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Sun Y, Xu X, Lin L, Xu K, Zheng Y, Ren C, Tao H, Wang X, Zhao H, Tu W, Bai X, Wang J, Huang Q, Li Y, Chen H, Li H, Bo X. A graph neural network-based interpretable framework reveals a novel DNA fragility-associated chromatin structural unit. Genome Biol 2023; 24:90. [PMID: 37095580 PMCID: PMC10124043 DOI: 10.1186/s13059-023-02916-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/22/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND DNA double-strand breaks (DSBs) are among the most deleterious DNA lesions, and they can cause cancer if improperly repaired. Recent chromosome conformation capture techniques, such as Hi-C, have enabled the identification of relationships between the 3D chromatin structure and DSBs, but little is known about how to explain these relationships, especially from global contact maps, or their contributions to DSB formation. RESULTS Here, we propose a framework that integrates graph neural network (GNN) to unravel the relationship between 3D chromatin structure and DSBs using an advanced interpretable technique GNNExplainer. We identify a new chromatin structural unit named the DNA fragility-associated chromatin interaction network (FaCIN). FaCIN is a bottleneck-like structure, and it helps to reveal a universal form of how the fragility of a piece of DNA might be affected by the whole genome through chromatin interactions. Moreover, we demonstrate that neck interactions in FaCIN can serve as chromatin structural determinants of DSB formation. CONCLUSIONS Our study provides a more systematic and refined view enabling a better understanding of the mechanisms of DSB formation under the context of the 3D genome.
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Affiliation(s)
- Yu Sun
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Xiang Xu
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Lin Lin
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Kang Xu
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Yang Zheng
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Chao Ren
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Huan Tao
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Xu Wang
- 4Paradigm Inc, Beijing, China
| | | | | | - Xuemei Bai
- The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Junting Wang
- The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Qiya Huang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yaru Li
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Hebing Chen
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China.
| | - Hao Li
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China.
| | - Xiaochen Bo
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China.
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2
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Long-read sequencing unveils high-resolution HPV integration and its oncogenic progression in cervical cancer. Nat Commun 2022; 13:2563. [PMID: 35538075 PMCID: PMC9091225 DOI: 10.1038/s41467-022-30190-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 04/19/2022] [Indexed: 01/03/2023] Open
Abstract
Integration of human papillomavirus (HPV) DNA into the human genome is considered as a key event in cervical carcinogenesis. Here, we perform comprehensive characterization of large-range virus-human integration events in 16 HPV16-positive cervical tumors using the Nanopore long-read sequencing technology. Four distinct integration types characterized by the integrated HPV DNA segments are identified with Type B being particularly notable as lacking E6/E7 genes. We further demonstrate that multiple clonal integration events are involved in the use of shared breakpoints, the induction of inter-chromosomal translocations and the formation of extrachromosomal circular virus-human hybrid structures. Combined with the corresponding RNA-seq data, we highlight LINC00290, LINC02500 and LENG9 as potential driver genes in cervical cancer. Finally, we reveal the spatial relationship of HPV integration and its various structural variations as well as their functional consequences in cervical cancer. These findings provide insight into HPV integration and its oncogenic progression in cervical cancer. The molecular mechanisms underlying cervical carcinogenesis following integration of HPV DNA into the human genome remain elusive. Here, the authors perform long-read sequencing in 16 HPV16-positive cervical tumors and identify distinct integration types, structural variations and potential driver genes.
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3
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Saayman X, Esashi F. Breaking the paradigm: early insights from mammalian DNA breakomes. FEBS J 2022; 289:2409-2428. [PMID: 33792193 PMCID: PMC9451923 DOI: 10.1111/febs.15849] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/04/2021] [Accepted: 03/29/2021] [Indexed: 12/13/2022]
Abstract
DNA double-strand breaks (DSBs) can result from both exogenous and endogenous sources and are potentially toxic lesions to the human genome. If improperly repaired, DSBs can threaten genome integrity and contribute to premature ageing, neurodegenerative disorders and carcinogenesis. Through decades of work on genome stability, it has become evident that certain regions of the genome are inherently more prone to breakage than others, known as genome instability hotspots. Recent advancements in sequencing-based technologies now enable the profiling of genome-wide distributions of DSBs, also known as breakomes, to systematically map these instability hotspots. Here, we review the application of these technologies and their implications for our current understanding of the genomic regions most likely to drive genome instability. These breakomes ultimately highlight both new and established breakage hotspots including actively transcribed regions, loop boundaries and early-replicating regions of the genome. Further, these breakomes challenge the paradigm that DNA breakage primarily occurs in hard-to-replicate regions. With these advancements, we begin to gain insights into the biological mechanisms both invoking and protecting against genome instability.
