1
|
Li F, Ming W, Lu W, Wang Y, Dong X, Bai Y. Bioinformatics advances in eccDNA identification and analysis. Oncogene 2024; 43:3021-3036. [PMID: 39209966 DOI: 10.1038/s41388-024-03138-6] [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: 03/20/2024] [Revised: 08/09/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024]
Abstract
Extrachromosomal circular DNAs (eccDNAs) are a unique class of chromosome-originating circular DNA molecules, which are closely linked to oncogene amplification. Due to recent technological advances, particularly in high-throughput sequencing technology, bioinformatics methods based on sequencing data have become primary approaches for eccDNA identification and functional analysis. Currently, eccDNA-relevant databases incorporate previously identified eccDNA and provide thorough functional annotations and predictions, thereby serving as a valuable resource for eccDNA research. In this review, we collected around 20 available eccDNA-associated bioinformatics tools, including identification tools and annotation databases, and summarized their properties and capabilities. We evaluated some of the eccDNA detection methods in simulated data to offer recommendations for future eccDNA detection. We also discussed the current limitations and prospects of bioinformatics methodologies in eccDNA research.
Collapse
Affiliation(s)
- Fuyu Li
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, PR China
| | - Wenlong Ming
- Institute for AI in Medicine, School of Artificial Intelligence, Nanjing University of Information Science and Technology, Nanjing, 210044, PR China.
| | - Wenxiang Lu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, PR China
| | - Ying Wang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, PR China
| | - Xianjun Dong
- Adams Center of Parkinson's Disease Research, Yale School of Medicine, Yale University, 100 College St, New Haven, CT, 06511, USA.
- Department of Neurology, Yale School of Medicine, Yale University, 100 College St, New Haven, CT, 06511, USA.
| | - Yunfei Bai
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, PR China.
| |
Collapse
|
2
|
Yuan XQ, Zhou N, Song SJ, Xie YX, Chen SQ, Yang TF, Peng X, Zhang CY, Zhu YH, Peng L. Decoding the genomic enigma: Approaches to studying extrachromosomal circular DNA. Heliyon 2024; 10:e36659. [PMID: 39263178 PMCID: PMC11388731 DOI: 10.1016/j.heliyon.2024.e36659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 08/19/2024] [Accepted: 08/20/2024] [Indexed: 09/13/2024] Open
Abstract
Extrachromosomal circular DNA (eccDNA), a pervasive yet enigmatic component of the eukaryotic genome, exists autonomously from its chromosomal counterparts. Ubiquitous in eukaryotes, eccDNA plays a critical role in the orchestration of cellular processes and the etiology of diseases, particularly cancers. However, the full scope of its influence on health and disease remains elusive, presenting a rich vein of research yet to be mined. Unraveling the complexities of eccDNA necessitates a distillation of methodologies - from biogenesis to functional analysis - a landscape we overview in this study with precision and clarity. Here, we systematically outline cutting-edge methodologies from high-throughput sequencing and bioinformatics to experimental validations, showcasing the intricate world of eccDNAs. We combed through a treasure trove of auxiliary research resources and analytical tools. Moreover, we chart a course for future inquiry, illuminating the horizon with potential groundbreaking strategies for designing eccDNA research projects and pioneering new methodological frontiers.
Collapse
Affiliation(s)
- Xiao-Qing Yuan
- Guangdong Provincial Key Laboratory of Cancer Pathogenesis and Precision Diagnosis and Treatment, Shenshan Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Shanwei, 516621, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Nan Zhou
- The Affiliated Brain Hospital, Guangzhou Medical University, Guangzhou, 510370, China
| | - Shi-Jian Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Yi-Xia Xie
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Shui-Qin Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Teng-Fei Yang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Xian Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
- Puai Medical College, Shaoyang University, Shaoyang, 422100, China
| | - Chao-Yang Zhang
- Research Unit Analytical Pathology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany
| | - Ying-Hua Zhu
- Department of Genetic Medicine, Dongguan Children's Hospital Affiliated to Guangdong Medical University, Dongguan, 523325, China
| | - Li Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| |
Collapse
|
3
|
Kraft K, Murphy SE, Jones MG, Shi Q, Bhargava-Shah A, Luong C, Hung KL, He BJ, Li R, Park SK, Weiser NE, Luebeck J, Bafna V, Boeke JD, Mischel PS, Boettiger AN, Chang HY. Enhancer activation from transposable elements in extrachromosomal DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.04.611262. [PMID: 39282372 PMCID: PMC11398463 DOI: 10.1101/2024.09.04.611262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]
Abstract
Extrachromosomal DNA (ecDNA) is a hallmark of aggressive cancer, contributing to both oncogene amplification and tumor heterogeneity. Here, we used Hi-C, super-resolution imaging, and long-read sequencing to explore the nuclear architecture of MYC-amplified ecDNA in colorectal cancer cells. Intriguingly, we observed frequent spatial proximity between ecDNA and 68 repetitive elements which we called ecDNA-interacting elements or EIEs. To characterize a potential regulatory role of EIEs, we focused on a fragment of the L1M4a1#LINE/L1 which we found to be co-amplified with MYC on ecDNA, gaining enhancer-associated chromatin marks in contrast to its normally silenced state. This EIE, in particular, existed as a naturally occurring structural variant upstream of MYC, gaining oncogenic potential in the transcriptionally permissive ecDNA environment. This EIE sequence is sufficient to enhance MYC expression and is required for cancer cell fitness. These findings suggest that silent repetitive genomic elements can be reactivated on ecDNA, leading to functional cooption and amplification. Repeat element activation on ecDNA represents a mechanism of accelerated evolution and tumor heterogeneity and may have diagnostic and therapeutic potential.
Collapse
Affiliation(s)
- Katerina Kraft
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sedona E Murphy
- Present address: Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Matthew G Jones
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aarohi Bhargava-Shah
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H Institute and Department of Pathology, Stanford University, Stanford, CA, 94305 USA
| | - Christy Luong
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Chemical and Systems Biology, Stanford, CA 94305, USA
| | - King L Hung
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Britney J He
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Seung K Park
- Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Natasha E Weiser
- Sarafan ChEM-H Institute and Department of Pathology, Stanford University, Stanford, CA, 94305 USA
| | - Jens Luebeck
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Paul S Mischel
- Sarafan ChEM-H Institute and Department of Pathology, Stanford University, Stanford, CA, 94305 USA
| | - Alistair N Boettiger
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
4
|
Rossini R, Oshaghi M, Nekrasov M, Bellanger A, Domaschenz R, Dijkwel Y, Abdelhalim M, Collas P, Tremethick D, Paulsen J. Loss of multi-level 3D genome organization during breast cancer progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.26.568711. [PMID: 38076897 PMCID: PMC10705249 DOI: 10.1101/2023.11.26.568711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Breast cancer entails intricate alterations in genome organization and expression. However, how three-dimensional (3D) chromatin structure changes in the progression from a normal to a breast cancer malignant state remains unknown. To address this, we conducted an analysis combining Hi-C data with lamina-associated domains (LADs), epigenomic marks, and gene expression in an in vitro model of breast cancer progression. Our results reveal that while the fundamental properties of topologically associating domains (TADs) are overall maintained, significant changes occur in the organization of compartments and subcompartments. These changes are closely correlated with alterations in the expression of oncogenic genes. We also observe a restructuring of TAD-TAD interactions, coinciding with a loss of spatial compartmentalization and radial positioning of the 3D genome. Notably, we identify a previously unrecognized interchromosomal insertion event, wherein a locus on chromosome 8 housing the MYC oncogene is inserted into a highly active subcompartment on chromosome 10. This insertion is accompanied by the formation of de novo enhancer contacts and activation of MYC, illustrating how structural genomic variants can alter the 3D genome to drive oncogenic states. In summary, our findings provide evidence for the loss of genome organization at multiple scales during breast cancer progression revealing novel relationships between genome 3D structure and oncogenic processes.
Collapse
Affiliation(s)
- Roberto Rossini
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Mohammadsaleh Oshaghi
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Maxim Nekrasov
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Aurélie Bellanger
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Renae Domaschenz
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Yasmin Dijkwel
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Mohamed Abdelhalim
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0424 Oslo, Norway
| | - David Tremethick
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jonas Paulsen
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, 0316 Oslo, Norway
| |
Collapse
|
5
|
Zhou B, Purmann C, Guo H, Shin G, Huang Y, Pattni R, Meng Q, Greer SU, Roychowdhury T, Wood RN, Ho M, zu Dohna H, Abyzov A, Hallmayer JF, Wong WH, Ji HP, Urban AE. Resolving the 22q11.2 deletion using CTLR-Seq reveals chromosomal rearrangement mechanisms and individual variance in breakpoints. Proc Natl Acad Sci U S A 2024; 121:e2322834121. [PMID: 39042694 PMCID: PMC11295037 DOI: 10.1073/pnas.2322834121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 06/15/2024] [Indexed: 07/25/2024] Open
Abstract
We developed a generally applicable method, CRISPR/Cas9-targeted long-read sequencing (CTLR-Seq), to resolve, haplotype-specifically, the large and complex regions in the human genome that had been previously impenetrable to sequencing analysis, such as large segmental duplications (SegDups) and their associated genome rearrangements. CTLR-Seq combines in vitro Cas9-mediated cutting of the genome and pulse-field gel electrophoresis to isolate intact large (i.e., up to 2,000 kb) genomic regions that encompass previously unresolvable genomic sequences. These targets are then sequenced (amplification-free) at high on-target coverage using long-read sequencing, allowing for their complete sequence assembly. We applied CTLR-Seq to the SegDup-mediated rearrangements that constitute the boundaries of, and give rise to, the 22q11.2 Deletion Syndrome (22q11DS), the most common human microdeletion disorder. We then performed de novo assembly to resolve, at base-pair resolution, the full sequence rearrangements and exact chromosomal breakpoints of 22q11.2DS (including all common subtypes). Across multiple patients, we found a high degree of variability for both the rearranged SegDup sequences and the exact chromosomal breakpoint locations, which coincide with various transposons within the 22q11.2 SegDups, suggesting that 22q11DS can be driven by transposon-mediated genome recombination. Guided by CTLR-Seq results from two 22q11DS patients, we performed three-dimensional chromosomal folding analysis for the 22q11.2 SegDups from patient-derived neurons and astrocytes and found chromosome interactions anchored within the SegDups to be both cell type-specific and patient-specific. Lastly, we demonstrated that CTLR-Seq enables cell-type specific analysis of DNA methylation patterns within the deletion haplotype of 22q11DS.
