L1 retrotransposons, cancer stem cells and oncogenesis

Retrotransposons have played a central role in human genome evolution. The accumulation of heritable L1, Alu and SVA retrotransposon insertions continues to generate structural variation within and between populations, and can result in spontaneous genetic disease. Recent works have reported somatic L1 retrotransposition in tumours, which in some cases may contribute to oncogenesis. Intriguingly, L1 mobilization appears to occur almost exclusively in cancers of epithelial cell origin. In this review, we discuss how L1 retrotransposition could potentially trigger neoplastic transformation, based on the established correlation between L1 activity and cellular plasticity, and the proven capacity of L1‐mediated insertional mutagenesis to decisively alter gene expression and functional output.

[1]  K. Kinzler,et al.  Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer. , 1992, Cancer research.

[2]  Ryan E. Mills,et al.  Which transposable elements are active in the human genome? , 2007, Trends in genetics : TIG.

[3]  J. V. Moran,et al.  Dynamic interactions between transposable elements and their hosts , 2011, Nature Reviews Genetics.

[4]  R. Cardiff,et al.  Lineage analysis of basal epithelial cells reveals their unexpected plasticity and supports a cell of origin model for prostate cancer heterogeneity , 2013, Nature Cell Biology.

[5]  H. Kazazian,et al.  Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans. , 2011, Genome research.

[6]  G. Swergold Identification, characterization, and cell specificity of a human LINE-1 promoter , 1990, Molecular and cellular biology.

[7]  C. Tufarelli,et al.  Isolation of cancer-specific chimeric transcripts induced by hypomethylation of the LINE-1 antisense promoter. , 2009, Genomics.

[8]  T. Bestor,et al.  Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L , 2004, Nature.

[9]  M. Batzer,et al.  Repetitive Elements May Comprise Over Two-Thirds of the Human Genome , 2011, PLoS genetics.

[10]  D. Largaespada,et al.  Extensive somatic L1 retrotransposition in colorectal tumors , 2012, Genome research.

[11]  C. Walsh,et al.  Single-Neuron Sequencing Analysis of L1 Retrotransposition and Somatic Mutation in the Human Brain , 2012, Cell.

[12]  Zhijin Wu,et al.  DNA hypomethylation arises later in prostate cancer progression than CpG island hypermethylation and contributes to metastatic tumor heterogeneity. , 2008, Cancer research.

[13]  Jef D Boeke,et al.  High Frequency Retrotransposition in Cultured Mammalian Cells , 1996, Cell.

[14]  R. Buffenstein Negligible senescence in the longest living rodent, the naked mole-rat: insights from a successfully aging species , 2008, Journal of Comparative Physiology B.

[15]  D. Hanahan,et al.  Hallmarks of Cancer: The Next Generation , 2011, Cell.

[16]  K. Ramos,et al.  Activation of human long interspersed nuclear element 1 retrotransposition by benzo(a)pyrene, an ubiquitous environmental carcinogen. , 2006, Cancer research.

[17]  C. Lilley,et al.  APOBEC3A Is a Potent Inhibitor of Adeno-Associated Virus and Retrotransposons , 2006, Current Biology.

[18]  H. Kazazian,et al.  Mapping the LINE1 ORF1 protein interactome reveals associated inhibitors of human retrotransposition , 2013, Nucleic acids research.

[19]  E. Ostertag,et al.  L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism. , 2009, Genes & development.

[20]  J. Löwer,et al.  APOBEC3 Proteins Inhibit Human LINE-1 Retrotransposition* , 2006, Journal of Biological Chemistry.

[21]  Ryan E. Mills,et al.  Active Alu retrotransposons in the human genome. , 2008, Genome research.

[22]  J. V. Moran,et al.  LINE-1 elements in structural variation and disease. , 2011, Annual review of genomics and human genetics.

[23]  H. Kazazian,et al.  High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. , 2010, Genome research.

[24]  M. Knuiman,et al.  Dietary Benzo[a]pyrene Intake from Meat and the Risk of Colorectal Cancer , 2010, Cancer Epidemiology, Biomarkers & Prevention.

[25]  Gene W. Yeo,et al.  L1 retrotransposition in human neural progenitor cells , 2009, Nature.

