1s suggest certain loci can “escape” methylation and thus contribute to somatic retrotransposition throughout development and in cancer (Pitkänen et...
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Research: Pedigree-based estimation of human mobile element retrotransposition rates
- Julie Feusier,
- W. Scott Watkins,
- Jainy Thomas,
- Andrew Farrell,
- David J. Witherspoon,
- Lisa Baird,
- Hongseok Ha,
- Jinchuan Xing,
- and Lynn B. Jorde
Genome Res. October 2019 29: 1567-1577; doi:10.1101/gr.247965.118
..., for example, are active and have been extensively studied in the human brain (for review, see Faulkner and Billon 2018) and in tumors (for review, see Burns 2017).Inherited retrotransposition events occur either in the parental gametes or in early embryogenesis of the individual, with the latter leading...
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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
..., gastrointestinal cancers, including esophageal (Doucet-O'Hare et al. 2015; Secrier et al. 2016), gastric (Ewing et al. 2015), and colorectal cancers (Lee et al. 2012; Solyom et al. 2012), reportedly carry extensive somatic L1 insertions. The rate of L1 insertions varies substantially among individual tumors...
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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
...endogenous somatic L1 insertions, L1 mobilization events have been uncovered in a plethora of tumor types, including lung, ovarian, breast, colorectal, prostate, liver, pancreatic, gastric, endometrial, and esophageal cancers (Iskow et al. 2010; Lee et al. 2012; Solyom et al. 2012; Shukla et al. 2013; Helman...
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Research: Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution
- Adam D. Ewing,
- Anthony Gacita,
- Laura D. Wood,
- Florence Ma,
- Dongmei Xing,
- Min-Sik Kim,
- Srikanth S. Manda,
- Gabriela Abril,
- Gavin Pereira,
- Alvin Makohon-Moore,
- Leendert H.J. Looijenga,
- Ad J.M. Gillis,
- Ralph H. Hruban,
- Robert A. Anders,
- Katharine E. Romans,
- Akhilesh Pandey,
- Christine A. Iacobuzio-Donahue,
- Bert Vogelstein,
- Kenneth W. Kinzler,
- Haig H. Kazazian, Jr.,
- and Szilvia Solyom
Genome Res. October 2015 25: 1536-1545; Published in Advance August 10, 2015, doi:10.1101/gr.196238.115
...–6019); in red, poly(A) tail. Early somatic retrotransposition in tumors Genome Research 1539 www..org Figure 3. Representative examples of further somatic L1 insertions in colon cancer patient 2BV and gastric cancer patient 2043. (A) L1 insertions in colorectal cancer (all detectable by conventional PCR), from...
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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: Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing
- Elena Helman,
- Michael S. Lawrence,
- Chip Stewart,
- Carrie Sougnez,
- Gad Getz,
- and Matthew Meyerson
Genome Res. July 2014 24: 1053-1063; Published in Advance May 13, 2014, doi:10.1101/gr.163659.113
.... In addition to novel germline polymorphisms, we find 810 somatic retrotransposon insertions primarily in lung squamous, head and neck, colorectal, and endometrial carcinomas. Many somatic retrotransposon insertions occur in known cancer genes. We find that high somatic retrotransposition rates in tumors...
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Research: Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling
- Lu Liu,
- He Chen,
- Cheng Sun,
- Jianyun Zhang,
- Juncheng Wang,
- Meijie Du,
- Jie Li,
- Lin Di,
- Jie Shen,
- Shuang Geng,
- Yuhong Pang,
- Yingying Luo,
- Chen Wu,
- Yusi Fu,
- Zhe Zheng,
- Jianbin Wang,
- and Yanyi Huang
Genome Res. January 2022 32: 44-54; Published in Advance December 28, 2021, doi:10.1101/gr.275453.121
...mM EDTA, and 0.5% Triton X-100 [Sigma-Aldrich T9284]) in a well of a 96-well plate.Single-cell isolation from a tumor tissueWe ground the colorectal cancer sample (∼0.1 cm3) using a dounce glass tissue grinder. The cells were then washed, resuspended in PBS, and filtered through a Falcon 40-µm cell...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...leading to the clonal evolution of cancer cells (Qing et al. 2020; Chakravarty and Solit 2021). Somatic mutations in key genes and their regulatory sequences, especially oncogenes, tumor suppressors, and DNA repair genes, are frequently found in cancers and contribute to tumor progression and therapeutic...
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