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Annapragada AV, Niknafs N, White JR, Bruhm DC, Cherry C, Medina JE, Adleff V, Hruban C, Mathios D, Foda ZH, Phallen J, Scharpf RB, Velculescu VE. Genome-wide repeat landscapes in cancer and cell-free DNA. Sci Transl Med 2024; 16:eadj9283. [PMID: 38478628 PMCID: PMC11323656 DOI: 10.1126/scitranslmed.adj9283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 02/16/2024] [Indexed: 03/22/2024]
Abstract
Genetic changes in repetitive sequences are a hallmark of cancer and other diseases, but characterizing these has been challenging using standard sequencing approaches. We developed a de novo kmer finding approach, called ARTEMIS (Analysis of RepeaT EleMents in dISease), to identify repeat elements from whole-genome sequencing. Using this method, we analyzed 1.2 billion kmers in 2837 tissue and plasma samples from 1975 patients, including those with lung, breast, colorectal, ovarian, liver, gastric, head and neck, bladder, cervical, thyroid, or prostate cancer. We identified tumor-specific changes in these patients in 1280 repeat element types from the LINE, SINE, LTR, transposable element, and human satellite families. These included changes to known repeats and 820 elements that were not previously known to be altered in human cancer. Repeat elements were enriched in regions of driver genes, and their representation was altered by structural changes and epigenetic states. Machine learning analyses of genome-wide repeat landscapes and fragmentation profiles in cfDNA detected patients with early-stage lung or liver cancer in cross-validated and externally validated cohorts. In addition, these repeat landscapes could be used to noninvasively identify the tissue of origin of tumors. These analyses reveal widespread changes in repeat landscapes of human cancers and provide an approach for their detection and characterization that could benefit early detection and disease monitoring of patients with cancer.
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Affiliation(s)
- Akshaya V. Annapragada
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Noushin Niknafs
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - James R. White
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Daniel C. Bruhm
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Christopher Cherry
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jamie E. Medina
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Vilmos Adleff
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Carolyn Hruban
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Dimitrios Mathios
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Zachariah H. Foda
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jillian Phallen
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Robert B. Scharpf
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Victor E. Velculescu
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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Lerat E. Recent Bioinformatic Progress to Identify Epigenetic Changes Associated to Transposable Elements. Front Genet 2022; 13:891194. [PMID: 35646069 PMCID: PMC9140218 DOI: 10.3389/fgene.2022.891194] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Transposable elements (TEs) are recognized for their great impact on the functioning and evolution of their host genomes. They are associated to various deleterious effects, which has led to the evolution of regulatory epigenetic mechanisms to control their activity. Despite these negative effects, TEs are also important actors in the evolution of genomes by promoting genetic diversity and new regulatory elements. Consequently, it is important to study the epigenetic modifications associated to TEs especially at a locus-specific level to determine their individual influence on gene functioning. To this aim, this short review presents the current bioinformatic tools to achieve this task.
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Affiliation(s)
- Emmanuelle Lerat
- Univ Lyon, Univ Lyon 1, CNRS, VetAgro Sup, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
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Correa M, Lerat E, Birmelé E, Samson F, Bouillon B, Normand K, Rizzon C. The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality. Genome Biol Evol 2021; 13:6273345. [PMID: 33973013 PMCID: PMC8155550 DOI: 10.1093/gbe/evab062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2021] [Indexed: 12/13/2022] Open
Abstract
Transposable elements (TEs) are major components of eukaryotic genomes and represent approximately 45% of the human genome. TEs can be important sources of novelty in genomes and there is increasing evidence that TEs contribute to the evolution of gene regulation in mammals. Gene duplication is an evolutionary mechanism that also provides new genetic material and opportunities to acquire new functions. To investigate how duplicated genes are maintained in genomes, here, we explored the TE environment of duplicated and singleton genes. We found that singleton genes have more short-interspersed nuclear elements and DNA transposons in their vicinity than duplicated genes, whereas long-interspersed nuclear elements and long-terminal repeat retrotransposons have accumulated more near duplicated genes. We also discovered that this result is highly associated with the degree of essentiality of the genes with an unexpected accumulation of short-interspersed nuclear elements and DNA transposons around the more-essential genes. Our results underline the importance of taking into account the TE environment of genes to better understand how duplicated genes are maintained in genomes.
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Affiliation(s)
- Margot Correa
- Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), UMR CNRS 8071, ENSIIE, USC INRA, Université d'Evry Val d'Essonne, Evry, France
| | - Emmanuelle Lerat
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France
| | - Etienne Birmelé
- Laboratoire MAP5 UMR 8145, Université de Paris, Paris, France
| | - Franck Samson
- Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), UMR CNRS 8071, ENSIIE, USC INRA, Université d'Evry Val d'Essonne, Evry, France
| | - Bérengère Bouillon
- Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), UMR CNRS 8071, ENSIIE, USC INRA, Université d'Evry Val d'Essonne, Evry, France
| | - Kévin Normand
- Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), UMR CNRS 8071, ENSIIE, USC INRA, Université d'Evry Val d'Essonne, Evry, France
| | - Carène Rizzon
- Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), UMR CNRS 8071, ENSIIE, USC INRA, Université d'Evry Val d'Essonne, Evry, France
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Lannes R, Rizzon C, Lerat E. Does the Presence of Transposable Elements Impact the Epigenetic Environment of Human Duplicated Genes? Genes (Basel) 2019; 10:genes10030249. [PMID: 30917603 PMCID: PMC6470583 DOI: 10.3390/genes10030249] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/22/2019] [Accepted: 03/22/2019] [Indexed: 02/07/2023] Open
Abstract
Epigenetic modifications have an important role to explain part of the intra- and inter-species variation in gene expression. They also have a role in the control of transposable elements (TEs) whose activity may have a significant impact on genome evolution by promoting various mutations, which are expected to be mostly deleterious. A change in the local epigenetic landscape associated with the presence of TEs is expected to affect the expression of neighboring genes since these modifications occurring at TE sequences can spread to neighboring sequences. In this work, we have studied how the epigenetic modifications of genes are conserved and what the role of TEs is in this conservation. For that, we have compared the conservation of the epigenome associated with human duplicated genes and the differential presence of TEs near these genes. Our results show higher epigenome conservation of duplicated genes from the same family when they share similar TE environment, suggesting a role for the differential presence of TEs in the evolutionary divergence of duplicates through variation in the epigenetic landscape.