[26]  P. Freeman,et al.  L1 Hybridization Enrichment: A Method for Directly Accessing De Novo L1 Insertions in the Human Germline , 2011, Human mutation.

[27]  R. Richardson,et al.  Prominin1 marks intestinal stem cells that are susceptible to neoplastic transformation , 2008, Nature.

[28]  A. Rasedee,et al.  Cytotoxicity of nickel zinc ferrite nanoparticles on cancer cells of epithelial origin , 2013, International journal of nanomedicine.

[29]  M. Tang,et al.  Preferential Formation of Benzo[a]pyrene Adducts at Lung Cancer Mutational Hotspots in P53 , 1996, Science.

[30]  Fred H. Gage,et al.  L1 retrotransposition in neurons is modulated by MeCP2 , 2010, Nature.

[31]  Jörg D. Becker,et al.  Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen , 2009, Cell.

[32]  J. Boeke,et al.  Reverse transcriptase encoded by a human transposable element. , 1991, Science.

[33]  P. Deininger,et al.  Mammalian non-LTR retrotransposons: for better or worse, in sickness and in health. , 2008, Genome research.

[34]  Josef Gotzmann,et al.  Molecular aspects of epithelial cell plasticity: implications for local tumor invasion and metastasis. , 2004, Mutation research.

[35]  Andrew F. Neuwald,et al.  Natural Mutagenesis of Human Genomes by Endogenous Retrotransposons , 2010, Cell.

[36]  S. Altschul,et al.  Identification of FAP locus genes from chromosome 5q21. , 1991, Science.

[37]  A. Mutirangura,et al.  LINE‐ 1 hypomethylation level as a potential prognostic factor for epithelial ovarian cancer , 2008, International journal of gynecological cancer : official journal of the International Gynecological Cancer Society.

[38]  H. Wang,et al.  Mesenchymal and stem-like cell properties targeted in suppression of chronically-induced breast cell carcinogenesis. , 2013, Cancer letters.

[39]  J. V. Moran,et al.  A YY1-binding site is required for accurate human LINE-1 transcription initiation. , 2004, Nucleic acids research.

[40]  T. Hubbard,et al.  A census of human cancer genes , 2004, Nature Reviews Cancer.

[41]  J. Kaprio,et al.  Environmental and heritable factors in the causation of cancer--analyses of cohorts of twins from Sweden, Denmark, and Finland. , 2000, The New England journal of medicine.

[42]  N. Yang,et al.  L1 retrotransposition is suppressed by endogenously encoded small interfering RNAs in human cultured cells , 2006, Nature Structural &Molecular Biology.

[43]  M. Esteller,et al.  Epigenetic Disruption of the PIWI Pathway in Human Spermatogenic Disorders , 2012, PloS one.

[44]  J. V. Moran,et al.  Hot L1s account for the bulk of retrotransposition in the human population , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[45]  T. Eickbush,et al.  Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: A mechanism for non-LTR retrotransposition , 1993, Cell.

[46]  J. V. Moran,et al.  LINE-1 retrotransposition in human embryonic stem cells. , 2007, Human molecular genetics.

[47]  R. Löwer,et al.  The non-autonomous retrotransposon SVA is trans-mobilized by the human LINE-1 protein machinery , 2011, Nucleic acids research.

[48]  Thierry Heidmann,et al.  LINE-mediated retrotransposition of marked Alu sequences , 2003, Nature Genetics.

[49]  Gregory J. Hannon,et al.  Small RNAs as Guardians of the Genome , 2009, Cell.

[50]  Ronald H. A. Plasterk,et al.  Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi , 2003, Nature.

[51]  William Wheeler,et al.  Detectable clonal mosaicism and its relationship to aging and cancer , 2012, Nature Genetics.

[52]  A. Fornace,et al.  Induction of B2 RNA polymerase III transcription by heat shock: enrichment for heat shock induced sequences in rodent cells by hybridization subtraction. , 1986, Nucleic acids research.

[53]  H. Hohjoh,et al.  Cytoplasmic ribonucleoprotein complexes containing human LINE‐1 protein and RNA. , 1996, The EMBO journal.