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Affiliation(s)
- Xanita Saayman
- Sir William Dunn School of Pathology, University of Oxford, UK
| | - Fumiko Esashi
- Sir William Dunn School of Pathology, University of Oxford, UK
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4
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FusionAI: Predicting fusion breakpoint from DNA sequence with deep learning. iScience 2021; 24:103164. [PMID: 34646994 PMCID: PMC8501764 DOI: 10.1016/j.isci.2021.103164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 07/16/2021] [Accepted: 09/21/2021] [Indexed: 12/12/2022] Open
Abstract
Identifying the molecular mechanisms related to genomic breakage is an important goal of cancer mechanism studies. Among diverse locations of structural variants, fusion genes, which have the breakpoints in the gene bodies and are typically identified from the split reads of RNA-seq data, can provide a highlighted structural variant resource for studying the genomic breakages with expression and potential pathogenic impacts. In this study, we developed FusionAI, which utilizes deep learning to predict gene fusion breakpoints based on DNA sequence and let us identify fusion breakage code and genomic context. FusionAI leverages the known fusion breakpoints to provide a prediction model of the fusion genes from the primary genomic sequences via deep learning, thereby helping researchers a more accurate selection of fusion genes and better understand genomic breakage. FusionAI predicts fusion gene breakpoints from a DNA sequence FusonAI reduce the effort for validating fusion genes with other tools High feature importance regions were apart 100nt from the exon junction BPs High feature importance regions were overlapped with 44 human genomic features
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5
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Bowry A, Kelly RDW, Petermann E. Hypertranscription and replication stress in cancer. Trends Cancer 2021; 7:863-877. [PMID: 34052137 DOI: 10.1016/j.trecan.2021.04.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/23/2021] [Accepted: 04/30/2021] [Indexed: 12/18/2022]
Abstract
Replication stress results from obstacles to replication fork progression, including ongoing transcription, which can cause transcription-replication conflicts. Oncogenic signaling can promote global increases in transcription activity, also termed hypertranscription. Despite the widely accepted importance of oncogene-induced hypertranscription, its study remains neglected compared with other causes of replication stress and genomic instability in cancer. A growing number of recent studies are reporting that oncogenes, such as RAS, and targeted cancer treatments, such as bromodomain and extraterminal motif (BET) bromodomain inhibitors, increase global transcription, leading to R-loop accumulation, transcription-replication conflicts, and the activation of replication stress responses. Here we discuss our mechanistic understanding of hypertranscription-induced replication stress and the resulting cellular responses, in the context of oncogenes and targeted cancer therapies.
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Affiliation(s)
- Akhil Bowry
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Richard D W Kelly
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK.
| | - Eva Petermann
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK.
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6
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Bouwman BAM, Agostini F, Garnerone S, Petrosino G, Gothe HJ, Sayols S, Moor AE, Itzkovitz S, Bienko M, Roukos V, Crosetto N. Genome-wide detection of DNA double-strand breaks by in-suspension BLISS. Nat Protoc 2020; 15:3894-3941. [PMID: 33139954 DOI: 10.1038/s41596-020-0397-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023]
Abstract
sBLISS (in-suspension breaks labeling in situ and sequencing) is a versatile and widely applicable method for identification of endogenous and induced DNA double-strand breaks (DSBs) in any cell type that can be brought into suspension. sBLISS provides genome-wide profiles of the most consequential DNA lesion implicated in a variety of pathological, but also physiological, processes. In sBLISS, after in situ labeling, DSB ends are linearly amplified, followed by next-generation sequencing and DSB landscape analysis. Here, we present a step-by-step experimental protocol for sBLISS, as well as a basic computational analysis. The main advantages of sBLISS are (i) the suspension setup, which renders the protocol user-friendly and easily scalable; (ii) the possibility of adapting it to a high-throughput or single-cell workflow; and (iii) its flexibility and its applicability to virtually every cell type, including patient-derived cells, organoids, and isolated nuclei. The wet-lab protocol can be completed in 1.5 weeks and is suitable for researchers with intermediate expertise in molecular biology and genomics. For the computational analyses, basic-to-intermediate bioinformatics expertise is required.
