Retroelements (RE) have been proposed as important players in cancerogenesis. Different cancer types are characterized by a different level of tumor-specific RE insertions. In previous studies, small cohorts of hematological malignancies, such as acute myeloid leukemia, multiple myeloma, and chronic lymphocytic leukemia have been characterized by a low level of RE insertional activity. Acute lymphoblastic leukemia (ALL) in adults and childhood acute leukemias have not been studied in this context. We performed a search for new RE insertions (Alu and L1) in 44 childhood ALL, 14 childhood acute myeloid leukemia, and 14 adult ALL samples using a highly sensitive NGS-based approach. First, we evaluated the method sensitivity revealing the 1% detection threshold for the proportion of cells with specific RE insertion. Following this result, we did not identify new tumor-specific RE insertions in the tested cohort of acute leukemia samples at the established level of sensitivity. Additionally, we analyzed the transcription levels of active L1 copies and found them increased. Thus, the increased transcription of active L1 copies is not sufficient for overt elevation of L1 retrotranspositional activity in leukemia.

Center of Life Sciences Skolkovo Institute of Science and Technology 121205 Moscow Russia

Central European Institute of Technology Masaryk University 625 00 Brno Czech Republic

Department of Genomics of Adaptive Immunity Shemyakin Ovchinnikov Institute of Bioorganic Chemistry 117997 Moscow Russia

Department of Internal Medicine Hematology and Oncology University Hospital Brno and Faculty of Medicine Masaryk University 625 00 Brno Czech Republic

Department of Molecular Technologies Pirogov Russian National Research Medical University 117997 Moscow Russia

Dmitry Rogachev National Medical and Research Center of Pediatric Hematology Oncology and Immunology 117997 Moscow Russia

Institute of Medical Genetics and Genomics University Hospital Brno and Faculty of Medicine Masaryk University 625 00 Brno Czech Republic

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Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., et al. Initial sequencing and analysis of the human genome. Nature. 2001;409:860–921. PubMed

Goodier J.L. Restricting retrotransposons: A review. Mob. DNA. 2016;7:16. doi: 10.1186/s13100-016-0070-z. PubMed DOI PMC

Khan H., Smit A., Boissinot S. Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res. 2006;16:78–87. doi: 10.1101/gr.4001406. PubMed DOI PMC

Penzkofer T., Jager M., Figlerowicz M., Badge R., Mundlos S., Robinson P.N., Zemojtel T. L1Base 2: More retrotransposition-active LINE-1s, more mammalian genomes. Nucleic Acids Res. 2017;45:D68–D73. doi: 10.1093/nar/gkw925. PubMed DOI PMC

Kazazian H.H., Jr., Moran J.V. Mobile DNA in Health and Disease. N. Engl. J. Med. 2017;377:361–370. doi: 10.1056/NEJMra1510092. PubMed DOI PMC

Deininger P. Alu elements: Know the SINEs. Genome Biol. 2011;12:236. doi: 10.1186/gb-2011-12-12-236. PubMed DOI PMC

Belancio V.P., Roy-Engel A.M., Deininger P.L. All y’all need to know ‘bout retroelements in cancer. Semin. Cancer Biol. 2010;20:200–210. doi: 10.1016/j.semcancer.2010.06.001. PubMed DOI PMC

Bundo M., Toyoshima M., Okada Y., Akamatsu W., Ueda J., Nemoto-Miyauchi T., Sunaga F., Toritsuka M., Ikawa D., Kakita A., et al. Increased l1 retrotransposition in the neuronal genome in schizophrenia. Neuron. 2014;81:306–313. doi: 10.1016/j.neuron.2013.10.053. PubMed DOI

Rodriguez-Martin B., Alvarez E.G., Baez-Ortega A., Zamora J., Supek F., Demeulemeester J., Santamarina M., Ju Y.S., Temes J., Garcia-Souto D., et al. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nat. Genet. 2020;52:306–319. doi: 10.1038/s41588-019-0562-0. PubMed DOI PMC