[54]  D. C. Hancks,et al.  Active human retrotransposons: variation and disease. , 2012, Current opinion in genetics & development.

[55]  A. F. Scott,et al.  Isolation of an active human transposable element. , 1991, Science.

[56]  Evan E. Eichler,et al.  LINE-1 Retrotransposition Activity in Human Genomes , 2010, Cell.

[57]  Lovelace J. Luquette,et al.  Landscape of Somatic Retrotransposition in Human Cancers , 2012, Science.

[58]  Ingo Ruczinski,et al.  Detectable clonal mosaicism from birth to old age and its relationship to cancer , 2012, Nature Genetics.

[59]  J. Dahlstrom,et al.  Prognostic value of LINE-1 retrotransposon expression and its subcellular localization in breast cancer , 2012, Breast Cancer Research and Treatment.

[60]  J. V. Moran,et al.  Cis-preferential LINE-1 reverse transcriptase activity in ribonucleoprotein particles , 2006, Nature Structural &Molecular Biology.

[61]  M. Plummer,et al.  International agency for research on cancer. , 2020, Archives of pathology.

[62]  G. Berx,et al.  Regulatory networks defining EMT during cancer initiation and progression , 2013, Nature Reviews Cancer.

[63]  A. Mutirangura,et al.  Line-1 hypomethylation in multistage carcinogenesis of the uterine cervix. , 2007, Asian Pacific journal of cancer prevention : APJCP.

[64]  Steven A. Roberts,et al.  An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers , 2013, Nature Genetics.

[65]  M. Speek,et al.  Retroelements in human disease. , 2013, Gene.

[66]  S. Yamanaka,et al.  Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors , 2006, Cell.

[67]  M. Speek,et al.  L1 Antisense Promoter Drives Tissue-Specific Transcription of Human Genes , 2006, Journal of biomedicine & biotechnology.

[68]  H. Kazazian,et al.  MOV10 RNA Helicase Is a Potent Inhibitor of Retrotransposition in Cells , 2012, PLoS genetics.

[69]  C. Sander,et al.  A novel class of small RNAs bind to MILI protein in mouse testes , 2006, Nature.

[70]  J. Boeke,et al.  Effect of reverse transcriptase inhibitors on LINE-1 and Ty1 reverse transcriptase activities and on LINE-1 retrotransposition , 2011, BMC Biochemistry.

[71]  Jef D Boeke,et al.  Human L1 Retrotransposon Encodes a Conserved Endonuclease Required for Retrotransposition , 1996, Cell.

[72]  J. V. Moran,et al.  Determination of L1 retrotransposition kinetics in cultured cells. , 2000, Nucleic acids research.

[73]  Fredrik Nyberg,et al.  Contribution of environmental factors to cancer risk. , 2003, British medical bulletin.

[74]  Eduardo Eyras,et al.  DGCR8 HITS-CLIP reveals novel functions for the Microprocessor , 2012, Nature Structural &Molecular Biology.

[75]  M. Speek Antisense Promoter of Human L1 Retrotransposon Drives Transcription of Adjacent Cellular Genes , 2001, Molecular and Cellular Biology.

[76]  H. Clevers,et al.  Intestinal Tumorigenesis Initiated by Dedifferentiation and Acquisition of Stem-Cell-like Properties , 2013, Cell.

[77]  J. Yodoi,et al.  Persistent oxidative stress in cancer , 1995, FEBS letters.

[78]  J. Mattick,et al.  Somatic retrotransposition alters the genetic landscape of the human brain , 2011, Nature.

[79]  C. Huttenhower,et al.  Epigenomic diversity of colorectal cancer indicated by LINE-1 methylation in a database of 869 tumors , 2010, Molecular Cancer.

[80]  J. Kawai,et al.  The regulated retrotransposon transcriptome of mammalian cells , 2009, Nature Genetics.

[81]  J. V. Moran,et al.  Distinct mechanisms for trans-mediated mobilization of cellular RNAs by the LINE-1 reverse transcriptase. , 2007, Genome research.

[82]  J. Siemiatycki,et al.  Lung cancer risk associated with occupational exposure to nickel, chromium VI, and cadmium in two population-based case-control studies in Montreal. , 2010, American journal of industrial medicine.