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Affiliation(s)
- Britta A M Bouwman
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| | - Federico Agostini
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Silvano Garnerone
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Sergi Sayols
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Magda Bienko
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Nicola Crosetto
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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7
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Oster S, Aqeilan RI. Programmed DNA Damage and Physiological DSBs: Mapping, Biological Significance and Perturbations in Disease States. Cells 2020; 9:cells9081870. [PMID: 32785139 PMCID: PMC7463922 DOI: 10.3390/cells9081870] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/02/2020] [Accepted: 08/05/2020] [Indexed: 12/12/2022] Open
Abstract
DNA double strand breaks (DSBs) are known to be the most toxic and threatening of the various types of breaks that may occur to the DNA. However, growing evidence continuously sheds light on the regulatory roles of programmed DSBs. Emerging studies demonstrate the roles of DSBs in processes such as T and B cell development, meiosis, transcription and replication. A significant recent progress in the last few years has contributed to our advanced knowledge regarding the functions of DSBs is the development of many next generation sequencing (NGS) methods, which have considerably advanced our capabilities. Other studies have focused on the implications of programmed DSBs on chromosomal aberrations and tumorigenesis. This review aims to summarize what is known about DNA damage in its physiological context. In addition, we will examine the advancements of the past several years, which have made an impact on the study of genome landscape and its organization.
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Affiliation(s)
- Sara Oster
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 9112001, Israel;
| | - Rami I. Aqeilan
- The Concern Foundation Laboratories, The Lautenberg Center for Immunology and Cancer Research, Department of Immunology and Cancer Research-IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 9112001, Israel;
- Department of Cancer Biology and Genetics, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, USA
- Correspondence:
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8
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Benzene induces rapid leukemic transformation after prolonged hematotoxicity in a murine model. Leukemia 2020; 35:595-600. [PMID: 32503976 DOI: 10.1038/s41375-020-0894-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 11/09/2022]
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9
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Vitamin D in Triple-Negative and BRCA1-Deficient Breast Cancer-Implications for Pathogenesis and Therapy. Int J Mol Sci 2020; 21:ijms21103670. [PMID: 32456160 PMCID: PMC7279503 DOI: 10.3390/ijms21103670] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 02/08/2023] Open
Abstract
Several studies show that triple-negative breast cancer (TNBC) patients have the lowest vitamin D concentration among all breast cancer types, suggesting that this vitamin may induce a protective effect against TNBC. This effect of the active metabolite of vitamin D, 1α,25-dihydroxyvitamin D3 (1,25(OH)2D), can be attributed to its potential to modulate proliferation, differentiation, apoptosis, inflammation, angiogenesis, invasion and metastasis and is supported by many in vitro and animal studies, but its exact mechanism is poorly known. In a fraction of TNBCs that harbor mutations that cause the loss of function of the DNA repair-associated breast cancer type 1 susceptibility (BRCA1) gene, 1,25(OH)2D may induce protective effects by activating its receptor and inactivating cathepsin L-mediated degradation of tumor protein P53 binding protein 1 (TP53BP1), preventing deficiency in DNA double-strand break repair and contributing to genome stability. Similar effects can be induced by the interaction of 1,25(OH)2D with proteins of the growth arrest and DNA damage-inducible 45 (GADD45) family. Further studies on TNBC cell lines with exact molecular characteristics and clinical trials with well-defined cases are needed to determine the mechanism of action of vitamin D in TNBC to assess its preventive and therapeutic potential.
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