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Manjón AG, Manzo SG, Prekovic S, Potgeter L, van Schaik T, Liu NQ, Flach K, Peric-Hupkes D, Joosten S, Teunissen H, Friskes A, Ilic M, Hintzen D, Franceschini-Santos VH, Zwart W, de Wit E, van Steensel B, Medema RH. Perturbations in 3D genome organization can promote acquired drug resistance. Cell Rep 2023; 42:113124. [PMID: 37733591 DOI: 10.1016/j.celrep.2023.113124] [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: 02/18/2021] [Revised: 08/05/2023] [Accepted: 08/25/2023] [Indexed: 09/23/2023] Open
Abstract
Acquired drug resistance is a major problem in the treatment of cancer. hTERT-immortalized, untransformed RPE-1 cells can acquire resistance to Taxol by derepressing the ABCB1 gene, encoding for the multidrug transporter P-gP. Here, we investigate how the ABCB1 gene is derepressed. ABCB1 activation is associated with reduced H3K9 trimethylation, increased H3K27 acetylation, and ABCB1 displacement from the nuclear lamina. While altering DNA methylation and H3K27 methylation had no major impact on ABCB1 expression, nor did it promote resistance, disrupting the nuclear lamina component Lamin B Receptor did promote the acquisition of a Taxol-resistant phenotype in a subset of cells. CRISPRa-mediated gene activation supported the notion that lamina dissociation influences ABCB1 derepression. We propose a model in which nuclear lamina dissociation of a repressed gene allows for its activation, implying that deregulation of the 3D genome topology could play an important role in tumor evolution and the acquisition of drug resistance.
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Affiliation(s)
- Anna G Manjón
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Stefano Giustino Manzo
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | - Stefan Prekovic
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Center for Molecular Medicine, University Medical Center Utrecht and Utrecht University, 3584 CX Utrecht, the Netherlands
| | - Leon Potgeter
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Tom van Schaik
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Ning Qing Liu
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Department of Hematology, Erasmus Medical Center (MC) Cancer Institute, Rotterdam, the Netherlands
| | - Koen Flach
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Daniel Peric-Hupkes
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Stacey Joosten
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Anoek Friskes
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Mila Ilic
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Dorine Hintzen
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Vinícius H Franceschini-Santos
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Wilbert Zwart
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands
| | - Bas van Steensel
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands.
| | - René H Medema
- Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands; Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, the Netherlands.
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2
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Maslova A, Plotnikov V, Nuriddinov M, Gridina M, Fishman V, Krasikova A. Hi-C analysis of genomic contacts revealed karyotype abnormalities in chicken HD3 cell line. BMC Genomics 2023; 24:66. [PMID: 36750787 PMCID: PMC9906895 DOI: 10.1186/s12864-023-09158-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND Karyotype abnormalities are frequent in immortalized continuous cell lines either transformed or derived from primary tumors. Chromosomal rearrangements can cause dramatic changes in gene expression and affect cellular phenotype and behavior during in vitro culture. Structural variations of chromosomes in many continuous mammalian cell lines are well documented, but chromosome aberrations in cell lines from other vertebrate models often remain understudied. The chicken LSCC-HD3 cell line (HD3), generated from erythroid precursors, was used as an avian model for erythroid differentiation and lineage-specific gene expression. However, karyotype abnormalities in the HD3 cell line were not assessed. In the present study, we applied high-throughput chromosome conformation capture to analyze 3D genome organization and to detect chromosome rearrangements in the HD3 cell line. RESULTS We obtained Hi-C maps of genomic interactions for the HD3 cell line and compared A/B compartments and topologically associating domains between HD3 and several other cell types. By analysis of contact patterns in the Hi-C maps of HD3 cells, we identified more than 25 interchromosomal translocations of regions ≥ 200 kb on both micro- and macrochromosomes. We classified most of the observed translocations as unbalanced, leading to the formation of heteromorphic chromosomes. In many cases of microchromosome rearrangements, an entire microchromosome together with other macro- and microchromosomes participated in the emergence of a derivative chromosome, resembling "chromosomal fusions'' between acrocentric microchromosomes. Intrachromosomal inversions, deletions and duplications were also detected in HD3 cells. Several of the identified simple and complex chromosomal rearrangements, such as between GGA2 and GGA1qter; GGA5, GGA4p and GGA7p; GGA4q, GGA6 and GGA19; and duplication of the sex chromosome GGAW, were confirmed by FISH. CONCLUSIONS In the erythroid progenitor HD3 cell line, in contrast to mature and immature erythrocytes, the genome is organized into distinct topologically associating domains. The HD3 cell line has a severely rearranged karyotype with most of the chromosomes engaged in translocations and can be used in studies of genome structure-function relationships. Hi-C proved to be a reliable tool for simultaneous assessment of the spatial genome organization and chromosomal aberrations in karyotypes of birds with a large number of microchromosomes.
