Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking

Weischenfeldt, Joachim, Dubash, Taronish, Drainas, Alexandros P, Mardin, Balca R, Chen, Yuanyuan, Stütz, Adrian M, Waszak, Sebastian M, Bosco, Graziella +24 more·2017·Nature Genetics

Cited by (423)

Items 101–200 of 423

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  2. Transcriptional dysregulation by aberrant enhancer activation and rewiring in cancer
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  3. Facultative CTCF sites moderate mammary super-enhancer activity and regulate juxtaposed gene in non-mammary cells
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  4. Effective normalization for copy number variation in Hi-C data
    N. Servant, Nelle Varoquaux, E. Heard, E. Barillot, Jean-Philippe Vert · 2017 · BMC Bioinformatics
  5. Functional analysis of structural variants in single cells using Strand-seq
    Hyobin Jeong, Karen Grimes, Kerstin Katharina Rauwolf, Peter‐Martin Bruch, Tobias Rausch, Patrick Hasenfeld, Eva Benito, Tobias Roider, Radhakrishnan Sabarinathan, David Porubskỳ et al. · 2022 · Nature Biotechnology
  6. Pervasive structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs
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  7. TAD fusion score: discovery and ranking the contribution of deletions to genome structure
    Linh Ngoc Huynh, Fereydoun Hormozdiari · 2019 · Genome biology
  8. Copy number variation profile in the placental and parental genomes of recurrent pregnancy loss families
    Laura Kasak, Kristiina Rull, Siim Sõber, Maris Laan · 2017 · Scientific Reports
  9. An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
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  10. Enhancer reprogramming in tumor progression: a new route towards cancer cell plasticity
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  11. SVFX: a machine learning framework to quantify the pathogenicity of structural variants
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  13. Genome-guided discovery of cancer therapeutic targets
    Prathyusha Konda, Simon Garinet, Eliezer M. Van Allen, Srinivas Raghavan Viswanathan · 2023 · Cell Reports
  14. Structural variants in the 3D genome as drivers of disease
    Varun K. A. Sreenivasan, Verónica Yumiceba, Malte Spielmann · 2025 · Nature Reviews Genetics
  15. The IGF1R/INSR Inhibitor BI 885578 Selectively Inhibits Growth of IGF2-Overexpressing Colorectal Cancer Tumors and Potentiates the Efficacy of Anti-VEGF Therapy
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  16. Making Use of Cancer Genomic Databases
    Chad J. Creighton · 2018 · Current Protocols in Molecular Biology
  17. 3D disorganization and rearrangement of genome provide insights into pathogenesis of NAFLD by integrated Hi-C, Nanopore, and RNA sequencing
    Li-Na Xu, L. Yin, Yan Qi, Xuemei Tan, Meng Gao, Jin-Yong Peng · 2021 · Acta Pharmaceutica Sinica B
  18. 3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression
    Katelyn L. Mortenson, Courtney Dawes, Emily R Wilson, Nathan E. Patchen, Hailey E Johnson, J. Gertz, Swneke D. Bailey, Yang Liu, K. Varley, Xiao-Yang Zhang · 2024 · Nature Communications
  19. Nuclear topology modulates the mutational landscapes of cancer genomes
    Kyle S. Smith, Lin L. Liu, Shridar Ganesan, Franziska Michor, Subhajyoti De · 2017 · Nature Structural & Molecular Biology
  20. Insights into Impact of DNA Copy Number Alteration and Methylation on the Proteogenomic Landscape of Human Ovarian Cancer via a Multi-omics Integrative Analysis
    Xiaoyu Song, Jiayi Ji, Kevin J. Gleason, Fan Yang, John A. Martignetti, Lin Chen, Pei Wang · 2019 · Molecular & Cellular Proteomics
  21. Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway
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  22. Somatic structural variant formation is guided by and influences genome architecture
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  23. Super-enhancers and novel therapeutic targets in colorectal cancer
    Qian Liu, Lijuan Guo, Zhiyuan Lou, Xueping Xiang, Jimin Shao · 2022 · Cell Death and Disease
  24. Effects of super-enhancers in cancer metastasis: mechanisms and therapeutic targets
