Pan-cancer analysis identifies tumor-specific antigens derived from transposable elements
Open accessAbstract
Cryptic promoters within transposable elements (TEs) can be transcriptionally reactivated in tumors to create new TE-chimeric transcripts, which can produce immunogenic antigens. We performed a comprehensive screen for these TE exaptation events in 33 TCGA tumor types, 30 GTEx adult tissues and 675 cancer cell lines, and identified 1,068 TE-exapted candidates with the potential to generate shared tumor-specific TE-chimeric antigens (TS-TEAs). Whole-lysate and HLA-pulldown mass spectrometry data confirmed that TS-TEAs are presented on the surface of cancer cells. In addition, we highlight tumor-specific membrane proteins transcribed from TE promoters that constitute aberrant epitopes on the extracellular surface of cancer cells. Altogether, we showcase the high pan-cancer prevalence of TS-TEAs and atypical membrane proteins that could potentially be therapeutically exploited and targeted.
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A prior study uncovered the presence of tumor-specific antigens originating from certain repetitive sequences in various cancers, potentially eliciting immune responses.
“Intriguingly, a prior study uncovered the presence of tumor-specific antigens originating from certain repetitive sequences in various cancers, potentially eliciting immune responses25.”
From Multi-omics analysis identifies glioblastoma dependency on H3K9me3 methyltransferase activity (2025) · cites this paper as [25]
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The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works
STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709 · see citing works
Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889 · see citing works
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437 · see citing works
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Liao, Y., Smyth, G. K., & Shi, W. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt656 · Cited by 27,219 · see citing works
Cerami, E., Gao, J., Dogrusoz, U., Gross, B. E., Sumer, S. O., Aksoy, B. A., Jacobsen, A., Byrne, C. J., Heuer, M. L., Larsson, E., et al. (2012) · Cancer Discovery · doi:10.1158/2159-8290.cd-12-0095 · Cited by 17,455 · see citing works
Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal
Gao, J., Aksoy, B. A., Dogrusoz, U., Dresdner, G., Gross, B., Sumer, S. O., Sun, Y., Jacobsen, A., Sinha, R., Larsson, E., et al. (2013) · Science Signaling · doi:10.1126/scisignal.2004088 · Cited by 15,160 · see citing works
Krogh, A., Larsson, B., von Heijne, G., & Sonnhammer, E. L. L. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4315 · Cited by 12,654 · see citing works
Trapnell, C., Roberts, A., Goff, L. A., Pertea, G. M., Kim, D., Kelley, D. R., Pimentel, H., Salzberg, S. L., Rinn, J. L., & Pachter, L. S. (2012) · Nature Protocols · doi:10.1038/nprot.2012.016 · Cited by 11,930 · see citing works
Complex heatmaps reveal patterns and correlations in multidimensional genomic data
Gu, Z., Eils, R., & Schlesner, M. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw313 · Cited by 10,122 · see citing works
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480 · see citing works
DNA methylation patterns and epigenetic memory
Bird, A. (2002) · Genes & Development · doi:10.1101/gad.947102 · Cited by 7,124 · see citing works
Pfam: the protein families database
Finn, R. D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Heger, A., Hetherington, K., Holm, L., Mistry, J., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1223 · Cited by 6,148 · see citing works
The Immune Landscape of Cancer
Thorsson, V., Gibbs, D. L., Brown, S. D., Wolf, D., Bortone, D. S., Ou Yang, T.-H., Porta-Pardo, E., Gao, G. F., Plaisier, C. L., Eddy, J. A., et al. (2018) · Immunity · doi:10.1016/j.immuni.2018.03.023 · Cited by 5,870 · see citing works
The MaxQuant computational platform for mass spectrometry-based shotgun proteomics
Tyanova, S., Temu, T., & Cox, J. (2016) · Nature Protocols · doi:10.1038/nprot.2016.136 · Cited by 4,691 · see citing works
GENCODE: The reference human genome annotation for The ENCODE Project
Harrow, J., Frankish, A., Gonzalez, J. M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B. L., Barrell, D., Zadissa, A., Searle, S., et al. (2012) · Genome Research · doi:10.1101/gr.135350.111 · Cited by 4,585 · see citing works
Jones, P. A., & Baylin, S. B. (2007) · Cell · doi:10.1016/j.cell.2007.01.029 · Cited by 4,515 · see citing works
Next-generation characterization of the Cancer Cell Line Encyclopedia
Ghandi, M., Huang, F. W., Jané-Valbuena, J., Kryukov, G. V., Lo, C. C., McDonald, E. R., Barretina, J., Gelfand, E. T., Bielski, C. M., Li, H., et al. (2019) · Nature · doi:10.1038/s41586-019-1186-3 · Cited by 3,394 · see citing works
Car t cell immunotherapy for human cancer
June, C. H., O’Connor, R. S., Kawalekar, O. U., Ghassemi, S., & Milone, M. C. (2018) · Science · doi:10.1126/science.aar6711 · Cited by 3,207 · see citing works
A decade of exploring the cancer epigenome—biological and translational implications
Baylin, S. B., & Jones, P. A. (2011) · Nature Reviews Cancer · doi:10.1038/nrc3130 · Cited by 2,871 · see citing works
Leinonen, R., Sugawara, H., & Shumway, M. F. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1019 · Cited by 2,760 · see citing works
Sharma, S., Kelly, T. K., & Jones, P. A. (2010) · Carcinogenesis · doi:10.1093/carcin/bgp220 · Cited by 2,637 · see citing works
The UCSC Table Browser data retrieval tool
Karolchik, D. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh103 · Cited by 2,269 · see citing works
Comprehensive Characterization of Cancer Driver Genes and Mutations
Bailey, M. H., Tokheim, C., Porta-Pardo, E., Sengupta, S., Bertrand, D., Weerasinghe, A., Colaprico, A., Wendl, M. C., Kim, J., Reardon, B., et al. (2018) · Cell · doi:10.1016/j.cell.2018.02.060 · Cited by 2,256 · see citing works
Self-citationSmith, T. S., Heger, A., & Sudbery, I. M. (2017) · Genome Research · doi:10.1101/gr.209601.116 · Cited by 2,072 · see citing works
Transposable elements and the epigenetic regulation of the genome
Slotkin, R. K., & Martienssen, R. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2072 · Cited by 2,044 · see citing works
Chiappinelli, K. B., Strissel, P. L., Desrichard, A., Li, H., Henke, C., Akman, B., Hein, A., Rote, N. S., Cope, L. M., Snyder, A., et al. (2015) · Cell · doi:10.1016/j.cell.2015.07.011 · Cited by 2,022 · see citing works
Proteogenomics connects somatic mutations to signalling in breast cancer
CPTAC, N., Mertins, P., Mani, D. R., Ruggles, K. V., Gillette, M. A., Clauser, K. R., Wang, P., Wang, X., Qiao, J. W., Cao, S., et al. (2016) · Nature · doi:10.1038/nature18003 · Cited by 1,676 · see citing works
CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features
Kang, Y.-J., Yang, D.-C., Kong, L., Hou, M. L., Meng, Y.-Q., Wei, L., & Gao, G. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx428 · Cited by 1,619 · see citing works
Roulois, D., Loo Yau, H., Singhania, R., Wang, Y., Danesh, A., Shen, S. Y., Han, H., Liang, G., Jones, P. A., Pugh, T. J., et al. (2015) · Cell · doi:10.1016/j.cell.2015.07.056 · Cited by 1,527 · see citing works