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Affiliation(s)
- A. Maslova
- grid.15447.330000 0001 2289 6897Saint Petersburg State University, Saint Petersburg, Russia
| | - V. Plotnikov
- grid.15447.330000 0001 2289 6897Saint Petersburg State University, Saint Petersburg, Russia
| | - M. Nuriddinov
- grid.418953.2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - M. Gridina
- grid.418953.2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - V. Fishman
- grid.418953.2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - A. Krasikova
- grid.15447.330000 0001 2289 6897Saint Petersburg State University, Saint Petersburg, Russia
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3
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Xu Z, Lee DS, Chandran S, Le VT, Bump R, Yasis J, Dallarda S, Marcotte S, Clock B, Haghani N, Cho CY, Akdemir K, Tyndale S, Futreal PA, McVicker G, Wahl GM, Dixon JR. Structural variants drive context-dependent oncogene activation in cancer. Nature 2022; 612:564-572. [PMID: 36477537 PMCID: PMC9810360 DOI: 10.1038/s41586-022-05504-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/01/2022] [Indexed: 12/12/2022]
Abstract
Higher-order chromatin structure is important for the regulation of genes by distal regulatory sequences1,2. Structural variants (SVs) that alter three-dimensional (3D) genome organization can lead to enhancer-promoter rewiring and human disease, particularly in the context of cancer3. However, only a small minority of SVs are associated with altered gene expression4,5, and it remains unclear why certain SVs lead to changes in distal gene expression and others do not. To address these questions, we used a combination of genomic profiling and genome engineering to identify sites of recurrent changes in 3D genome structure in cancer and determine the effects of specific rearrangements on oncogene activation. By analysing Hi-C data from 92 cancer cell lines and patient samples, we identified loci affected by recurrent alterations to 3D genome structure, including oncogenes such as MYC, TERT and CCND1. By using CRISPR-Cas9 genome engineering to generate de novo SVs, we show that oncogene activity can be predicted by using 'activity-by-contact' models that consider partner region chromatin contacts and enhancer activity. However, activity-by-contact models are only predictive of specific subsets of genes in the genome, suggesting that different classes of genes engage in distinct modes of regulation by distal regulatory elements. These results indicate that SVs that alter 3D genome organization are widespread in cancer genomes and begin to illustrate predictive rules for the consequences of SVs on oncogene activation.
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Affiliation(s)
- Zhichao Xu
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA,These authors contributed equally
| | - Dong-Sung Lee
- Department of Life Sciences, University of Seoul, Seoul, South Korea,These authors contributed equally
| | - Sahaana Chandran
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Victoria T. Le
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Rosalind Bump
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Jean Yasis
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Sofia Dallarda
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Samantha Marcotte
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Benjamin Clock
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Nicholas Haghani
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Chae Yun Cho
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Kadir Akdemir
- Department of Genomic Medicine; UT MD Anderson Cancer Center; Houston, TX, 77030; USA
| | - Selene Tyndale
- Integrative Biology Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - P. Andrew Futreal
- Department of Genomic Medicine; UT MD Anderson Cancer Center; Houston, TX, 77030; USA
| | - Graham McVicker
- Integrative Biology Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Geoffrey M. Wahl
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA
| | - Jesse R. Dixon
- Gene Expression Laboratory; Salk Institute for Biological Studies; La Jolla, CA, 92037; USA,Correspondence:
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4
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Abstract
The change in cell state from normal to malignant is driven fundamentally by oncogenic mutations in cooperation with epigenetic alterations of chromatin. These alterations in chromatin can be a consequence of environmental stressors or germline and/or somatic mutations that directly alter the structure of chromatin machinery proteins, their levels, or their regulatory function. These changes can result in an inability of the cell to differentiate along a predefined lineage path, or drive a hyperactive, highly proliferative state with addiction to high levels of transcriptional output. We discuss how these genetic alterations hijack the chromatin machinery for the oncogenic process to reveal unique vulnerabilities and novel targets for cancer therapy.
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Affiliation(s)
- Berkley Gryder
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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5
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Lindsly S, Jia W, Chen H, Liu S, Ronquist S, Chen C, Wen X, Stansbury C, Dotson GA, Ryan C, Rehemtulla A, Omenn GS, Wicha M, Li SC, Muir L, Rajapakse I. Functional organization of the maternal and paternal human 4D Nucleome. iScience 2021; 24:103452. [PMID: 34877507 PMCID: PMC8633971 DOI: 10.1016/j.isci.2021.103452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/16/2021] [Accepted: 11/09/2021] [Indexed: 11/19/2022] Open
Abstract
Every human somatic cell inherits a maternal and a paternal genome, which work together to give rise to cellular phenotypes. However, the allele-specific relationship between gene expression and genome structure through the cell cycle is largely unknown. By integrating haplotype-resolved genome-wide chromosome conformation capture, mature and nascent mRNA, and protein binding data from a B lymphoblastoid cell line, we investigate this relationship both globally and locally. We introduce the maternal and paternal 4D Nucleome, enabling detailed analysis of the mechanisms and dynamics of genome structure and gene function for diploid organisms. Our analyses find significant coordination between allelic expression biases and local genome conformation, and notably absent expression bias in universally essential cell cycle and glycolysis genes. We propose a model in which coordinated biallelic expression reflects prioritized preservation of essential gene sets.