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Affiliation(s)
- Romain Lannes
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, F-69622 Villeurbanne, France.
| | - Carène Rizzon
- Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Université d'Evry Val d'Essonne, UMR CNRS 8071, ENSIIE, USC INRA, 23 bvd de France, 91037, Evry CEDEX Paris, France.
| | - Emmanuelle Lerat
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, F-69622 Villeurbanne, France.
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Renault S, Genty M, Gabori A, Boisneau C, Esnault C, Dugé de Bernonville T, Augé-Gouillou C. The epigenetic regulation of HsMar1, a human DNA transposon. BMC Genet 2019; 20:17. [PMID: 30764754 PMCID: PMC6375154 DOI: 10.1186/s12863-019-0719-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/29/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Both classes of transposable elements (DNA and RNA) are tightly regulated at the transcriptional level leading to the inactivation of transposition via epigenetic mechanisms. Due to the high copies number of these elements, the hypothesis has emerged that their regulation can coordinate a regulatory network of genes. Herein, we investigated whether transposition regulation of HsMar1, a human DNA transposon, differs in presence or absence of endogenous HsMar1 copies. In the case where HsMar1 transposition is regulated, the number of repetitive DNA sequences issued by HsMar1 and distributed in the human genome makes HsMar1 a good candidate to regulate neighboring gene expression by epigenetic mechanisms. RESULTS A recombinant active HsMar1 copy was inserted in HeLa (human) and CHO (hamster) cells and its genomic excision monitored. We show that HsMar1 excision is blocked in HeLa cells, whereas CHO cells are competent to promote HsMar1 excision. We demonstrate that de novo HsMar1 insertions in HeLa cells (human) undergo rapid silencing by cytosine methylation and apposition of H3K9me3 marks, whereas de novo HsMar1 insertions in CHO cells (hamster) are not repressed and enriched in H3K4me3 modifications. The overall analysis of HsMar1 endogenous copies in HeLa cells indicates that neither full-length endogenous inactive copies nor their Inverted Terminal Repeats seem to be specifically silenced, and are, in contrast, devoid of epigenetic marks. Finally, the setmar gene, derived from HsMar1, presents H3K4me3 modifications as expected for a human housekeeping gene. CONCLUSIONS Our work highlights that de novo and old HsMar1 are not similarly regulated by epigenetic mechanisms. Old HsMar1 are generally detected as lacking epigenetic marks, irrespective their localisation relative to the genes. Considering the putative existence of a network associating HsMar1 old copies and SETMAR, two non-mutually exclusive hypotheses are proposed: active and inactive HsMar1 copies are not similarly regulated or/and regulations concern only few loci (and few genes) that cannot be detected at the whole genome level.
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Affiliation(s)
- Sylvaine Renault
- EA 6306 Instabilité génétique et cancer, Université de Tours, UFR Sciences et Techniques, UFR Pharmacie, 31 Avenue Monge, 37200 Tours, France
- UMR 1253, iBrain, University of Tours, INSERM, Tours, France
| | - Murielle Genty
- EA 6306 Instabilité génétique et cancer, Université de Tours, UFR Sciences et Techniques, UFR Pharmacie, 31 Avenue Monge, 37200 Tours, France
- UMR 1253, iBrain, University of Tours, INSERM, Tours, France
| | - Alison Gabori
- EA 6306 Instabilité génétique et cancer, Université de Tours, UFR Sciences et Techniques, UFR Pharmacie, 31 Avenue Monge, 37200 Tours, France
| | - Catherine Boisneau
- UMR CITERES CNRS 7324, Université de Tours, 35 Allée Ferdinand de Lesseps, 37200 Tours, France
| | - Charles Esnault
- EA 6306 Instabilité génétique et cancer, Université de Tours, UFR Sciences et Techniques, UFR Pharmacie, 31 Avenue Monge, 37200 Tours, France
| | | | - Corinne Augé-Gouillou
- EA 6306 Instabilité génétique et cancer, Université de Tours, UFR Sciences et Techniques, UFR Pharmacie, 31 Avenue Monge, 37200 Tours, France
- UMR 1253, iBrain, University of Tours, INSERM, Tours, France
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Sekhon A, Singh R, Qi Y. DeepDiff: DEEP-learning for predicting DIFFerential gene expression from histone modifications. Bioinformatics 2018; 34:i891-i900. [DOI: 10.1093/bioinformatics/bty612] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Arshdeep Sekhon
- Department of Computer Science, University of Virginia, Charlottesville, VA, USA
| | - Ritambhara Singh
- Department of Computer Science, University of Virginia, Charlottesville, VA, USA
| | - Yanjun Qi
- Department of Computer Science, University of Virginia, Charlottesville, VA, USA
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