Epigenetic inheritance at the agouti locus in the mouse
Morgan, H. D., Sutherland, H. G. E., Martin, D. I. K., & Whitelaw, E. (1999) · Nature Genetics · doi:10.1038/15490 · Cited by 1,476 · see citing works
Jurtz, V. I., Paul, S., Andreatta, M., Marcatili, P., Peters, B., & Nielsen, M. (2017) · The Journal of Immunology · doi:10.4049/jimmunol.1700893 · Cited by 1,476 · see citing works
The chromatin accessibility landscape of primary human cancers
Corces, M. R., Granja, J. M., Shams, S., Louie, B. H., Seoane, J. A., Zhou, W., Silva, T. C., Groeneveld, C., Wong, C. K., Cho, S. W., et al. (2018) · Science · doi:10.1126/science.aav1898 · Cited by 1,230 · see citing works
BioMart – biological queries made easy
Smedley, D. P., Haider, S. A., Ballester, B., Holland, R., London, D., Þórisson, G. Á., & Kasprzyk, A. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-22 · Cited by 1,119 · see citing works
Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer
Zhang, H., Liu, T., Zhang, Z., Payne, S. H., Zhang, B., McDermott, J. E., Zhou, J.-Y., Petyuk, V. A., Chen, L., Ray, D., et al. (2016) · Cell · doi:10.1016/j.cell.2016.05.069 · Cited by 1,029 · see citing works
Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients
Kahles, A., Lehmann, K.-V., Toussaint, N. C., Hüser, M., Stark, S. G., Sachsenberg, T. T., Stegle, O., Kohlbacher, O., Sander, C., Johnson, R., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.07.001 · Cited by 892 · see citing works
Regulation of translation via mRNA structure in prokaryotes and eukaryotes
Kozak, M. (2005) · Gene · doi:10.1016/j.gene.2005.06.037 · Cited by 747 · see citing works
OpenMS: a flexible open-source software platform for mass spectrometry data analysis
Röst, H. L., Sachsenberg, T. T., Aiche, S., Bielow, C., Weisser, H., Aicheler, F., Andreotti, S., Ehrlich, H., Gutenbrunner, P., Kenar, E., et al. (2016) · Nature Methods · doi:10.1038/nmeth.3959 · Cited by 680 · see citing works
A comprehensive transcriptional portrait of human cancer cell lines
Klijn, C. N., Durinck, S., Stawiski, E. W., Haverty, P. M., Jiang, Z., Liu, H., Degenhardt, J. D., Mayba, O., Gnad, F., Liu, J., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.3080 · Cited by 650 · see citing works
CAR T cells in solid tumors: challenges and opportunities
Marofi, F., Motavalli, R., Safonov, V. A., Thangavelu, L., Yumashev, A. V., Alexander, M., Shomali, N., Chartrand, M. S., Pathak, Y., Jarahian, M., et al. (2021) · Stem Cell Research & Therapy · doi:10.1186/s13287-020-02128-1 · Cited by 582 · see citing works
Transposable elements in cancer
Burns, K. H. (2017) · Nature Reviews Cancer · doi:10.1038/nrc.2017.35 · Cited by 572 · cited 2× · see citing works
“Tumor-specific TE-chimeric proteins (TS-TEPs) are abundantly detected in tumors Next, we predicted the protein products of these TE-chimeric transcripts using two methods as follows: (1) the longest open reading frame and (2) the first start codon with a ‘strong’ Kozak context (Methods).”
BackgroundMethodDNA methylation loss promotes immune evasion of tumours with high mutation and copy number load
Jung, H., Kim, H. S., Kim, J. Y., Sun, J., Ahn, J. S., Ahn, M., Park, K., Esteller, M., Lee, S., & Choi, J. K. (2019) · Nature Communications · doi:10.1038/s41467-019-12159-9 · Cited by 537 · see citing works
Noncoding regions are the main source of targetable tumor-specific antigens
Laumont, C. M., Vincent, K., Hesnard, L., Audemard, E. O., Bonneil, É., Laverdure, J., Gendron, P., Courcelles, M., Hardy, M., Côté, C., et al. (2018) · Science Translational Medicine · doi:10.1126/scitranslmed.aau5516 · Cited by 520 · see citing works
Bassani‐Sternberg, M., Pletscher-Frankild, S., Jensen, L. J., & Mann, M. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.042812 · Cited by 412 · see citing works
Transposable elements drive widespread expression of oncogenes in human cancers
Jang, H. J., Shah, N. M., Du, A. Y., Dailey, Z. Z., Pehrsson, E. C., Godoy, P. M., Zhang, D., Li, D., Xing, X., Kim, S., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0373-3 · Cited by 395 · see citing works
Self-citationWang, T., Zeng, J., Lowe, C. B., Sellers, R. G., Salama, S. R., Yang, M., Burgess, S. M., Brachmann, R. K., & Haussler, D. H. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0703637104 · Cited by 389 · see citing works
Self-citationLamprecht, B., Walter, K., Kreher, S., Kumar, R., Hummel, M., Lenze, D., Köchert, K., Bouhlel, M. A., Richter, J., Soler, E., et al. (2010) · Nature Medicine · doi:10.1038/nm.2129 · Cited by 376 · see citing works
Transposable elements in human genetic disease
Payer, L. M., & Burns, K. H. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0165-8 · Cited by 344 · cited 2× · see citing works
“Tumor-specific TE-chimeric proteins (TS-TEPs) are abundantly detected in tumors Next, we predicted the protein products of these TE-chimeric transcripts using two methods as follows: (1) the longest open reading frame and (2) the first start codon with a ‘strong’ Kozak context (Methods).”
BackgroundMethodDNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats
Brocks, D., Schmidt, C. R., Daskalakis, M., Jang, H. S., Shah, N. M., Li, D., Li, J., Zhang, B., Hou, Y., Laudato, S., et al. (2017) · Nature Genetics · doi:10.1038/ng.3889 · Cited by 339 · see citing works
Self-citationThe Human Epigenome Browser at Washington University
Zhou, X., Maricque, B. B., Xie, M., Li, D., Sundaram, V., Martin, E. A., Koebbe, B. C., Nielsen, C. B., Hirst, M., Farnham, P., et al. (2011) · Nature Methods · doi:10.1038/nmeth.1772 · Cited by 309 · see citing works
Self-citationKong, Y., Rose, C. M., Cass, A. A., Williams, A. G., Darwish, M., Lianoglou, S., Haverty, P. M., Tong, A.-J., Blanchette, C., Albert, M. L., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-13035-2 · Cited by 285 · see citing works
HLA typing from RNA-Seq sequence reads
Boegel, S., Löwer, M., Schäfer, M. K. E., Bukur, T., de Graaf, J., Boisguérin, V., Türeci, Ö., Diken, M., Castle, J. C., & Şahin, U. (2012) · Genome Medicine · doi:10.1186/gm403 · Cited by 269 · see citing works
Making Better Chimeric Antigen Receptors for Adoptive T-cell Therapy
Maus, M. V., & June, C. H. (2016) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-15-1433 · Cited by 269 · see citing works
Leonova, K. I., Brodsky, L., Lipchick, B. C., Pal, M., Novototskaya, L. R., Chenchik, A. A., Sen, G. C., Komarova, E. A., & Gudkov, A. V. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1216922110 · Cited by 260 · see citing works
Alternative transcription initiation leads to expression of a novel ALK isoform in cancer
Wiesner, T., Lee, W., Obenauf, A. C., Ran, L., Murali, R., Zhang, Q. F., Wong, E. W. P., Hu, W., Scott, S. N., Shah, R. H., et al. (2015) · Nature · doi:10.1038/nature15258 · Cited by 248 · see citing works
Endogenous retroviral promoter exaptation in human cancer
Babaian, A., & Mager, D. L. (2016) · Mobile DNA · doi:10.1186/s13100-016-0080-x · Cited by 246 · cited 1× · see citing works
“would be any of the following six categories: (1) none, (2) normal, (3) truncated, (4) chimeric normal, (5) chimeric truncated or (6) frameshift (Fig.”
BackgroundCAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses
Haberle, V., Forrest, A. R. R., Hayashizaki, Y., Carninci, P., & Lenhard, B. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv054 · Cited by 237 · see citing works
CAR T Cells in Solid Tumors: Blueprints for Building Effective Therapies
Knochelmann, H. M., Smith, A. S., Dwyer, C. J., Wyatt, M. M., Mehrotra, S., & Paulos, C. M. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.01740 · Cited by 186 · see citing works
Andrysík, Z., Galbraith, M. D., Guarnieri, A. L., Zaccara, S., Sullivan, K. D., Pandey, A., MacBeth, M. L., Inga, A., & Espinosa, J. M. (2017) · Genome Research · doi:10.1101/gr.220533.117 · Cited by 154 · see citing works
Newey, A., Griffiths, B. L., Michaux, J., Pak, H. S., Stevenson, B. J., Woolston, A., Semiannikova, M., Spain, G., Barber, L. J., Matthews, N., et al. (2019) · Journal for ImmunoTherapy of Cancer · doi:10.1186/s40425-019-0769-8 · Cited by 142 · see citing works
Mass spectrometry-based antigen discovery for cancer immunotherapy
Bassani‐Sternberg, M., & Coukos, G. (2016) · Current Opinion in Immunology · doi:10.1016/j.coi.2016.04.005 · Cited by 139 · see citing works
Onco-exaptation of an endogenous retroviral LTR drives IRF5 expression in Hodgkin lymphoma
Babaian, A., Romanish, M. T., Gagnier, L., Kuo, L. Y., Karimi, M. M., Steidl, C., & Mager, D. L. (2016) · Oncogene · doi:10.1038/onc.2015.308 · Cited by 121 · cited 1× · see citing works
“would be any of the following six categories: (1) none, (2) normal, (3) truncated, (4) chimeric normal, (5) chimeric truncated or (6) frameshift (Fig.”
Backgroundp53 directly represses human LINE1 transposonsPreprint
Tiwari, B., Jones, A. E., Caillet, C. J., Das, S., Royer, S. K., & Abrams, J. (2020) · Genes & Development · doi:10.1101/gad.343186.120 · Cited by 113 · see citing works
Attig, J., Young, G. R., Hosie, L., Perkins, D., Encheva-Yokoya, V., Stoye, J. P., Snijders, A. P., Ternette, N., & Kassiotis, G. (2019) · Genome Research · doi:10.1101/gr.248922.119 · Cited by 110 · see citing works
Bonaventura, P., Alcazer, V., Mutez, V., Tonon, L., Martin, J., Chuvin, N., Michel, E., Boulos, R. E., Estornes, Y., Valladeau‐Guilemond, J., et al. (2022) · Science Advances · doi:10.1126/sciadv.abj3671 · Cited by 110 · see citing works
McKerrow, W., Wang, X., Mendez‐Dorantes, C., Mita, P., Cao, S., Grivainis, M., Ding, L., LaCava, J., Burns, K. H., Boeke, J. D., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2115999119 · Cited by 107 · see citing works
pblat: a multithread blat algorithm speeding up aligning sequences to genomes
Wang, M., & Kong, L. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-2597-8 · Cited by 106 · see citing works
Scholtalbers, J., Boegel, S., Bukur, T., Byl, M., Goerges, S., Sorn, P., Löewer, M., Şahin, U., & Castle, J. C. (2015) · Genome Medicine · doi:10.1186/s13073-015-0240-5 · Cited by 89 · see citing works
FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies
Abugessaisa, I., Noguchi, S., Hasegawa, A., Harshbarger, J., Kondo, A., Lizio, M., Severin, J., Carninci, P., Kawaji, H., & Kasukawa, T. (2017) · Scientific Data · doi:10.1038/sdata.2017.107 · Cited by 77 · see citing works
Lock, F. E., Rebollo, R., Miceli-Royer, K., Gagnier, L., Kuah, S., Babaian, A., Sistiaga-Poveda, M., Lai, C. B., Nemirovsky, O., Serrano, I., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1405507111 · Cited by 75 · cited 1× · see citing works
“would be any of the following six categories: (1) none, (2) normal, (3) truncated, (4) chimeric normal, (5) chimeric truncated or (6) frameshift (Fig.”
BackgroundMass Spectrometry Based Immunopeptidomics for the Discovery of Cancer Neoantigens
Bassani‐Sternberg, M. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-7537-2_14 · Cited by 73 · see citing works
P53 and the defenses against genome instability caused by transposons and repetitive elements
Levine, A. J., Ting, D. T., & Greenbaum, B. D. (2016) · BioEssays · doi:10.1002/bies.201600031 · Cited by 72 · see citing works
NanoCAGE: A High-Resolution Technique to Discover and Interrogate Cell TranscriptomesPreprint
Salimullah, M., Salimullah, M., Sakai, M., & Plessy, C. (2011) · Cold Spring Harbor Protocols · doi:10.1101/pdb.prot5559 · Cited by 63 · see citing works
BO-LSTM: classifying relations via long short-term memory networks along biomedical ontologies
Lamúrias, A., Sousa, D., Clarke, L. A., & Couto, F. M. (2019) · BMC Bioinformatics · doi:10.1186/s12859-018-2584-5 · Cited by 62 · see citing works
Transposable elements and human cancer: A causal relationship?
Chénais, B. (2012) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2012.09.001 · Cited by 61 · cited 1× · see citing works
“would be any of the following six categories: (1) none, (2) normal, (3) truncated, (4) chimeric normal, (5) chimeric truncated or (6) frameshift (Fig.”
BackgroundReverse Transcriptase Inhibition Disrupts Repeat Element Life Cycle in Colorectal Cancer.