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Affiliation(s)
- Stephen Lindsly
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wenlong Jia
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Haiming Chen
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sijia Liu
- MIT-IBM Watson AI Lab, IBM Research, Cambridge, MA 02142, USA
| | - Scott Ronquist
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Can Chen
- Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xingzhao Wen
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Cooper Stansbury
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gabrielle A. Dotson
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Charles Ryan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alnawaz Rehemtulla
- Department of Hematology/Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gilbert S. Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Human Genetics, and School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Max Wicha
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Hematology/Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Lindsey Muir
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Indika Rajapakse
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA
- Corresponding author
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6
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Zhu Y, Gujar AD, Wong CH, Tjong H, Ngan CY, Gong L, Chen YA, Kim H, Liu J, Li M, Mil-Homens A, Maurya R, Kuhlberg C, Sun F, Yi E, deCarvalho AC, Ruan Y, Verhaak RGW, Wei CL. Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription. Cancer Cell 2021; 39:694-707.e7. [PMID: 33836152 PMCID: PMC8119378 DOI: 10.1016/j.ccell.2021.03.006] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/05/2020] [Accepted: 03/12/2021] [Indexed: 12/13/2022]
Abstract
Extrachromosomal, circular DNA (ecDNA) is emerging as a prevalent yet less characterized oncogenic alteration in cancer genomes. We leverage ChIA-PET and ChIA-Drop chromatin interaction assays to characterize genome-wide ecDNA-mediated chromatin contacts that impact transcriptional programs in cancers. ecDNAs in glioblastoma patient-derived neurosphere and prostate cancer cell cultures are marked by widespread intra-ecDNA and genome-wide chromosomal interactions. ecDNA-chromatin contact foci are characterized by broad and high-level H3K27ac signals converging predominantly on chromosomal genes of increased expression levels. Prostate cancer cells harboring synthetic ecDNA circles composed of characterized enhancers result in the genome-wide activation of chromosomal gene transcription. Deciphering the chromosomal targets of ecDNAs at single-molecule resolution reveals an association with actively expressed oncogenes spatially clustered within ecDNA-directed interaction networks. Our results suggest that ecDNA can function as mobile transcriptional enhancers to promote tumor progression and manifest a potential synthetic aneuploidy mechanism of transcription control in cancer.
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Affiliation(s)
- Yanfen Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Amit D Gujar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Chee-Hong Wong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Harianto Tjong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Chew Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Liang Gong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Yi-An Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Jihe Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Meihong Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Adam Mil-Homens
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Rahul Maurya
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Chris Kuhlberg
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Fanyue Sun
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Eunhee Yi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Ana C deCarvalho
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
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7
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Liu X, Sun Q, Wang Q, Hu C, Chen X, Li H, Czajkowsky DM, Shao Z. Epithelial Cells in 2D and 3D Cultures Exhibit Large Differences in Higher-order Genomic Interactions. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 20:101-109. [PMID: 33631432 PMCID: PMC9510857 DOI: 10.1016/j.gpb.2020.06.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 03/09/2020] [Accepted: 08/09/2020] [Indexed: 02/07/2023]
Abstract
Recent studies have characterized the genomic structures of many eukaryotic cells, often focusing on their relation to gene expression. However, these studies have largely investigated cells grown in 2D cultures, although the transcriptomes of 3D-cultured cells are generally closer to their in vivo phenotypes. To examine the effects of spatial constraints on chromosome conformation, we investigated the genomic architecture of mouse hepatocytes grown in 2D and 3D cultures using in situ Hi-C. Our results reveal significant differences in higher-order genomic interactions, notably in compartment identity and strength as well as in topologically associating domain (TAD)–TAD interactions, but only minor differences are found at the TAD level. Our RNA-seq analysis reveals an up-regulated expression of genes involved in physiological hepatocyte functions in the 3D-cultured cells. These genes are associated with a subset of structural changes, suggesting that differences in genomic structure are critically important for transcriptional regulation. However, there are also many structural differences that are not directly associated with changes in gene expression, whose cause remains to be determined. Overall, our results indicate that growth in 3D significantly alters higher-order genomic interactions, which may be consequential for a subset of genes that are important for the physiological functioning of the cell.
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Affiliation(s)
- Xin Liu
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiu Sun
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qi Wang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Science and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Chuansheng Hu
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xuecheng Chen
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hua Li
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniel M Czajkowsky
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Zhifeng Shao
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
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8
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TCF7L2 silencing results in altered gene expression patterns accompanied by local genomic reorganization. Neoplasia 2021; 23:257-269. [PMID: 33422939 PMCID: PMC7809436 DOI: 10.1016/j.neo.2020.12.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 12/15/2020] [Accepted: 12/29/2020] [Indexed: 11/27/2022] Open
Abstract
Canonical Wnt signaling is crucial for intestinal homeostasis as TCF4, the major Wnt signaling effector in the intestines, is required for stem cell maintenance. The capability of TCF4 to maintain the stem cell phenotype is contingent upon β-catenin, a potent transcriptional activator, which interacts with histone acetyltransferases and chromatin remodeling complexes. We used RNAi to explore the influence of TCF4 on chromatin structure (Hi-C) and gene expression (RNA sequencing) across a 72-hour time series in colon cancer. We found that TCF4 reduction results in a disproportionate up-regulation of gene expression, including a powerful induction of SOX2. Integration of RNA sequencing and Hi-C data revealed a TAD boundary loss, which occurred concomitantly with the over-expression of a cluster of CEACAM genes on chromosome 19. We identified EMT and E2F as the 2 most deregulated pathways upon TCF4 depletion and LUM, TMPO, and AURKA as highly influential genes in these networks using measures of centrality. Results from gene expression, chromatin structure, and centrality analyses were integrated to generate a list of candidate transcription factors crucial for colon cancer cell homeostasis. The top ranked factor was c-JUN, an oncoprotein known to interact with TCF4 and β-catenin, confirming the usefulness of this approach.
