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Bao Y, Sui X, Wang X, Qu N, Xie Y, Cong Y, Cao X. Extrachromosomal circular DNA landscape of breast cancer with lymph node metastasis. Int J Cancer 2024; 155:756-765. [PMID: 38693790 DOI: 10.1002/ijc.34985] [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: 12/02/2023] [Revised: 03/15/2024] [Accepted: 04/02/2024] [Indexed: 05/03/2024]
Abstract
Breast cancer (BC) is a complex disease with diverse manifestations, often resulting in lymph node metastasis (LNM) and impacting patient prognosis. Extrachromosomal circular DNA (eccDNA) has emerged as a key player in tumorigenesis, yet its contribution to BC LNM remains elusive. Here, we examined primary tumors and matched LNM tissues from 19 BC patients using the Circle-Seq method. We identified a median count of 44,682 eccDNA in primary tumor tissues and 38,057 in their paired LNM tissues. Furthermore, a ladder-like size distribution is observed in both primary tumor and LNM tissues. Meanwhile, similar repeat sequence distribution and GC content are identified from both primary tissue and LNM tissues. Finally, we found that eccDNA from both groups are flanked with palindromic trinucleotide motifs. These observations indicate that eccDNA of primary tumor and LNM tissues are from similar chromosomal origins. However, a subset of miRNA-associated eccDNA displayed selective enrichment in metastatic lesions, such as miR-6730 and miR-548AA1 genes. This observation implicates the function of miRNA-related eccDNA in the metastatic cascade. Our study uncovers the potential significance of these unique eccDNA molecules, shedding light on their role in cancer metastasis.
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Affiliation(s)
- Yuhan Bao
- Breast Center, The Second Hospital of Shandong University, Jinan, China
| | - Xiaolong Sui
- Department of Pathology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Xiaofei Wang
- Department of Ultrasound, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Nina Qu
- Department of Ultrasound, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Yanjie Xie
- Department of Ultrasound, Laiyang Central Hospital of Yantai City, Yantai, China
| | - Yizi Cong
- Department of Breast Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Xiaoli Cao
- Department of Ultrasound, Yantai Yuhuangding Hospital, Shandong University, Yantai, China
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Li B, Zhao S, Li S, Li C, Liu W, Li L, Cui B, Liu X, Chen H, Zhang J, Ren Y, Liu F, Yang M, Jiang T, Liu Y, Qiu X. Novel molecular subtypes of intracranial germ cell tumors expand therapeutic opportunities. Neuro Oncol 2024; 26:1335-1351. [PMID: 38430549 DOI: 10.1093/neuonc/noae038] [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: 08/29/2023] [Indexed: 03/04/2024] Open
Abstract
BACKGROUND Intracranial germ cell tumors (IGCTs) are a rare group of malignancies that are clinically classified as germinomas and nongerminomatous germ cell tumors (NGGCTs). Previous studies have found that somatic mutations involving the mitogen-activated protein kinase/mTOR signaling pathway are common early events. However, a comprehensive genomic understanding of IGCTs is still lacking. METHODS We established a cohort including over 100 IGCTs and conducted genomic and transcriptomic sequencing. RESULTS We identified novel recurrent driver genomic aberrations, including USP28 truncation mutations and high-level copy number amplification of KRAS and CRKL caused by replication of extrachromosomal DNA. Three distinct subtypes associated with unique genomic and clinical profiles were identified with transcriptome analysis: Immune-hot, MYC/E2F, and SHH. Both immune-hot and MYC/E2F were predominantly identified in germinomas and shared similar mutations involving the RAS/MAPK signaling pathway. However, the immune-hot group showed an older disease onset age and a significant immune response. MYC/E2F was characterized by a younger disease onset age and increased genomic instability, with a higher proportion of tumors showing whole-genome doubling. Additionally, the SHH subtype was mostly identified in NGGCTs. CONCLUSIONS Novel genomic aberrations and molecular subtypes were identified in IGCTs. These findings provide molecular basis for the potential introduction of new treatment strategies in this setting.
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Affiliation(s)
- Bo Li
- Department of Radiation Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Shuang Zhao
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shouwei Li
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Chunde Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wei Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Lin Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bowen Cui
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xing Liu
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Huiyuan Chen
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jing Zhang
- Department of Radiation Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yin Ren
- Department of Radiation Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Fei Liu
- Department of Radiation Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ming Yang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Jinan, China
| | - Tao Jiang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yu Liu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Pediatric Hematology & Oncology Ministry of Health, Department of Hematology & Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoguang Qiu
- Department of Radiation Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
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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.
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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.
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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.
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Van Arsdale A, Turker L, Chang YC, Gould J, Harmon B, Maggi EC, Meshcheryakova O, Brown MP, Luong D, Van Doorslaer K, Einstein MH, Kuo DYS, Zheng D, Haas BJ, Lenz J, Montagna C. Structure and transcription of integrated HPV DNA in vulvar carcinomas. NPJ Genom Med 2024; 9:35. [PMID: 38898085 PMCID: PMC11187145 DOI: 10.1038/s41525-024-00418-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 05/02/2024] [Indexed: 06/21/2024] Open
Abstract
HPV infections are associated with a fraction of vulvar cancers. Through hybridization capture and DNA sequencing, HPV DNA was detected in five of thirteen vulvar cancers. HPV16 DNA was integrated into human DNA in three of the five. The insertions were in introns of human NCKAP1, C5orf67, and LRP1B. Integrations in NCKAP1 and C5orf67 were flanked by short direct repeats in the human DNA, consistent with HPV DNA insertions at sites of abortive, staggered, endonucleolytic incisions. The insertion in C5orf67 was present as a 36 kbp, human-HPV-hetero-catemeric DNA as either an extrachromosomal circle or a tandem repeat within the human genome. The human circularization/repeat junction was defined at single nucleotide resolution. The integrated viral DNA segments all retained an intact upstream regulatory region and the adjacent viral E6 and E7 oncogenes. RNA sequencing revealed that the only HPV genes consistently transcribed from the integrated viral DNAs were E7 and E6*I. The other two HPV DNA+ tumors had coinfections, but no evidence for integration. HPV-positive and HPV-negative vulvar cancers exhibited contrasting human, global gene expression patterns partially overlapping with previously observed differences between HPV-positive and HPV-negative cervical and oropharyngeal cancers. A substantial fraction of the differentially expressed genes involved immune system function. Thus, transcription and HPV DNA integration in vulvar cancers resemble those in other HPV-positive cancers. This study emphasizes the power of hybridization capture coupled with DNA and RNA sequencing to identify a broad spectrum of HPV types, determine human genome integration status of viral DNAs, and elucidate their structures.
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Affiliation(s)
- Anne Van Arsdale
- Department of Obstetrics Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Lauren Turker
- Department of Obstetrics Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Lankenau Medical Center, Wynnewood, PA, 19096, USA
| | - Yoke-Chen Chang
- Rutgers Cancer Institute of New Jersey, 195 Little Albany St., New Brunswick, NJ, 08901, USA
| | - Joshua Gould
- Broad Institute, Cambridge, MA, 02142, USA
- Cellarity, Cambridge, MA, 02140, USA
| | - Bryan Harmon
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Elaine C Maggi
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Twist Biosciences, South San Francisco, CA, 94080, USA
| | - Olga Meshcheryakova
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Maxwell P Brown
- Broad Institute, Cambridge, MA, 02142, USA
- Verve Therapeutics, Boston, MA, 02215, USA
| | - Dana Luong
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, College of Agriculture and Life Sciences BIO5 Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Mark H Einstein
- Department of Obstetrics, Gynecology, and Women's Health, Rutgers New Jersey Medical School, Newark, NJ, 07102, USA
| | - Dennis Y S Kuo
- Department of Obstetrics Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | | | - Jack Lenz
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Cristina Montagna
- Department of Obstetrics Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
- Rutgers Cancer Institute of New Jersey, 195 Little Albany St., New Brunswick, NJ, 08901, USA.
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Lim BY, Guo Z, Lim JQ, Ko TK, Lee ECY, Kannan B, Lee JY, Lim AH, Li Z, Ng CCY, Busmanis I, Chan JY. Whole genome sequencing of HER2-positive metastatic extramammary Paget's disease: a case report. Orphanet J Rare Dis 2024; 19:223. [PMID: 38831459 PMCID: PMC11149212 DOI: 10.1186/s13023-024-03169-y] [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: 11/20/2023] [Accepted: 03/30/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND Extramammary Paget's disease (EMPD) is a rare cancer that occurs within the epithelium of the skin, arising predominantly in areas with high apocrine gland concentration such as the vulva, scrotum, penis and perianal regions. Here, we aim to integrate clinicopathological data with genomic analysis of aggressive, rapidly-progressing de novo metastatic EMPD responding to HER2-directed treatment in combination with other agents, to attain a more comprehensive understanding of the disease landscape. METHODS Immunohistochemical staining on the scrotal wall tumor and bone marrow metastasis demonstrated HER2 overexpression. Whole genome sequencing of the tumor and matched blood was performed. RESULTS Notable copy number gains (log2FC > 0.9) on chromosomes 7 and 8 were detected (n = 81), with 92.6% of these unique genes specifically located on chromosome 8. Prominent cancer-associated genes include ZNF703, HOOK3, DDHD2, LSM1, NSD3, ADAM9, BRF2, KAT6A and FGFR1. Interestingly, ERBB2 gene did not exhibit high copy number gain (log2FC = 0.4) although 90% of tumor cells stained HER2-positive. Enrichment in pathways associated with transforming growth factor-beta (TGFβ) (FDR = 0.0376, Enrichment Ratio = 8.12) and fibroblast growth factor receptor (FGFR1) signaling (FDR = 0.0082, Enrichment Ratio = 2.3) was detected. Amplicon structure analysis revealed that this was a simple-linear amplification event. CONCLUSION Whole genome sequencing revealed the underlying copy number variation landscape in HER2-positive metastatic EMPD. The presence of alternative signalling pathways and genetic variants suggests potential interactions with HER2 signalling, which possibly contributed to the HER2 overexpression and observed response to HER2-directed therapy combined with other agents in a comprehensive treatment regimen.
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Affiliation(s)
- Boon Yee Lim
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | - Zexi Guo
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | - Jing Quan Lim
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Tun Kiat Ko
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | | | - Bavani Kannan
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | - Jing Yi Lee
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | - Abner Herbert Lim
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | - Zhimei Li
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | | | - Inny Busmanis
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Jason Yongsheng Chan
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore.
- Duke-NUS Medical School, Singapore, Singapore.
- Divison of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.
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7
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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.