Rajurkar, M., Parikh, A. R., Solovyov, A., You, E., Kulkarni, A. S., Chu, C., Xu, K. H., Jaicks, C., Taylor, M. S., Wu, C., et al. (2022) · Cancer Discovery · doi:10.1158/2159-8290.cd-21-1117 · Cited by 61 · see citing works
TagDust2: a generic method to extract reads from sequencing data
Lassmann, T. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0454-y · Cited by 60 · see citing works
Transposons, p53 and Genome Security
Tiwari, B., Jones, A. E., & Abrams, J. (2018) · Trends in Genetics · doi:10.1016/j.tig.2018.08.003 · Cited by 50 · see citing works
An atlas of transposable element-derived alternative splicing in cancer
Clayton, E. A., Rishishwar, L., Huang, T.-C., Gulati, S., Ban, D., McDonald, J. F., & Jordan, I. K. (2020) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2019.0342 · Cited by 48 · see citing works
Cumbie, J. S., Ivanchenko, M. G., & Megraw, M. S. (2015) · BMC Genomics · doi:10.1186/s12864-015-1670-6 · Cited by 46 · see citing works
Bonaventura, P., Alcazer, V., Mutez, V., Tonon, L., Martin, J., Chuvin, N., Boulos, R. E., Estornes, Y., Valladeau‐Guilemond, J., Viari, A., et al. (2021) · Regular and Young Investigator Award Abstracts · doi:10.1136/jitc-2021-sitc2021.691 · Cited by 9 · see citing works
Flagged first, then by citations
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Sorted by citations
Repetitive DNA sequence detection and its role in the human genome
Liao, X., Zhu, W., Zhou, J., Li, H., Xu, X., Zhang, B., & Gao, X. (2023) · Communications Biology · doi:10.1038/s42003-023-05322-y · Cited by 180 · see citing works
Activation of human endogenous retroviruses and its physiological consequences
Dopkins, N., & Nixon, D. F. (2024) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-023-00674-z · Cited by 122 · see citing works
“…two exons of a gene, splicing often goes awry in malignant conditions 136 , resulting in non-canonical trans-splicing between exons and overabundant HERV RNAs, thereby forming junction between exons and transposable element (JET) mRNAs, which are translated to form recurrent TSAs 131,132,135 (Fig.”
Clinical advances of mRNA vaccines for cancer immunotherapy
Yaremenko, A. V., Khan, M. M., Zhen, X., Tang, Y., & Tao, W. (2025) · Med · doi:10.1016/j.medj.2024.11.015 · Cited by 127 · see citing works
Mendez‐Dorantes, C., & Burns, K. H. (2023) · Genes & Development · doi:10.1101/gad.351051.123 · Cited by 106 · see citing works
Prediction of tumor-reactive T cell receptors from scRNA-seq data for personalized T cell therapy
Tan, C. L., Lindner, K. A. M., Boschert, T., Meng, Z., Rodriguez-Ehrenfried, A., Roia, A. D., Haltenhof, G., Faenza, A., Imperatore, F., Bunse, L., et al. (2024) · Nature Biotechnology · doi:10.1038/s41587-024-02161-y · Cited by 80 · see citing works
The Somatic Mosaicism across Human Tissues Network
Coorens, T. H. H., Oh, J. W., Choi, Y. A., Lim, N. S., Zhao, B., Voshall, A., Abyzov, A. S., Antonacci-Fulton, L. L., Aparicio, S. A. J. R., Ardlie, K., et al. (2025) · Nature · doi:10.1038/s41586-025-09096-7 · Cited by 79 · see citing works
“The reference mutation sets from four donor tissues were inferred from the analysis of bulk whole genome sequencing data.”
Self-citationSplicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy
Li, G., Mahajan, S., Ma, S., Jeffery, E. D., Zhang, X., Bhattacharjee, A., Venkatasubramanian, M., Weirauch, M. T., Miraldi, E. R., Grimes, H. L., et al. (2024) · Science Translational Medicine · doi:10.1126/scitranslmed.ade2886 · Cited by 82 · see citing works
“Moreover, transposable elements have been reported to contribute to a subset of alternative splicing events ( 76 ) and give rise to neoantigens ( 77 – 80 ), including endogenous retrovirus ( 81 ).”
BackgroundComputational immunogenomic approaches to predict response to cancer immunotherapies
Addala, V., Newell, F., Pearson, J. V., Redwood, A., Robinson, B. W. S., Creaney, J., & Waddell, N. (2023) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-023-00830-6 · Cited by 77 · see citing works
“Profiling of ITH and monitoring tumour evolution to enable the targeting of clonal neoantigens could enable the design of vaccines against the broadest possible range of tumour neoantigens present in each patient’s tumour.”
Towards targeting transposable elements for cancer therapy
Liang, Y., Qu, X., Shah, N. M., & Wang, T. (2024) · Nature reviews. Cancer · doi:10.1038/s41568-023-00653-8 · Cited by 70 · see citing works
Self-citationTransposable element exonization generates a reservoir of evolving and functional protein isoforms
Arribas, Y. A., Baudon, B., Rotival, M., Suárez, G., Bonté, P., Casas, V., Roubert, A., Klein, P., Bonnin, E., Mchich, B., et al. (2024) · Cell · doi:10.1016/j.cell.2024.11.011 · Cited by 55 · see citing works
Jang, H. J., Shah, N. M., Maeng, J. H., Liang, Y., Basri, N. L., Ge, J., Qu, X., Mahlokozera, T., Tzeng, S., Williams, R. B., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01880-x · Cited by 51 · see citing works
“We previously discovered that TE-chimeric transcripts (a subtype of TE-derived transcripts) often initiate from cryptic TE promoters in a tumor-specific manner 32 .”
InfluentialSelf-citationLanciano, S., Philippe, C., Sarkar, A., Pratella, D., Domrane, C., Doucet, A. J., van Essen, D., Saccani, S., Ferry, L., Defossez, P., et al. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100498 · Cited by 50 · see citing works
“13,20,50,103 As an example, the promoter of an L1PA2 element residing within an intron of the BCAS3 gene is unmethylated, marked by active chromatin signatures (H3K4me3 and histone 3 lysine 27 acetylation [H3K27ac]), and bound by ESR1, both internally and in its immediate upstream region (Figure…”
BackgroundChimeraTE: a pipeline to detect chimeric transcripts derived from genes and transposable elements
de Oliveira, D. S., Fablet, M., Larue, A. E. A., Vallier, A., Carareto, C. M. A., Rebollo, R., & Vieira, C. P. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad671 · Cited by 37 · see citing works
Noviello, T., Giacomo, A. M. D., Caruso, F. P., Covre, A., Mortarini, R., Scala, G., Costa, M. C., Coral, S., Fridman, W. H., Sautès‐Fridman, C., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-40994-4 · Cited by 38 · see citing works
Regulation and function of transposable elements in cancer genomes
Lee, M., Ahmad, S. F., & Xu, J. (2024) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-024-05195-2 · Cited by 32 · see citing works
“…studies support the notion that concurrent upregulation of TEs and antigen presentation genes upon viral mimicry induction results in increased presentation of TE-derived peptides on tumor cells, providing a novel source of tumor-associated “neoantigens” to signal cellular immunity [127, 128].”
BackgroundKanholm, T., Rentia, U., Hadley, M. M., Karlow, J. A., Cox, O. L., Diab, N., Bendall, M. L., Dawson, T., McDonald, J. I., Xie, W., et al. (2023) · Cancer Research · doi:10.1158/0008-5472.can-22-3485 · Cited by 30 · see citing works
Advances in understanding LINE-1 regulation and function in the human genome
Li, X., & Liu, N. (2025) · Trends in Genetics · doi:10.1016/j.tig.2025.04.011 · Cited by 30 · see citing works
SCAR: Single-cell and Spatially-resolved Cancer Resources
Deng, Y., Chen, P., Xiao, J., Li, M., Shen, J., Qin, S., Jia, T., Li, C., Chang, A., Zhang, W., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad753 · Cited by 28 · see citing works
“The TSAs were sourced from a large-scale pan-cancer study that comprehensively analyzed TCGA datasets, identifying a variety of cell surface proteins highly expressed in and specific to tumor tissues ( 50 ).”