[83]  P. Andersen,et al.  Genetic and environmental influences on premature death in adult adoptees. , 1988, The New England journal of medicine.

[84]  G. Giorgi,et al.  LINE-1 retrotransposition in human neuroblastoma cells is affected by oxidative stress , 2011, Cell and Tissue Research.

[85]  L. Rozek,et al.  A Prospective Study of LINE-1DNA Methylation and Development of Adiposity in School-Age Children , 2013, PloS one.

[86]  M. Batzer,et al.  Extensive individual variation in L1 retrotransposition capability contributes to human genetic diversity. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[87]  N. Yang,et al.  An important role for RUNX3 in human L1 transcription and retrotransposition. , 2003, Nucleic acids research.

[88]  H. Hohjoh,et al.  Sequence‐specific single‐strand RNA binding protein encoded by the human LINE‐1 retrotransposon , 1997, The EMBO journal.

[89]  E. Barillot,et al.  LINE-1 Activity in Facultative Heterochromatin Formation during X Chromosome Inactivation , 2010, Cell.

[90]  Ravi Sachidanandam,et al.  A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. , 2008, Molecular cell.

[91]  T. Heidmann,et al.  Trex1 Prevents Cell-Intrinsic Initiation of Autoimmunity , 2008, Cell.

[92]  N. Perrimon,et al.  An endogenous small interfering RNA pathway in Drosophila , 2008, Nature.

[93]  M. Batzer,et al.  Reading TE leaves: new approaches to the identification of transposable element insertions. , 2011, Genome research.

[94]  G. Faulkner Retrotransposons: Mobile and mutagenic from conception to death , 2011, FEBS letters.

[95]  M. Shimura,et al.  All APOBEC3 family proteins differentially inhibit LINE-1 retrotransposition , 2007, Nucleic acids research.

[96]  Mireya Plass,et al.  The Microprocessor controls the activity of mammalian retrotransposons , 2013, Nature Structural &Molecular Biology.

[97]  Tom Royce,et al.  A comprehensive catalogue of somatic mutations from a human cancer genome , 2010, Nature.

[98]  D. Valle,et al.  Mobile Interspersed Repeats Are Major Structural Variants in the Human Genome , 2010, Cell.

[99]  International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome , 2001, Nature.

[100]  M. Stenglein,et al.  APOBEC3B and APOBEC3F Inhibit L1 Retrotransposition by a DNA Deamination-independent Mechanism* , 2006, Journal of Biological Chemistry.

[101]  W. Burhans,et al.  Retrotransposition is associated with genome instability during chronological aging , 2011, Proceedings of the National Academy of Sciences.

[102]  J. V. Moran,et al.  L1 retrotransposition in nondividing and primary human somatic cells. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[103]  M. Batzer,et al.  LSU Digital Commons LSU Digital Commons Mobile element scanning (ME-Scan) identifies thousands of novel Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations Alu insertions in diverse human populations , 2022 .

[104]  K. Burns,et al.  Long Interspersed Element–1 (LINE-1): Passenger or Driver in Human Neoplasms? , 2013, PLoS genetics.

[105]  W. J. Esselman,et al.  Identification of APOBEC3DE as Another Antiretroviral Factor from the Human APOBEC Family , 2006, Journal of Virology.

[106]  M. Emerman,et al.  Antiretroelement activity of APOBEC3H was lost twice in recent human evolution. , 2008, Cell host & microbe.

[107]  L. Peshkin,et al.  Genome sequencing reveals insights into physiology and longevity of the naked mole rat , 2011, Nature.

[108]  S. Antonarakis,et al.  Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man , 1988, Nature.

[109]  Thierry Heidmann,et al.  Human LINE retrotransposons generate processed pseudogenes , 2000, Nature Genetics.

[110]  J. Piriyapongsa,et al.  Hypomethylation of Intragenic LINE-1 Represses Transcription in Cancer Cells through AGO2 , 2011, PloS one.

[111]  P. Deininger,et al.  Nickel stimulates L1 retrotransposition by a post-transcriptional mechanism. , 2005, Journal of molecular biology.