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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
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8
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Conway JR, Gillani R, Crowdis J, Reardon B, Park J, Han S, Titchen B, Benamar M, Haq R, Van Allen EM. Somatic structural variants drive distinct modes of oncogenesis in melanoma. J Clin Invest 2024; 134:e177270. [PMID: 38758740 PMCID: PMC11213511 DOI: 10.1172/jci177270] [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: 11/07/2023] [Accepted: 05/07/2024] [Indexed: 05/19/2024] Open
Abstract
The diversity of structural variants (SVs) in melanoma and how they impact oncogenesis are incompletely known. We performed harmonized analysis of SVs across melanoma histologic and genomic subtypes, and we identified distinct global properties between subtypes. These included the frequency and size of SVs and SV classes, their relation to chromothripsis events, and the impact on cancer-related genes of SVs that alter topologically associated domain (TAD) boundaries. Following our prior identification of double-stranded break repair deficiency in a subset of triple-wild-type cutaneous melanoma, we identified MRE11 and NBN loss-of-function SVs in melanomas with this mutational signature. Experimental knockouts of MRE11 and NBN, followed by olaparib cell viability assays in melanoma cells, indicated that dysregulation of each of these genes may cause sensitivity to PARP inhibitors in cutaneous melanomas. Broadly, harmonized analysis of melanoma SVs revealed distinct global genomic properties and molecular drivers, which may have biological and therapeutic impact.
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Affiliation(s)
- Jake R. Conway
- Division of Medical Sciences, Harvard University, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Riaz Gillani
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Jett Crowdis
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Brendan Reardon
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jihye Park
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Seunghun Han
- Division of Medical Sciences, Harvard University, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Breanna Titchen
- Division of Medical Sciences, Harvard University, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Rizwan Haq
- Center for Cancer Precision Medicine and
| | - Eliezer M. Van Allen
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Center for Cancer Precision Medicine and
- Parker Institute for Cancer Immunotherapy, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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9
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Pal Choudhuri S, Girard L, Lim JYS, Wise JF, Freitas B, Yang D, Wong E, Hamilton S, Chien VD, Kim YJ, Gilbreath C, Zhong J, Phat S, Myers DT, Christensen CL, Mazloom-Farsibaf H, Stanzione M, Wong KK, Hung YP, Farago AF, Meador CB, Dyson NJ, Lawrence MS, Wu S, Drapkin BJ. Acquired Cross-Resistance in Small Cell Lung Cancer due to Extrachromosomal DNA Amplification of MYC Paralogs. Cancer Discov 2024; 14:804-827. [PMID: 38386926 PMCID: PMC11061613 DOI: 10.1158/2159-8290.cd-23-0656] [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: 06/08/2023] [Revised: 12/15/2023] [Accepted: 02/20/2024] [Indexed: 02/24/2024]
Abstract
Small cell lung cancer (SCLC) presents as a highly chemosensitive malignancy but acquires cross-resistance after relapse. This transformation is nearly inevitable in patients but has been difficult to capture in laboratory models. Here, we present a preclinical system that recapitulates acquired cross-resistance, developed from 51 patient-derived xenograft (PDX) models. Each model was tested in vivo against three clinical regimens: cisplatin plus etoposide, olaparib plus temozolomide, and topotecan. These drug-response profiles captured hallmark clinical features of SCLC, such as the emergence of treatment-refractory disease after early relapse. For one patient, serial PDX models revealed that cross-resistance was acquired through MYC amplification on extrachromosomal DNA (ecDNA). Genomic and transcriptional profiles of the full PDX panel revealed that MYC paralog amplifications on ecDNAs were recurrent in relapsed cross-resistant SCLC, and this was corroborated in tumor biopsies from relapsed patients. We conclude that ecDNAs with MYC paralogs are recurrent drivers of cross-resistance in SCLC. SIGNIFICANCE SCLC is initially chemosensitive, but acquired cross-resistance renders this disease refractory to further treatment and ultimately fatal. The genomic drivers of this transformation are unknown. We use a population of PDX models to discover that amplifications of MYC paralogs on ecDNA are recurrent drivers of acquired cross-resistance in SCLC. This article is featured in Selected Articles from This Issue, p. 695.
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Affiliation(s)
- Shreoshi Pal Choudhuri
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Internal Medicine and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Luc Girard
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jun Yi Stanley Lim
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jillian F. Wise
- Massachusetts General Hospital Cancer Center, Krantz Family Center for Cancer Research, Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Braeden Freitas
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Internal Medicine and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Di Yang
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Internal Medicine and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Edmond Wong
- Massachusetts General Hospital Cancer Center, Krantz Family Center for Cancer Research, Harvard Medical School, Boston, Massachusetts
| | - Seth Hamilton
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Internal Medicine and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Victor D. Chien
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Internal Medicine and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yoon Jung Kim
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Collin Gilbreath
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jun Zhong
- Massachusetts General Hospital Cancer Center, Krantz Family Center for Cancer Research, Harvard Medical School, Boston, Massachusetts
| | - Sarah Phat
- Massachusetts General Hospital Cancer Center, Krantz Family Center for Cancer Research, Harvard Medical School, Boston, Massachusetts
| | - David T. Myers
- Massachusetts General Hospital Cancer Center, Krantz Family Center for Cancer Research, Harvard Medical School, Boston, Massachusetts
| | | | - Hanieh Mazloom-Farsibaf
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Marcello Stanzione
- Massachusetts General Hospital Cancer Center, Krantz Family Center for Cancer Research, Harvard Medical School, Boston, Massachusetts
| | - Kwok-Kin Wong
- Perlmutter Cancer Center, NYU Langone Health, New York, New York
| | - Yin P. Hung
- Massachusetts General Hospital Cancer Center, Krantz Family Center for Cancer Research, Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Anna F. Farago
- Massachusetts General Hospital Cancer Center, Krantz Family Center for Cancer Research, Harvard Medical School, Boston, Massachusetts
| | - Catherine B. Meador
- Massachusetts General Hospital Cancer Center, Krantz Family Center for Cancer Research, Harvard Medical School, Boston, Massachusetts
| | - Nicholas J. Dyson
- Massachusetts General Hospital Cancer Center, Krantz Family Center for Cancer Research, Harvard Medical School, Boston, Massachusetts
| | - Michael S. Lawrence
- Massachusetts General Hospital Cancer Center, Krantz Family Center for Cancer Research, Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Sihan Wu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Benjamin J. Drapkin
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Internal Medicine and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
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10
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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.
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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
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11
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Chen Z, Huang H, Hong H, Huang H, Weng H, Yu L, Xiao J, Wang Z, Fang X, Yao Y, Yue JX, Lin T. Full-spectral genome analysis of natural killer/T cell lymphoma highlights impacts of genome instability in driving its progression. Genome Med 2024; 16:48. [PMID: 38566223 PMCID: PMC10986005 DOI: 10.1186/s13073-024-01324-5] [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: 08/12/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Natural killer/T cell lymphoma (NKTCL) is a clinically and genetically heterogeneous disease with poor prognosis. Genome sequencing and mutation characterization provides a powerful approach for patient stratification, treatment target discovery, and etiology identification. However, previous studies mostly concentrated on base-level mutations in primary NKTCL, whereas the large-scale genomic alterations in NKTCL and the mutational landscapes in relapsed/refractory NKTCL remain largely unexplored. METHODS Here, we assembled whole-genome sequencing and whole-exome sequencing data from 163 patients with primary or relapsed/refractory NKTCL and compared their somatic mutational landscapes at both nucleotide and structure levels. RESULTS Our study not only confirmed previously reported common NKTCL mutational targets like STAT3, TP53, and DDX3X but also unveiled several novel high-frequency mutational targets such as PRDM9, DST, and RBMX. In terms of the overall mutational landscape, we observed striking differences between primary and relapsed/refractory NKTCL patient groups, with the latter exhibits higher levels of tumor mutation burden, copy number variants (CNVs), and structural variants (SVs), indicating a strong signal of genomic instability. Complex structural rearrangements such as chromothripsis and focal amplification are also significantly enriched in relapsed/refractory NKTCL patients, exerting a substantial impact on prognosis. Accordingly, we devised a novel molecular subtyping system (i.e., C0-C4) with distinct prognosis by integrating potential driver mutations at both nucleotide and structural levels, which further provides an informative guidance for novel treatments that target these specific driver mutations and genome instability as a whole. CONCLUSIONS The striking differences underlying the mutational landscapes between the primary and relapsed/refractory NKTCL patients highlight the importance of genomic instability in driving the progression of NKTCL. Our newly proposed molecular subtyping system is valuable in assisting patient stratification and novel treatment design towards a better prognosis in the age of precision medicine.
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Affiliation(s)
- Zegeng Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - He Huang
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Huangming Hong
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, 610041, China
| | - Huageng Huang
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Huawei Weng
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, 610041, China
| | - Le Yu
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, 610041, China
| | - Jian Xiao
- Department of Medical Oncology, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510655, China
| | - Zhao Wang
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Xiaojie Fang
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Yuyi Yao
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Jia-Xing Yue
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
| | - Tongyu Lin
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, 610041, China.
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12
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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.
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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.
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13
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Noorani I, Luebeck J, Rowan A, Grönroos E, Barbe V, Fabian M, Nicoll JAR, Boche D, Bafna V, Mischel PS, Swanton C. Oncogenic extrachromosomal DNA identification using whole-genome sequencing from formalin-fixed glioblastomas. Ann Oncol 2024:S0923-7534(24)00085-1. [PMID: 38555024 DOI: 10.1016/j.annonc.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 03/15/2024] [Indexed: 04/02/2024] Open
Affiliation(s)
- I Noorani
- The Francis Crick Institute, London, UK; Department of Neuromuscular Diseases, Institute of Neurology, University College London; National Hospital for Neurology and Neurosurgery, London, UK
| | - J Luebeck
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA
| | - A Rowan
- The Francis Crick Institute, London, UK
| | | | - V Barbe
- The Francis Crick Institute, London, UK
| | - M Fabian
- Department of Cellular Pathology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - J A R Nicoll
- Department of Cellular Pathology, University Hospital Southampton NHS Foundation Trust, Southampton, UK; Clinical Neurosciences, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - D Boche
- Clinical Neurosciences, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - V Bafna
- Department of Cellular Pathology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - P S Mischel
- Department of Pathology, Stanford University School of Medicine and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - C Swanton
- The Francis Crick Institute, London, UK
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14
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Chen L, Zhang C, Xue R, Liu M, Bai J, Bao J, Wang Y, Jiang N, Li Z, Wang W, Wang R, Zheng B, Yang A, Hu J, Liu K, Shen S, Zhang Y, Bai M, Wang Y, Zhu Y, Yang S, Gao Q, Gu J, Gao D, Wang XW, Nakagawa H, Zhang N, Wu L, Rozen SG, Bai F, Wang H. Deep whole-genome analysis of 494 hepatocellular carcinomas. Nature 2024; 627:586-593. [PMID: 38355797 DOI: 10.1038/s41586-024-07054-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
Over half of hepatocellular carcinoma (HCC) cases diagnosed worldwide are in China1-3. However, whole-genome analysis of hepatitis B virus (HBV)-associated HCC in Chinese individuals is limited4-8, with current analyses of HCC mainly from non-HBV-enriched populations9,10. Here we initiated the Chinese Liver Cancer Atlas (CLCA) project and performed deep whole-genome sequencing (average depth, 120×) of 494 HCC tumours. We identified 6 coding and 28 non-coding previously undescribed driver candidates. Five previously undescribed mutational signatures were found, including aristolochic-acid-associated indel and doublet base signatures, and a single-base-substitution signature that we termed SBS_H8. Pentanucleotide context analysis and experimental validation confirmed that SBS_H8 was distinct to the aristolochic-acid-associated SBS22. Notably, HBV integrations could take the form of extrachromosomal circular DNA, resulting in elevated copy numbers and gene expression. Our high-depth data also enabled us to characterize subclonal clustered alterations, including chromothripsis, chromoplexy and kataegis, suggesting that these catastrophic events could also occur in late stages of hepatocarcinogenesis. Pathway analysis of all classes of alterations further linked non-coding mutations to dysregulation of liver metabolism. Finally, we performed in vitro and in vivo assays to show that fibrinogen alpha chain (FGA), determined as both a candidate coding and non-coding driver, regulates HCC progression and metastasis. Our CLCA study depicts a detailed genomic landscape and evolutionary history of HCC in Chinese individuals, providing important clinical implications.