MethodStem cell activity-coupled suppression of endogenous retrovirus governs adult tissue regeneration
Lyu, Y., Kim, S., Humphrey, E., Nayak, R., Guan, Y., Liang, Q., Kim, K. H., Tan, Y., Dou, J., Sun, H., et al. (2024) · Cell · doi:10.1016/j.cell.2024.10.007 · Cited by 29 · see citing works
FLIBase: a comprehensive repository of full-length isoforms across human cancers and tissues
Shi, Q., Li, X., Liu, Y., Chen, Z., & He, X. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad745 · Cited by 24 · see citing works
Transposable elements as instructors of the immune system
Schmidleithner, L., Stüve, P., & Feuerer, M. (2025) · Nature reviews. Immunology · doi:10.1038/s41577-025-01172-3 · Cited by 32 · see citing works
“It has long been speculated that TEs may be translated into protein in tumours, as changes in the epigenetic landscape of tumour cells often lead to an increase in TE transcription 47,63,66,69 .”
LINE-1 transposable element renaissance in aging and age-related diseases
Li, X., Yu, H., Li, D., & Liu, N. (2024) · Ageing Research Reviews · doi:10.1016/j.arr.2024.102440 · Cited by 23 · see citing works
Self-citationTransposable elements regulate thymus development and function
Larouche, J., Laumont, C. M., Trofimov, A., Vincent, K., Hesnard, L., Brochu, S., Côté, C., Humeau, J., Bonneil, É., Lanoix, J., et al. (2023) · eLife · doi:10.7554/elife.91037 · Cited by 26 · see citing works
Ilik, İ., Xu, Y., Zhang, Z. Z., & Aktaş, T. (2025) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-025-00867-8 · Cited by 26 · see citing works
“Several studies have revealed that the primary source of major histocompatibility complex (MHC) class I-associated peptides is non-coding regions of the genome, which include TEs 263–266 .”
The neoantigens derived from transposable elements – A hidden treasure for cancer immunotherapy
Hu, Z., Guo, X., Li, Z., Meng, Z., & Huang, S. (2024) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2024.189126 · Cited by 21 · see citing works
Leveraging real-world data to advance biomarker discovery and precision oncology
Luo, J., & Solit, D. B. (2025) · Cancer Cell · doi:10.1016/j.ccell.2025.03.012 · Cited by 21 · see citing works
The cryptic immunopeptidome in health and disease
Kina, E., Larouche, J., Thibault, P., & Perreault, C. (2024) · Trends in Genetics · doi:10.1016/j.tig.2024.09.003 · Cited by 20 · see citing works
Xiang, Y.-Q., Qian, Y., Li, Z., Wang, J., Tian, R., Meng, W.-K., Bu, J.-B., Huang, F., Ai, Z.-P., Wu, D.-Y., et al. (2026) · Science · doi:10.1126/science.adv5257 · Cited by 16 · see citing works
Single-cell omics sequencing technologies: the long-read generation
Wen, L., & Tang, F. (2025) · Trends in Genetics · doi:10.1016/j.tig.2025.07.012 · Cited by 17 · see citing works
CircRNA: Unlocking new frontiers in therapeutic and vaccine development
Bahrulolum, H., Rouzbahani, F. N., Hoseini, Z. S., Chaharmahali, M., & Hosseini, S. M. (2025) · Molecular Therapy · doi:10.1016/j.ymthe.2025.10.038 · Cited by 18 · see citing works
Snowbarger, J. M., Koganti, P., & Spruck, C. (2024) · Biomolecules · doi:10.3390/biom14101250 · Cited by 13 · see citing works
“Shah et al. recently identified several chimeric, RE-derived proteins on the surfaces of cancer cells [191].”
BackgroundMethodZhu, J., Wang, Y., Huang, Q., & Liu, Z. (2025) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2025.149128 · Cited by 16 · see citing works
Zhang, R., Wu, M., Xiang, D., Zhu, J., Zhang, Q., Zhong, H., Peng, Y., Wang, Z., Ma, G., Li, G., et al. (2024) · Cell stem cell · doi:10.1016/j.stem.2024.07.006 · Cited by 17 · see citing works
Self-citationEfficient profiling of total RNA in single cells with STORM-seqPreprint
Johnson, B. K., Majewski, M. F., Jang, H. J., Siwicki, R. A., Wegener, M., Semwal, A., Morrison, J., Gallik, K., Hagemann-Jensen, M., Foy, K. K., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.14.484332 · Cited by 16 · see citing works
Self-citationMaeng, J. H., Jang, H. J., Du, A. Y., Tzeng, S., & Wang, T. (2023) · Genome Research · doi:10.1101/gr.277061.122 · Cited by 16 · see citing works
“Of note, the cell line used in this study, H1299, is TP53 null, which is known to be associated with an increased number of TE-chimeric transcripts (Shah et al. 2023).”
BackgroundInfluentialSelf-citationTransposable elements as genome regulators in normal and malignant haematopoiesis
Prokopov, D., Tunbak, H., Leddy, E., Drylie, B., Camera, F., & Deniz, Ö. (2025) · Blood Cancer Journal · doi:10.1038/s41408-025-01295-9 · Cited by 14 · see citing works
“…their role in transcriptomic diversity, in some cases TE-derived transcripts are translated into proteins, which may lead to the formation of novel TE-chimeric antigens or cryptic ORFs [39 – 42], that are recognised by immune cells and in fl uence immune responses in haematopoietic malignancies.”
Viral mimicry in cancer therapy
Rosenberg, L., & Vabret, N. (2025) · Trends in cancer · doi:10.1016/j.trecan.2025.08.010 · Cited by 15 · see citing works
Uncovering the role of LINE-1 in the evolution of lung adenocarcinoma
Zhang, T., Wei, Z., Wirth, C., Díaz‐Gay, M., Yin, J., Cecati, M., Marchegiani, F., Hoang, P. H., Leduc, C., Baine, M. K., et al. (2025) · Nature · doi:10.1038/s41586-025-09825-y · Cited by 25 · see citing works
“…and transposable elements are the subject of increasing research into their role in stabilizing the genome, their dynamic relationship with DNA methylation and their potential to be therapeutically targeted 38 , possibly exploiting tumour-specific antigens derived from transposable elements 60 .”
Relevance of mutation-derived neoantigens and non-classical antigens for anticancer therapies
Aparicio, B., Theunissen, P., Hervás‐Stubbs, S., Fortes, P., & Sarobe, P. (2024) · Human Vaccines & Immunotherapeutics · doi:10.1080/21645515.2024.2303799 · Cited by 16 · see citing works
“139”
A single-cell transposable element atlas of human cell identity
Reyes-Gopar, H., Marston, J. L., Singh, B., Greenig, M., Lin, J., Ostrowski, M., Randall, K. N., Sandoval‐Motta, S., Dopkins, N., Lawrence, E., et al. (2025) · Cell Reports Methods · doi:10.1016/j.crmeth.2025.101086 · Cited by 13 · see citing works
“TE transcription is believed to be more complex, 29,45,46 but reference TE gene models are not available.”