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9
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Wu Y, Xu Y. Bioinformatics for The Prognostic Value and Function of Cubilin (CUBN) in Colorectal Cancer. Med Sci Monit 2020; 26:e922447. [PMID: 33235183 PMCID: PMC7702664 DOI: 10.12659/msm.922447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background Cubilin (CUBN) gene was reported to be a novel risk variant for colorectal cancer (CRC). Previous studies have shown that germline variants in known cancer driver genes are predictive of patient outcome, but no study has systematically analyzed CRC to identify CUBN that can predict patient outcome and function by using bioinformatics. Material/Methods The association in expression, clinicopathological parameters, and survival were analyzed by using Oncomine, UNCLA, and GEPIA, while CUBN alterations and related functional networks were identified using cBioPortal. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathways (KEGG) of CUBN in CRC were explored by using LinkOmics. Gene set enrichment analysis (GSEA) examined target networks of kinases, miRNAs, and transcription factors. Results We found that CUBN was overexpressed in CRC. Patients who were in advanced TNM stage tended to express higher CUBN mRNA levels, while those who received radiotherapy tended to express relatively lower CUBN mRNA levels. Higher expression of CUBN was found to be associated with shorter overall survival (OS) and disease-free survival (DFS). Moreover, functional networks analysis suggested that CUBN can regulate mismatch repair, terpenoid backbone biosynthesis, base excision repair, and proteasome via vitamin digestion and absorption pathway to influence CRC occurrence. Conclusions These findings suggested that CUBN could serve as a prognostic and therapeutic biomarker of CRC in the future.
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Affiliation(s)
- Yibin Wu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China (mainland)
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China (mainland)
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10
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Abstract
Identifying structural variation (SV) is essential for genome interpretation but has been historically difficult due to limitations inherent to available genome technologies. Detection methods that use ensemble algorithms and emerging sequencing technologies have enabled the discovery of thousands of SVs, uncovering information about their ubiquity, relationship to disease and possible effects on biological mechanisms. Given the variability in SV type and size, along with unique detection biases of emerging genomic platforms, multiplatform discovery is necessary to resolve the full spectrum of variation. Here, we review modern approaches for investigating SVs and proffer that, moving forwards, studies integrating biological information with detection will be necessary to comprehensively understand the impact of SV in the human genome.
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Affiliation(s)
- Steve S Ho
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan E Mills
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
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11
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Virk RKA, Wu W, Almassalha LM, Bauer GM, Li Y, VanDerway D, Frederick J, Zhang D, Eshein A, Roy HK, Szleifer I, Backman V. Disordered chromatin packing regulates phenotypic plasticity. SCIENCE ADVANCES 2020; 6:eaax6232. [PMID: 31934628 PMCID: PMC6949045 DOI: 10.1126/sciadv.aax6232] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 11/08/2019] [Indexed: 05/19/2023]
Abstract
Three-dimensional supranucleosomal chromatin packing plays a profound role in modulating gene expression by regulating transcription reactions through mechanisms such as gene accessibility, binding affinities, and molecular diffusion. Here, we use a computational model that integrates disordered chromatin packing (CP) with local macromolecular crowding (MC) to study how physical factors, including chromatin density, the scaling of chromatin packing, and the size of chromatin packing domains, influence gene expression. We computationally and experimentally identify a major role of these physical factors, specifically chromatin packing scaling, in regulating phenotypic plasticity, determining responsiveness to external stressors by influencing both intercellular transcriptional malleability and heterogeneity. Applying CPMC model predictions to transcriptional data from cancer patients, we identify an inverse relationship between patient survival and phenotypic plasticity of tumor cells.
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Affiliation(s)
- Ranya K. A. Virk
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Wenli Wu
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Luay M. Almassalha
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Medical Scientist Training Program, Feinberg School of Medicine, Northwestern University, Chicago, IL 60211, USA
- Department of Internal Medicine, Northwestern University, Chicago, IL 60211, USA
| | - Greta M. Bauer
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Yue Li
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Applied Physics Program, Northwestern University, Evanston, IL 60208, USA
| | - David VanDerway
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Jane Frederick
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Di Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Adam Eshein
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Hemant K. Roy
- Section of Gastroenterology, Boston Medical Center/Boston University School of Medicine, Boston, MA 02118, USA
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Corresponding author. (V.B.); (I.S.)
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Corresponding author. (V.B.); (I.S.)
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12
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Bushnell GG, Hardas TP, Hartfield RM, Zhang Y, Oakes RS, Ronquist S, Chen H, Rajapakse I, Wicha MS, Jeruss JS, Shea LD. Biomaterial Scaffolds Recruit an Aggressive Population of Metastatic Tumor Cells In Vivo. Cancer Res 2019; 79:2042-2053. [PMID: 30808673 PMCID: PMC6467791 DOI: 10.1158/0008-5472.can-18-2502] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 12/21/2018] [Accepted: 02/18/2019] [Indexed: 12/28/2022]
Abstract
For most cancers, metastasis is the point at which clinical treatment shifts from curative intent to extending survival. Biomaterial implants acting as a synthetic premetastatic niche recruit metastatic cancer cells and provide a survival advantage, and their use as a diagnostic platform requires assessing their relevance to disease progression. Here, we showed that scaffold-captured tumor cells (SCAF) were 30 times more metastatic to the lung than primary tumor (PT) cells, similar to cells derived from lung micrometastases (LUNG). SCAF cells were more aggressive in vitro, demonstrated higher levels of migration, invasion, and mammosphere formation, and had a greater proportion of cancer stem cells than PT. SCAF cells were highly enriched for gene expression signatures associated with metastasis and had associated genomic structural changes, including globally enhanced entropy. Collectively, our findings demonstrate that SCAF cells are distinct from PT and more closely resemble LUNG, indicating that tumor cells retrieved from scaffolds are reflective of cells at metastatic sites. SIGNIFICANCE: These findings suggest that metastatic tumor cells captured by a biomaterial scaffold may serve as a diagnostic for molecular staging of metastasis.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/79/8/2042/F1.large.jpg.