Collapse
Affiliation(s)
- Bo Zhou
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
- Stanford Maternal and Child Health Research Institute, Stanford University School of Medicine, Stanford, CA94305
| | - Carolin Purmann
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
- Stanford Maternal and Child Health Research Institute, Stanford University School of Medicine, Stanford, CA94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
| | - Hanmin Guo
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
- Stanford Maternal and Child Health Research Institute, Stanford University School of Medicine, Stanford, CA94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
- Department of Statistics, Stanford University, Stanford, CA94305
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305
| | - GiWon Shin
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | - Yiling Huang
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
| | - Qingxi Meng
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | - Stephanie U. Greer
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | - Tanmoy Roychowdhury
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN55905
| | - Raegan N. Wood
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | - Marcus Ho
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
| | - Heinrich zu Dohna
- Department of Biology, American University of Beirut, Beirut1107 2020, Lebanon
| | - Alexej Abyzov
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN55905
| | - Joachim F. Hallmayer
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
| | - Wing H. Wong
- Department of Statistics, Stanford University, Stanford, CA94305
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305
| | - Hanlee P. Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | - Alexander E. Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
- Stanford Maternal and Child Health Research Institute, Stanford University School of Medicine, Stanford, CA94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
- Program on Genetics of Brain Function, Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA94305
| |
Collapse
|
6
|
Tsiakanikas P, Athanasopoulou K, Darioti IA, Agiassoti VT, Theocharis S, Scorilas A, Adamopoulos PG. Beyond the Chromosome: Recent Developments in Decoding the Significance of Extrachromosomal Circular DNA (eccDNA) in Human Malignancies. Life (Basel) 2024; 14:922. [PMID: 39202666 PMCID: PMC11355349 DOI: 10.3390/life14080922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/13/2024] [Accepted: 07/23/2024] [Indexed: 09/03/2024] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is a form of a circular double-stranded DNA that exists independently of conventional chromosomes. eccDNA exhibits a broad and random distribution across eukaryotic cells and has been associated with tumor-related properties due to its ability to harbor the complete gene information of oncogenes. The complex and multifaceted mechanisms underlying eccDNA formation include pathways such as DNA damage repair, breakage-fusion-bridge (BFB) mechanisms, chromothripsis, and cell apoptosis. Of note, eccDNA plays a pivotal role in tumor development, genetic heterogeneity, and therapeutic resistance. The high copy number and transcriptional activity of oncogenes carried by eccDNA contribute to the accelerated growth of tumors. Notably, the amplification of oncogenes on eccDNA is implicated in the malignant progression of cancer cells. The improvement of high-throughput sequencing techniques has greatly enhanced our knowledge of eccDNA by allowing for a detailed examination of its genetic structures and functions. However, we still lack a comprehensive and efficient annotation for eccDNA, while challenges persist in the study and understanding of the functional role of eccDNA, emphasizing the need for the development of robust methodologies. The potential clinical applications of eccDNA, such as its role as a measurable biomarker or therapeutic target in diseases, particularly within the spectrum of human malignancies, is a promising field for future research. In conclusion, eccDNA represents a quite dynamic and multifunctional genetic entity with far-reaching implications in cancer pathogenesis and beyond. Further research is essential to unravel the molecular pathways of eccDNA formation, elucidate its functional roles, and explore its clinical applications. Addressing these aspects is crucial for advancing our understanding of genomic instability and developing novel strategies for tailored therapeutics, especially in cancer.
Collapse
Affiliation(s)
- Panagiotis Tsiakanikas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Konstantina Athanasopoulou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Ioanna A. Darioti
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Vasiliki Taxiarchoula Agiassoti
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 15772 Athens, Greece; (V.T.A.)
| | - Stamatis Theocharis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 15772 Athens, Greece; (V.T.A.)
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Panagiotis G. Adamopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| |
Collapse
|
7
|
Mortenson KL, Dawes C, Wilson ER, Patchen NE, Johnson HE, Gertz J, Bailey SD, Liu Y, Varley KE, Zhang X. 3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression. Nat Commun 2024; 15:6130. [PMID: 39033128 PMCID: PMC11271278 DOI: 10.1038/s41467-024-50387-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 07/05/2024] [Indexed: 07/23/2024] Open
Abstract
Cancer genomes are composed of many complex structural alterations on chromosomes and extrachromosomal DNA (ecDNA), making it difficult to identify non-coding enhancer regions that are hijacked to activate oncogene expression. Here, we describe a 3D genomics-based analysis called HAPI (Highly Active Promoter Interactions) to characterize enhancer hijacking. HAPI analysis of HiChIP data from 34 cancer cell lines identified enhancer hijacking events that activate both known and potentially novel oncogenes such as MYC, CCND1, ETV1, CRKL, and ID4. Furthermore, we found enhancer hijacking among multiple oncogenes from different chromosomes, often including MYC, on the same complex amplicons such as ecDNA. We characterized a MYC-ERBB2 chimeric ecDNA, in which ERBB2 heavily hijacks MYC's enhancers. Notably, CRISPRi of the MYC promoter led to increased interaction of ERBB2 with MYC enhancers and elevated ERBB2 expression. Our HAPI analysis tool provides a robust strategy to detect enhancer hijacking and reveals novel insights into oncogene activation.
Collapse
Affiliation(s)
- Katelyn L Mortenson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Courtney Dawes
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Emily R Wilson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Nathan E Patchen
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Hailey E Johnson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Swneke D Bailey
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Surgery and Human Genetics, McGill University, Montreal, QC, Canada
| | - Yang Liu
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Katherine E Varley
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
| | - Xiaoyang Zhang
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
| |
Collapse
|
8
|
Dyshlovoy SA, Paigin S, Afflerbach AK, Lobermeyer A, Werner S, Schüller U, Bokemeyer C, Schuh AH, Bergmann L, von Amsberg G, Joosse SA. Applications of Nanopore sequencing in precision cancer medicine. Int J Cancer 2024. [PMID: 39031959 DOI: 10.1002/ijc.35100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/25/2024] [Accepted: 06/25/2024] [Indexed: 07/22/2024]
Abstract
Oxford Nanopore Technologies sequencing, also referred to as Nanopore sequencing, stands at the forefront of a revolution in clinical genetics, offering the potential for rapid, long read, and real-time DNA and RNA sequencing. This technology is currently making sequencing more accessible and affordable. In this comprehensive review, we explore its potential regarding precision cancer diagnostics and treatment. We encompass a critical analysis of clinical cases where Nanopore sequencing was successfully applied to identify point mutations, splice variants, gene fusions, epigenetic modifications, non-coding RNAs, and other pivotal biomarkers that defined subsequent treatment strategies. Additionally, we address the challenges of clinical applications of Nanopore sequencing and discuss the current efforts to overcome them.
Collapse
Affiliation(s)
- Sergey A Dyshlovoy
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Oxford, UK
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefanie Paigin
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Ann-Kristin Afflerbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Annabelle Lobermeyer
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Werner
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Institute for Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Paediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Carsten Bokemeyer
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna H Schuh
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Oxford, UK
| | - Lina Bergmann
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gunhild von Amsberg
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Martini-Klinik, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon A Joosse
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| |
Collapse
|
9
|
Purshouse K, Pollard SM, Bickmore WA. Imaging extrachromosomal DNA (ecDNA) in cancer. Histochem Cell Biol 2024; 162:53-64. [PMID: 38625562 PMCID: PMC7616135 DOI: 10.1007/s00418-024-02280-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2024] [Indexed: 04/17/2024]
Abstract
Extrachromosomal DNA (ecDNA) are circular regions of DNA that are found in many cancers. They are an important means of oncogene amplification, and correlate with treatment resistance and poor prognosis. Consequently, there is great interest in exploring and targeting ecDNA vulnerabilities as potential new therapeutic targets for cancer treatment. However, the biological significance of ecDNA and their associated regulatory control remains unclear. Light microscopy has been a central tool in the identification and characterisation of ecDNA. In this review we describe the different cellular models available to study ecDNA, and the imaging tools used to characterise ecDNA and their regulation. The insights gained from quantitative imaging are discussed in comparison with genome sequencing and computational approaches. We suggest that there is a crucial need for ongoing innovation using imaging if we are to achieve a full understanding of the dynamic regulation and organisation of ecDNA and their role in tumourigenesis.