Unmasked: transposable elements as drivers and targets in cancer
Grinwald, M., Saintilnord, W. N., & Wang, T. (2025) · Trends in Genetics · doi:10.1016/j.tig.2025.08.002 · Cited by 14 · see citing works
Self-citationTargeting G Protein–Coupled Receptors in Immuno-Oncological Therapies
Stagg, J., & Gutkind, J. S. (2024) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-061724-080852 · Cited by 13 · see citing works
Rethinking ovarian cancer III: the past decade and future directions
Balkwill, F. R., Laumont, C. M., Burdett, N. L., Saux, O. L., Garsed, D. W., Grither, W. R., Nijhuis, A. M., Recouvreux, M. S., Kang, Z., Zhang, R., et al. (2026) · Nature reviews. Cancer · doi:10.1038/s41568-026-00916-0 · Cited by 12 · see citing works
Xu, B., Li, X., Zhang, S., Lian, M., Huang, W., Zhang, Y., Wang, Y., & Huang, Z. (2023) · Mobile DNA · doi:10.1186/s13100-023-00300-x · Cited by 12 · see citing works
“Recently, Shah et al. validated a total of 673 L1 chimeric transcripts in 10 tumor cell lines by CAGE-seq, including DM53 and NCI-H1623 cell lines, which were associated with 174 genes (Supplementary Table 7) [20].”
BackgroundZhao, Z., Chen, Y., Zou, X., Lin, L. S., Zhou, X., Cheng, X., Yang, G., Xu, Q., Gong, L., Li, L., et al. (2024) · Science Advances · doi:10.1126/sciadv.adl5606 · Cited by 13 · see citing works
“AFEs, another form of alternative transcription initiation, have been reported to show widespread dysregulation in tumors ( 8 – 11 ).”
BackgroundWang, Z., Ying, Y., Wang, M., Chen, Q., Wang, Y., Yu, X., He, W. A., Li, J., Zeng, S., & Xu, C. (2023) · iScience · doi:10.1016/j.isci.2023.108482 · Cited by 11 · see citing works
Li, D., Xia, L., Zhang, X., Liu, Y., Wang, Z., Guo, Q., Huang, P., Leng, W., & Qin, S. (2024) · Computer Methods and Programs in Biomedicine · doi:10.1016/j.cmpb.2024.108193 · Cited by 11 · see citing works
Self-citationExploring the Relationship of Transposable Elements and Ageing: Causes and Consequences
Merenciano, M., Larue, A. E. A., Garambois, C., Nunes, W. V. B., & Vieira, C. P. (2025) · Genome Biology and Evolution · doi:10.1093/gbe/evaf088 · Cited by 13 · see citing works
Li, Y., Liu, Y., Xie, Y., Wang, Y., Wang, J., Wang, H., Lin, X., & Xie, D. (2025) · BMC Cancer · doi:10.1186/s12885-025-13888-5 · Cited by 10 · see citing works
“Two recent pancancer studies of TE expression demonstrated that chimeric TE-gene transcripts exist in the vast majority of tumors, and a list of shared tumor specific TE chimeric antigens (TS-TEAs) [3, 4] has promising therapeutic value for creating pancancer vaccines.”
InfluentialTransposable elements in health and disease: Molecular basis and clinical implications
Hong, Y., & Liu, N. (2025) · Chinese Medical Journal · doi:10.1097/cm9.0000000000003775 · Cited by 10 · see citing works
“[115,125] 130] Thus, TEs’ ability to stimulate innate immune sensors and generate tumor-specific antigens makes them promising targets for cancer immunotherapy.”
InfluentialLocus-specific human endogenous retroviruses reveal lymphoma subtypes
Singh, B., Dopkins, N., Fei, T., Marston, J. L., Michael, S., Reyes-Gopar, H., Curty, G., Heymann, J. J., Chadburn, A., Martin, P., et al. (2025) · iScience · doi:10.1016/j.isci.2025.112541 · Cited by 10 · see citing works
Gu, X., Wang, M., & Zhang, X.-O. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad1048 · Cited by 9 · see citing works
Patel, D., Tiusanen, V., Karttunen, K., Pihlajamaa, P., & Sahu, B. (2025) · Communications Biology · doi:10.1038/s42003-025-08413-0 · Cited by 9 · see citing works
“To study the effect of CMEi onTE-derived chimeric transcripts, we performedTEProf2 16 analysis on RNA-seq data.”
InfluentialGlaser, J., Cova, G., Fauler, B., Prada‐Medina, C. A., Stanislas, V., Phan, M. H. Q., Schöpflin, R., Aktas, Y., Franke, M., Andrey, G., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02248-5 · Cited by 10 · see citing works
Human Endogenous Retroviruses and Diseases
Chen, C., Cui, Y., Wang, S., Yang, Y., Liu, Z., Jin, S., Shen, F., Gaipl, U. S., Ma, H., & Zhou, J. (2025) · MedComm · doi:10.1002/mco2.70452 · Cited by 10 · see citing works
“Importantly, HERVs RNAs form tumor-specific antigens through abnormal splicing events (including exon-transposition factor linkers), making them promising immunotherapy targets across multiple malignancies including bladder, kidney, and breast cancers [123–129].”
Charting the regulatory landscape of TP53 on transposable elements in cancerPreprint
Qu, X., Liang, Y., McCornack, C. R., Xing, X., Schmidt, H. K., Tomlinson, C., Fronick, C. C., Belter, E. A., Macias-Velasco, J. F., & Wang, T. (2025) · Genome Research · doi:10.1101/gr.279398.124 · Cited by 9 · see citing works
Self-citationMulti-omics analysis identifies glioblastoma dependency on H3K9me3 methyltransferase activity
Xie, Q., Du, Y., Ghosh, S., Rajendran, S., Cohen-Gadol, A. A., Baizabal, J.-M., Nephew, K. P., Han, L., & Shen, J. (2025) · NPJ Precision Oncology · doi:10.1038/s41698-025-00829-5 · Cited by 10 · see citing works
Targeting transposable elements in cancer: developments and opportunities
Wang, Z.-Y., Ge, L., Ouyang, Y., Jin, X., & Jiang, Y. (2024) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2024.189143 · Cited by 11 · see citing works
Zhang, H., Shi, G., Li, Y., Wang, C., Zhang, Y., Luo, Y., Xu, J. M., Qiu, Y., Ma, J., Yang, J. Y., et al. (2025) · Translational research · doi:10.1016/j.trsl.2025.05.007 · Cited by 8 · see citing works
Zeisig, B. B., Tsai, C., Virely, C., Fung, T. K., Akin, A. T., Troadec, E., Jiao, B., Thompson, I. R., Lau, P. N. I., Li, N., et al. (2025) · Blood · doi:10.1182/blood.2025028560 · Cited by 9 · see citing works
Long-read transcriptome landscapes of primary and metastatic liver cancers at transcript resolution
Chen, Z., Shi, Q., Zhao, Y., Xu, M., Liu, Y., Li, X., Liu, L., Sun, M., Wu, X., Shao, Z., et al. (2024) · Biomarker Research · doi:10.1186/s40364-023-00554-w · Cited by 8 · see citing works
Li, Z., Zhao, Y., Huang, P. F., Wu, Z., Ouyang, D., Nyarko, A. O., Ai, L., Zhang, Z., & Chang, S. (2024) · Scientific Reports · doi:10.1038/s41598-024-73274-2 · Cited by 8 · see citing works
Chour, M., Porteu, F., Depil, S., & Alcazer, V. (2024) · American Journal of Hematology · doi:10.1002/ajh.27501 · Cited by 9 · see citing works
“The use of these ERE promoters generates chimeric transcripts that can lead to neoantigens 14 or oncoproteins, 53 although their contribution to disease is still debated.”