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Affiliation(s)
- Lei Chen
- National Center for Liver Cancer/Eastern Hepatobiliary Surgery Hospital, Shanghai, China.
| | - Chong Zhang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking University, Beijing, China
| | - Ruidong Xue
- Peking University-Yunnan Baiyao International Medical Research Center, International Cancer Institute, Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Translational Cancer Research Center, Peking University First Hospital, Beijing, China
| | - Mo Liu
- Centre for Computational Biology and Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Jian Bai
- Berry Oncology Corporation, Beijing, China
| | - Jinxia Bao
- Model Animal Research Center, Medical School, Nanjing University, Nanjing, China
| | - Yin Wang
- Berry Oncology Corporation, Beijing, China
| | - Nanhai Jiang
- Centre for Computational Biology and Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Zhixuan Li
- National Center for Liver Cancer/Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Wenwen Wang
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Ruiru Wang
- Berry Oncology Corporation, Beijing, China
| | - Bo Zheng
- National Center for Liver Cancer/Eastern Hepatobiliary Surgery Hospital, Shanghai, China
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | | | - Ji Hu
- National Center for Liver Cancer/Eastern Hepatobiliary Surgery Hospital, Shanghai, China
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Ke Liu
- Berry Oncology Corporation, Beijing, China
| | - Siyun Shen
- National Center for Liver Cancer/Eastern Hepatobiliary Surgery Hospital, Shanghai, China
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Yangqianwen Zhang
- National Center for Liver Cancer/Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Mixue Bai
- National Center for Liver Cancer/Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Yan Wang
- Berry Oncology Corporation, Beijing, China
| | - Yanjing Zhu
- National Center for Liver Cancer/Eastern Hepatobiliary Surgery Hospital, Shanghai, China
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Shuai Yang
- National Center for Liver Cancer/Eastern Hepatobiliary Surgery Hospital, Shanghai, China
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai, China
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jin Gu
- MOE Key Laboratory for Bioinformatics, Department of Automation, Tsinghua University, Beijing, China
| | - Dong Gao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, CAS, Shanghai, China
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ning Zhang
- Peking University-Yunnan Baiyao International Medical Research Center, International Cancer Institute, Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Translational Cancer Research Center, Peking University First Hospital, Beijing, China
| | - Lin Wu
- Berry Oncology Corporation, Beijing, China.
| | - Steven G Rozen
- Centre for Computational Biology and Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore.
| | - Fan Bai
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking University, Beijing, China.
| | - Hongyang Wang
- National Center for Liver Cancer/Eastern Hepatobiliary Surgery Hospital, Shanghai, China.
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15
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Chen JP, Diekmann C, Wu H, Chen C, Della Chiara G, Berrino E, Georgiadis KL, Bouwman BAM, Virdi M, Harbers L, Bellomo SE, Marchiò C, Bienko M, Crosetto N. scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells. Nat Commun 2024; 15:1768. [PMID: 38409079 PMCID: PMC10897160 DOI: 10.1038/s41467-024-45972-y] [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: 03/07/2023] [Accepted: 02/08/2024] [Indexed: 02/28/2024] Open
Abstract
Extrachromosomal circular DNAs (eccDNAs) have emerged as important intra-cellular mobile genetic elements that affect gene copy number and exert in trans regulatory roles within the cell nucleus. Here, we describe scCircle-seq, a method for profiling eccDNAs and unraveling their diversity and complexity in single cells. We implement and validate scCircle-seq in normal and cancer cell lines, demonstrating that most eccDNAs vary largely between cells and are stochastically inherited during cell division, although their genomic landscape is cell type-specific and can be used to accurately cluster cells of the same origin. eccDNAs are preferentially produced from chromatin regions enriched in H3K9me3 and H3K27me3 histone marks and are induced during replication stress conditions. Concomitant sequencing of eccDNAs and RNA from the same cell uncovers the absence of correlation between eccDNA copy number and gene expression levels, except for a few oncogenes, including MYC, contained within a large eccDNA in colorectal cancer cells. Lastly, we apply scCircle-seq to one prostate cancer and two breast cancer specimens, revealing cancer-specific eccDNA landscapes and a higher propensity of eccDNAs to form in amplified genomic regions. scCircle-seq is a scalable tool that can be used to dissect the complexity of eccDNAs across different cell and tissue types, and further expands the potential of eccDNAs for cancer diagnostics.
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Affiliation(s)
- Jinxin Phaedo Chen
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden.
| | - Constantin Diekmann
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
| | - Honggui Wu
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, PR China
- School of Life Sciences, Peking University, Beijing, PR China
| | - Chong Chen
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | | | - Enrico Berrino
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Konstantinos L Georgiadis
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Britta A M Bouwman
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
| | - Mohit Virdi
- Human Technopole, Viale Rita Levi-Montalcini 1, 22157, Milan, Italy
| | - Luuk Harbers
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
| | - Sara Erika Bellomo
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
| | - Caterina Marchiò
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Magda Bienko
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden.
- Human Technopole, Viale Rita Levi-Montalcini 1, 22157, Milan, Italy.
| | - Nicola Crosetto
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden.
- Human Technopole, Viale Rita Levi-Montalcini 1, 22157, Milan, Italy.
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16
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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.
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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.
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17
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Al-Ghabkari A, Huang B, Park M. Aberrant MET Receptor Tyrosine Kinase Signaling in Glioblastoma: Targeted Therapy and Future Directions. Cells 2024; 13:218. [PMID: 38334610 PMCID: PMC10854665 DOI: 10.3390/cells13030218] [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: 11/08/2023] [Revised: 11/27/2023] [Accepted: 01/12/2024] [Indexed: 02/10/2024] Open
Abstract
Brain tumors represent a heterogeneous group of neoplasms characterized by a high degree of aggressiveness and a poor prognosis. Despite recent therapeutic advances, the treatment of brain tumors, including glioblastoma (GBM), an aggressive primary brain tumor associated with poor prognosis and resistance to therapy, remains a significant challenge. Receptor tyrosine kinases (RTKs) are critical during development and in adulthood. Dysregulation of RTKs through activating mutations and gene amplification contributes to many human cancers and provides attractive therapeutic targets for treatment. Under physiological conditions, the Met RTK, the hepatocyte growth factor/scatter factor (HGF/SF) receptor, promotes fundamental signaling cascades that modulate epithelial-to-mesenchymal transition (EMT) involved in tissue repair and embryogenesis. In cancer, increased Met activity promotes tumor growth and metastasis by providing signals for proliferation, survival, and migration/invasion. Recent clinical genomic studies have unveiled multiple mechanisms by which MET is genetically altered in GBM, including focal amplification, chromosomal rearrangements generating gene fusions, and a splicing variant mutation (exon 14 skipping, METex14del). Notably, MET overexpression contributes to chemotherapy resistance in GBM by promoting the survival of cancer stem-like cells. This is linked to distinctive Met-induced pathways, such as the upregulation of DNA repair mechanisms, which can protect tumor cells from the cytotoxic effects of chemotherapy. The development of MET-targeted therapies represents a major step forward in the treatment of brain tumours. Preclinical studies have shown that MET-targeted therapies (monoclonal antibodies or small molecule inhibitors) can suppress growth and invasion, enhancing the efficacy of conventional therapies. Early-phase clinical trials have demonstrated promising results with MET-targeted therapies in improving overall survival for patients with recurrent GBM. However, challenges remain, including the need for patient stratification, the optimization of treatment regimens, and the identification of mechanisms of resistance. This review aims to highlight the current understanding of mechanisms underlying MET dysregulation in GBM. In addition, it will focus on the ongoing preclinical and clinical assessment of therapies targeting MET dysregulation in GBM.
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Affiliation(s)
- Abdulhameed Al-Ghabkari
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada; (A.A.-G.); (B.H.)
| | - Bruce Huang
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada; (A.A.-G.); (B.H.)
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Morag Park
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada; (A.A.-G.); (B.H.)
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
- Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada
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18
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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.
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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
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19
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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.
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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
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20
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Dehkordi SR, Wong ITL, Ni J, Luebeck J, Zhu K, Prasad G, Krockenberger L, Xu G, Chowdhury B, Rajkumar U, Caplin A, Muliaditan D, Coruh C, Jin Q, Turner K, Teo SX, Pang AWC, Alexandrov LB, Chua CEL, Furnari FB, Paulson TG, Law JA, Chang HY, Yue F, DasGupta R, Zhao J, Mischel PS, Bafna V. Breakage fusion bridge cycles drive high oncogene copy number, but not intratumoral genetic heterogeneity or rapid cancer genome change. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571349. [PMID: 38168210 PMCID: PMC10760206 DOI: 10.1101/2023.12.12.571349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Oncogene amplification is a major driver of cancer pathogenesis. Breakage fusion bridge (BFB) cycles, like extrachromosomal DNA (ecDNA), can lead to high copy numbers of oncogenes, but their impact on intratumoral heterogeneity, treatment response, and patient survival are not well understood due to difficulty in detecting them by DNA sequencing. We describe a novel algorithm that detects and reconstructs BFB amplifications using optical genome maps (OGMs), called OM2BFB. OM2BFB showed high precision (>93%) and recall (92%) in detecting BFB amplifications in cancer cell lines, PDX models and primary tumors. OM-based comparisons demonstrated that short-read BFB detection using our AmpliconSuite (AS) toolkit also achieved high precision, albeit with reduced sensitivity. We detected 371 BFB events using whole genome sequences from 2,557 primary tumors and cancer lines. BFB amplifications were preferentially found in cervical, head and neck, lung, and esophageal cancers, but rarely in brain cancers. BFB amplified genes show lower variance of gene expression, with fewer options for regulatory rewiring relative to ecDNA amplified genes. BFB positive (BFB (+)) tumors showed reduced heterogeneity of amplicon structures, and delayed onset of resistance, relative to ecDNA(+) tumors. EcDNA and BFB amplifications represent contrasting mechanisms to increase the copy numbers of oncogene with markedly different characteristics that suggest different routes for intervention.