    Shenglan Liu, Wei Dai, Bei Jin, Feng Jiang, Hao Huang, Wen Hou, Jin‐Xia Lan, Yanli Jin, Weijie Peng, Jingxuan Pan · 2024 · Molecular Cancer
  25. IRS4 promotes the progression of non-small cell lung cancer and confers resistance to EGFR-TKI through the activation of PI3K/Akt and Ras-MAPK pathways
    Peiqi Hao, Ying Huang, Jun Peng, Jiaojiao Yu, Xiao‐Xi Guo, Fan Bao, Ziqin Dian, Su An, Tian‐Rui Xu · 2021 · Experimental Cell Research
  26. Structure–function relationships explain CTCF zinc finger mutation phenotypes in cancer
    Charles G. Bailey, Shailendra K. Gupta, Cynthia Metierre, Punkaja M. S. Amarasekera, Patrick O’Young, Wunna Kyaw, Tatyana Laletin, Habib Francis, Crystal Semaan, Mehdi Sharifi Tabar et al. · 2021 · Cellular and Molecular Life Sciences
  27. Epigenetic Mechanisms Regulating Adaptive Responses to Targeted Kinase Inhibitors in Cancer
    Steven P. Angus, Jon S. Zawistowski, Gary L. Johnson · 2017 · The Annual Review of Pharmacology and Toxicology
  28. Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations
    Avantika Lal, Daniele Ramazzotti, Ziming Weng, Keli Liu, James M. Ford, Arend Sidow · 2019 · BMC Medical Genomics
  29. Spotlight on the Granules (Grainyhead-Like Proteins) – From an Evolutionary Conserved Controller of Epithelial Trait to Pioneering the Chromatin Landscape
    Vignesh Sundararajan, Qing You Pang, Mahesh Arjandas Choolani, Ruby Yun‐Ju Huang · 2020 · Frontiers in Molecular Biosciences
  30. Rewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying neurogliomal synaptic communication
    Chaitali Chakraborty, Itzel Nissen, Craig A. Vincent, Anna‐Carin Hägglund, Andreas Hörnblad, Silvia Remeseiro · 2023 · Nature Communications
  31. Selective and mechanistic sources of recurrent rearrangements across the cancer genome
    Jeremiah A. Wala, Ofer Shapira, Yilong Li, David Craft, Steven E. Schumacher, Marcin B. Imielinski, James E. Haber, Nicola D. Roberts, Xiaotong Yao, Chip Stewart et al. · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  32. Hijacked enhancer–promoter and silencer–promoter loops in cancer
    Xiaotao Wang, Feng Yue · 2024 · Current Opinion in Genetics & Development
  33. Ultraconserved Elements Occupy Specific Arenas of Three-Dimensional Mammalian Genome Organization
    Ruth B. McCole, Jelena Erceg, Wren Saylor, Chao-ting Wu · 2018 · Cell Reports
  34. Determinants and role of chromatin organization in acute leukemia
    Celestia Fang, Sridhar Rao, John D. Crispino, Panagiotis Ntziachristos · 2020 · Leukemia
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    Tingting Liu, Juan Wang, Hongbo Yang, Qiushi Jin, Xiaotao Wang, Yihao Fu, Yu Luan, Qixuan Wang, Mark W. Youngblood, Xinyan Lu et al. · 2023 · Cancer Research
  36. Broad H3K4me3 domains: Maintaining cellular identity and their implication in super‐enhancer hijacking
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  37. Enhancer-gene rewiring in the pathogenesis of Quebec Platelet Disorder
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  38. Spatial promoter–enhancer hubs in cancer: organization, regulation, and function
    Zhao, Jingru, Faryabi, Robert B. · 2023 · Trends in Cancer
  39. A guide to visualizing the spatial epigenome with super‐resolution microscopy
    Jianquan Xu, Yang Liu · 2019 · FEBS Journal
  40. Gene Fusions Create Partner and Collateral Dependencies Essential to Cancer Cell Survival
    Riaz Gillani, Bo Kyung A. Seong, Jett P. Crowdis, Jake R. Conway, Neekesh V. Dharia, Saif I. Alimohamed, Brian J. Haas, Kyuho Han, Jihye Park, Felix Dietlein et al. · 2021 · Cancer Research
  41. Unravelling the tumour genome: The evolutionary and clinical impacts of structural variants in tumourigenesis
    Alhafidz Hamdan, Ailith Ewing · 2022 · The Journal of Pathology
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    Xiaoru Ling, Xinyi Liu, Shaoshuai Jiang, Lili Fan, Junjun Ding · 2022 · Cell Regeneration
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    Vinícius G. Contessoto, Olga Dudchenko, Erez Lieberman Aiden, Peter Guy Wolynes, José N. Onuchic, Michele Di Pierro · 2023 · Nature Communications
  44. Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae
    Li E. Cheng, Shijun Zhao, Tianyi Li, Sha Hou, Zhouqing Luo, Jinsheng Xu, Wenfei Yu, Shuangying Jiang, Marco Monti, Daniel Schindler et al. · 2024 · Nature Communications