Potential and development of cellular vesicle vaccines in cancer immunotherapy
Zhao, W., Li, X., Guan, J., Yan, S., Teng, L., Sun, X., Dong, Y., Wang, H., & Tao, W. (2025) · Discover Oncology · doi:10.1007/s12672-025-01781-3 · Cited by 7 · see citing works
MacKenzie, T. M. G., Cisneros, R., Maynard, R. D., & Snyder, M. P. (2023) · Cells · doi:10.3390/cells12141860 · Cited by 7 · see citing works
“antigens is the activation of cryptic promoters within transposable elements near genes in cancer, highlighting the importance of specific promoters and their molecular context within the cancer phenotype [46].”
BackgroundTu, Z., Bassal, M. A., Bell, G. W., Zhang, Y., Hu, Y. P., Quintana, L. M., Gokul, D., Tenen, D. G., & Karnoub, A. E. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.09.025 · Cited by 7 · see citing works
Deciphering lung adenocarcinoma evolution and the role of LINE-1 retrotranspositionPreprint
Zhang, T., Zhao, W., Wirth, C., Díaz‐Gay, M., Yin, J., Cecati, M., Marchegiani, F., Hoang, P. H., Leduc, C., Baine, M. K., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.03.14.643063 · Cited by 7 · see citing works
Alternative splicing of transposable elements in human breast cancer
Nesta, A. V., Veiga, D. F. T., Banchereau, J., Anczuków, O., & Beck, C. R. (2025) · Mobile DNA · doi:10.1186/s13100-025-00341-4 · Cited by 7 · see citing works
“Some of these events result in tumor-specific TE-chimeric antigens [65] and are emerging as an important source of neoantigens [53].”
Combination Therapy Approaches to Enhance the Efficacy of ERV-Targeting Vaccines in Cancer
Gracia-Hernandez, M., Maldonado, M. D. M., Schlom, J., & Hamilton, D. H. (2025) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-24-1192 · Cited by 6 · see citing works
“ERV-derived immunogenic epitopes can be derived via canonical ERV ORFs, chimeric endogenous retroelement–exon tumor antigens (69), or noncanonical splicing junctions between exons and transposable elements (70).”
Exploring transposable elements: new horizons in cancer diagnostics and therapeutics
Chaaban, A., Sleem, R., Santina, J., Rima, M., & Ibrahim, J.-N. (2025) · Mobile DNA · doi:10.1186/s13100-025-00366-9 · Cited by 9 · see citing works
“For instance, although still in the research phase, vaccine designs targeting TE-derived antigens have been proposed [91, 93].”
InfluentialTransposable elements drive species-specific and tissue-specific transcriptomes in human development
Zhang, Y., She, J., Hu, X., Jin, Y., Zhao, J., Hou, S., Tao, C., Du, M., & Yang, E. (2025) · Genome biology · doi:10.1186/s13059-025-03855-5 · Cited by 7 · see citing works
“TE-initiated transcripts have recently been identified using transcript assembly from short-read RNA-seq data [22, 24].”
Transposable element DNA and RNA: Drivers of gene expression, evolution, and disease
Ho, J., Douse, C. H., & Marazzi, I. (2026) · Cell · doi:10.1016/j.cell.2026.05.003 · Cited by 8 · see citing works
Kazachenka, A., Loong, J. H. C., Attig, J., Young, G. R., Ganguli, P., Devonshire, G., Grehan, N., Fitzgerald, R. C., Edwards, P. A., Grehan, N., et al. (2023) · NAR Cancer · doi:10.1093/narcan/zcad040 · Cited by 6 · see citing works
Long-range alternative splicing contributes to neoantigen specificity in glioblastoma
Ji, M., Yu, Q., Yang, X., Yu, X., Wang, J., Xiao, C., An, N. A., Han, C., Li, C., & Ding, W. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae503 · Cited by 6 · see citing works
Meng, X., Nie, Z., Wang, Q., Hu, Y., Deng, Y., Ai, N., Huang, Z., Li, Y., Yuan, Y., Xiao, J., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf1235 · Cited by 5 · see citing works
“Notably, widespread activation of TE-derived promoters can generate chimeric transcripts that fuse TE sequences with downstream genes, potentially encoding TE-gene fusion proteins or truncated TE-encoded polypeptides [ 12 –14 ].”
InfluentialKarttunen, K., Patel, D., & Sahu, B. (2024) · BioEssays · doi:10.1002/bies.202400059 · Cited by 4 · see citing works
“[29] Chimeric TE-transcripts also encode immunogenic antigens that are presented on the surface of cancer cells, [67] presenting a promising opportunity to exploit these neoantigens and TE-produced double-stranded RNA (dsRNA) in cancer immunotherapies (reviewed recently by Reid Cahn et al. [68] and…”
Activating the dark genome to illuminate cancer vaccine targets
Kwok, D. W., Okada, H., & Costello, J. (2024) · Nature Genetics · doi:10.1038/s41588-024-01850-3 · Cited by 5 · see citing works
A pan-cancer atlas of therapeutic T cell targetsPreprint
Li, G., Guzmán-Bringas, O. U., Sharma, A., Dellacherie, M. O., Sekhri, P., Yamin, R., Stepec, D., Burq, M., Clotea, I., Tardio, E., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.22.634237 · Cited by 5 · see citing works
Lee, S., Ho, Y. Y., Hao, S., Ouyang, Y., Liew, U. L., Goyal, A., Li, S., Barbour, J. A., He, M., Huang, Y., et al. (2025) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2025.108568 · Cited by 4 · see citing works
STING agonist-primed supramolecular oncolytic hydrogel vaccine for tuning tumors against themselves
Guo, M., Xie, S., Jiang, C., Tang, M., Zhang, W., Xiong, L., Shang, Q., An, X., & Wang, F. (2026) · Journal of Controlled Release · doi:10.1016/j.jconrel.2026.115032 · Cited by 4 · see citing works
Immunologic specificity in glioblastoma: Antigen discovery and translational implications
Hill, C. M., Wang, A. Z., Hsueh, B., Ramirez, R., Sherpa, N. D., Costa, M. A., Williams, O., Mao, L., & Dunn, G. P. (2025) · Neuro-Oncology Advances · doi:10.1093/noajnl/vdaf028 · Cited by 4 · see citing works
“252 While TE-derived antigens have been classified as tumor-specific, 93,253 the study indicated that many TEs are expressed at low levels in normal tissues.”
Cancer Immunotherapy: How to Exploit Transposable Elements?
Lanciano, S., & Cristofari, G. (2023) · Clinical Chemistry · doi:10.1093/clinchem/hvad091 · Cited by 4 · see citing works
Pan-cancer analysis reveals multifaceted roles of retrotransposon-fusion RNAsPreprint
Lee, B., Park, J., Voshall, A., Maury, E. A., Kang, Y., Kim, Y. J., Lee, J.-Y., Shim, H.-R., Kim, H.-J., Lee, J. W., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.16.562422 · Cited by 5 · see citing works
“…of TE-derived peptides, several studies including our previous work suggested that reactivated transposons trigger innate immune responses 17,18,20,42 and might play a more complex, long-term immune-modulatory role in primary tumors leading to the observation of anti-correlation between cancer…”
BackgroundCheng, C. C. Y., Cheung, M. F., Lee, A. Y., Wu, Q., Chow, S. H.-C., Ang, J. Y. J., Riquelme Medina, I., Lo, G., Wu, H., Yang, W., et al. (2025) · Communications Biology · doi:10.1038/s42003-025-09154-w · Cited by 3 · see citing works
“Forexample,globalDNAhypo-methylationcanactivatelong-terminalrepeat(LTR)retrotransposons, includingendogenousretroviruses(ERVs),whichcanfunctionasalter-nativepromotersforoncogenes 30,31 .”