Collapse
Affiliation(s)
- Karin Purshouse
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Centre for Regenerative Medicine, Institute for Regeneration and Repair & Cancer Research UK Scotland Centre, University of Edinburgh, Edinburgh, UK
- Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh, UK
| | - Steven M Pollard
- Centre for Regenerative Medicine, Institute for Regeneration and Repair & Cancer Research UK Scotland Centre, University of Edinburgh, Edinburgh, UK
- Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
10
|
Mortenson KL, Dawes C, Wilson ER, Patchen NE, Johnson HE, Gertz J, Bailey SD, Liu Y, Varley KE, Zhang X. 3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576965. [PMID: 38328209 PMCID: PMC10849656 DOI: 10.1101/2024.01.23.576965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Cancer genomes are composed of many complex structural alterations on chromosomes and extrachromosomal DNA (ecDNA), making it difficult to identify non-coding enhancer regions that are hijacked to activate oncogene expression. Here, we describe a 3D genomics-based analysis called HAPI (Highly Active Promoter Interactions) to characterize enhancer hijacking. HAPI analysis of HiChIP data from 34 cancer cell lines identified enhancer hijacking events that activate both known and potentially novel oncogenes such as MYC, CCND1 , ETV1 , CRKL , and ID4 . Furthermore, we found enhancer hijacking among multiple oncogenes from different chromosomes, often including MYC , on the same complex amplicons such as ecDNA. We characterized a MYC - ERBB2 chimeric ecDNA, in which ERBB2 heavily hijacks MYC 's enhancers. Notably, CRISPRi of the MYC promoter led to increased interaction of ERBB2 with MYC enhancers and elevated ERBB2 expression. Our HAPI analysis tool provides a robust strategy to detect enhancer hijacking and reveals novel insights into oncogene activation.
Collapse
|
11
|
Zhu K, Jones MG, Luebeck J, Bu X, Yi H, Hung KL, Wong ITL, Zhang S, Mischel PS, Chang HY, Bafna V. CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580594. [PMID: 38405779 PMCID: PMC10888815 DOI: 10.1101/2024.02.15.580594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Extrachromosomal DNA (ecDNA) is a central mechanism for focal oncogene amplification in cancer, occurring in approximately 15% of early stage cancers and 30% of late-stage cancers. EcDNAs drive tumor formation, evolution, and drug resistance by dynamically modulating oncogene copy-number and rewiring gene-regulatory networks. Elucidating the genomic architecture of ecDNA amplifications is critical for understanding tumor pathology and developing more effective therapies. Paired-end short-read (Illumina) sequencing and mapping have been utilized to represent ecDNA amplifications using a breakpoint graph, where the inferred architecture of ecDNA is encoded as a cycle in the graph. Traversals of breakpoint graph have been used to successfully predict ecDNA presence in cancer samples. However, short-read technologies are intrinsically limited in the identification of breakpoints, phasing together of complex rearrangements and internal duplications, and deconvolution of cell-to-cell heterogeneity of ecDNA structures. Long-read technologies, such as from Oxford Nanopore Technologies, have the potential to improve inference as the longer reads are better at mapping structural variants and are more likely to span rearranged or duplicated regions. Here, we propose CoRAL (Complete Reconstruction of Amplifications with Long reads), for reconstructing ecDNA architectures using long-read data. CoRAL reconstructs likely cyclic architectures using quadratic programming that simultaneously optimizes parsimony of reconstruction, explained copy number, and consistency of long-read mapping. CoRAL substantially improves reconstructions in extensive simulations and 9 datasets from previously-characterized cell-lines as compared to previous short-read-based tools. As long-read usage becomes wide-spread, we anticipate that CoRAL will be a valuable tool for profiling the landscape and evolution of focal amplifications in tumors.
Collapse
Affiliation(s)
- Kaiyuan Zhu
- Department of Computer Science & Engineering, UC San Diego, La Jolla, CA, USA
- These authors contributed equally to this work
| | - Matthew G. Jones
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- These authors contributed equally to this work
| | - Jens Luebeck
- Department of Computer Science & Engineering, UC San Diego, La Jolla, CA, USA
| | - Xinxin Bu
- Bioinformatics Undergraduate Program, School of Biological Sciences, UC San Diego, La Jolla, CA, USA
| | - Hyerim Yi
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - King L. Hung
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Ivy Tsz-Lo Wong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan Chemistry, Engineering, and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA, USA
| | - Shu Zhang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Paul S. Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan Chemistry, Engineering, and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA, USA
| | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Vineet Bafna
- Department of Computer Science & Engineering, UC San Diego, La Jolla, CA, USA
- Halicioglu Data Science Institute, UC San Diego, La Jolla, CA, USA
| |
Collapse
|
12
|
Ng AWT, McClurg DP, Wesley B, Zamani SA, Black E, Miremadi A, Giger O, Hoopen RT, Devonshire G, Redmond AM, Grehan N, Jammula S, Blasko A, Li X, Aparicio S, Tavaré S, Nowicki-Osuch K, Fitzgerald RC. Disentangling oncogenic amplicons in esophageal adenocarcinoma. Nat Commun 2024; 15:4074. [PMID: 38744814 PMCID: PMC11094127 DOI: 10.1038/s41467-024-47619-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 04/08/2024] [Indexed: 05/16/2024] Open
Abstract
Esophageal adenocarcinoma is a prominent example of cancer characterized by frequent amplifications in oncogenes. However, the mechanisms leading to amplicons that involve breakage-fusion-bridge cycles and extrachromosomal DNA are poorly understood. Here, we use 710 esophageal adenocarcinoma cases with matched samples and patient-derived organoids to disentangle complex amplicons and their associated mechanisms. Short-read sequencing identifies ERBB2, MYC, MDM2, and HMGA2 as the most frequent oncogenes amplified in extrachromosomal DNAs. We resolve complex extrachromosomal DNA and breakage-fusion-bridge cycles amplicons by integrating of de-novo assemblies and DNA methylation in nine long-read sequenced cases. Complex amplicons shared between precancerous biopsy and late-stage tumor, an enrichment of putative enhancer elements and mobile element insertions are potential drivers of complex amplicons' origin. We find that patient-derived organoids recapitulate extrachromosomal DNA observed in the primary tumors and single-cell DNA sequencing capture extrachromosomal DNA-driven clonal dynamics across passages. Prospectively, long-read and single-cell DNA sequencing technologies can lead to better prediction of clonal evolution in esophageal adenocarcinoma.
Collapse
Affiliation(s)
- Alvin Wei Tian Ng
- Early Cancer Institute, University of Cambridge, Cambridge, CB2 0XZ, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | | | - Ben Wesley
- Irving Institute for Cancer Dynamics, Columbia University, New York, USA
| | - Shahriar A Zamani
- Early Cancer Institute, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Emily Black
- Early Cancer Institute, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Ahmad Miremadi
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Olivier Giger
- Department of Pathology, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Rogier Ten Hoopen
- Department of Oncology, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Ginny Devonshire
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Aisling M Redmond
- Early Cancer Institute, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Nicola Grehan
- Early Cancer Institute, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Sriganesh Jammula
- Early Cancer Institute, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Adrienn Blasko
- Early Cancer Institute, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Xiaodun Li
- Early Cancer Institute, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Simon Tavaré
- Irving Institute for Cancer Dynamics, Columbia University, New York, USA
- Department of Statistics, Columbia University, New York, USA
- Department of Biological Sciences, Columbia University, New York, USA
| | | | | |
Collapse
|
13
|
Wu H, Liu S, Wu D, Zhou H, Wu G. Tumor extrachromosomal DNA: Biogenesis and recent advances in the field. Biomed Pharmacother 2024; 174:116588. [PMID: 38613997 DOI: 10.1016/j.biopha.2024.116588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/02/2024] [Accepted: 04/10/2024] [Indexed: 04/15/2024] Open
Abstract
Extrachromosomal DNA (ecDNA) is a self-replicating circular DNA originating from the chromosomal genome and exists outside the chromosome. It contains specific gene sequences and non-coding regions that regulate transcription. Recent studies have demonstrated that ecDNA is present in various malignant tumors. Malignant tumor development and poor prognosis may depend on ecDNA's distinctive ring structure, which assists in amplifying oncogenes. During cell division, an uneven distribution of ecDNA significantly enhances tumor cells' heterogeneity, allowing tumor cells to adapt to changes in the tumor microenvironment and making them more resistant to treatments. The application of ecDNA as a cancer biomarker and therapeutic target holds great potential. This article examines the latest advancements in this area and discusses the potential clinical applications of ecDNA.
Collapse
Affiliation(s)
- Haomin Wu
- Department of General Surgery, the First Hospital of China Medical University, 155# Nanjing Street, Shenyang 110001, China
| | - Shiqi Liu
- Department of General Surgery, the First Hospital of China Medical University, 155# Nanjing Street, Shenyang 110001, China
| | - Di Wu
- Department of General Surgery, the First Hospital of China Medical University, 155# Nanjing Street, Shenyang 110001, China
| | - Haonan Zhou
- Department of General Surgery, the First Hospital of China Medical University, 155# Nanjing Street, Shenyang 110001, China
| | - Gang Wu
- Department of General Surgery, the First Hospital of China Medical University, 155# Nanjing Street, Shenyang 110001, China.
| |
Collapse
|
14
|
Zhou L, Tang W, Ye B, Zou L. Characterization, biogenesis model, and current bioinformatics of human extrachromosomal circular DNA. Front Genet 2024; 15:1385150. [PMID: 38746056 PMCID: PMC11092383 DOI: 10.3389/fgene.2024.1385150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/12/2024] [Indexed: 05/16/2024] Open
Abstract
Human extrachromosomal circular DNA, or eccDNA, has been the topic of extensive investigation in the last decade due to its prominent regulatory role in the development of disorders including cancer. With the rapid advancement of experimental, sequencing and computational technology, millions of eccDNA records are now accessible. Unfortunately, the literature and databases only provide snippets of this information, preventing us from fully understanding eccDNAs. Researchers frequently struggle with the process of selecting algorithms and tools to examine eccDNAs of interest. To explain the underlying formation mechanisms of the five basic classes of eccDNAs, we categorized their characteristics and functions and summarized eight biogenesis theories. Most significantly, we created a clear procedure to help in the selection of suitable techniques and tools and thoroughly examined the most recent experimental and bioinformatics methodologies and data resources for identifying, measuring and analyzing eccDNA sequences. In conclusion, we highlighted the current obstacles and prospective paths for eccDNA research, specifically discussing their probable uses in molecular diagnostics and clinical prediction, with an emphasis on the potential contribution of novel computational strategies.