  45. Dynamic Interplay between Structural Variations and 3D Genome Organization in Pancreatic Cancer
    Yong-Xing Du, Zong-Ting Gu, Zong-Ze Li, Zan Yuan, Yue Zhao, Xiao-Hao Zheng, Xiao-Chen Bo, He-Bing Chen, Cheng-Feng Wang · 2022 · Advancement of science
  46. Etiology of super-enhancer reprogramming and activation in cancer
    Royce W. Zhou, Ramon E. Parsons · 2023 · Epigenetics & Chromatin
  47. Modeling double strand break susceptibility to interrogate structural variation in cancer
    Tracy J. Ballinger, Britta A. M. Bouwman, Reza Mirzazadeh, Silvano Garnerone, Nicola Crosetto, Colin A M Semple · 2019 · Genome biology
  48. 3D chromosomal landscapes in hematopoiesis and immunity
    A. Kloetgen, Palaniraja Thandapani, A. Tsirigos, lannis Aifantis · 2019 · Trends in immunology
  49. Three-dimensional genome: developmental technologies and applications in precision medicine
    Yingqi Li, Tao Tao, Likun Du, Xiao Ming Zhu · 2020 · Journal of Human Genetics
  50. Generation of onco-enhancer enhances chromosomal remodeling and accelerates tumorigenesis
    Peiwei Chai, Jie Yu, Ruobing Jia, Xuyang Wen, Tianyi Ding, Xiaoyu Zhang, Hongyan Ni, Renbing Jia, Shengfang Ge, He Zhang et al. · 2020 · Nucleic Acids Research
  51. Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway
    Jian Carrot‐Zhang, Xiaotong Yao, Siddhartha H. K. Devarakonda, Aditya S. Deshpande, Jeffrey S. Damrauer, Tiago C. Silva, Christopher K. Wong, Hyo Young Choi, Ina Felau, A. Gordon Robertson et al. · 2021 · Cell Reports
  52. Serine hydroxymethyltransferase 2 expression promotes tumorigenesis in rhabdomyosarcoma with 12q13-q14 amplification
    Thanh Nguyen, Prasantha L. Vemu, Gregory E. Hoy, Salah Boudjadi, Bishwanath Chatterjee, Jack F. Shern, Javed Iqbal Khan, Wenyue Sun, Frederic G. Barr · 2021 · Journal of Clinical Investigation
  53. MeCP2 and transcriptional control of eukaryotic gene expression
    Ghanan Bin Akhtar, Marjorie Buist, Mojgan Rastegar · 2022 · European Journal of Cell Biology
  54. Intermingling of chromosome territories
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  55. Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers
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  57. Analysis of Hi-C Data for Discovery of Structural Variations in Cancer
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    Marina Saisana, S M Griffin, Felicity E. B. May · 2021 · Gastric Cancer
  59. Superenhancers as master gene regulators and novel therapeutic targets in brain tumors
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  60. The 3D genome and its impacts on human health and disease
    Siqi Wang, Zhengyu Luo, Weiguang Liu, Tengfei Hu, Zhongying Zhao, Michael G Rosenfeld, Xiaoyuan Song · 2023 · Life Medicine
  61. When 3D genome changes cause disease: the impact of structural variations in congenital disease and cancer
    Joachim Weischenfeldt, Daniel M. Ibrahim · 2023 · Current Opinion in Genetics & Development
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    Andrea Esposito, Carlo Annunziatella, Simona Bianco, Andrea M. Chiariello, Luca Fiorillo, Mario Nicodemi · 2018 · WIREs Systems Biology and Medicine
  63. Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells
    Karen Grimes, Hyobin Jeong, Amanda Amoah, Nuo Xu, Julian Niemann, Benjamin Raeder, Patrick Hasenfeld, Catherine Stober, Tobias Rausch, Eva Benito et al. · 2024 · Nature Genetics
  64. Mechanism of ERBB2 gene overexpression by the formation of super-enhancer with genomic structural abnormalities in lung adenocarcinoma without clinically actionable genetic alterations
    Syuzo Kaneko, Ken Takasawa, Ken Asada, Kouya Shiraishi, Noriko Ikawa, Hidenori Machino, Norio Shinkai, Maiko Matsuda, Mari Masuda, Shungo Adachi et al. · 2024 · Molecular Cancer
  65. Insulin receptor substrate 4 (IRS4) is a constitutive active oncogenic driver collaborating with HER2 and causing therapeutic resistance
    Gerjon J. Ikink, John Hilkens · 2017 · Molecular & Cellular Oncology
  66. Single-cell systems biology: Probing the basic unit of information flow
    Simona Patange, Michelle Girvan, Daniel R. Larson · 2017 · Current Opinion in Systems Biology