Tubio J.M., Li Y., Ju Y.S., Martincorena I., Cooke S.L., Tojo M., Gundem G., Pipinikas C.P., Zamora J., Raine K., et al. Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. Science. 2014;345:1251343. doi: 10.1126/science.1251343. PubMed DOI PMC

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium Pan-cancer analysis of whole genomes. Nature. 2020;578:82–93. doi: 10.1038/s41586-020-1969-6. PubMed DOI PMC

Kulpa D.A., Moran J.V. Cis-preferential LINE-1 reverse transcriptase activity in ribonucleoprotein particles. Nat. Struct. Mol. Biol. 2006;13:655–660. doi: 10.1038/nsmb1107. PubMed DOI

Helman E., Lawrence M.S., Stewart C., Sougnez C., Getz G., Meyerson M. Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing. Genome Res. 2014;24:1053–1063. doi: 10.1101/gr.163659.113. PubMed DOI PMC

Lee E., Iskow R., Yang L., Gokcumen O., Haseley P., Luquette L.J., 3rd, Lohr J.G., Harris C.C., Ding L., Wilson R.K., et al. Landscape of somatic retrotransposition in human cancers. Science. 2012;337:967–971. doi: 10.1126/science.1222077. PubMed DOI PMC

Feusier J., Watkins W.S., Thomas J., Farrell A., Witherspoon D.J., Baird L., Ha H., Xing J., Jorde L.B. Pedigree-based estimation of human mobile element retrotransposition rates. Genome Res. 2019;29:1567–1577. doi: 10.1101/gr.247965.118. PubMed DOI PMC

Goubert C., Thomas J., Payer L.M., Kidd J.M., Feusier J., Watkins W.S., Burns K.H., Jorde L.B., Feschotte C. TypeTE: A tool to genotype mobile element insertions from whole genome resequencing data. Nucleic Acids Res. 2020;48:e36. doi: 10.1093/nar/gkaa074. PubMed DOI PMC

Komkov A.Y., Minervina A.A., Nugmanov G.A., Saliutina M.V., Khodosevich K.V., Lebedev Y.B., Mamedov I.Z. An advanced enrichment method for rare somatic retroelement insertions sequencing. Mob. DNA. 2018;9:31. doi: 10.1186/s13100-018-0136-1. PubMed DOI PMC

Loh J.W., Ha H., Lin T., Sun N., Burns K.H., Xing J. Integrated Mobile Element Scanning (ME-Scan) method for identifying multiple types of polymorphic mobile element insertions. Mob. DNA. 2020;11:12. doi: 10.1186/s13100-020-00207-x. PubMed DOI PMC

Mamedov I.Z., Arzumanyan E.S., Amosova A.L., Lebedev Y.B., Sverdlov E.D. Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach. Nucleic Acids Res. 2005;33:e16. doi: 10.1093/nar/gni018. PubMed DOI PMC

Shukla R., Upton K.R., Munoz-Lopez M., Gerhardt D.J., Fisher M.E., Nguyen T., Brennan P.M., Baillie J.K., Collino A., Ghisletti S., et al. Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell. 2013;153:101–111. doi: 10.1016/j.cell.2013.02.032. PubMed DOI PMC

Solyom S., Ewing A.D., Rahrmann E.P., Doucet T., Nelson H.H., Burns M.B., Harris R.S., Sigmon D.F., Casella A., Erlanger B., et al. Extensive somatic L1 retrotransposition in colorectal tumors. Genome Res. 2012;22:2328–2338. doi: 10.1101/gr.145235.112. PubMed DOI PMC

Upton K.R., Gerhardt D.J., Jesuadian J.S., Richardson S.R., Sanchez-Luque F.J., Bodea G.O., Ewing A.D., Salvador-Palomeque C., van der Knaap M.S., Brennan P.M., et al. Ubiquitous l1 mosaicism in hippocampal neurons. Cell. 2015;161:228–239. doi: 10.1016/j.cell.2015.03.026. PubMed DOI PMC