Collapse
Affiliation(s)
- Lina Zhou
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Wenyi Tang
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Bo Ye
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Lingyun Zou
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
- School of Medicine, Jinan University, Guangzhou, Guangdong, China
| |
Collapse
|
15
|
Katoh M, Loriot Y, Brandi G, Tavolari S, Wainberg ZA, Katoh M. FGFR-targeted therapeutics: clinical activity, mechanisms of resistance and new directions. Nat Rev Clin Oncol 2024; 21:312-329. [PMID: 38424198 DOI: 10.1038/s41571-024-00869-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2024] [Indexed: 03/02/2024]
Abstract
Fibroblast growth factor (FGF) signalling via FGF receptors (FGFR1-4) orchestrates fetal development and contributes to tissue and whole-body homeostasis, but can also promote tumorigenesis. Various agents, including pan-FGFR inhibitors (erdafitinib and futibatinib), FGFR1/2/3 inhibitors (infigratinib and pemigatinib), as well as a range of more-specific agents, have been developed and several have entered clinical use. Erdafitinib is approved for patients with urothelial carcinoma harbouring FGFR2/3 alterations, and futibatinib and pemigatinib are approved for patients with cholangiocarcinoma harbouring FGFR2 fusions and/or rearrangements. Clinical benefit from these agents is in part limited by hyperphosphataemia owing to off-target inhibition of FGFR1 as well as the emergence of resistance mutations in FGFR genes, activation of bypass signalling pathways, concurrent TP53 alterations and possibly epithelial-mesenchymal transition-related isoform switching. The next generation of small-molecule inhibitors, such as lirafugratinib and LOXO-435, and the FGFR2-specific antibody bemarituzumab are expected to have a reduced risk of hyperphosphataemia and the ability to overcome certain resistance mutations. In this Review, we describe the development and current clinical role of FGFR inhibitors and provide perspective on future research directions including expansion of the therapeutic indications for use of FGFR inhibitors, combination of these agents with immune-checkpoint inhibitors and the application of novel technologies, such as artificial intelligence.
Collapse
Affiliation(s)
| | - Yohann Loriot
- Drug Development Department (DITEP), Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
- INSERM U981, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Giovanni Brandi
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Simona Tavolari
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Zev A Wainberg
- Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Masaru Katoh
- M & M Precision Medicine, Tokyo, Japan.
- Department of Omics Network, National Cancer Center, Tokyo, Japan.
| |
Collapse
|
16
|
Yan X, Mischel P, Chang H. Extrachromosomal DNA in cancer. Nat Rev Cancer 2024; 24:261-273. [PMID: 38409389 DOI: 10.1038/s41568-024-00669-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/18/2024] [Indexed: 02/28/2024]
Abstract
Extrachromosomal DNA (ecDNA) has recently been recognized as a major contributor to cancer pathogenesis that is identified in most cancer types and is associated with poor outcomes. When it was discovered over 60 years ago, ecDNA was considered to be rare, and its impact on tumour biology was not well understood. The application of modern imaging and computational techniques has yielded powerful new insights into the importance of ecDNA in cancer. The non-chromosomal inheritance of ecDNA during cell division results in high oncogene copy number, intra-tumoural genetic heterogeneity and rapid tumour evolution that contributes to treatment resistance and shorter patient survival. In addition, the circular architecture of ecDNA results in altered patterns of gene regulation that drive elevated oncogene expression, potentially enabling the remodelling of tumour genomes. The generation of clusters of ecDNAs, termed ecDNA hubs, results in interactions between enhancers and promoters in trans, yielding a new paradigm in oncogenic transcription. In this Review, we highlight the rapid advancements in ecDNA research, providing new insights into ecDNA biogenesis, maintenance and transcription and its role in promoting tumour heterogeneity. To conclude, we delve into a set of unanswered questions whose answers will pave the way for the development of ecDNA targeted therapeutic approaches.
Collapse
Affiliation(s)
- Xiaowei Yan
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Paul Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
| | - Howard Chang
- Department of Dermatology, Stanford University, Stanford, CA, USA.
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| |
Collapse
|
17
|
Wang S, Wu CY, He MM, Yong JX, Chen YX, Qian LM, Zhang JL, Zeng ZL, Xu RH, Wang F, Zhao Q. Machine learning-based extrachromosomal DNA identification in large-scale cohorts reveals its clinical implications in cancer. Nat Commun 2024; 15:1515. [PMID: 38373991 PMCID: PMC10876971 DOI: 10.1038/s41467-024-45479-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 01/24/2024] [Indexed: 02/21/2024] Open
Abstract
The clinical implications of extrachromosomal DNA (ecDNA) in cancer therapy remain largely elusive. Here, we present a comprehensive analysis of ecDNA amplification spectra and their association with clinical and molecular features in multiple cohorts comprising over 13,000 pan-cancer patients. Using our developed computational framework, GCAP, and validating it with multifaceted approaches, we reveal a consistent pan-cancer pattern of mutual exclusivity between ecDNA amplification and microsatellite instability (MSI). In addition, we establish the role of ecDNA amplification as a risk factor and refine genomic subtypes in a cohort from 1015 colorectal cancer patients. Importantly, our investigation incorporates data from four clinical trials focused on anti-PD-1 immunotherapy, demonstrating the pivotal role of ecDNA amplification as a biomarker for guiding checkpoint blockade immunotherapy in gastrointestinal cancer. This finding represents clinical evidence linking ecDNA amplification to the effectiveness of immunotherapeutic interventions. Overall, our study provides a proof-of-concept of identifying ecDNA amplification from cancer whole-exome sequencing (WES) data, highlighting the potential of ecDNA amplification as a valuable biomarker for facilitating personalized cancer treatment.
Collapse
Affiliation(s)
- Shixiang Wang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Chen-Yi Wu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Ming-Ming He
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Jia-Xin Yong
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Yan-Xing Chen
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Li-Mei Qian
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Jin-Ling Zhang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Zhao-Lei Zeng
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Rui-Hua Xu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
- Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, China.
| | - Feng Wang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
| | - Qi Zhao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
| |
Collapse
|
18
|
Abstract
Long non-coding RNAs (lncRNAs) are significant contributors in maintaining genomic integrity through epigenetic regulation. LncRNAs can interact with chromatin-modifying complexes in both cis and trans pathways, drawing them to specific genomic loci and influencing gene expression via DNA methylation, histone modifications, and chromatin remodeling. They can also operate as building blocks to assemble different chromatin-modifying components, facilitating their interactions and gene regulatory functions. Deregulation of these molecules has been associated with various human diseases, including cancer, cardiovascular disease, and neurological disorders. Thus, lncRNAs are implicated as potential diagnostic indicators and therapeutic targets. This review discusses the current understanding of how lncRNAs mediate epigenetic control, genomic integrity, and their putative functions in disease pathogenesis.
Collapse
Affiliation(s)
- Ganesan Arunkumar
- The LncRNA, Epigenetics, and Genome Organization Laboratory, Department of Cell Biology and Physiology, School of Medicine, University of New Mexico, Albuquerque, NM, USA
| |
Collapse
|
19
|
Fang M, Fang J, Luo S, Liu K, Yu Q, Yang J, Zhou Y, Li Z, Sun R, Guo C, Qu K. eccDNA-pipe: an integrated pipeline for identification, analysis and visualization of extrachromosomal circular DNA from high-throughput sequencing data. Brief Bioinform 2024; 25:bbae034. [PMID: 38349061 PMCID: PMC10862650 DOI: 10.1093/bib/bbae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/22/2023] [Accepted: 01/11/2024] [Indexed: 02/15/2024] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is currently attracting considerable attention from researchers due to its significant impact on tumor biogenesis. High-throughput sequencing (HTS) methods for eccDNA identification are continually evolving. However, an efficient pipeline for the integrative and comprehensive analysis of eccDNA obtained from HTS data is still lacking. Here, we introduce eccDNA-pipe, an accessible software package that offers a user-friendly pipeline for conducting eccDNA analysis starting from raw sequencing data. This dataset includes data from various sequencing techniques such as whole-genome sequencing (WGS), Circle-seq and Circulome-seq, obtained through short-read sequencing or long-read sequencing. eccDNA-pipe presents a comprehensive solution for both upstream and downstream analysis, encompassing quality control and eccDNA identification in upstream analysis and downstream tasks such as eccDNA length distribution analysis, differential analysis of genes enriched with eccDNA and visualization of eccDNA structures. Notably, eccDNA-pipe automatically generates high-quality publication-ready plots. In summary, eccDNA-pipe provides a comprehensive and user-friendly pipeline for customized analysis of eccDNA research.