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Affiliation(s)
- Siavash Raeisi Dehkordi
- Department of Computer Science and Engineering, University of California San Diego, 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
| | - Jing Ni
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 USA
| | - Jens Luebeck
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, San Diego, CA, USA
| | - Kaiyuan Zhu
- 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
| | - Lena Krockenberger
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Guanghui Xu
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Biswanath Chowdhury
- 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
| | - Ann Caplin
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Daniel Muliaditan
- Laboratory of Precision Oncology and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Ceyda Coruh
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- ClearNote Health, San Diego, CA 92121 USA
| | - Qiushi Jin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | | | - Shu Xian Teo
- Singapore Nuclear Research and Safety Initiative, National University of Singapore
| | | | - Ludmil B Alexandrov
- Moores Cancer Center, UC San Diego Health, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA
| | | | - Frank B Furnari
- Department of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Thomas G Paulson
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | - Ramanuj DasGupta
- Laboratory of Precision Oncology and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Jean Zhao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 USA
| | - Paul S Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
- Halıcıoğlu Data Science Institute, University of California at San Diego, La Jolla, CA, USA
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21
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Zhu Q, Zhao X, Zhang Y, Li Y, Liu S, Han J, Sun Z, Wang C, Deng D, Wang S, Tang Y, Huang Y, Jiang S, Tian C, Chen X, Yuan Y, Li Z, Yang T, Lai T, Liu Y, Yang W, Zou X, Zhang M, Cui H, Liu C, Jin X, Hu Y, Chen A, Xu X, Li G, Hou Y, Liu L, Liu S, Fang L, Chen W, Wu L. Single cell multi-omics reveal intra-cell-line heterogeneity across human cancer cell lines. Nat Commun 2023; 14:8170. [PMID: 38071219 PMCID: PMC10710513 DOI: 10.1038/s41467-023-43991-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Human cancer cell lines have long served as tools for cancer research and drug discovery, but the presence and the source of intra-cell-line heterogeneity remain elusive. Here, we perform single-cell RNA-sequencing and ATAC-sequencing on 42 and 39 human cell lines, respectively, to illustrate both transcriptomic and epigenetic heterogeneity within individual cell lines. Our data reveal that transcriptomic heterogeneity is frequently observed in cancer cell lines of different tissue origins, often driven by multiple common transcriptional programs. Copy number variation, as well as epigenetic variation and extrachromosomal DNA distribution all contribute to the detected intra-cell-line heterogeneity. Using hypoxia treatment as an example, we demonstrate that transcriptomic heterogeneity could be reshaped by environmental stress. Overall, our study performs single-cell multi-omics of commonly used human cancer cell lines and offers mechanistic insights into the intra-cell-line heterogeneity and its dynamics, which would serve as an important resource for future cancer cell line-based studies.
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Affiliation(s)
- Qionghua Zhu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
| | - Xin Zhao
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yuanhang Zhang
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yanping Li
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Shang Liu
- BGI Research, 518083, Shenzhen, China
| | - Jingxuan Han
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Zhiyuan Sun
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Chunqing Wang
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Daqi Deng
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | | | - Yisen Tang
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | | | - Siyuan Jiang
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Chi Tian
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Xi Chen
- BGI Research, 518083, Shenzhen, China
| | - Yue Yuan
- BGI Research, 518083, Shenzhen, China
| | - Zeyu Li
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Tao Yang
- China National GeneBank, 518120, Shenzhen, China
| | - Tingting Lai
- China National GeneBank, 518120, Shenzhen, China
| | - Yiqun Liu
- China National GeneBank, 518120, Shenzhen, China
| | - Wenzhen Yang
- China National GeneBank, 518120, Shenzhen, China
| | - Xuanxuan Zou
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | | | - Huanhuan Cui
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, China
| | | | - Xin Jin
- BGI Research, 518083, Shenzhen, China
| | - Yuhui Hu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Ao Chen
- BGI Research, 518083, Shenzhen, China
- JFL-BGI STOmics Center, Jinfeng Laboratory, 401329, Chongqing, China
- The Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong, China
| | - Xun Xu
- BGI Research, 518083, Shenzhen, China
| | - Guipeng Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Yong Hou
- BGI Research, 518083, Shenzhen, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, 518100, Shenzhen, China
| | - Longqi Liu
- BGI Research, 518083, Shenzhen, China.
- BGI Research, 310012, Hangzhou, China.
- Shenzhen Bay Laboratory, 518000, Shenzhen, China.
| | - Shiping Liu
- BGI Research, 518083, Shenzhen, China.
- The Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong, China.
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, 518100, Shenzhen, China.
- BGI Research, 310012, Hangzhou, China.
- Shenzhen Bay Laboratory, 518000, Shenzhen, China.
| | - Liang Fang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, China.
| | - Wei Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
| | - Liang Wu
- BGI Research, 518083, Shenzhen, China.
- JFL-BGI STOmics Center, Jinfeng Laboratory, 401329, Chongqing, China.
- BGI Research, 401329, Chongqing, China.
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22
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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.
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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.
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23
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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.
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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.
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24
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Espejo Valle-Inclán J, Cortés-Ciriano I. ReConPlot: an R package for the visualization and interpretation of genomic rearrangements. Bioinformatics 2023; 39:btad719. [PMID: 38058190 PMCID: PMC10710371 DOI: 10.1093/bioinformatics/btad719] [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: 02/24/2023] [Revised: 09/13/2023] [Accepted: 12/05/2023] [Indexed: 12/08/2023] Open
Abstract
MOTIVATION Whole-genome sequencing studies of human tumours have revealed that complex forms of structural variation, collectively known as complex genome rearrangements (CGRs), are pervasive across diverse cancer types. Detection, classification, and mechanistic interpretation of CGRs requires the visualization of complex patterns of somatic copy number aberrations (SCNAs) and structural variants (SVs). However, there is a lack of tools specifically designed to facilitate the visualization and study of CGRs. RESULTS We present ReConPlot (REarrangement and COpy Number PLOT), an R package that provides functionalities for the joint visualization of SCNAs and SVs across one or multiple chromosomes. ReConPlot is based on the popular ggplot2 package, thus allowing customization of plots and the generation of publication-quality figures with minimal effort. Overall, ReConPlot facilitates the exploration, interpretation, and reporting of CGR patterns. AVAILABILITY AND IMPLEMENTATION The R package ReConPlot is available at https://github.com/cortes-ciriano-lab/ReConPlot. Detailed documentation and a tutorial with examples are provided with the package.
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Affiliation(s)
- Jose Espejo Valle-Inclán
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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25
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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.
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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.
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26
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Wu S, Tao T, Zhang L, Zhu X, Zhou X. Extrachromosomal DNA (ecDNA): Unveiling its role in cancer progression and implications for early detection. Heliyon 2023; 9:e21327. [PMID: 38027570 PMCID: PMC10643110 DOI: 10.1016/j.heliyon.2023.e21327] [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: 05/25/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
Extrachromosomal DNA (ecDNA) is a special class of circular DNA in eukaryotes, which is independent of conventional chromosomes. These circular molecules play important roles in biology, especially in cancer biology. The emergence of sequencing technologies such as CCDA-seq and Amplicon Architect has led to a progressive unraveling of the mystery of ecDNA. Consequently, insights into its function and potential applications have begun to surface. Among these studies, the most noteworthy research pertains to cancer-related investigations into ecDNA. Numerous studies have underscored the significance of ecDNA in the pathogenesis of cancer and its role in accelerating cancer evolution. This review provides an overview of the source, structure, and function of ecDNA, while compiling recent advancements in ecDNA in the field of cancer. Nonetheless, further research is imperative to determine its effectiveness and specificity as a biomarker for early cancer detection.
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Affiliation(s)
- Shuhong Wu
- Department of Immunology, School of Medicine, Nantong University, Nantong, China
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
| | - Tao Tao
- Department of Gastroenterology, Zibo Central Hospital, Zibo, China
| | - Lin Zhang
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
| | - Xiao Zhu
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
- Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou Medical College, Hangzhou, China
| | - Xiaorong Zhou
- Department of Immunology, School of Medicine, Nantong University, Nantong, China
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27
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Lin D, Zou Y, Li X, Wang J, Xiao Q, Gao X, Lin F, Zhang N, Jiao M, Guo Y, Teng Z, Li S, Wei Y, Zhou F, Yin R, Zhang S, Xing L, Xu W, Wu X, Yang B, Xiao K, Wu C, Tao Y, Yang X, Zhang J, Hu S, Dong S, Li X, Ye S, Hong Z, Pan Y, Yang Y, Sun H, Cao G. MGA-seq: robust identification of extrachromosomal DNA and genetic variants using multiple genetic abnormality sequencing. Genome Biol 2023; 24:247. [PMID: 37904244 PMCID: PMC10614391 DOI: 10.1186/s13059-023-03081-x] [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: 02/05/2023] [Accepted: 10/04/2023] [Indexed: 11/01/2023] Open
Abstract
Genomic abnormalities are strongly associated with cancer and infertility. In this study, we develop a simple and efficient method - multiple genetic abnormality sequencing (MGA-Seq) - to simultaneously detect structural variation, copy number variation, single-nucleotide polymorphism, homogeneously staining regions, and extrachromosomal DNA (ecDNA) from a single tube. MGA-Seq directly sequences proximity-ligated genomic fragments, yielding a dataset with concurrent genome three-dimensional and whole-genome sequencing information, enabling approximate localization of genomic structural variations and facilitating breakpoint identification. Additionally, by utilizing MGA-Seq, we map focal amplification and oncogene coamplification, thus facilitating the exploration of ecDNA's transcriptional regulatory function.