Evrony G.D., Lee E., Park P.J., Walsh C.A. Resolving rates of mutation in the brain using single-neuron genomics. Elife. 2016;5:e12966. doi: 10.7554/eLife.12966. PubMed DOI PMC

Komkov A.Y., Urazbakhtin S.Z., Saliutina M.V., Komech E.A., Shelygin Y.A., Nugmanov G.A., Shubin V.P., Smirnova A.O., Bobrov M.Y., Tsukanov A.S., et al. SeqURE—A new copy-capture based method for sequencing of unknown Retroposition events. Mob. DNA. 2020;11:33. doi: 10.1186/s13100-020-00228-6. PubMed DOI PMC

Kurnosov A.A., Ustyugova S.V., Nazarov V.I., Minervina A.A., Komkov A.Y., Shugay M., Pogorelyy M.V., Khodosevich K.V., Mamedov I.Z., Lebedev Y.B. The evidence for increased L1 activity in the site of human adult brain neurogenesis. PLoS ONE. 2015;10:e0117854. doi: 10.1371/journal.pone.0117854. PubMed DOI PMC

Kivioja T., Vaharautio A., Karlsson K., Bonke M., Enge M., Linnarsson S., Taipale J. Counting absolute numbers of molecules using unique molecular identifiers. Nat. Methods. 2012;9:72–74. doi: 10.1038/nmeth.1778. PubMed DOI

Nugmanov G.A., Komkov A.Y., Saliutina M.V., Minervina A.A., Lebedev Y.B., Mamedov I.Z. A Pipeline for the Error-free Identification of Somatic Alu Insertions in High-throughput Sequencing Data. Mol. Biol. 2019;53:138–146. doi: 10.1134/S0026893319010114. PubMed DOI

Fagerberg L., Hallstrom B.M., Oksvold P., Kampf C., Djureinovic D., Odeberg J., Habuka M., Tahmasebpoor S., Danielsson A., Edlund K., et al. Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Mol. Cell. Proteom. 2014;13:397–406. doi: 10.1074/mcp.M113.035600. PubMed DOI PMC

Gerousi M., Psomopoulos F., Kotta K., Tsagiopoulou M., Stavroyianni N., Anagnostopoulos A., Anastasiadis A., Gkanidou M., Kotsianidis I., Ntoufa S., et al. The Calcitriol/Vitamin D Receptor System Regulates Key Immune Signaling Pathways in Chronic Lymphocytic Leukemia. Cancers. 2021;13:285. doi: 10.3390/cancers13020285. PubMed DOI PMC

Cajuso T., Sulo P., Tanskanen T., Katainen R., Taira A., Hanninen U.A., Kondelin J., Forsstrom L., Valimaki N., Aavikko M., et al. Retrotransposon insertions can initiate colorectal cancer and are associated with poor survival. Nat. Commun. 2019;10:4022. doi: 10.1038/s41467-019-11770-0. PubMed DOI PMC

Miki Y., Nishisho I., Horii A., Miyoshi Y., Utsunomiya J., Kinzler K.W., Vogelstein B., Nakamura Y. Disruption of the APC gene by a retrotransposal insertion of L1 sequence in a colon cancer. Cancer Res. 1992;52:643–645. PubMed

Cuellar T.L., Herzner A.M., Zhang X., Goyal Y., Watanabe C., Friedman B.A., Janakiraman V., Durinck S., Stinson J., Arnott D., et al. Silencing of retrotransposons by SETDB1 inhibits the interferon response in acute myeloid leukemia. J. Cell Biol. 2017;216:3535–3549. doi: 10.1083/jcb.201612160. PubMed DOI PMC