Bright side of the dark genome: antigens for next-gen cancer vaccines
Wang, X., & Fox, B. A. (2026) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2025-014075 · Cited by 6 · see citing works
“167 DPV-001 is also being combined with ICB for the treatment of metastatic/recurrent HNSCC with a reported tripling of responses and increased PFS and OS in a cohort of 18 patients.”
Decoding immunotherapy response through computational modeling
Li, B., Luo, R., Huang, K., Liu, J., Zhao, W., & Zhou, X. (2026) · Nature Communications · doi:10.1038/s41467-026-71364-5 · Cited by 3 · see citing works
Recurrent ZC3H18 mutations stabilize oncogenic endogenous retroviral RNA
Tanu, T., Cox, A. M., Karlow, J. A., Sharma, P., Sun, K., He, X., Babu, S., Roelofs, M. K., Jeon, E., Chen, J., et al. (2026) · Cell Reports · doi:10.1016/j.celrep.2026.117526 · Cited by 5 · see citing works
“15 Transposable elements are upregulated in multiple cancer types, with the ERV class of retroelements being most affected.”
Grundy, E. E., Shaw, L. C., Wang, L., Lee, A. V., Argueta, J. C., Powell, D. J., Ostrowski, M., Jones, R. B., Cruz, C. C., Gordish‐Dressman, H., et al. (2024) · Mobile DNA · doi:10.1186/s13100-024-00333-w · Cited by 3 · see citing works
“Beyond targeting whole TEs as tumor associated antigens, a more effective approach may be to target chimeric TE-derived transcripts, which derive from cryptic promoters within TEs [70].”
BackgroundResultZhu, S., Chen, C., Wang, M., Liu, Y., Li, B., Qi, X., Song, M., Liu, X., Feng, J., & Liu, J. (2024) · Scientific Reports · doi:10.1038/s41598-024-83022-1 · Cited by 3 · see citing works
Xu, J., Liu, J., Wang, Y., Peng, L., Wang, L., Ji, L., Yang, Y., You, B., Huang, Y., Fang, S., et al. (2025) · Translational Oncology · doi:10.1016/j.tranon.2025.102369 · Cited by 3 · see citing works
“Their activity is tightly regulated by epigenetic modifications, primarily DNA methylation, which repress transcription [16 – 18].”
Xu, Y., Huang, Z., Zhang, Y., Gong, M., Wang, Z., Guo, P., Zhang, F., Yang, J., Liang, G., Dong, L., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-70645-3 · Cited by 3 · see citing works
Choudalakis, M., Bashtrykov, P., & Jeltsch, A. (2024) · Mobile DNA · doi:10.1186/s13100-024-00315-y · Cited by 3 · see citing works
DNA virus infections shape transposable elements activity in vitro and in vivoPreprint
Tan, J., Franke, V., Neugebauer, E., Pennisi, S., Schaechtle, M. A., Lagisquet, J., Kuderna, A. K., Wälter, S., Welker, I., Ensser, A., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.18.589901 · Cited by 3 · see citing works
RAmbler resolves complex repeats in human Chromosomes 8, 19, and XPreprint
Chakravarty, S., Logsdon, G. A., & Lonardi, S. (2025) · Genome Research · doi:10.1101/gr.279308.124 · Cited by 3 · see citing works
Genomics guiding personalized first-line immunotherapy response in lung and bladder tumors
Iglesias, J. B., Gallardo‐Gómez, M., Oitabén, A., Lázaro-Quintela, M., León‐Mateos, L., Alves, J. M., Pino-González, M., Juaneda‐Magdalena, L., García-Benito, C., Abdulkader, I., et al. (2025) · Journal of Translational Medicine · doi:10.1186/s12967-025-06323-7 · Cited by 2 · see citing works
Exploiting TCR Repertoire Analysis to Select Therapeutic TCRs for Cancer Immunotherapy
Demaël, U. M., Rirkkrai, T., Okuş, F. Z., Tiffeau-Mayer, A., & Stauss, H. J. (2025) · Cells · doi:10.3390/cells14151223 · Cited by 2 · see citing works
“…literature has explored contributions from the “dark proteome”, including peptides arising from endogenous retroviruses and trans-posable elements [13], aberrant splice variants [14], frameshift mutations [14], circular RNAs [15], and microbial sources [16,17], all of which are processed…”
Molecular effects of transposable element sequences in mammalian cells
Wen, M., & Welch, J. D. (2025) · Genome biology · doi:10.1186/s13059-025-03883-1 · Cited by 2 · see citing works
“Although these mechanisms may contribute to disease in some contexts [13, 15, 17, 100], in other contexts, TEs may serve helpful roles [48, 56].”
Qiao, N., Chen, J., Liu, Y., Chen, Z. J., & Chen, S. J. (2026) · MedScience · doi:10.1007/s11684-026-1210-6 · Cited by 2 · see citing works
Harnessing transposable elements for cancer therapy
Liu, Y., & Han, L. (2023) · Trends in cancer · doi:10.1016/j.trecan.2023.05.005 · Cited by 2 · see citing works
Spermine Synthase : A Potential Prognostic Marker for Lower-Grade Gliomas
Liu, C., Li, H., Hu, X., Yan, M., Fu, Z., Zhang, H., Wang, Y., & Du, N. (2024) · Journal of Korean Neurosurgical Society · doi:10.3340/jkns.2024.0080 · Cited by 2 · see citing works
“Before data collection, written informed consent was acquired per the provided guidelines since the TCGA and GTEx databases are publicly accessible 45,48) .”
Method
- Authors
- Shah, N. M., Jang, H. J., Liang, Y., Maeng, J. H., Tzeng, S.-C., Wu, A., Basri, N. L., Qu, X., Fan, C., Li, A., Katz, B., Li, D., Xing, X., Evans, B. S., & Wang, T.
- Affiliations
- Washington University in St. Louis (US)
- Van Andel Institute (US)
- Donald Danforth Plant Science Center (US)
- Corresponding author
- Wang, Ting
- ORCID
- Venue
- Nature Genetics
- Published
- 2023-03-27
- Volume
- 55
- Issue
- 4
- Pages
- 631-639
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC13152471
- OpenAlex
- W4360999762
- Cited by
- 175
- References
- 70
- Citations by year
- 2026: 40 · 2025: 61 · 2024: 46 · 2023: 27 · 2022: 1
- FWCI
- 22.95
- Type
- journal article
- Language
- en
- Open access
- green
- pmc.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion)
- Funders
- National Human Genome Research Institute (R01HG007175, U01HG009391)
- National Institute of General Medical Sciences (T32GM007067)
- National Institute of Environmental Health Sciences (U24ES026699)
- Topics
- Health Sciences › Medicine › Oncology › Cancer Immunotherapy and Biomarkers
- Life Sciences › Immunology and Microbiology › Immunology › Immunotherapy and Immune Responses
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Keywords
- transposable elements, cryptic promoter, tumor-specific antigens, cancer immunotherapy, membrane proteins, pan-cancer analysis, cancer cell lines
- MeSH terms
- Adult, Antigens, Neoplasm, Cell Line, DNA Transposable Elements, Humans, Neoplasms, Promoter Regions, Genetic
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