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Affiliation(s)
- Da Lin
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yanyan Zou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xinyu Li
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinyue Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qin Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaochen Gao
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fei Lin
- Reproductive Medical Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Ningyuan Zhang
- Reproductive Medical Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Ming Jiao
- Department of Laboratory Animal Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Guo
- Department of Laboratory Animal Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhaowei Teng
- The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Shiyi Li
- Baylor College of Medicine, Houston, TX, USA
- Department of Radiation & Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yongchang Wei
- Department of Radiation & Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Fuling Zhou
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Rong Yin
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Siheng Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Lingyu Xing
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Weize Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xiaofeng Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Bing Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Ke Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Chengchao Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yingfeng Tao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xiaoqing Yang
- Hospital of Huazhong Agricultural University, Wuhan, China
| | - Jing Zhang
- Department of Medical Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sheng Hu
- Department of Medical Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuang Dong
- Department of Medical Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyu Li
- Department of Medical Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shengwei Ye
- Department of Gastrointestinal Surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhidan Hong
- Dapartment of Reproductive Medicine Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yihang Pan
- Precision Medicine Center, Scientific Research Center, School of Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Yuqin Yang
- Department of Laboratory Animal Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haixiang Sun
- Reproductive Medical Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
- College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China.
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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28
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Rodriguez-Fos E, Planas-Fèlix M, Burkert M, Puiggròs M, Toedling J, Thiessen N, Blanc E, Szymansky A, Hertwig F, Ishaque N, Beule D, Torrents D, Eggert A, Koche RP, Schwarz RF, Haase K, Schulte JH, Henssen AG. Mutational topography reflects clinical neuroblastoma heterogeneity. CELL GENOMICS 2023; 3:100402. [PMID: 37868040 PMCID: PMC10589636 DOI: 10.1016/j.xgen.2023.100402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/13/2023] [Accepted: 08/11/2023] [Indexed: 10/24/2023]
Abstract
Neuroblastoma is a pediatric solid tumor characterized by strong clinical heterogeneity. Although clinical risk-defining genomic alterations exist in neuroblastomas, the mutational processes involved in their generation remain largely unclear. By examining the topography and mutational signatures derived from all variant classes, we identified co-occurring mutational footprints, which we termed mutational scenarios. We demonstrate that clinical neuroblastoma heterogeneity is associated with differences in the mutational processes driving these scenarios, linking risk-defining pathognomonic variants to distinct molecular processes. Whereas high-risk MYCN-amplified neuroblastomas were characterized by signs of replication slippage and stress, homologous recombination-associated signatures defined high-risk non-MYCN-amplified patients. Non-high-risk neuroblastomas were marked by footprints of chromosome mis-segregation and TOP1 mutational activity. Furthermore, analysis of subclonal mutations uncovered differential activity of these processes through neuroblastoma evolution. Thus, clinical heterogeneity of neuroblastoma patients can be linked to differences in the mutational processes that are active in their tumors.
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Affiliation(s)
- Elias Rodriguez-Fos
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mercè Planas-Fèlix
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Burkert
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Montserrat Puiggròs
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center – Center for Genomic Regulation – Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Joern Toedling
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nina Thiessen
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Eric Blanc
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Annabell Szymansky
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Falk Hertwig
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Naveed Ishaque
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Dieter Beule
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - David Torrents
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center – Center for Genomic Regulation – Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Angelika Eggert
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Richard P. Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roland F. Schwarz
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- BIFOLD – Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
| | - Kerstin Haase
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johannes H. Schulte
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Anton G. Henssen
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
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Fu W, MacGregor DR, Comont D, Saski CA. Sequence Characterization of Extra-Chromosomal Circular DNA Content in Multiple Blackgrass ( Alopecurus myosuroides) Populations. Genes (Basel) 2023; 14:1905. [PMID: 37895254 PMCID: PMC10606437 DOI: 10.3390/genes14101905] [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: 09/15/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Alopecurus myosuroides (blackgrass) is a problematic weed of Western European winter wheat, and its success is largely due to widespread multiple-herbicide resistance. Previous analysis of F2 seed families derived from two distinct blackgrass populations exhibiting equivalent non-target site resistance (NTSR) phenotypes shows resistance is polygenic and evolves from standing genetic variation. Using a CIDER-seq pipeline, we show that herbicide-resistant (HR) and herbicide-sensitive (HS) F3 plants from these F2 seed families as well as the parent populations they were derived from carry extra-chromosomal circular DNA (eccDNA). We identify the similarities and differences in the coding structures within and between resistant and sensitive populations. Although the numbers and size of detected eccDNAs varied between the populations, comparisons between the HR and HS blackgrass populations identified shared and unique coding content, predicted genes, and functional protein domains. These include genes related to herbicide detoxification such as Cytochrome P450s, ATP-binding cassette transporters, and glutathione transferases including AmGSTF1. eccDNA content was mapped to the A. myosuroides reference genome, revealing genomic regions at the distal end of chromosome 5 and the near center of chromosomes 1 and 7 as regions with a high number of mapped eccDNA gene density. Mapping to 15 known herbicide-resistant QTL regions showed that the eccDNA coding sequences matched twelve, with four QTL matching HS coding sequences; only one region contained HR coding sequences. These findings establish that, like other pernicious weeds, blackgrass has eccDNAs that contain homologs of chromosomal genes, and these may contribute genetic heterogeneity and evolutionary innovation to rapidly adapt to abiotic stresses, including herbicide treatment.
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Affiliation(s)
- Wangfang Fu
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
| | - Dana R. MacGregor
- Rothamsted Research, Protecting Crops and the Environment, Harpenden, Hertfordshire AL5 2JQ, UK; (D.R.M.); (D.C.)
| | - David Comont
- Rothamsted Research, Protecting Crops and the Environment, Harpenden, Hertfordshire AL5 2JQ, UK; (D.R.M.); (D.C.)
| | - Christopher A. Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
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30
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Mu Q, Chai R, Pang B, Yang Y, Liu H, Zhao Z, Bao Z, Song D, Zhu Z, Yan M, Jiang B, Mo Z, Tang J, Sa JK, Cho HJ, Chang Y, Chan KHY, Loi DSC, Tam SST, Chan AKY, Wu AR, Liu Z, Poon WS, Ng HK, Chan DTM, Iavarone A, Nam DH, Jiang T, Wang J. Identifying predictors of glioma evolution from longitudinal sequencing. Sci Transl Med 2023; 15:eadh4181. [PMID: 37792958 DOI: 10.1126/scitranslmed.adh4181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 09/01/2023] [Indexed: 10/06/2023]
Abstract
Clonal evolution drives cancer progression and therapeutic resistance. Recent studies have revealed divergent longitudinal trajectories in gliomas, but early molecular features steering posttreatment cancer evolution remain unclear. Here, we collected sequencing and clinical data of initial-recurrent tumor pairs from 544 adult diffuse gliomas and performed multivariate analysis to identify early molecular predictors of tumor evolution in three diffuse glioma subtypes. We found that CDKN2A deletion at initial diagnosis preceded tumor necrosis and microvascular proliferation that occur at later stages of IDH-mutant glioma. Ki67 expression at diagnosis was positively correlated with acquiring hypermutation at recurrence in the IDH-wild-type glioma. In all glioma subtypes, MYC gain or MYC-target activation at diagnosis was associated with treatment-induced hypermutation at recurrence. To predict glioma evolution, we constructed CELLO2 (Cancer EvoLution for LOngitudinal data version 2), a machine learning model integrating features at diagnosis to forecast hypermutation and progression after treatment. CELLO2 successfully stratified patients into subgroups with distinct prognoses and identified a high-risk patient group featured by MYC gain with worse post-progression survival, from the low-grade IDH-mutant-noncodel subtype. We then performed chronic temozolomide-induction experiments in glioma cell lines and isogenic patient-derived gliomaspheres and demonstrated that MYC drives temozolomide resistance by promoting hypermutation. Mechanistically, we demonstrated that, by binding to open chromatin and transcriptionally active genomic regions, c-MYC increases the vulnerability of key mismatch repair genes to treatment-induced mutagenesis, thus triggering hypermutation. This study reveals early predictors of cancer evolution under therapy and provides a resource for precision oncology targeting cancer dynamics in diffuse gliomas.
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Affiliation(s)
- Quanhua Mu
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
- SIAT-HKUST Joint Laboratory of Cell Evolution and Digital Health, Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen, Guangdong 518045, China
| | - Ruichao Chai
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Bo Pang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Yingxi Yang
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
| | - Hanjie Liu
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Zheng Zhao
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Zhaoshi Bao
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Dong Song
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
| | - Zhihan Zhu
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
| | - Mengli Yan
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
| | - Biaobin Jiang
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
| | - Zongchao Mo
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
| | - Jihong Tang
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
| | - Jason K Sa
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul 06351, Korea
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Korea
| | - Hee Jin Cho
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul 06351, Korea
| | - Yuzhou Chang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Kaitlin Hao Yi Chan
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
| | - Danson Shek Chun Loi
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
| | - Sindy Sing Ting Tam
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
| | - Aden Ka Yin Chan
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, SAR 999077, China
| | - Angela Ruohao Wu
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
| | - Zhaoqi Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Wai Sang Poon
- CUHK Otto Wong Brain Tumour Centre, Department of Surgery, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Ho Keung Ng
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, SAR 999077, China
| | - Danny Tat Ming Chan
- CUHK Otto Wong Brain Tumour Centre, Department of Surgery, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Antonio Iavarone
- Department of Neurological Surgery, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Do-Hyun Nam
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul 06351, Korea
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 110745, Korea
- Department of Health Science and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University School of Medicine, Seoul 110745, Korea
- Chinese Glioma Genome Atlas (CGGA) and Asian Glioma Genome Atlas (AGGA) Research Networks
| | - Tao Jiang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
- Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- Chinese Glioma Genome Atlas (CGGA) and Asian Glioma Genome Atlas (AGGA) Research Networks
- Research Unit of Accurate Diagnosis, Treatment, and Translational Medicine of Brain Tumors, Chinese Academy of Medical Sciences, Beijing 100070, China
| | - Jiguang Wang
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, SAR 999077, China
- SIAT-HKUST Joint Laboratory of Cell Evolution and Digital Health, Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen, Guangdong 518045, China
- Chinese Glioma Genome Atlas (CGGA) and Asian Glioma Genome Atlas (AGGA) Research Networks
- Hong Kong Center for Neurodegenerative Diseases, InnoHK, Hong Kong, SAR 999077, China
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31
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [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).