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Affiliation(s)
- Grace G Bushnell
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Tejaswini P Hardas
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Rachel M Hartfield
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Yining Zhang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Robert S Oakes
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Scott Ronquist
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Haiming Chen
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Indika Rajapakse
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan
- Department of Mathematics, University of Michigan, Ann Arbor, Michigan
| | - Max S Wicha
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Jacqueline S Jeruss
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan.
- Department of Surgery, University of Michigan, Ann Arbor, Michigan
| | - Lonnie D Shea
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan.
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan
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13
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Braun R, Ronquist S, Wangsa D, Chen H, Anthuber L, Gemoll T, Wangsa D, Koparde V, Hunn C, Habermann JK, Heselmeyer-Haddad K, Rajapakse I, Ried T. Single Chromosome Aneuploidy Induces Genome-Wide Perturbation of Nuclear Organization and Gene Expression. Neoplasia 2019; 21:401-412. [PMID: 30909073 PMCID: PMC6434407 DOI: 10.1016/j.neo.2019.02.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/22/2019] [Accepted: 02/26/2019] [Indexed: 12/21/2022] Open
Abstract
Chromosomal aneuploidy is a defining feature of carcinomas and results in tumor-entity specific genomic imbalances. For instance, most sporadic colorectal carcinomas carry extra copies of chromosome 7, an aneuploidy that emerges already in premalignant adenomas, and is maintained throughout tumor progression and in derived cell lines. A comprehensive understanding on how chromosomal aneuploidy affects nuclear organization and gene expression, i.e., the nucleome, remains elusive. We now analyzed a cell line established from healthy colon mucosa with a normal karyotype (46,XY) and its isogenic derived cell line that acquired an extra copy of chromosome 7 as its sole anomaly (47,XY,+7). We studied structure/function relationships consequent to aneuploidization using genome-wide chromosome conformation capture (Hi-C), RNA sequencing and protein profiling. The gain of chromosome 7 resulted in an increase of transcript levels of resident genes as well as genome-wide gene and protein expression changes. The Hi-C analysis showed that the extra copy of chromosome 7 is reflected in more interchromosomal contacts between the triploid chromosomes. Chromatin organization changes are observed genome-wide, as determined by changes in A/B compartmentalization and topologically associating domain (TAD) boundaries. Most notably, chromosome 4 shows a profound loss of chromatin organization, and chromosome 14 contains a large A/B compartment switch region, concurrent with resident gene expression changes. No changes to the nuclear position of the additional chromosome 7 territory were observed when measuring distances of chromosome painting probes by interphase FISH. Genome and protein data showed enrichment in signaling pathways crucial for malignant transformation, such as the HGF/MET-axis. We conclude that a specific chromosomal aneuploidy has profound impact on nuclear structure and function, both locally and genome-wide. Our study provides a benchmark for the analysis of cancer nucleomes with complex karyotypes.
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Affiliation(s)
- Rüdiger Braun
- Section of Cancer Genomics, National Cancer Institute, Center for Cancer Research, NIH, Bethesda, MD, USA
| | - Scott Ronquist
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Darawalee Wangsa
- Section of Cancer Genomics, National Cancer Institute, Center for Cancer Research, NIH, Bethesda, MD, USA
| | - Haiming Chen
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Lena Anthuber
- Section of Cancer Genomics, National Cancer Institute, Center for Cancer Research, NIH, Bethesda, MD, USA
| | - Timo Gemoll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Danny Wangsa
- Section of Cancer Genomics, National Cancer Institute, Center for Cancer Research, NIH, Bethesda, MD, USA
| | - Vishal Koparde
- CCR Collaborative Bioinformatics Resource (CCBR), Center for Cancer Research, NCI, Bethesda, MD, USA; Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, USA
| | - Cynthia Hunn
- Section of Cancer Genomics, National Cancer Institute, Center for Cancer Research, NIH, Bethesda, MD, USA
| | - Jens K Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Kerstin Heselmeyer-Haddad
- Section of Cancer Genomics, National Cancer Institute, Center for Cancer Research, NIH, Bethesda, MD, USA
| | - Indika Rajapakse
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Mathematics, University of Michigan, Ann Arbor, MI, USA.
| | - Thomas Ried
- Section of Cancer Genomics, National Cancer Institute, Center for Cancer Research, NIH, Bethesda, MD, USA.
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14
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Wang Y, Song F, Zhang B, Zhang L, Xu J, Kuang D, Li D, Choudhary MNK, Li Y, Hu M, Hardison R, Wang T, Yue F. The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions. Genome Biol 2018; 19:151. [PMID: 30286773 PMCID: PMC6172833 DOI: 10.1186/s13059-018-1519-9] [Citation(s) in RCA: 323] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 08/29/2018] [Indexed: 12/20/2022] Open
Abstract
Here, we introduce the 3D Genome Browser, http://3dgenome.org , which allows users to conveniently explore both their own and over 300 publicly available chromatin interaction data of different types. We design a new binary data format for Hi-C data that reduces the file size by at least a magnitude and allows users to visualize chromatin interactions over millions of base pairs within seconds. Our browser provides multiple methods linking distal cis-regulatory elements with their potential target genes. Users can seamlessly integrate thousands of other omics data to gain a comprehensive view of both regulatory landscape and 3D genome structure.