Collapse
Affiliation(s)
- Minghao Fang
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
- Institute of Advanced Technology, University of Science and Technology of China, Hefei, 230027, China
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, 230088, China
| | - Jingwen Fang
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
- HanGene Biotech, Xiaoshan Innovation Polis, Hangzhou, Zhejiang 311200, China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, 215123, China
| | - Songwen Luo
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Ke Liu
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Qiaoni Yu
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Jiaxuan Yang
- HanGene Biotech, Xiaoshan Innovation Polis, Hangzhou, Zhejiang 311200, China
| | - Youyang Zhou
- HanGene Biotech, Xiaoshan Innovation Polis, Hangzhou, Zhejiang 311200, China
| | - Zongkai Li
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Ruoming Sun
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Chuang Guo
- Department of Rheumatology and Immunology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230021, China
- School of Pharmacy, Bengbu Medical University, Bengbu, 233030, China
| | - Kun Qu
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
- Institute of Advanced Technology, University of Science and Technology of China, Hefei, 230027, China
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, 230088, China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, 215123, China
| |
Collapse
|
20
|
Wu N, Wei L, Zhu Z, Liu Q, Li K, Mao F, Qiao J, Zhao X. Innovative insights into extrachromosomal circular DNAs in gynecologic tumors and reproduction. Protein Cell 2024; 15:6-20. [PMID: 37233789 PMCID: PMC10762679 DOI: 10.1093/procel/pwad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/03/2023] [Indexed: 05/27/2023] Open
Abstract
Originating but free from chromosomal DNA, extrachromosomal circular DNAs (eccDNAs) are organized in circular form and have long been found in unicellular and multicellular eukaryotes. Their biogenesis and function are poorly understood as they are characterized by sequence homology with linear DNA, for which few detection methods are available. Recent advances in high-throughput sequencing technologies have revealed that eccDNAs play crucial roles in tumor formation, evolution, and drug resistance as well as aging, genomic diversity, and other biological processes, bringing it back to the research hotspot. Several mechanisms of eccDNA formation have been proposed, including the breakage-fusion-bridge (BFB) and translocation-deletion-amplification models. Gynecologic tumors and disorders of embryonic and fetal development are major threats to human reproductive health. The roles of eccDNAs in these pathological processes have been partially elucidated since the first discovery of eccDNA in pig sperm and the double minutes in ovarian cancer ascites. The present review summarized the research history, biogenesis, and currently available detection and analytical methods for eccDNAs and clarified their functions in gynecologic tumors and reproduction. We also proposed the application of eccDNAs as drug targets and liquid biopsy markers for prenatal diagnosis and the early detection, prognosis, and treatment of gynecologic tumors. This review lays theoretical foundations for future investigations into the complex regulatory networks of eccDNAs in vital physiological and pathological processes.
Collapse
Affiliation(s)
- Ning Wu
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Ling Wei
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Zhipeng Zhu
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Qiang Liu
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Kailong Li
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Fengbiao Mao
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Jie Qiao
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
- Beijing Advanced Innovation Center for Genomics, Beijing 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China
| | - Xiaolu Zhao
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| |
Collapse
|
21
|
Agustinus AS, David Y. Thinking outside the chromosome: epigenetic mechanisms in non-canonical chromatin species. Nat Struct Mol Biol 2024; 31:8-10. [PMID: 38253662 PMCID: PMC10964953 DOI: 10.1038/s41594-023-01200-7] [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] [Indexed: 01/24/2024]
Abstract
Here we investigate the role of epigenetics in the formation, transcription regulation, maintenance and termination of several non-canonical chromatin structures. Using two examples, we demonstrate how studying non-canonical structures may reveal underlying mechanisms with implications for disease and propose intriguing epigenetic avenues for further exploration.
Collapse
Affiliation(s)
- Albert S Agustinus
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pharmacology Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Yael David
- Pharmacology Graduate Program, Weill Cornell Medicine, New York, NY, USA.
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Tri-institutional PhD Program in Chemical Biology, New York, NY, USA.
| |
Collapse
|
22
|
Zhao X, Zhao H, Liu Y, Guo Z. Methods, bioinformatics tools and databases in ecDNA research: An overview. Comput Biol Med 2023; 167:107680. [PMID: 37976817 DOI: 10.1016/j.compbiomed.2023.107680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/25/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
Abstract
Extrachromosomal DNA (ecDNA), derived from chromosomes, is a cancer-specific circular DNA molecule. EcDNA drives tumor initiation and progression, which is associated with poor clinical outcomes and drug resistance in a wide range of cancers. Although ecDNA was first discovered in 1965, tremendous technological revolutions in recent years have provided crucial new insights into its key biological functions and regulatory mechanisms. Here, we provide a thorough overview of the methods, bioinformatics tools, and database resources used in ecDNA research, mainly focusing on their performance, strengths, and limitations. This study can provide important reference for selecting the most appropriate method in ecDNA research. Furthermore, we offer suggestions for the current bioinformatics analysis of ecDNA and provide an outlook to the future research.
Collapse
Affiliation(s)
- Xinyu Zhao
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Huan Zhao
- Key Laboratory of Marine Bio-resource Restoration and Habitat Reparation, Dalian Ocean University, Dalian, 116023, China
| | - Yupeng Liu
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Zhiyun Guo
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, 610031, China.
| |
Collapse
|
23
|
Chapman OS, Luebeck J, Sridhar S, Wong ITL, Dixit D, Wang S, Prasad G, Rajkumar U, Pagadala MS, Larson JD, He BJ, Hung KL, Lange JT, Dehkordi SR, Chandran S, Adam M, Morgan L, Wani S, Tiwari A, Guccione C, Lin Y, Dutta A, Lo YY, Juarez E, Robinson JT, Korshunov A, Michaels JEA, Cho YJ, Malicki DM, Coufal NG, Levy ML, Hobbs C, Scheuermann RH, Crawford JR, Pomeroy SL, Rich JN, Zhang X, Chang HY, Dixon JR, Bagchi A, Deshpande AJ, Carter H, Fraenkel E, Mischel PS, Wechsler-Reya RJ, Bafna V, Mesirov JP, Chavez L. Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma. Nat Genet 2023; 55:2189-2199. [PMID: 37945900 PMCID: PMC10703696 DOI: 10.1038/s41588-023-01551-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/22/2023] [Indexed: 11/12/2023]
Abstract
Circular extrachromosomal DNA (ecDNA) in patient tumors is an important driver of oncogenic gene expression, evolution of drug resistance and poor patient outcomes. Applying computational methods for the detection and reconstruction of ecDNA across a retrospective cohort of 481 medulloblastoma tumors from 465 patients, we identify circular ecDNA in 82 patients (18%). Patients with ecDNA-positive medulloblastoma were more than twice as likely to relapse and three times as likely to die within 5 years of diagnosis. A subset of tumors harbored multiple ecDNA lineages, each containing distinct amplified oncogenes. Multimodal sequencing, imaging and CRISPR inhibition experiments in medulloblastoma models reveal intratumoral heterogeneity of ecDNA copy number per cell and frequent putative 'enhancer rewiring' events on ecDNA. This study reveals the frequency and diversity of ecDNA in medulloblastoma, stratified into molecular subgroups, and suggests copy number heterogeneity and enhancer rewiring as oncogenic features of ecDNA.
Collapse
Affiliation(s)
- Owen S Chapman
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, San Diego, CA, USA
- Department of Medicine, University of California San Diego, San Diego, CA, USA
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Jens Luebeck
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, San Diego, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Sunita Sridhar
- Department of Medicine, University of California San Diego, San Diego, CA, USA
- Department of Pediatrics, UC San Diego and Rady Children's Hospital, San Diego, CA, USA
| | - Ivy Tsz-Lo Wong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Deobrat Dixit
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
- Department of Neurology and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Shanqing Wang
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Gino Prasad
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Utkrisht Rajkumar
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Meghana S Pagadala
- Medical Scientist Training Program, University of California San Diego, San Diego, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, San Diego, CA, USA
| | - Jon D Larson
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Britney Jiayu He
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - King L Hung
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Joshua T Lange
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Siavash R Dehkordi
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | | | - Miriam Adam
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ling Morgan
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Sameena Wani
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Ashutosh Tiwari
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Caitlin Guccione
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, San Diego, CA, USA
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Yingxi Lin
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Aditi Dutta
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Yan Yuen Lo
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital and Healthcare Center, San Diego, CA, USA
| | - Edwin Juarez
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - James T Robinson
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Andrey Korshunov
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - John-Edward A Michaels
- Papé Pediatric Research Institute, Department of Pediatrics and Knight Cancer Insitute, Oregon Health and Sciences University, Portland, OR, USA
| | - Yoon-Jae Cho
- Papé Pediatric Research Institute, Department of Pediatrics and Knight Cancer Insitute, Oregon Health and Sciences University, Portland, OR, USA
| | - Denise M Malicki
- Division of Pathology, UC San Diego and Rady Children's Hospital, San Diego, CA, USA
| | - Nicole G Coufal
- Department of Pediatrics, UC San Diego and Rady Children's Hospital, San Diego, CA, USA
| | - Michael L Levy
- Division of Pathology, UC San Diego and Rady Children's Hospital, San Diego, CA, USA
| | - Charlotte Hobbs
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital and Healthcare Center, San Diego, CA, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA, USA
- Department of Pathology, University of California San Diego, San Diego, CA, USA
| | - John R Crawford
- Department of Pediatrics, University of California Irvine and Children's Hospital Orange County, Irvine, CA, USA
| | - Scott L Pomeroy
- Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jeremy N Rich
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xinlian Zhang
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, San Diego, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jesse R Dixon
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Anindya Bagchi
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | | | - Hannah Carter
- Department of Medicine, University of California San Diego, San Diego, CA, USA
- Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paul S Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Robert J Wechsler-Reya
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
- Department of Neurology and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
- Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Jill P Mesirov
- Department of Medicine, University of California San Diego, San Diego, CA, USA
- Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Lukas Chavez
- Department of Medicine, University of California San Diego, San Diego, CA, USA.
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA.
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital and Healthcare Center, San Diego, CA, USA.