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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
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32
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Li C, Chen L, Pan G, Zhang W, Li SC. Deciphering complex breakage-fusion-bridge genome rearrangements with Ambigram. Nat Commun 2023; 14:5528. [PMID: 37684230 PMCID: PMC10491683 DOI: 10.1038/s41467-023-41259-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: 10/13/2022] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Breakage-fusion-bridge (BFB) is a complex rearrangement that leads to tumor malignancy. Existing models for detecting BFBs rely on the ideal BFB hypothesis, ruling out the possibility of BFBs entangled with other structural variations, that is, complex BFBs. We propose an algorithm Ambigram to identify complex BFB and reconstruct the rearranged structure of the local genome during the cancer subclone evolution process. Ambigram handles data from short, linked, long, and single-cell sequences, and optical mapping technologies. Ambigram successfully deciphers the gold- or silver-standard complex BFBs against the state-of-the-art in multiple cancers. Ambigram dissects the intratumor heterogeneity of complex BFB events with single-cell reads from melanoma and gastric cancer. Furthermore, applying Ambigram to liver and cervical cancer data suggests that the BFB mechanism may mediate oncovirus integrations. BFB also exists in noncancer genomics. Investigating the complete human genome reference with Ambigram suggests that the BFB mechanism may be involved in two genome reorganizations of Homo Sapiens during evolution. Moreover, Ambigram discovers the signals of recurrent foldback inversions and complex BFBs in whole genome data from the 1000 genome project, and congenital heart diseases, respectively.
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Affiliation(s)
- Chaohui Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Lingxi Chen
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Guangze Pan
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Wenqian Zhang
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, China.
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33
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Luo X, Zhang L, Cui J, An Q, Li H, Zhang Z, Sun G, Huang W, Li Y, Li C, Jia W, Zou L, Zhao G, Xiao F. Small extrachromosomal circular DNAs as biomarkers for multi-cancer diagnosis and monitoring. Clin Transl Med 2023; 13:e1393. [PMID: 37649244 PMCID: PMC10468585 DOI: 10.1002/ctm2.1393] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Small extrachromosomal circular DNAs (eccDNAs) have the potential to be cancer biomarkers. However, the formation mechanisms and functions of small eccDNAs selected in carcinogenesis are not clear, and whether the small eccDNA profile in the plasma of cancer patients represents that in cancer tissues remains to be elucidated. METHODS A novel sequencing workflow based on the nanopore sequencing platform was used to sequence naturally existing full-length small eccDNAs in tissues and plasma collected from 25 cancer patients (including prostate cancer, hepatocellular carcinoma and colorectal cancer), and from an independent validation cohort (including 7 cancer plasma and 14 healthy plasma). RESULTS Compared with those in non-cancer tissues, small eccDNAs detected in cancer tissues had a significantly larger number and size (P = 0.040 and 2.2e-16, respectively), along with more even distribution and different formation mechanisms. Although small eccDNAs had different general characteristics and genomic annotation between cancer tissues and the paired plasma, they had similar formation mechanisms and cancer-related functions. Small eccDNAs originated from some specific genes had great multi-cancer diagnostic value in tissues (AUC ≥ 0.8) and plasma (AUC > 0.9), especially increasing the accuracy of multi-cancer prediction of CEA/CA19-9 levels. The high multi-cancer diagnostic value of small eccDNAs originated from ALK&ETV6 could be extrapolated from tissues (AUC = 0.804) to plasma and showed high positive predictive value (100%) and negative predictive value (82.35%) in a validation cohort. CONCLUSIONS As independent and stable circular DNA molecules, small eccDNAs in both tissues and plasma can be used as ideal biomarkers for cost-effective multi-cancer diagnosis and monitoring.
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Affiliation(s)
- Xuanmei Luo
- Peking University Fifth School of Clinical MedicineBeijing HospitalNational Center of GerontologyBeijingChina
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Lili Zhang
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Jian Cui
- Department of General SurgeryBeijing HospitalBeijingChina
| | - Qi An
- Department of General SurgeryBeijing HospitalBeijingChina
| | - Hexin Li
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Zaifeng Zhang
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Gaoyuan Sun
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Wei Huang
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Yifei Li
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Chang Li
- Peking University Fifth School of Clinical MedicineBeijing HospitalNational Center of GerontologyBeijingChina
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Wenzhuo Jia
- Department of General SurgeryBeijing HospitalBeijingChina
- National Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Lihui Zou
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Gang Zhao
- Department of General SurgeryBeijing HospitalBeijingChina
- National Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Fei Xiao
- Peking University Fifth School of Clinical MedicineBeijing HospitalNational Center of GerontologyBeijingChina
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
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34
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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.
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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
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35
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Chang L, Deng E, Wang J, Zhou W, Ao J, Liu R, Su D, Fan X. Single-cell third-generation sequencing-based multi-omics uncovers gene expression changes governed by ecDNA and structural variants in cancer cells. Clin Transl Med 2023; 13:e1351. [PMID: 37517066 PMCID: PMC10387328 DOI: 10.1002/ctm2.1351] [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: 02/24/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 08/01/2023] Open
Abstract
BACKGROUND Cancer cells often exhibit large-scale genomic variations, such as circular extrachromosomal DNA (ecDNA) and structural variants (SVs), which have been highly correlated with the initiation and progression of cancer. Currently, no adequate method exists to unveil how these variations regulate gene expression in heterogeneous cancer cell populations at a single-cell resolution. METHODS Here, we developed a single-cell multi-omics sequencing method, scGTP-seq, to analyse ecDNA and SVs using long-read sequencing technologies. RESULTS AND CONCLUSIONS We demonstrated that our method can efficiently detect ecDNA and SVs and illustrated how these variations affect transcriptomic changes in various cell lines. Finally, we applied and validated this method in a clinical sample of hepatocellular carcinoma (HCC), demonstrating a feasible way to monitor the evolution of ecDNA and SVs during cancer progression.
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Affiliation(s)
- Lei Chang
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Innovation centre for Advanced Interdisciplinary MedicineThe Fifth Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
- Present address:
Department of Cellular and Molecular MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Enze Deng
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
| | - Jun Wang
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
| | - Wei Zhou
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
| | - Jian Ao
- Innovation centre for Advanced Interdisciplinary MedicineThe Fifth Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
| | - Rong Liu
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
| | - Dan Su
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
- The Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouGuangdong ProvinceP. R. China
| | - Xiaoying Fan
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Innovation centre for Advanced Interdisciplinary MedicineThe Fifth Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
- The Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouGuangdong ProvinceP. R. China
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36
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Hung KL, Jones MG, Wong ITL, Lange JT, Luebeck J, Scanu E, He BJ, Brückner L, Li R, González RC, Schmargon R, Dörr JR, Belk JA, Bafna V, Werner B, Huang W, Henssen AG, Mischel PS, Chang HY. Coordinated inheritance of extrachromosomal DNA species in human cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.18.549597. [PMID: 37503111 PMCID: PMC10371175 DOI: 10.1101/2023.07.18.549597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The chromosomal theory of inheritance has dominated human genetics, including cancer genetics. Genes on the same chromosome segregate together while genes on different chromosomes assort independently, providing a fundamental tenet of Mendelian inheritance. Extrachromosomal DNA (ecDNA) is a frequent event in cancer that drives oncogene amplification, dysregulated gene expression and intratumoral heterogeneity, including through random segregation during cell division. Distinct ecDNA sequences, herein termed ecDNA species, can co-exist to facilitate intermolecular cooperation in cancer cells. However, how multiple ecDNA species within a tumor cell are assorted and maintained across somatic cell generations to drive cancer cell evolution is not known. Here we show that cooperative ecDNA species can be coordinately inherited through mitotic co-segregation. Imaging and single-cell analyses show that multiple ecDNAs encoding distinct oncogenes co-occur and are correlated in copy number in human cancer cells. EcDNA species are coordinately segregated asymmetrically during mitosis, resulting in daughter cells with simultaneous copy number gains in multiple ecDNA species prior to any selection. Computational modeling reveals the quantitative principles of ecDNA co-segregation and co-selection, predicting their observed distributions in cancer cells. Finally, we show that coordinated inheritance of ecDNAs enables co-amplification of specialized ecDNAs containing only enhancer elements and guides therapeutic strategies to jointly deplete cooperating ecDNA oncogenes. Coordinated inheritance of ecDNAs confers stability to oncogene cooperation and novel gene regulatory circuits, allowing winning combinations of epigenetic states to be transmitted across cell generations.
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Affiliation(s)
- King L. Hung
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Matthew G. Jones
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Ivy Tsz-Lo Wong
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Joshua T. Lange
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Jens Luebeck
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Elisa Scanu
- Department of Mathematics, Queen Mary University of London, London, UK
| | - Britney Jiayu He
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Lotte Brückner
- Max-Delbrück-Centrum für Molekulare Medizin (BIMSB/BIH), Berlin, Germany
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité—Universitätsmedizin Berlin, Lindenberger Weg 80, 13125, Berlin, Germany
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Rocío Chamorro González
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité—Universitätsmedizin Berlin, Lindenberger Weg 80, 13125, Berlin, Germany
- Department of Pediatric Oncology/Hematology, Charité—Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Rachel Schmargon
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité—Universitätsmedizin Berlin, Lindenberger Weg 80, 13125, Berlin, Germany
- Department of Pediatric Oncology/Hematology, Charité—Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Jan R. Dörr
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité—Universitätsmedizin Berlin, Lindenberger Weg 80, 13125, Berlin, Germany
- Department of Pediatric Oncology/Hematology, Charité—Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Julia A. Belk
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Benjamin Werner
- Evolutionary Dynamics Group, Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Weini Huang
- Department of Mathematics, Queen Mary University of London, London, UK
- Group of Theoretical Biology, The State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, Guangzhou, China
| | - Anton G. Henssen
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité—Universitätsmedizin Berlin, Lindenberger Weg 80, 13125, Berlin, Germany
- Department of Pediatric Oncology/Hematology, Charité—Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center DKFZ, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Berlin Institute of Health, Anna-Louisa-Karsch-Str. 2, 10178, Berlin, Germany
| | - Paul S. Mischel
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
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37
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Lin M, Chen Y, Xia S, He Z, Yu X, Huang L, Lin S, Liang B, Huang Z, Mei S, Liu D, Zheng L, Luo Y. Integrative profiling of extrachromosomal circular DNA in placenta and maternal plasma provides insights into the biology of fetal growth restriction and reveals potential biomarkers. Front Genet 2023; 14:1128082. [PMID: 37476414 PMCID: PMC10354665 DOI: 10.3389/fgene.2023.1128082] [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: 12/20/2022] [Accepted: 02/24/2023] [Indexed: 07/22/2023] Open
Abstract
Introduction: Fetal growth restriction (FGR) is a placenta-mediated pregnancy complication that predisposes fetuses to perinatal complications. Maternal plasma cell-free DNA harbors DNA originating from placental trophoblasts, which is promising for the prenatal diagnosis and prediction of pregnancy complications. Extrachromosomal circular DNA (eccDNA) is emerging as an ideal biomarker and target for several diseases. Methods: We utilized eccDNA sequencing and bioinformatic pipeline to investigate the characteristics and associations of eccDNA in placenta and maternal plasma, the role of placental eccDNA in the pathogenesis of FGR, and potential plasma eccDNA biomarkers of FGR. Results: Using our bioinformatics pipelines, we identified multi-chromosomal-fragment and single-fragment eccDNA in placenta, but almost exclusively single-fragment eccDNA in maternal plasma. Relative to that in plasma, eccDNA in placenta was larger and substantially more abundant in exons, untranslated regions, promoters, repetitive elements [short interspersed nuclear elements (SINEs)/Alu, SINEs/mammalian-wide interspersed repeats, long terminal repeats/endogenous retrovirus-like elements, and single recognition particle RNA], and transcription factor binding motifs. Placental multi-chromosomal-fragment eccDNA was enriched in confident enhancer regions predicted to pertain to genes in apoptosis, energy, cell growth, and autophagy pathways. Placental eccDNA-associated genes whose abundance differed between the FGR and control groups were associated with immunity-related gene ontology (GO) terms. The combined analysis of plasma and placental eccDNA-associated genes in the FGR and control groups led to the identification of potential biomarkers that were assigned to the GO terms of the epigenetic regulation of gene expression and nutrient-related processes, respectively. Conclusion: Together, our results highlight links between placenta functions and multi-chromosomal-fragment and single-fragment eccDNA. The integrative analysis of placental and plasma eccDNA confirmed the potential of these molecules as disease-specific biomarkers of FGR.