[112]  Jef D. Boeke,et al.  Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes , 2004, Nature.

[113]  J. V. Moran,et al.  Epigenetic silencing of engineered L1 retrotransposition events in human embryonic carcinoma cells , 2010, Nature.

[114]  Piero Carninci,et al.  Edinburgh Research Explorer Endogenous Retrotransposition Activates Oncogenic Pathways in Hepatocellular Carcinoma Endogenous Retrotransposition Activates Oncogenic Pathways in Hepatocellular Carcinoma , 2022 .

[115]  Y. Kohara,et al.  Role of the Dnmt3 family in de novo methylation of imprinted and repetitive sequences during male germ cell development in the mouse. , 2007, Human molecular genetics.

[116]  M. Batzer,et al.  The impact of retrotransposons on human genome evolution , 2009, Nature Reviews Genetics.

[117]  D. Hanahan,et al.  The Hallmarks of Cancer , 2000, Cell.

[118]  J. V. Moran,et al.  Cellular inhibitors of long interspersed element 1 and Alu retrotransposition. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[119]  Y. Asmann,et al.  A Transposon-Based Genetic Screen in Mice Identifies Genes Altered in Colorectal Cancer , 2009, Science.

[120]  Jianrong Wang,et al.  Chromatin signature discovery via histone modification profile alignments , 2012, Nucleic acids research.

[121]  Jef D Boeke,et al.  Human L1 element target‐primed reverse transcription in vitro , 2002, The EMBO journal.

[122]  K. Kinzler,et al.  Identification of a gene located at chromosome 5q21 that is mutated in colorectal cancers. , 1991, Science.

[123]  Shuji Ogino,et al.  A cohort study of tumoral LINE-1 hypomethylation and prognosis in colon cancer. , 2008, Journal of the National Cancer Institute.

[124]  M. Malim,et al.  Endogenous MOV10 inhibits the retrotransposition of endogenous retroelements but not the replication of exogenous retroviruses , 2012, Retrovirology.

[125]  J. V. Moran,et al.  Reprogramming somatic cells into iPS cells activates LINE-1 retroelement mobility. , 2012, Human molecular genetics.

[126]  A. F. Scott,et al.  Origin of the human L1 elements: Proposed progenitor genes deduced from a consensus DNA sequence☆ , 1987, Genomics.

[127]  G. Grimaldi,et al.  Defining the beginning and end of KpnI family segments. , 1984, The EMBO journal.

[128]  J. V. Moran,et al.  Ribonucleoprotein particle formation is necessary but not sufficient for LINE-1 retrotransposition. , 2005, Human molecular genetics.

[129]  S. Martin,et al.  Ribonucleoprotein particles with LINE-1 RNA in mouse embryonal carcinoma cells , 1991, Molecular and cellular biology.

[130]  I. Weissman,et al.  Stem cells, cancer, and cancer stem cells , 2001, Nature.

[131]  Aaron N. Chang,et al.  MicroRNA-494 Within an Oncogenic MicroRNA Megacluster Regulates G1/S Transition in Liver Tumorigenesis Through Suppression of Mutated in Colorectal Cancer , 2013, Hepatology.

[132]  Gene W. Yeo,et al.  Wnt-mediated activation of NeuroD1 and retro-elements during adult neurogenesis , 2009, Nature Neuroscience.

[133]  Y. Sakaki,et al.  Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes , 2008, Nature.

[134]  Jialiang Liang,et al.  A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts. , 2010, Cell stem cell.

[135]  Jef D. Boeke,et al.  Human L1 Retrotransposition: cisPreference versus trans Complementation , 2001, Molecular and Cellular Biology.

[136]  N. A. Temiz,et al.  Evidence for APOBEC3B mutagenesis in multiple human cancers , 2013, Nature Genetics.

[137]  Ping Zhang,et al.  APOBEC3G Inhibits MicroRNA-mediated Repression of Translation by Interfering with the Interaction between Argonaute-2 and MOV10* , 2012, The Journal of Biological Chemistry.

[138]  P. Deininger,et al.  Somatic expression of LINE-1 elements in human tissues , 2010, Nucleic acids research.