- Moores Cancer Center, University of California San Diego, San Diego, CA, USA.
| |
Collapse
|
24
|
Cheng H, Ma W, Wang K, Chu H, Bao G, Liao Y, Yuan Y, Gou Y, Dong L, Yang J, Cai H. ATACAmp: a tool for detecting ecDNA/HSRs from bulk and single-cell ATAC-seq data. BMC Genomics 2023; 24:678. [PMID: 37950200 PMCID: PMC10638764 DOI: 10.1186/s12864-023-09792-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND High oncogene expression in cancer cells is a major cause of rapid tumor progression and drug resistance. Recent cancer genome research has shown that oncogenes as well as regulatory elements can be amplified in the form of extrachromosomal DNA (ecDNA) or subsequently integrated into chromosomes as homogeneously staining regions (HSRs). These genome-level variants lead to the overexpression of the corresponding oncogenes, resulting in poor prognosis. Most existing detection methods identify ecDNA using whole genome sequencing (WGS) data. However, these techniques usually detect many false positive regions owing to chromosomal DNA interference. RESULTS In the present study, an algorithm called "ATACAmp" that can identify ecDNA/HSRs in tumor genomes using ATAC-seq data has been described. High chromatin accessibility, one of the characteristics of ecDNA, makes ATAC-seq naturally enriched in ecDNA and reduces chromosomal DNA interference. The algorithm was validated using ATAC-seq data from cell lines that have been experimentally determined to contain ecDNA regions. ATACAmp accurately identified the majority of validated ecDNA regions. AmpliconArchitect, the widely used ecDNA detecting tool, was used to detect ecDNA regions based on the WGS data of the same cell lines. Additionally, the Circle-finder software, another tool that utilizes ATAC-seq data, was assessed. The results showed that ATACAmp exhibited higher accuracy than AmpliconArchitect and Circle-finder. Moreover, ATACAmp supported the analysis of single-cell ATAC-seq data, which linked ecDNA to specific cells. CONCLUSIONS ATACAmp, written in Python, is freely available on GitHub under the MIT license: https://github.com/chsmiss/ATAC-amp . Using ATAC-seq data, ATACAmp offers a novel analytical approach that is distinct from the conventional use of WGS data. Thus, this method has the potential to reduce the cost and technical complexity associated ecDNA analysis.
Collapse
Affiliation(s)
- Hansen Cheng
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Chengdu, Sichuan, 610064, China
| | - Wenhao Ma
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Chengdu, Sichuan, 610064, China
| | - Kun Wang
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Chengdu, Sichuan, 610064, China
| | - Han Chu
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Chengdu, Sichuan, 610064, China
| | - Guangchao Bao
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Chengdu, Sichuan, 610064, China
| | - Yu Liao
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Chengdu, Sichuan, 610064, China
| | - Yawen Yuan
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Chengdu, Sichuan, 610064, China
| | - Yixiong Gou
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Chengdu, Sichuan, 610064, China
| | - Liting Dong
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Chengdu, Sichuan, 610064, China
| | - Jian Yang
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Chengdu, Sichuan, 610064, China.
| | - Haoyang Cai
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, No.29 Wangjiang Road, Chengdu, Sichuan, 610064, China.
| |
Collapse
|
25
|
Li Z, Wang B, Liang H, Li Y, Zhang Z, Han L. A three-stage eccDNA based molecular profiling significantly improves the identification, prognosis assessment and recurrence prediction accuracy in patients with glioma. Cancer Lett 2023; 574:216369. [PMID: 37640198 DOI: 10.1016/j.canlet.2023.216369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/15/2023] [Accepted: 08/24/2023] [Indexed: 08/31/2023]
Abstract
Glioblastoma (GBM) progression is influenced by intratumoral heterogeneity. Emerging evidence has emphasized the pivotal role of extrachromosomal circular DNA (eccDNA) in accelerating tumor heterogeneity, particularly in GBM. However, the eccDNA landscape of GBM has not yet been elucidated. In this study, we first identified the eccDNA profiles in GBM and adjacent tissues using circle- and RNA-sequencing data from the same samples. A three-stage model was established based on eccDNA-carried genes that exhibited consistent upregulation and downregulation trends at the mRNA level. Combinations of machine learning algorithms and stacked ensemble models were used to improve the performance and robustness of the three-stage model. In stage 1, a total of 113 combinations of machine learning algorithms were constructed and validated in multiple external cohorts to accurately distinguish between low-grade glioma (LGG) and GBM in patients with glioma. The model with the highest area under the curve (AUC) across all cohorts was selected for interpretability analysis. In stage 2, a total of 101 combinations of machine learning algorithms were established and validated for prognostic prediction in patients with glioma. This prognostic model performed well in multiple glioma cohorts. Recurrent GBM is invariably associated with aggressive and refractory disease. Therefore, accurate prediction of recurrence risk is crucial for developing individualized treatment strategies, monitoring patient status, and improving clinical management. In stage 3, a large-scale GBM cohort (including primary and recurrent GBM samples) was used to fit the GBM recurrence prediction model. Multiple machine learning and stacked ensemble models were fitted to select the model with the best performance. Finally, a web tool was developed to facilitate the clinical application of the three-stage model.
Collapse
Affiliation(s)
- Zesheng Li
- Tianjin Neurological Institute, Key Laboratory of Post-Neuro Injury, Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Bo Wang
- Tianjin Neurological Institute, Key Laboratory of Post-Neuro Injury, Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Hao Liang
- Tianjin Neurological Institute, Key Laboratory of Post-Neuro Injury, Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Ying Li
- Tianjin Neurological Institute, Key Laboratory of Post-Neuro Injury, Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Zhenyu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 480082, China.
| | - Lei Han
- Tianjin Neurological Institute, Key Laboratory of Post-Neuro Injury, Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, 300052, China.
| |
Collapse
|
26
|
Li F, Ming W, Lu W, Wang Y, Li X, Dong X, Bai Y. FLED: a full-length eccDNA detector for long-reads sequencing data. Brief Bioinform 2023; 24:bbad388. [PMID: 37930031 PMCID: PMC10632013 DOI: 10.1093/bib/bbad388] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/24/2023] [Accepted: 09/30/2023] [Indexed: 11/07/2023] Open
Abstract
Reconstructing the full-length sequence of extrachromosomal circular DNA (eccDNA) from short sequencing reads has proved challenging given the similarity of eccDNAs and their corresponding linear DNAs. Previous sequencing methods were unable to achieve high-throughput detection of full-length eccDNAs. Herein, a novel algorithm was developed, called Full-Length eccDNA Detection (FLED), to reconstruct the sequence of eccDNAs based on the strategy that combined rolling circle amplification and nanopore long-reads sequencing technology. Seven human epithelial and cancer cell line samples were analyzed by FLED and over 5000 full-length eccDNAs were identified per sample. The structures of identified eccDNAs were validated by both Polymerase Chain Reaction (PCR) and Sanger sequencing. Compared to other published nanopore-based eccDNA detectors, FLED exhibited higher sensitivity. In cancer cell lines, the genes overlapped with eccDNA regions were enriched in cancer-related pathways and cis-regulatory elements can be predicted in the upstream or downstream of intact genes on eccDNA molecules, and the expressions of these cancer-related genes were dysregulated in tumor cell lines, indicating the regulatory potency of eccDNAs in biological processes. The proposed method takes advantage of nanopore long reads and enables unbiased reconstruction of full-length eccDNA sequences. FLED is implemented using Python3 which is freely available on GitHub (https://github.com/FuyuLi/FLED).
Collapse
Affiliation(s)
- Fuyu Li
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, P. R. China
| | - Wenlong Ming
- Institute for AI in Medicine, School of Artificial Intelligence, Nanjing University of Information Science and Technology, Nanjing, 210044, P. R. China
| | - Wenxiang Lu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, P. R. China
| | - Ying Wang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, P. R. China
| | - Xiaohan Li
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, P. R. China
| | - Xianjun Dong
- Genomics and Bioinformatics Hub, Brigham and Women's Hospital, Boston, MA 02115, USA
- Precision Neurology Program, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Yunfei Bai
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, P. R. China
| |
Collapse
|
27
|
dos Santos CR, Hansen LB, Rojas-Triana M, Johansen AZ, Perez-Moreno M, Regenberg B. Variation of extrachromosomal circular DNA in cancer cell lines. Comput Struct Biotechnol J 2023; 21:4207-4214. [PMID: 37705597 PMCID: PMC10495552 DOI: 10.1016/j.csbj.2023.08.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/26/2023] [Accepted: 08/26/2023] [Indexed: 09/15/2023] Open
Abstract
The presence of oncogene carrying eccDNAs is strongly associated with carcinogenesis and poor patient survival. Tumour biopsies and in vitro cancer cell lines are frequently utilized as models to investigate the role of eccDNA in cancer. However, eccDNAs are often lost during the in vitro growth of cancer cell lines, questioning the reproducibility of studies utilizing cancer cell line models. Here, we conducted a comprehensive analysis of eccDNA variability in seven cancer cell lines (MCA3D, PDV, HaCa4, CarC, MIA-PaCa-2, AsPC-1, and PC-3). We compared the content of unique eccDNAs between triplicates of each cell line and found that the number of unique eccDNA is specific to each cell line, while the eccDNA sequence content varied greatly among triplicates (∼ 0-1% eccDNA coordinate commonality). In the PC-3 cell line, we found that the large eccDNA (ecDNA) with MYC is present in high-copy number in an NCI cell line isolate but not present in ATCC isolates. Together, these results reveal that the sequence content of eccDNA is highly variable in cancer cell lines. This highlights the importance of testing cancer cell lines before use, and to enrich for subclones in cell lines with the desired eccDNA to get relatively pure population for studying the role of eccDNA in cancer.
