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Zwaig M, Baguette A, Hu B, Johnston M, Lakkis H, Nakada EM, Faury D, Juretic N, Ellezam B, Weil AG, Karamchandani J, Majewski J, Blanchette M, Taylor MD, Gallo M, Kleinman CL, Jabado N, Ragoussis J. Detection and genomic analysis of BRAF fusions in Juvenile Pilocytic Astrocytoma through the combination and integration of multi-omic data. BMC Cancer 2022; 22:1297. [PMID: 36503484 PMCID: PMC9743522 DOI: 10.1186/s12885-022-10359-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Juvenile Pilocytic Astrocytomas (JPAs) are one of the most common pediatric brain tumors, and they are driven by aberrant activation of the mitogen-activated protein kinase (MAPK) signaling pathway. RAF-fusions are the most common genetic alterations identified in JPAs, with the prototypical KIAA1549-BRAF fusion leading to loss of BRAF's auto-inhibitory domain and subsequent constitutive kinase activation. JPAs are highly vascular and show pervasive immune infiltration, which can lead to low tumor cell purity in clinical samples. This can result in gene fusions that are difficult to detect with conventional omics approaches including RNA-Seq. METHODS To this effect, we applied RNA-Seq as well as linked-read whole-genome sequencing and in situ Hi-C as new approaches to detect and characterize low-frequency gene fusions at the genomic, transcriptomic and spatial level. RESULTS Integration of these datasets allowed the identification and detailed characterization of two novel BRAF fusion partners, PTPRZ1 and TOP2B, in addition to the canonical fusion with partner KIAA1549. Additionally, our Hi-C datasets enabled investigations of 3D genome architecture in JPAs which showed a high level of correlation in 3D compartment annotations between JPAs compared to other pediatric tumors, and high similarity to normal adult astrocytes. We detected interactions between BRAF and its fusion partners exclusively in tumor samples containing BRAF fusions. CONCLUSIONS We demonstrate the power of integrating multi-omic datasets to identify low frequency fusions and characterize the JPA genome at high resolution. We suggest that linked-reads and Hi-C could be used in clinic for the detection and characterization of JPAs.
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Affiliation(s)
- Melissa Zwaig
- grid.14709.3b0000 0004 1936 8649McGill Genome Centre and Department of Human Genetics, McGill University, Montreal, Canada
| | - Audrey Baguette
- grid.414980.00000 0000 9401 2774Quantitative Life Sciences and Lady Davis Institute for Medical Research, Montreal, Quebec Canada
| | - Bo Hu
- grid.14709.3b0000 0004 1936 8649McGill Genome Centre and Department of Human Genetics, McGill University, Montreal, Canada
| | - Michael Johnston
- grid.22072.350000 0004 1936 7697Alberta Children‘s Hospital Research Institute, Charbonneau Cancer Institute, and Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB Canada
| | - Hussein Lakkis
- grid.414980.00000 0000 9401 2774Department of Human Genetics and Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec Canada
| | - Emily M. Nakada
- grid.63984.300000 0000 9064 4811The Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Damien Faury
- grid.63984.300000 0000 9064 4811The Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Nikoleta Juretic
- grid.63984.300000 0000 9064 4811The Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Benjamin Ellezam
- grid.14848.310000 0001 2292 3357Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, QC, H3T 1C5 Canada
| | - Alexandre G. Weil
- grid.14848.310000 0001 2292 3357Department of Pediatric Neurosurgery, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C5 Canada
| | - Jason Karamchandani
- grid.14709.3b0000 0004 1936 8649Department of Pathology, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4 Canada
| | - Jacek Majewski
- grid.14709.3b0000 0004 1936 8649McGill Genome Centre and Department of Human Genetics, McGill University, Montreal, Canada
| | - Mathieu Blanchette
- grid.14709.3b0000 0004 1936 8649School of Computer Science and McGill Center for Bioinformatics, McGill University, Montréal, Québec Canada
| | - Michael D. Taylor
- grid.42327.300000 0004 0473 9646Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children Research Institute, Toronto, Canada
| | - Marco Gallo
- grid.22072.350000 0004 1936 7697Alberta Children‘s Hospital Research Institute, Charbonneau Cancer Institute, and Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB Canada
| | - Claudia L. Kleinman
- grid.414980.00000 0000 9401 2774Department of Human Genetics and Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec Canada
| | - Nada Jabado
- grid.63984.300000 0000 9064 4811Department of Human Genetics, Department of Pediatrics, and The Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Jiannis Ragoussis
- grid.14709.3b0000 0004 1936 8649McGill Genome Centre and Department of Human Genetics, McGill University, Montreal, Canada
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Wang WJ, Li LY, Cui JW. Chromosome structural variation in tumorigenesis: mechanisms of formation and carcinogenesis. Epigenetics Chromatin 2020; 13:49. [PMID: 33168103 PMCID: PMC7654176 DOI: 10.1186/s13072-020-00371-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/29/2020] [Indexed: 12/23/2022] Open
Abstract
With the rapid development of next-generation sequencing technology, chromosome structural variation has gradually gained increased clinical significance in tumorigenesis. However, the molecular mechanism(s) underlying this structural variation remain poorly understood. A search of the literature shows that a three-dimensional chromatin state plays a vital role in inducing structural variation and in the gene expression profiles in tumorigenesis. Structural variants may result in changes in copy number or deletions of coding sequences, as well as the perturbation of structural chromatin features, especially topological domains, and disruption of interactions between genes and their regulatory elements. This review focuses recent work aiming at elucidating how structural variations develop and misregulate oncogenes and tumor suppressors, to provide general insights into tumor formation mechanisms and to provide potential targets for future anticancer therapies.