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Affiliation(s)
- Yanli Wang
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Fan Song
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Bo Zhang
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Lijun Zhang
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State Hershey, Hershey, PA, 17033, USA
| | - Jie Xu
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State Hershey, Hershey, PA, 17033, USA
| | - Da Kuang
- Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Daofeng Li
- Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Mayank N K Choudhary
- Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Ross Hardison
- Center for Computational Biology and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Ting Wang
- Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63108, USA.
| | - Feng Yue
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, 16802, USA.
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State Hershey, Hershey, PA, 17033, USA.
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15
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Behrisch M, Schreck T, Krüger R, Gehlenborg N, Lekschas F, Pfister H. Visual Pattern-Driven Exploration of Big Data. 2018 INTERNATIONAL SYMPOSIUM ON BIG DATA VISUAL AND IMMERSIVE ANALYTICS (BDVA) : KONSTANZ, GERMANY, OCTOBER 17 -19, 2018. IEEE INTERNATIONAL SYMPOSIUM ON BIG DATA VISUAL AND IMMERSIVE ANALYTICS (4TH : 2018 : KONSTANZ, GERMANY) 2018; 2018:10.1109/BDVA.2018.8534028. [PMID: 31396383 PMCID: PMC6687327 DOI: 10.1109/bdva.2018.8534028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Pattern extraction algorithms are enabling insights into the ever-growing amount of today's datasets by translating reoccurring data properties into compact representations. Yet, a practical problem arises: With increasing data volumes and complexity also the number of patterns increases, leaving the analyst with a vast result space. Current algorithmic and especially visualization approaches often fail to answer central overview questions essential for a comprehensive understanding of pattern distributions and support, their quality, and relevance to the analysis task. To address these challenges, we contribute a visual analytics pipeline targeted on the pattern-driven exploration of result spaces in a semi-automatic fashion. Specifically, we combine image feature analysis and unsupervised learning to partition the pattern space into interpretable, coherent chunks, which should be given priority in a subsequent in-depth analysis. In our analysis scenarios, no ground-truth is given. Thus, we employ and evaluate novel quality metrics derived from the distance distributions of our image feature vectors and the derived cluster model to guide the feature selection process. We visualize our results interactively, allowing the user to drill down from overview to detail into the pattern space and demonstrate our techniques in two case studies on Earth observation and biomedical genomic data.
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16
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Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı GG, Chakraborty A, Bann DV, Wang Y, Clark R, Zhang L, Yang H, Liu T, Iyyanki S, An L, Pool C, Sasaki T, Rivera-Mulia JC, Ozadam H, Lajoie BR, Kaul R, Buckley M, Lee K, Diegel M, Pezic D, Ernst C, Hadjur S, Odom DT, Stamatoyannopoulos JA, Broach JR, Hardison RC, Ay F, Noble WS, Dekker J, Gilbert DM, Yue F. Integrative detection and analysis of structural variation in cancer genomes. Nat Genet 2018; 50:1388-1398. [PMID: 30202056 PMCID: PMC6301019 DOI: 10.1038/s41588-018-0195-8] [Citation(s) in RCA: 211] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/16/2018] [Indexed: 01/19/2023]
Abstract
Structural variants (SVs) can contribute to oncogenesis through a variety of mechanisms. Despite their importance, the identification of SVs in cancer genomes remains challenging. Here, we present a framework that integrates optical mapping, high-throughput chromosome conformation capture (Hi-C), and whole-genome sequencing to systematically detect SVs in a variety of normal or cancer samples and cell lines. We identify the unique strengths of each method and demonstrate that only integrative approaches can comprehensively identify SVs in the genome. By combining Hi-C and optical mapping, we resolve complex SVs and phase multiple SV events to a single haplotype. Furthermore, we observe widespread structural variation events affecting the functions of noncoding sequences, including the deletion of distal regulatory sequences, alteration of DNA replication timing, and the creation of novel three-dimensional chromatin structural domains. Our results indicate that noncoding SVs may be underappreciated mutational drivers in cancer genomes.
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Affiliation(s)
- Jesse R Dixon
- Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Jie Xu
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Vishnu Dileep
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Ye Zhan
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Fan Song
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, USA
| | - Victoria T Le
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | | | - Darrin V Bann
- Division of Otolaryngology, Head & Neck Surgery, Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Yanli Wang
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, USA
| | - Royden Clark
- Penn State College of Medicine, Informatics and Technology, Hershey, PA, USA
| | - Lijun Zhang
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Hongbo Yang
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Tingting Liu
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Sriranga Iyyanki
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Lin An
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, USA
| | - Christopher Pool
- Division of Otolaryngology, Head & Neck Surgery, Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Takayo Sasaki
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | | | - Hakan Ozadam
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Bryan R Lajoie
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Rajinder Kaul
- Altius institute for Biomedical Sciences, Seattle, WA, USA
| | | | - Kristen Lee
- Altius institute for Biomedical Sciences, Seattle, WA, USA
| | - Morgan Diegel
- Altius institute for Biomedical Sciences, Seattle, WA, USA
| | - Dubravka Pezic
- Research Department of Cancer Biology, Cancer Institute, University College London, London, UK
| | - Christina Ernst
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Suzana Hadjur
- Research Department of Cancer Biology, Cancer Institute, University College London, London, UK
| | - Duncan T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics, Heidelberg, Germany
| | | | - James R Broach
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Ross C Hardison
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA, USA
| | - Ferhat Ay
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.
- School of Medicine, University of California San Diego, La Jolla, CA, USA.
| | | | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL, USA.
| | - Feng Yue
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA.