Collapse
Affiliation(s)
| | | | - Monica Rojas-Triana
- Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark
| | - Astrid Zedlitz Johansen
- Department of Oncology, Copenhagen University Hospital, Herlev and Gentofte, DK-2730 Herlev, Denmark
| | - Mirna Perez-Moreno
- Cell biology and Physiology, Department of Biology, University of Copenhagen, Denmark
| | - Birgitte Regenberg
- Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark
| |
Collapse
|
28
|
Abstract
DNA sequencing has revolutionized medicine over recent decades. However, analysis of large structural variation and repetitive DNA, a hallmark of human genomes, has been limited by short-read technology, with read lengths of 100-300 bp. Long-read sequencing (LRS) permits routine sequencing of human DNA fragments tens to hundreds of kilobase pairs in size, using both real-time sequencing by synthesis and nanopore-based direct electronic sequencing. LRS permits analysis of large structural variation and haplotypic phasing in human genomes and has enabled the discovery and characterization of rare pathogenic structural variants and repeat expansions. It has also recently enabled the assembly of a complete, gapless human genome that includes previously intractable regions, such as highly repetitive centromeres and homologous acrocentric short arms. With the addition of protocols for targeted enrichment, direct epigenetic DNA modification detection, and long-range chromatin profiling, LRS promises to launch a new era of understanding of genetic diversity and pathogenic mutations in human populations.
Collapse
Affiliation(s)
- Peter E Warburton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; ,
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert P Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; ,
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| |
Collapse
|
29
|
Zhou RW, Parsons RE. Etiology of super-enhancer reprogramming and activation in cancer. Epigenetics Chromatin 2023; 16:29. [PMID: 37415185 DOI: 10.1186/s13072-023-00502-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/10/2023] [Indexed: 07/08/2023] Open
Abstract
Super-enhancers are large, densely concentrated swaths of enhancers that regulate genes critical for cell identity. Tumorigenesis is accompanied by changes in the super-enhancer landscape. These aberrant super-enhancers commonly form to activate proto-oncogenes, or other genes upon which cancer cells depend, that initiate tumorigenesis, promote tumor proliferation, and increase the fitness of cancer cells to survive in the tumor microenvironment. These include well-recognized master regulators of proliferation in the setting of cancer, such as the transcription factor MYC which is under the control of numerous super-enhancers gained in cancer compared to normal tissues. This Review will cover the expanding cell-intrinsic and cell-extrinsic etiology of these super-enhancer changes in cancer, including somatic mutations, copy number variation, fusion events, extrachromosomal DNA, and 3D chromatin architecture, as well as those activated by inflammation, extra-cellular signaling, and the tumor microenvironment.
Collapse
Affiliation(s)
- Royce W Zhou
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Molecular Medicine Program, University of California San Francisco Internal Medicine Residency, San Francisco, CA, USA
| | - Ramon E Parsons
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
30
|
Vízkeleti L, Spisák S. Rewired Metabolism Caused by the Oncogenic Deregulation of MYC as an Attractive Therapeutic Target in Cancers. Cells 2023; 12:1745. [PMID: 37443779 PMCID: PMC10341379 DOI: 10.3390/cells12131745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
MYC is one of the most deregulated oncogenes on multiple levels in cancer. As a node transcription factor, MYC plays a diverse regulatory role in many cellular processes, including cell cycle and metabolism, both in physiological and pathological conditions. The relentless growth and proliferation of tumor cells lead to an insatiable demand for energy and nutrients, which requires the rewiring of cellular metabolism. As MYC can orchestrate all aspects of cellular metabolism, its altered regulation plays a central role in these processes, such as the Warburg effect, and is a well-established hallmark of cancer development. However, our current knowledge of MYC suggests that its spatial- and concentration-dependent contribution to tumorigenesis depends more on changes in the global or relative expression of target genes. As the direct targeting of MYC is proven to be challenging due to its relatively high toxicity, understanding its underlying regulatory mechanisms is essential for the development of tumor-selective targeted therapies. The aim of this review is to comprehensively summarize the diverse forms of MYC oncogenic deregulation, including DNA-, transcriptional- and post-translational level alterations, and their consequences for cellular metabolism. Furthermore, we also review the currently available and potentially attractive therapeutic options that exploit the vulnerability arising from the metabolic rearrangement of MYC-driven tumors.
Collapse
Affiliation(s)
- Laura Vízkeleti
- Department of Bioinformatics, Faculty of Medicine, Semmelweis University, 1094 Budapest, Hungary;
| | - Sándor Spisák
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary
| |
Collapse
|
31
|
Dong Y, He Q, Chen X, Yang F, He L, Zheng Y. Extrachromosomal DNA (ecDNA) in cancer: mechanisms, functions, and clinical implications. Front Oncol 2023; 13:1194405. [PMID: 37448518 PMCID: PMC10338009 DOI: 10.3389/fonc.2023.1194405] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/05/2023] [Indexed: 07/15/2023] Open
Abstract
Extrachromosomal DNA (ecDNA) is circular DNA that plays an important role in the development and heterogeneity of cancer. The rapid evolution of methods to detect ecDNA, including microscopic and sequencing approaches, has greatly enhanced our knowledge of the role of ecDNA in cancer development and evolution. Here, we review the molecular characteristics, functions, mechanisms of formation, and detection methods of ecDNA, with a focus on the potential clinical implications of ecDNA in cancer. Specifically, we consider the role of ecDNA in acquired drug resistance, as a diagnostic and prognostic biomarker, and as a therapeutic target in the context of cancer. As the pathological and clinical significance of ecDNA continues to be explored, it is anticipated that ecDNA will have broad applications in the diagnosis, prognosis, and treatment of patients with cancer.
Collapse
Affiliation(s)
- Yucheng Dong
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qi He
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xinyu Chen
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Fan Yang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li He
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Yongchang Zheng
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
32
|
Arshadi A, Tolomeo D, Venuto S, Storlazzi CT. Advancements in Focal Amplification Detection in Tumor/Liquid Biopsies and Emerging Clinical Applications. Genes (Basel) 2023; 14:1304. [PMID: 37372484 PMCID: PMC10298061 DOI: 10.3390/genes14061304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Focal amplifications (FAs) are crucial in cancer research due to their significant diagnostic, prognostic, and therapeutic implications. FAs manifest in various forms, such as episomes, double minute chromosomes, and homogeneously staining regions, arising through different mechanisms and mainly contributing to cancer cell heterogeneity, the leading cause of drug resistance in therapy. Numerous wet-lab, mainly FISH, PCR-based assays, next-generation sequencing, and bioinformatics approaches have been set up to detect FAs, unravel the internal structure of amplicons, assess their chromatin compaction status, and investigate the transcriptional landscape associated with their occurrence in cancer cells. Most of them are tailored for tumor samples, even at the single-cell level. Conversely, very limited approaches have been set up to detect FAs in liquid biopsies. This evidence suggests the need to improve these non-invasive investigations for early tumor detection, monitoring disease progression, and evaluating treatment response. Despite the potential therapeutic implications of FAs, such as, for example, the use of HER2-specific compounds for patients with ERBB2 amplification, challenges remain, including developing selective and effective FA-targeting agents and understanding the molecular mechanisms underlying FA maintenance and replication. This review details a state-of-the-art of FA investigation, with a particular focus on liquid biopsies and single-cell approaches in tumor samples, emphasizing their potential to revolutionize the future diagnosis, prognosis, and treatment of cancer patients.
Collapse
Affiliation(s)
| | | | | | - Clelia Tiziana Storlazzi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70125 Bari, Italy; (A.A.); (D.T.); (S.V.)
| |
Collapse
|
33
|
Wang W, Artiles KL, Machida S, Benkirane M, Jain N, Fire AZ. Combined direct/indirect detection allows identification of DNA termini in diverse sequencing datasets and supports a multiple-initiation-site model for HIV plus-strand synthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.12.544617. [PMID: 37398293 PMCID: PMC10312614 DOI: 10.1101/2023.06.12.544617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Replication of genetic material involves the creation of characteristic termini. Determining these termini is important to refine our understanding of the mechanisms involved in maintaining the genomes of cellular organisms and viruses. Here we describe a computational approach combining direct and indirect readouts to detect termini from next-generation short-read sequencing. While a direct inference of termini can come from mapping the most prominent start positions of captured DNA fragments, this approach is insufficient in cases where the DNA termini are not captured, whether for biological or technical reasons. Thus, a complementary (indirect) approach to terminus detection can be applied, taking advantage of the imbalance in coverage between forward and reverse sequence reads near termini. A resulting metric ("strand bias") can be used to detect termini even where termini are naturally blocked from capture or ends are not captured during library preparation (e.g., in tagmentation-based protocols). Applying this analysis to datasets where known DNA termini are present, such as from linear double-stranded viral genomes, yielded distinct strand bias signals corresponding to these termini. To evaluate the potential to analyze a more complex situation, we applied the analysis to examine DNA termini present early after HIV infection in a cell culture model. We observed both the known termini expected based on standard models of HIV reverse transcription (the U5-right-end and U3-left-end termini) as well as a signal corresponding to a previously described additional initiation site for plus-strand synthesis (cPPT [central polypurine tract]). Interestingly, we also detected putative terminus signals at additional sites. The strongest of these are a set that share several characteristics with the previously characterized plus-strand initiation sites (the cPPT and 3' PPT [polypurine tract] sites): (i) an observed spike in directly captured cDNA ends, an indirect terminus signal evident in localized strand bias, (iii) a preference for location on the plus-strand, (iv) an upstream purine-rich motif, and (v) a decrease in terminus signal at late time points after infection. These characteristics are consistent in duplicate samples in two different genotypes (wild type and integrase-lacking HIV). The observation of distinct internal termini associated with multiple purine-rich regions raises a possibility that multiple internal initiations of plus-strand synthesis might contribute to HIV replication.