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Affiliation(s)
- Wen-Jun Wang
- Cancer Center, The First Hospital of Jilin University, Jilin University, Changchun, 130021 Jilin China
| | - Ling-Yu Li
- Cancer Center, The First Hospital of Jilin University, Jilin University, Changchun, 130021 Jilin China
| | - Jiu-Wei Cui
- Cancer Center, The First Hospital of Jilin University, Jilin University, Changchun, 130021 Jilin China
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Menghi F, Barthel FP, Yadav V, Tang M, Ji B, Tang Z, Carter GW, Ruan Y, Scully R, Verhaak RGW, Jonkers J, Liu ET. The Tandem Duplicator Phenotype Is a Prevalent Genome-Wide Cancer Configuration Driven by Distinct Gene Mutations. Cancer Cell 2018; 34:197-210.e5. [PMID: 30017478 PMCID: PMC6481635 DOI: 10.1016/j.ccell.2018.06.008] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 05/04/2018] [Accepted: 06/14/2018] [Indexed: 12/14/2022]
Abstract
The tandem duplicator phenotype (TDP) is a genome-wide instability configuration primarily observed in breast, ovarian, and endometrial carcinomas. Here, we stratify TDP tumors by classifying their tandem duplications (TDs) into three span intervals, with modal values of 11 kb, 231 kb, and 1.7 Mb, respectively. TDPs with ∼11 kb TDs feature loss of TP53 and BRCA1. TDPs with ∼231 kb and ∼1.7 Mb TDs associate with CCNE1 pathway activation and CDK12 disruptions, respectively. We demonstrate that p53 and BRCA1 conjoint abrogation drives TDP induction by generating short-span TDP mammary tumors in genetically modified mice lacking them. Lastly, we show how TDs in TDP tumors disrupt heterogeneous combinations of tumor suppressors and chromatin topologically associating domains while duplicating oncogenes and super-enhancers.
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Affiliation(s)
- Francesca Menghi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Floris P Barthel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Vinod Yadav
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Ming Tang
- MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bo Ji
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Zhonghui Tang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | | | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Ralph Scully
- Division of Hematology Oncology, Department of Medicine, and Cancer Research Institute, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Jos Jonkers
- Oncode Institute and Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam 1066CX, the Netherlands
| | - Edison T Liu
- The Jackson Laboratory, Bar Harbor, ME 04609, USA.
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5
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Explaining cancer type specific mutations with transcriptomic and epigenomic features in normal tissues. Sci Rep 2018; 8:11456. [PMID: 30061703 PMCID: PMC6065413 DOI: 10.1038/s41598-018-29861-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 07/17/2018] [Indexed: 12/20/2022] Open
Abstract
Most cancer driver genes are involved in generic cellular processes such as DNA repair, cell proliferation and cell adhesion, yet their mutations are often confined to specific cancer types. To resolve this paradox, we explained mutation frequencies of selected genes across tumor types with four features in the corresponding normal tissues from cancer-free subjects: mRNA expression and chromatin accessibility of mutated genes, mRNA expressions of their neighbors in curated pathways and the protein-protein interaction network. Encouragingly, these transcriptomic/epigenomic features in normal tissues were closely associated with mutational/functional characteristics in tumors. First, chromatin accessibility was a necessary but not sufficient condition for frequent mutations. Second, variations of mutation frequencies in selected genes across tissue types were significantly associated with all four features. Third, the genes possessing significant associations between mutation frequency variations and pathway gene expression were enriched with documented cancer genes. We further proposed a novel bivariate gene set enrichment analysis and confirmed that the pathway gene expression was the dominant factor in cancer gene enrichment. These findings shed lights on the functional roles of genes in normal tissues in shaping the mutational landscape during tumor genome evolution.
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The tandem duplicator phenotype as a distinct genomic configuration in cancer. Proc Natl Acad Sci U S A 2016; 113:E2373-82. [PMID: 27071093 DOI: 10.1073/pnas.1520010113] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Next-generation sequencing studies have revealed genome-wide structural variation patterns in cancer, such as chromothripsis and chromoplexy, that do not engage a single discernable driver mutation, and whose clinical relevance is unclear. We devised a robust genomic metric able to identify cancers with a chromotype called tandem duplicator phenotype (TDP) characterized by frequent and distributed tandem duplications (TDs). Enriched only in triple-negative breast cancer (TNBC) and in ovarian, endometrial, and liver cancers, TDP tumors conjointly exhibit tumor protein p53 (TP53) mutations, disruption of breast cancer 1 (BRCA1), and increased expression of DNA replication genes pointing at rereplication in a defective checkpoint environment as a plausible causal mechanism. The resultant TDs in TDP augment global oncogene expression and disrupt tumor suppressor genes. Importantly, the TDP strongly correlates with cisplatin sensitivity in both TNBC cell lines and primary patient-derived xenografts. We conclude that the TDP is a common cancer chromotype that coordinately alters oncogene/tumor suppressor expression with potential as a marker for chemotherapeutic response.
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