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, USA.
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17
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Kerpedjiev P, Abdennur N, Lekschas F, McCallum C, Dinkla K, Strobelt H, Luber JM, Ouellette SB, Azhir A, Kumar N, Hwang J, Lee S, Alver BH, Pfister H, Mirny LA, Park PJ, Gehlenborg N. HiGlass: web-based visual exploration and analysis of genome interaction maps. Genome Biol 2018; 19:125. [PMID: 30143029 PMCID: PMC6109259 DOI: 10.1186/s13059-018-1486-1] [Citation(s) in RCA: 712] [Impact Index Per Article: 118.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 07/18/2018] [Indexed: 11/28/2022] Open
Abstract
We present HiGlass, an open source visualization tool built on web technologies that provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps alongside 1D genomic tracks, allowing users to combine various data types, synchronize multiple visualization modalities, and share fully customizable views with others. We demonstrate its utility in exploring different experimental conditions, comparing the results of analyses, and creating interactive snapshots to share with collaborators and the broader public. HiGlass is accessible online at http://higlass.io and is also available as a containerized application that can be run on any platform.
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Affiliation(s)
- Peter Kerpedjiev
- Department of Biomedical Informatics, Harvard Medical School, Countway Library, 10 Shattuck St, Boston, MA 02115 USA
| | - Nezar Abdennur
- Computational and Systems Biology Program, MIT, Cambridge, USA
| | - Fritz Lekschas
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA USA
| | - Chuck McCallum
- Department of Biomedical Informatics, Harvard Medical School, Countway Library, 10 Shattuck St, Boston, MA 02115 USA
| | - Kasper Dinkla
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA USA
| | - Hendrik Strobelt
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA USA
| | - Jacob M. Luber
- Department of Biomedical Informatics, Harvard Medical School, Countway Library, 10 Shattuck St, Boston, MA 02115 USA
- Bioinformatics and Integrative Genomics Program, Harvard Medical School, Boston, MA USA
| | - Scott B. Ouellette
- Department of Biomedical Informatics, Harvard Medical School, Countway Library, 10 Shattuck St, Boston, MA 02115 USA
| | - Alaleh Azhir
- Department of Biomedical Informatics, Harvard Medical School, Countway Library, 10 Shattuck St, Boston, MA 02115 USA
| | - Nikhil Kumar
- Department of Biomedical Informatics, Harvard Medical School, Countway Library, 10 Shattuck St, Boston, MA 02115 USA
| | - Jeewon Hwang
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA USA
| | - Soohyun Lee
- Department of Biomedical Informatics, Harvard Medical School, Countway Library, 10 Shattuck St, Boston, MA 02115 USA
| | - Burak H. Alver
- Department of Biomedical Informatics, Harvard Medical School, Countway Library, 10 Shattuck St, Boston, MA 02115 USA
| | - Hanspeter Pfister
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA USA
| | - Leonid A. Mirny
- Department of Physics, MIT, Cambridge, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, USA
| | - Peter J. Park
- Department of Biomedical Informatics, Harvard Medical School, Countway Library, 10 Shattuck St, Boston, MA 02115 USA
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Countway Library, 10 Shattuck St, Boston, MA 02115 USA
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18
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Diament A, Tuller T. Modeling three-dimensional genomic organization in evolution and pathogenesis. Semin Cell Dev Biol 2018; 90:78-93. [PMID: 30030143 DOI: 10.1016/j.semcdb.2018.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/08/2018] [Indexed: 12/17/2022]
Abstract
The regulation of gene expression is mediated via the complex three-dimensional (3D) conformation of the genetic material and its interactions with various intracellular factors. Various experimental and computational approaches have been developed in recent years for understating the relation between the 3D conformation of the genome and the phenotypes of cells in normal condition and diseases. In this review, we will discuss novel approaches for analyzing and modeling the 3D genomic conformation, focusing on deciphering disease-causing mutations that affect gene expression. We conclude that as this is a very challenging mission, an important direction should involve the comparative analysis of various 3D models from various organisms or cells.
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Affiliation(s)
- Alon Diament
- Dept. of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tamir Tuller
- Dept. of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel; The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 6997801, Israel.
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19
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Li R, Liu Y, Hou Y, Gan J, Wu P, Li C. 3D genome and its disorganization in diseases. Cell Biol Toxicol 2018; 34:351-365. [DOI: 10.1007/s10565-018-9430-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 03/26/2018] [Indexed: 01/25/2023]
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20
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Lekschas F, Bach B, Kerpedjiev P, Gehlenborg N, Pfister H. HiPiler: Visual Exploration of Large Genome Interaction Matrices with Interactive Small Multiples. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2018; 24:522-531. [PMID: 28866592 PMCID: PMC6038708 DOI: 10.1109/tvcg.2017.2745978] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
This paper presents an interactive visualization interface-HiPiler-for the exploration and visualization of regions-of-interest in large genome interaction matrices. Genome interaction matrices approximate the physical distance of pairs of regions on the genome to each other and can contain up to 3 million rows and columns with many sparse regions. Regions of interest (ROIs) can be defined, e.g., by sets of adjacent rows and columns, or by specific visual patterns in the matrix. However, traditional matrix aggregation or pan-and-zoom interfaces fail in supporting search, inspection, and comparison of ROIs in such large matrices. In HiPiler, ROIs are first-class objects, represented as thumbnail-like "snippets". Snippets can be interactively explored and grouped or laid out automatically in scatterplots, or through dimension reduction methods. Snippets are linked to the entire navigable genome interaction matrix through brushing and linking. The design of HiPiler is based on a series of semi-structured interviews with 10 domain experts involved in the analysis and interpretation of genome interaction matrices. We describe six exploration tasks that are crucial for analysis of interaction matrices and demonstrate how HiPiler supports these tasks. We report on a user study with a series of data exploration sessions with domain experts to assess the usability of HiPiler as well as to demonstrate respective findings in the data.