Collapse
|
34
|
Jiang R, Yang M, Zhang S, Huang M. Advances in sequencing-based studies of microDNA and ecDNA: Databases, identification methods, and integration with single-cell analysis. Comput Struct Biotechnol J 2023; 21:3073-3080. [PMID: 37273851 PMCID: PMC10238454 DOI: 10.1016/j.csbj.2023.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 06/06/2023] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is a class of circular DNA molecules that originate from genomic DNA but are separate from chromosomes. They are common in various organisms, with sizes ranging from a few hundred to millions of base pairs. A special type of large extrachromosomal DNA (ecDNA) is prevalent in cancer cells. Research on ecDNA has significantly contributed to our comprehension of cancer development, progression, evolution, and drug resistance. The use of next-generation (NGS) and third-generation sequencing (TGS) techniques to identify eccDNAs throughout the genome has become a trend in current research. Here, we briefly review current advances in the biological mechanisms and applications of two distinct types of eccDNAs: microDNA and ecDNA. In addition to presenting available identification tools based on sequencing data, we summarize the most recent efforts to integrate ecDNA with single-cell analysis and put forth suggestions to promote the process.
Collapse
Affiliation(s)
| | | | - Shufan Zhang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Moli Huang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| |
Collapse
|
35
|
Dharanipragada P, Zhang X, Liu S, Lomeli SH, Hong A, Wang Y, Yang Z, Lo KZ, Vega-Crespo A, Ribas A, Moschos SJ, Moriceau G, Lo RS. Blocking Genomic Instability Prevents Acquired Resistance to MAPK Inhibitor Therapy in Melanoma. Cancer Discov 2023; 13:880-909. [PMID: 36700848 PMCID: PMC10068459 DOI: 10.1158/2159-8290.cd-22-0787] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/27/2022] [Accepted: 01/23/2023] [Indexed: 01/27/2023]
Abstract
Blocking cancer genomic instability may prevent tumor diversification and escape from therapies. We show that, after MAPK inhibitor (MAPKi) therapy in patients and mice bearing patient-derived xenografts (PDX), acquired resistant genomes of metastatic cutaneous melanoma specifically amplify resistance-driver, nonhomologous end-joining (NHEJ), and homologous recombination repair (HRR) genes via complex genomic rearrangements (CGR) and extrachromosomal DNAs (ecDNA). Almost all sensitive and acquired-resistant genomes harbor pervasive chromothriptic regions with disproportionately high mutational burdens and significant overlaps with ecDNA and CGR spans. Recurrently, somatic mutations within ecDNA and CGR amplicons enrich for HRR signatures, particularly within acquired resistant tumors. Regardless of sensitivity or resistance, breakpoint-junctional sequence analysis suggests NHEJ as critical to double-stranded DNA break repair underlying CGR and ecDNA formation. In human melanoma cell lines and PDXs, NHEJ targeting by a DNA-PKCS inhibitor prevents/delays acquired MAPKi resistance by reducing the size of ecDNAs and CGRs early on combination treatment. Thus, targeting the causes of genomic instability prevents acquired resistance. SIGNIFICANCE Acquired resistance often results in heterogeneous, redundant survival mechanisms, which challenge strategies aimed at reversing resistance. Acquired-resistant melanomas recurrently evolve resistance-driving and resistance-specific amplicons via ecDNAs and CGRs, thereby nominating chromothripsis-ecDNA-CGR biogenesis as a resistance-preventive target. Specifically, targeting DNA-PKCS/NHEJ prevents resistance by suppressing ecDNA/CGR rearrangements in MAPKi-treated melanomas. This article is highlighted in the In This Issue feature, p. 799.
Collapse
Affiliation(s)
- Prashanthi Dharanipragada
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Xiao Zhang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Sixue Liu
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Shirley H. Lomeli
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Aayoung Hong
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Yan Wang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Zhentao Yang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Kara Z. Lo
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Agustin Vega-Crespo
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Antoni Ribas
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Division of Surgical Oncology, Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Stergios J. Moschos
- Division of Medical Oncology, Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Gatien Moriceau
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Roger S. Lo
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| |
Collapse
|
36
|
Zhong T, Wang W, Liu H, Zeng M, Zhao X, Guo Z. eccDNA Atlas: a comprehensive resource of eccDNA catalog. Brief Bioinform 2023; 24:7032933. [PMID: 36757087 DOI: 10.1093/bib/bbad037] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 02/10/2023] Open
Abstract
Extrachromosomal circular DNA (eccDNA) represents a large category of non-mitochondrial and non-plasmid circular extrachromosomal DNA, playing an indispensable role in various aspects such as tumorigenesis, immune responses. However, the information of characteristics and functions about eccDNA is fragmented, hiding behind abundant literatures and massive whole-genome sequencing (WGS) data, which has not been sufficiently used for the identification of eccDNAs. Therefore, establishing an integrated repository portal is essential for identifying and analyzing eccDNAs. Here, we developed eccDNA Atlas (http://lcbb.swjtu.edu.cn/eccDNAatlas), a user-friendly database of eccDNAs that aims to provide a high-quality and integrated resource for browsing, searching and analyzing eccDNAs from multiple species. eccDNA Atlas currently contains 629 987 eccDNAs and 8221 ecDNAs manually curated from literatures and 1105 ecDNAs predicted by AmpliconArchitect based on WGS data involved in 66 diseases, 57 tissues and 319 cell lines. The content of each eccDNA entry includes multiple aspects such as sequence, disease, function, characteristic, validation strategies. Furthermore, abundant annotations and analyzing utilities were provided to explore existing eccDNAs in eccDNA Atlas or user-defined eccDNAs including oncogenes, typical enhancers, super enhancers, CTCF-binding sites, SNPs, chromatin accessibility, eQTLs, gene expression, survival and genome visualization. Overall, eccDNA Atlas provides an integrated eccDNA data warehouse and serves as an important tool for future research.
Collapse
Affiliation(s)
- Tengwei Zhong
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Wenqing Wang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Houyan Liu
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Maolin Zeng
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Xinyu Zhao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Zhiyun Guo
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, P.R. China
| |
Collapse
|
37
|
Chen Y, Qiu Q, She J, Yu J. Extrachromosomal circular DNA in colorectal cancer: biogenesis, function and potential as therapeutic target. Oncogene 2023; 42:941-951. [PMID: 36859558 PMCID: PMC10038807 DOI: 10.1038/s41388-023-02640-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 03/03/2023]
Abstract
Extrachromosomal circular DNA (ecDNA) has gained renewed interest since its discovery more than half a century ago, emerging as critical driver of tumor evolution. ecDNA is highly prevalent in many types of cancers, including colorectal cancer (CRC), which is one of the most deadly cancers worldwide. ecDNAs play an essential role in regulating oncogene expression, intratumor heterogeneity, and resistance to therapy independently of canonical chromosomal alterations in CRC. Furthermore, the existence of ecDNAs is attributed to the patient's prognosis, since ecDNA-based oncogene amplification adversely affects clinical outcomes. Recent understanding of ecDNA put an extra layer of complexity in the pathogenesis of CRC. In this review, we will discuss the current understanding on mechanisms of biogenesis, and distinctive features of ecDNA in CRC. In addition, we will examine how ecDNAs mediate oncogene overexpression, gene regulation, and topological interactions with active chromatin, which facilitates genetic heterogeneity, accelerates CRC malignancy, and enhances rapid adaptation to therapy resistance. Finally, we will discuss the potential diagnostic and therapeutic implications of ecDNAs in CRC.
Collapse
Affiliation(s)
- Yinnan Chen
- Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Department of High Talent, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Quanpeng Qiu
- Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Department of High Talent, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Junjun She
- Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
- Department of High Talent, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
| | - Jun Yu
- Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
- Department of High Talent, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| |
Collapse
|
38
|
Unraveling the Impact of Intratumoral Heterogeneity on EGFR Tyrosine Kinase Inhibitor Resistance in EGFR-Mutated NSCLC. Int J Mol Sci 2023; 24:ijms24044126. [PMID: 36835536 PMCID: PMC9964908 DOI: 10.3390/ijms24044126] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
The advent of tyrosine kinase inhibitors (TKIs) for treating epidermal growth factor receptor (EGFR)-mutated non-small-cell lung cancer (NSCLC) has been a game changer in lung cancer therapy. However, patients often develop resistance to the drugs within a few years. Despite numerous studies that have explored resistance mechanisms, particularly in regards to collateral signal pathway activation, the underlying biology of resistance remains largely unknown. This review focuses on the resistance mechanisms of EGFR-mutated NSCLC from the standpoint of intratumoral heterogeneity, as the biological mechanisms behind resistance are diverse and largely unclear. There exist various subclonal tumor populations in an individual tumor. For lung cancer patients, drug-tolerant persister (DTP) cell populations may have a pivotal role in accelerating the evolution of tumor resistance to treatment through neutral selection. Cancer cells undergo various changes to adapt to the new tumor microenvironment caused by drug exposure. DTP cells may play a crucial role in this adaptation and may be fundamental in mechanisms of resistance. Intratumoral heterogeneity may also be precipitated by DNA gains and losses through chromosomal instability, and the role of extrachromosomal DNA (ecDNA) may play an important role. Significantly, ecDNA can increase oncogene copy number alterations and enhance intratumoral heterogeneity more effectively than chromosomal instability. Additionally, advances in comprehensive genomic profiling have given us insights into various mutations and concurrent genetic alterations other than EGFR mutations, inducing primary resistance in the context of tumor heterogeneity. Understanding the mechanisms of resistance is clinically crucial since these molecular interlayers in cancer-resistance mechanisms may help to devise novel and individualized anticancer therapeutic approaches.
Collapse
|