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Affiliation(s)
- Minhuan Lin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yiqing Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shuting Xia
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhiming He
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xuegao Yu
- Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Linhuan Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shaobin Lin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Binrun Liang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ziliang Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shiqiang Mei
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Dong Liu
- Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lingling Zheng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yanmin Luo
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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38
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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.
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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
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Choudhuri SP, Girard L, Lim JYS, Wise JF, Freitas B, Yang D, Wong E, Hamilton S, Chien VD, Gilbreath C, Zhong J, Phat S, Myers DT, Christensen CL, Stanzione M, Wong KK, Farago AF, Meador CB, Dyson NJ, Lawrence MS, Wu S, Drapkin BJ. Acquired Cross-resistance in Small Cell Lung Cancer due to Extrachromosomal DNA Amplification of MYC paralogs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.23.546278. [PMID: 37425738 PMCID: PMC10327110 DOI: 10.1101/2023.06.23.546278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Small cell lung cancer (SCLC) presents as a highly chemosensitive malignancy but acquires cross-resistance after relapse. This transformation is nearly inevitable in patients but has been difficult to capture in laboratory models. Here we present a pre-clinical system that recapitulates acquired cross-resistance in SCLC, developed from 51 patient-derived xenografts (PDXs). Each model was tested for in vivo sensitivity to three clinical regimens: cisplatin plus etoposide, olaparib plus temozolomide, and topotecan. These functional profiles captured hallmark clinical features, such as the emergence of treatment-refractory disease after early relapse. Serially derived PDX models from the same patient revealed that cross-resistance was acquired through a MYC amplification on extrachromosomal DNA (ecDNA). Genomic and transcriptional profiles of the full PDX panel revealed that this was not unique to one patient, as MYC paralog amplifications on ecDNAs were recurrent among cross-resistant models derived from patients after relapse. We conclude that ecDNAs with MYC paralogs are recurrent drivers of cross-resistance in SCLC. SIGNIFICANCE SCLC is initially chemosensitive, but acquired cross-resistance renders this disease refractory to further treatment and ultimately fatal. The genomic drivers of this transformation are unknown. We use a population of PDX models to discover that amplifications of MYC paralogs on ecDNA are recurrent drivers of acquired cross-resistance in SCLC.
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40
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Jiang X, Pan X, Li W, Han P, Yu J, Li J, Zhang H, Lv W, Zhang Y, He Y, Xiang X. Genome-wide characterization of extrachromosomal circular DNA in gastric cancer and its potential role in carcinogenesis and cancer progression. Cell Mol Life Sci 2023; 80:191. [PMID: 37369919 DOI: 10.1007/s00018-023-04838-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 05/03/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023]
Abstract
Extrachromosomal circular DNAs (eccDNAs) carrying random genomic segments are broadly found across different cancer types, but their molecular functions and impact in gastric cancer (GC) are rarely known. In this study, we aimed to investigate the potential role of eccDNA in GC. Using the Circle-seq strategy, we observed the eccDNA abundance in gastric cancer tissues (GCT) was aberrantly higher than that of normal adjacent tissues (NAT). The high abundance of eccDNAs carrying oncogene-segments in GCT may represent the DNA damage products of amplified oncogenes. Analysis of GCT over-represented eccDNA carrying enhancer (eccEnhancer) based on data from FANTOM5 project combined with TCGA database suggested the GC over-represented eccEnhancers may contribute to development of GC. GC over-represented eccDNAs carrying pre-miRNA (eccMIR) were enriched to multiple cancer-relevant signal pathways by KEGG analysis. We then synthesized the top six GC over-represented eccMIRs and found four of them enabled high expression of miRNAs and down-regulation of miRNA-target genes in MGC803 cells. Furthermore, we observed the inheritance of GC over-represented eccMIRs benefited host cell proliferation and promoted the aggressive features of host cells. Altogether, this study revealed the GC over-represented eccDNAs carrying functional genomic segments were related to the carcinogenesis of GC and presented the capability to facilitate cancer progression, suggesting the cancerous eccDNAs may serve as a dynamic reservoir for genome plasticity and rapid adaptive evolution of cancer. Therefore, blocking the pathways for eccDNAs generation may provide a novel therapeutic strategy for the treatment of gastric cancer.
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Affiliation(s)
- Xianming Jiang
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, Guangdong, China
| | - Xiaoguang Pan
- Department of Biology, University of Copenhagen, 2200, Copenhagen, Denmark
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, Shandong, China
| | - Wenchao Li
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, Guangdong, China
| | - Peng Han
- Department of Biology, University of Copenhagen, 2200, Copenhagen, Denmark
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, Shandong, China
| | - Jiaying Yu
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, Guangdong, China
| | - Jing Li
- College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shanxi, China
| | - Haoran Zhang
- College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, Shanxi, China
| | - Wei Lv
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, 266555, Shandong, China
- College of Life Sciences, University of Chinese Academy of Science, Beijing, 100049, China
| | - Ying Zhang
- Tomas Lindahl Nobel Laureate Laboratory, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China.
| | - Yulong He
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, Guangdong, China.
| | - Xi Xiang
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, Guangdong, China.
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41
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Pradella D, Zhang M, Gao R, Yao MA, Gluchowska KM, Florez YC, Mishra T, Rocca GL, Weigl M, Jiao Z, Nguyen HHM, Grimm F, Lisi M, Mastroleo C, Chen K, Luebeck J, Bafna V, Antonescu CR, Ventura A. Immortalization and transformation of primary cells mediated by engineered ecDNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.25.546239. [PMID: 37425909 PMCID: PMC10327150 DOI: 10.1101/2023.06.25.546239] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Focal gene amplifications are among the most common cancer-associated mutations, but their evolution and contribution to tumorigenesis have proven challenging to recapitulate in primary cells and model organisms. Here we describe a general approach to engineer large (>1 Mbp) focal amplifications mediated by extrachromosomal circular DNAs (ecDNAs, also known as "double minutes") in a spatiotemporally controlled manner in cancer cell lines and in primary cells derived from genetically engineered mice. With this strategy, ecDNA formation can be coupled with expression of fluorescent reporters or other selectable markers to enable the identification and tracking of ecDNA-containing cells. We demonstrate the feasibility of this approach by engineering MDM2-containing ecDNAs in near-diploid human cells, showing that GFP expression can be used to track ecDNA dynamics under physiological conditions or in the presence of specific selective pressures. We also apply this approach to generate mice harboring inducible Myc - and Mdm2 -containing ecDNAs analogous to those spontaneously occurring in human cancers. We show that the engineered ecDNAs rapidly accumulate in primary cells derived from these animals, promoting proliferation, immortalization, and transformation.
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42
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Saito-Adachi M, Hama N, Totoki Y, Nakamura H, Arai Y, Hosoda F, Rokutan H, Yachida S, Kato M, Fukagawa A, Shibata T. Oncogenic structural aberration landscape in gastric cancer genomes. Nat Commun 2023; 14:3688. [PMID: 37349325 PMCID: PMC10287692 DOI: 10.1038/s41467-023-39263-1] [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: 03/09/2022] [Accepted: 06/05/2023] [Indexed: 06/24/2023] Open
Abstract
Structural variants (SVs) are responsible for driver events in gastric cancer (GC); however, their patterns and processes remain poorly understood. Here, we examine 170 GC whole genomes to unravel the oncogenic structural aberration landscape in GC genomes and identify six rearrangement signatures (RSs). Non-random combinations of RSs elucidate distinctive GC subtypes comprising one or a few dominant RS that are associated with specific driver events (BRCA1/2 defects, mismatch repair deficiency, and TP53 mutation) and epidemiological backgrounds. Twenty-seven SV hotspots are identified as GC driver candidates. SV hotspots frequently constitute complexly clustered SVs involved in driver gene amplification, such as ERBB2, CCNE1, and FGFR2. Further deconstruction of the locally clustered SVs uncovers amplicon-generating profiles characterized by super-large SVs and intensive segmental amplifications, contributing to the extensive amplification of GC oncogenes. Comprehensive analyses using adjusted SV allele frequencies indicate the significant involvement of extra-chromosomal DNA in processes linked to specific RSs.
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Affiliation(s)
- Mihoko Saito-Adachi
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Natsuko Hama
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasushi Totoki
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hiromi Nakamura
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasuhito Arai
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Fumie Hosoda
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hirofumi Rokutan
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shinichi Yachida
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Mamoru Kato
- Division of Bioinformatics, National Cancer Center Research Institute, Tokyo, Japan
| | - Akihiko Fukagawa
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan.
- Laboratory of Molecular Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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43
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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.
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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.)
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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.
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45
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Yang M, Zhang S, Jiang R, Chen S, Huang M. Circlehunter: a tool to identify extrachromosomal circular DNA from ATAC-Seq data. Oncogenesis 2023; 12:28. [PMID: 37217468 DOI: 10.1038/s41389-023-00476-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/24/2023] Open
Abstract
In cancer, extrachromosomal circular DNA (ecDNA), or megabase-pair amplified circular DNA, plays an essential role in intercellular heterogeneity and tumor cell revolution because of its non-Mendelian inheritance. We developed circlehunter ( https://github.com/suda-huanglab/circlehunter ), a tool for identifying ecDNA from ATAC-Seq data using the enhanced chromatin accessibility of ecDNA. Using simulated data, we showed that circlehunter has an F1 score of 0.93 at 30× local depth and read lengths as short as 35 bp. Based on 1312 ecDNAs predicted from 94 publicly available datasets of ATAC-Seq assays, we found 37 oncogenes contained in these ecDNAs with amplification characteristics. In small cell lung cancer cell lines, ecDNA containing MYC leads to amplification of MYC and cis-regulates the expression of NEUROD1, resulting in an expression pattern consistent with the NEUROD1 high expression subtype and sensitive to Aurora kinase inhibitors. This showcases that circlehunter could serve as a valuable pipeline for the investigation of tumorigenesis.