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Ortega MA, Poirion O, Zhu X, Huang S, Wolfgruber TK, Sebra R, Garmire LX. Using single-cell multiple omics approaches to resolve tumor heterogeneity. Clin Transl Med 2017; 6:46. [PMID: 29285690 PMCID: PMC5746494 DOI: 10.1186/s40169-017-0177-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 12/06/2017] [Indexed: 12/31/2022] Open
Abstract
It has become increasingly clear that both normal and cancer tissues are composed of heterogeneous populations. Genetic variation can be attributed to the downstream effects of inherited mutations, environmental factors, or inaccurately resolved errors in transcription and replication. When lesions occur in regions that confer a proliferative advantage, it can support clonal expansion, subclonal variation, and neoplastic progression. In this manner, the complex heterogeneous microenvironment of a tumour promotes the likelihood of angiogenesis and metastasis. Recent advances in next-generation sequencing and computational biology have utilized single-cell applications to build deep profiles of individual cells that are otherwise masked in bulk profiling. In addition, the development of new techniques for combining single-cell multi-omic strategies is providing a more precise understanding of factors contributing to cellular identity, function, and growth. Continuing advancements in single-cell technology and computational deconvolution of data will be critical for reconstructing patient specific intra-tumour features and developing more personalized cancer treatments.
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Affiliation(s)
- Michael A. Ortega
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI USA
| | - Olivier Poirion
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI USA
| | - Xun Zhu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI USA
- Department of Molecular Biosciences and Bioengineering, Honolulu, HI USA
| | - Sijia Huang
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI USA
- Department of Molecular Biosciences and Bioengineering, Honolulu, HI USA
| | - Thomas K. Wolfgruber
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI USA
| | - Robert Sebra
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Lana X. Garmire
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI USA
- Department of Molecular Biosciences and Bioengineering, Honolulu, HI USA
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Chakraborty A, Ay F. Identification of copy number variations and translocations in cancer cells from Hi-C data. Bioinformatics 2017; 34:338-345. [PMID: 29048467 DOI: 10.1093/bioinformatics/btx664] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 09/21/2017] [Accepted: 10/17/2017] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Eukaryotic chromosomes adapt a complex and highly dynamic three-dimensional (3D) structure, which profoundly affects different cellular functions and outcomes including changes in epigenetic landscape and in gene expression. Making the scenario even more complex, cancer cells harbor chromosomal abnormalities [e.g. copy number variations (CNVs) and translocations] altering their genomes both at the sequence level and at the level of 3D organization. High-throughput chromosome conformation capture techniques (e.g. Hi-C), which are originally developed for decoding the 3D structure of the chromatin, provide a great opportunity to simultaneously identify the locations of genomic rearrangements and to investigate the 3D genome organization in cancer cells. Even though Hi-C data has been used for validating known rearrangements, computational methods that can distinguish rearrangement signals from the inherent biases of Hi-C data and from the actual 3D conformation of chromatin, and can precisely detect rearrangement locations de novo have been missing. RESULTS In this work, we characterize how intra and inter-chromosomal Hi-C contacts are distributed for normal and rearranged chromosomes to devise a new set of algorithms (i) to identify genomic segments that correspond to CNV regions such as amplifications and deletions (HiCnv), (ii) to call inter-chromosomal translocations and their boundaries (HiCtrans) from Hi-C experiments and (iii) to simulate Hi-C data from genomes with desired rearrangements and abnormalities (AveSim) in order to select optimal parameters for and to benchmark the accuracy of our methods. Our results on 10 different cancer cell lines with Hi-C data show that we identify a total number of 105 amplifications and 45 deletions together with 90 translocations, whereas we identify virtually no such events for two karyotypically normal cell lines. Our CNV predictions correlate very well with whole genome sequencing data among chromosomes with CNV events for a breast cancer cell line (r = 0.89) and capture most of the CNVs we simulate using Avesim. For HiCtrans predictions, we report evidence from the literature for 30 out of 90 translocations for eight of our cancer cell lines. Furthermore, we show that our tools identify and correctly classify relatively understudied rearrangements such as double minutes and homogeneously staining regions. Considering the inherent limitations of existing techniques for karyotyping (i.e. missing balanced rearrangements and those near repetitive regions), the accurate identification of CNVs and translocations in a cost-effective and high-throughput setting is still a challenge. Our results show that the set of tools we develop effectively utilize moderately sequenced Hi-C libraries (100-300 million reads) to identify known and de novo chromosomal rearrangements/abnormalities in well-established cancer cell lines. With the decrease in required number of cells and the increase in attainable resolution, we believe that our framework will pave the way towards comprehensive mapping of genomic rearrangements in primary cells from cancer patients using Hi-C. AVAILABILITY AND IMPLEMENTATION CNV calling: https://github.com/ay-lab/HiCnv, Translocation calling: https://github.com/ay-lab/HiCtrans and Hi-C simulation: https://github.com/ay-lab/AveSim. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Abhijit Chakraborty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Ferhat Ay
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.,School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, USA
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