Ardeljan D., Steranka J.P., Liu C., Li Z., Taylor M.S., Payer L.M., Gorbounov M., Sarnecki J.S., Deshpande V., Hruban R.H., et al. Cell fitness screens reveal a conflict between LINE-1 retrotransposition and DNA replication. Nat. Struct. Mol. Biol. 2020;27:168–178. doi: 10.1038/s41594-020-0372-1. PubMed DOI PMC

Den Nijs J.I., Gonggrijp H.S., Augustinus E., Leeksma C.H. Hot bands: A simple G-banding method for leukemic metaphases. Cancer Genet. Cytogenet. 1985;15:373–374. doi: 10.1016/0165-4608(85)90181-5. PubMed DOI

Gabert J., Beillard E., van der Velden V.H., Bi W., Grimwade D., Pallisgaard N., Barbany G., Cazzaniga G., Cayuela J.M., Cave H., et al. Standardization and quality control studies of ‘real-time’ quantitative reverse transcriptase polymerase chain reaction of fusion gene transcripts for residual disease detection in leukemia—A Europe Against Cancer program. Leukemia. 2003;17:2318–2357. doi: 10.1038/sj.leu.2403135. PubMed DOI

Meyer C., Schneider B., Reichel M., Angermueller S., Strehl S., Schnittger S., Schoch C., Jansen M.W., van Dongen J.J., Pieters R., et al. Diagnostic tool for the identification of MLL rearrangements including unknown partner genes. Proc. Natl. Acad. Sci. USA. 2005;102:449–454. doi: 10.1073/pnas.0406994102. PubMed DOI PMC

Afrin S., Zhang C.R.C., Meyer C., Stinson C.L., Pham T., Bruxner T.J.C., Venn N.C., Trahair T.N., Sutton R., Marschalek R., et al. Targeted Next-Generation Sequencing for Detecting MLL Gene Fusions in Leukemia. Mol. Cancer Res. 2018;16:279–285. doi: 10.1158/1541-7786.MCR-17-0569. PubMed DOI

Meyer C., Lopes B.A., Caye-Eude A., Cave H., Arfeuille C., Cuccuini W., Sutton R., Venn N.C., Oh S.H., Tsaur G., et al. Human MLL/KMT2A gene exhibits a second breakpoint cluster region for recurrent MLL-USP2 fusions. Leukemia. 2019;33:2306–2340. doi: 10.1038/s41375-019-0451-7. PubMed DOI PMC

Jansen M.W., van der Velden V.H., van Dongen J.J. Efficient and easy detection of MLL-AF4, MLL-AF9 and MLL-ENL fusion gene transcripts by multiplex real-time quantitative RT-PCR in TaqMan and LightCycler. Leukemia. 2005;19:2016–2018. doi: 10.1038/sj.leu.2403939. PubMed DOI

Blagodatskikh K.A., Kramarov V.M., Barsova E.V., Garkovenko A.V., Shcherbo D.S., Shelenkov A.A., Ustinova V.V., Tokarenko M.R., Baker S.C., Kramarova T.V., et al. Improved DOP-PCR (iDOP-PCR): A robust and simple WGA method for efficient amplification of low copy number genomic DNA. PLoS ONE. 2017;12:e0184507. doi: 10.1371/journal.pone.0184507. PubMed DOI PMC

Ye J., Coulouris G., Zaretskaya I., Cutcutache I., Rozen S., Madden T.L. Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction. BMC Bioinform. 2012;13:134. doi: 10.1186/1471-2105-13-134. PubMed DOI PMC

Schmieder R., Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011;27:863–864. doi: 10.1093/bioinformatics/btr026. PubMed DOI PMC

Shen W., Le S., Li Y., Hu F. SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLoS ONE. 2016;11:e0163962. doi: 10.1371/journal.pone.0163962. PubMed DOI PMC

Boratyn G.M., Thierry-Mieg J., Thierry-Mieg D., Busby B., Madden T.L. Magic-BLAST, an accurate RNA-seq aligner for long and short reads. BMC Bioinform. 2019;20:405. doi: 10.1186/s12859-019-2996-x. PubMed DOI PMC