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Affiliation(s)
- Manqiu Yang
- School of Biology and Basic Medical Sciences, Soochow University, 215123, Suzhou, China
| | - Shufan Zhang
- School of Biology and Basic Medical Sciences, Soochow University, 215123, Suzhou, China
| | - Rong Jiang
- School of Biology and Basic Medical Sciences, Soochow University, 215123, Suzhou, China
| | - Shaomu Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, 215006, Suzhou, China.
| | - Moli Huang
- School of Biology and Basic Medical Sciences, Soochow University, 215123, Suzhou, China.
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46
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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: 1] [Impact Index Per Article: 1.0] [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.
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47
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Raviram R, Raman A, Preissl S, Ning J, Wu S, Koga T, Zhang K, Brennan CW, Zhu C, Luebeck J, Van Deynze K, Han JY, Hou X, Ye Z, Mischel AK, Li YE, Fang R, Baback T, Mugford J, Han CZ, Glass CK, Barr CL, Mischel PS, Bafna V, Escoubet L, Ren B, Chen CC. Integrated analysis of single-cell chromatin state and transcriptome identified common vulnerability despite glioblastoma heterogeneity. Proc Natl Acad Sci U S A 2023; 120:e2210991120. [PMID: 37155843 PMCID: PMC10194019 DOI: 10.1073/pnas.2210991120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 03/09/2023] [Indexed: 05/10/2023] Open
Abstract
In 2021, the World Health Organization reclassified glioblastoma, the most common form of adult brain cancer, into isocitrate dehydrogenase (IDH)-wild-type glioblastomas and grade IV IDH mutant (G4 IDHm) astrocytomas. For both tumor types, intratumoral heterogeneity is a key contributor to therapeutic failure. To better define this heterogeneity, genome-wide chromatin accessibility and transcription profiles of clinical samples of glioblastomas and G4 IDHm astrocytomas were analyzed at single-cell resolution. These profiles afforded resolution of intratumoral genetic heterogeneity, including delineation of cell-to-cell variations in distinct cell states, focal gene amplifications, as well as extrachromosomal circular DNAs. Despite differences in IDH mutation status and significant intratumoral heterogeneity, the profiled tumor cells shared a common chromatin structure defined by open regions enriched for nuclear factor 1 transcription factors (NFIA and NFIB). Silencing of NFIA or NFIB suppressed in vitro and in vivo growths of patient-derived glioblastomas and G4 IDHm astrocytoma models. These findings suggest that despite distinct genotypes and cell states, glioblastoma/G4 astrocytoma cells share dependency on core transcriptional programs, yielding an attractive platform for addressing therapeutic challenges associated with intratumoral heterogeneity.
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Affiliation(s)
- Ramya Raviram
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Anugraha Raman
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego, La Jolla, CA92093
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jiangfang Ning
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN55455
| | - Shaoping Wu
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN55455
| | - Tomoyuki Koga
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN55455
| | - Kai Zhang
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Cameron W. Brennan
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Chenxu Zhu
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Jens Luebeck
- Department of Computer Science and Engineering, Halicioglu Data Science Institute, University of California San Diego, La Jolla, CA92093
| | - Kinsey Van Deynze
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Jee Yun Han
- Center for Epigenomics, University of California San Diego, La Jolla, CA92093
| | - Xiaomeng Hou
- Center for Epigenomics, University of California San Diego, La Jolla, CA92093
| | - Zhen Ye
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Anna K. Mischel
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Yang Eric Li
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Rongxin Fang
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
| | - Tomas Baback
- Department of Computer Science and Engineering, Biomedical Sciences Graduate Program, San Diego, CA92121
| | - Joshua Mugford
- Department of Computer Science and Engineering, Biomedical Sciences Graduate Program, San Diego, CA92121
| | - Claudia Z. Han
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
- Department of Medicine, University of California San Diego, La Jolla, CA92093
| | - Cathy L. Barr
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Division of Experimental & Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, ONM5T 0S8, Canada
- Department of Psychiatry, University of Toronto, Toronto, ONM5T 0S8, Canada
- Department of Physiology, University of Toronto, Toronto, ONM5T 0S8, Canada
| | - Paul S. Mischel
- Department of Pathology, Stanford University, Stanford, CA94305
| | - Vineet Bafna
- Department of Computer Science and Engineering, Halicioglu Data Science Institute, University of California San Diego, La Jolla, CA92093
| | - Laure Escoubet
- Department of Computer Science and Engineering, Biomedical Sciences Graduate Program, San Diego, CA92121
| | - Bing Ren
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA92093
- Center for Epigenomics, University of California San Diego, La Jolla, CA92093
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Clark C. Chen
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN55455
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48
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Chamorro González R, Conrad T, Stöber MC, Xu R, Giurgiu M, Rodriguez-Fos E, Kasack K, Brückner L, van Leen E, Helmsauer K, Dorado Garcia H, Stefanova ME, Hung KL, Bei Y, Schmelz K, Lodrini M, Mundlos S, Chang HY, Deubzer HE, Sauer S, Eggert A, Schulte JH, Schwarz RF, Haase K, Koche RP, Henssen AG. Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells. Nat Genet 2023; 55:880-890. [PMID: 37142849 PMCID: PMC10181933 DOI: 10.1038/s41588-023-01386-y] [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: 12/20/2021] [Accepted: 03/28/2023] [Indexed: 05/06/2023]
Abstract
Extrachromosomal DNAs (ecDNAs) are common in cancer, but many questions about their origin, structural dynamics and impact on intratumor heterogeneity are still unresolved. Here we describe single-cell extrachromosomal circular DNA and transcriptome sequencing (scEC&T-seq), a method for parallel sequencing of circular DNAs and full-length mRNA from single cells. By applying scEC&T-seq to cancer cells, we describe intercellular differences in ecDNA content while investigating their structural heterogeneity and transcriptional impact. Oncogene-containing ecDNAs were clonally present in cancer cells and drove intercellular oncogene expression differences. In contrast, other small circular DNAs were exclusive to individual cells, indicating differences in their selection and propagation. Intercellular differences in ecDNA structure pointed to circular recombination as a mechanism of ecDNA evolution. These results demonstrate scEC&T-seq as an approach to systematically characterize both small and large circular DNA in cancer cells, which will facilitate the analysis of these DNA elements in cancer and beyond.
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Affiliation(s)
- Rocío Chamorro González
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Thomas Conrad
- Genomics Technology Platform, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Maja C Stöber
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- Faculty of Life Science, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Robin Xu
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Mădălina Giurgiu
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
- Freie Universität Berlin, Berlin, Germany
| | - Elias Rodriguez-Fos
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Katharina Kasack
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses IZI-BB, Potsdam, Germany
| | - Lotte Brückner
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Eric van Leen
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Konstantin Helmsauer
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Heathcliff Dorado Garcia
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Maria E Stefanova
- RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - King L Hung
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Yi Bei
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
| | - Karin Schmelz
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marco Lodrini
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Stefan Mundlos
- RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Hedwig E Deubzer
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium, partner site Berlin, and German Cancer Research Center, Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Sascha Sauer
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium, partner site Berlin, and German Cancer Research Center, Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Johannes H Schulte
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium, partner site Berlin, and German Cancer Research Center, Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Institute for Computational Cancer Biology, Center for Integrated Oncology, Cancer Research Center Cologne Essen Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
| | - Kerstin Haase
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium, partner site Berlin, and German Cancer Research Center, Heidelberg, Germany
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anton G Henssen
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.
- Experimental and Clinical Research Center of the MDC and Charité Berlin, Berlin, Germany.
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.
- German Cancer Consortium, partner site Berlin, and German Cancer Research Center, Heidelberg, Germany.
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49
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Liu S, Dharanipragada P, Lomeli SH, Wang Y, Zhang X, Yang Z, Lim RJ, Dumitras C, Scumpia PO, Dubinett SM, Moriceau G, Johnson DB, Moschos SJ, Lo RS. Multi-organ landscape of therapy-resistant melanoma. Nat Med 2023; 29:1123-1134. [PMID: 37106167 PMCID: PMC10202813 DOI: 10.1038/s41591-023-02304-9] [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: 04/23/2022] [Accepted: 03/14/2023] [Indexed: 04/29/2023]
Abstract
Metastasis and failure of present-day therapies represent the most common causes of mortality in patients with cutaneous melanoma. To identify the underlying genetic and transcriptomic landscapes, in this study we analyzed multi-organ metastases and tumor-adjacent tissues from 11 rapid autopsies after treatment with MAPK inhibitor (MAPKi) and/or immune checkpoint blockade (ICB) and death due to acquired resistance. Either treatment elicits shared genetic alterations that suggest immune-evasive, cross-therapy resistance mechanisms. Large, non-clustered deletions, inversions and inter-chromosomal translocations dominate rearrangements. Analyzing data from separate melanoma cohorts including 345 therapy-naive patients and 35 patients with patient-matched pre-treatment and post-acquired resistance tumor samples, we performed cross-cohort analyses to identify MAPKi and ICB as respective contributors to gene amplifications and deletions enriched in autopsy versus therapy-naive tumors. In the autopsy cohort, private/late mutations and structural variants display shifted mutational and rearrangement signatures, with MAPKi specifically selecting for signatures of defective homologous-recombination, mismatch and base-excision repair. Transcriptomic signatures and crosstalks with tumor-adjacent macroenvironments nominated organ-specific adaptive pathways. An immune-desert, CD8+-macrophage-biased archetype, T-cell exhaustion and type-2 immunity characterized the immune contexture. This multi-organ analysis of therapy-resistant melanoma presents preliminary insights with potential to improve therapeutic strategies.
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Affiliation(s)
- Sixue Liu
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Prashanthi Dharanipragada
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shirley H Lomeli
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yan Wang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Xiao Zhang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Zhentao Yang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Raymond J Lim
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Camelia Dumitras
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Philip O Scumpia
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Dermatology, Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Steve M Dubinett
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Gatien Moriceau
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Douglas B Johnson
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Stergios J Moschos
- Division of Medical Oncology, Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Roger S Lo
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
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50
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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: 17] [Impact Index Per Article: 17.0] [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.
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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
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