  67. Functional Consequences of Chromosomal Rearrangements on Gene Expression: Not So Deleterious After All?
    Yad Ghavi-Helm · 2019 · Journal of Molecular Biology
  68. Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types
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  69. 3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome
    Michał Wlasnowolski, Michał Sadowski, Tymon Czarnota, Karolina Jodkowska, Przemysław Szałaj, Zhonghui Tang, Yijun Ruan, Dariusz Plewczyński · 2020 · Nucleic Acids Research
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  71. A modern challenge of polymer physics: Novel ways to study, interpret, and reconstruct chromatin structure
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  74. Immuno-oncology from the perspective of somatic evolution
    Santiago González, Nadezda V. Volkova, Philip A. Beer, Moritz Gerstung · 2017 · Seminars in Cancer Biology
  75. Therapeutic Effects of Curcumin against Bladder Cancer: A Review of Possible Molecular Pathways.
    M. Ashrafizadeh, Habib Yaribeygi, A. Sahebkar · 2020 · Anti-Cancer Agents in Medicinal Chemistry
  76. Chromatin Mechanisms Driving Cancer
    Berkley E. Gryder, Peter C. Scacheri, Thomas Ried, Javed Iqbal Khan · 2021 · Cold Spring Harbor Perspectives in Biology
  77. Application of Hi-C and other omics data analysis in human cancer and cell differentiation research
    Haiyan Gong, Yi Yang, Sichen Zhang, Ming-Hong Li, Xiao-Tong Zhang · 2021 · Computational and Structural Biotechnology Journal
  78. The importance of considering regulatory domains in genome-wide analyses – the nearest gene is often wrong!
    Ellora Hui Zhen Chua, Samen Yasar, Nathan Harmston · 2022 · Biology Open
  79. Super-enhancer hijacking drives ectopic expression of hedgehog pathway ligands in meningiomas
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  80. Insulin receptor substrate-4 is overexpressed in colorectal cancer and promotes retinoblastoma–cyclin-dependent kinase activation
    Patricia Sanmartín-Salinas, M. Val Toledo-Lobo, Fernando Noguerales-Fraguas, Miguel Toro Londoño, Antonio Jiménez-Ruı́z, Luis G. Guijarro · 2018 · Journal of Gastroenterology
  81. Physical mechanisms of chromatin spatial organization
    Andrea M. Chiariello, Simona Bianco, Andrea Esposito, Luca Fiorillo, Mattia Conte, Ehsan Irani, Francesco Musella, Alex Abraham, Antonella Prisco, Mario Nicodemi · 2021 · FEBS Journal
  82. The hierarchical folding dynamics of topologically associating domains are closely related to transcriptional abnormalities in cancers
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  83. Nuclear receptor activation shapes spatial genome organization essential for gene expression control: lessons learned from the vitamin D receptor
    T. Warwick, Marcel H. Schulz, R. Gilsbach, R. P. Brandes, S. Seuter · 2022 · Nucleic Acids Research
  84. 3D or Not 3D: Shaping the Genome during Development
    Juliane Glaser, Stefan Mundlos · 2021 · Cold Spring Harbor Perspectives in Biology
  85. Rare or Overlooked? Structural Disruption of Regulatory Domains in Human Neurocristopathies
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  86. Dynamic Interactions of Transcription Factors and Enhancer Reprogramming in Cancer Progression
    Emily Kate Zboril, Hannah Yoo, Lizhen Chen, Zhijie Liu · 2021 · Frontiers in Oncology
  87. Urinary transcript quantitation of CK20 and IGF2 for the non-invasive bladder cancer detection
    Karsten Salomo, Doreen Huebner, Manja U. Boehme, Alexander Herr, Werner Brabetz, Ulrike Heberling, Oliver W. Hakenberg, Daniela Jahn, Marc‐Oliver Grimm, Daniel Steinbach et al. · 2017 · Journal of Cancer Research and Clinical Oncology
  88. Characterization of Structural Variations in the Context of 3D Chromatin Structure.
    Kyukwang Kim, Junghyun Eom, Inkyung Jung · 2019 · PubMed Central
  89. Spatial 3D genome organization reveals intratumor heterogeneity in primary glioblastoma samples
    Qixuan Wang, Juan Wang, Radhika Mathur, Mark W. Youngblood, Qiushi Jin, Ye Hou, Lena Ann Stasiak, Yu Luan, Hengqiang Zhao, Stephanie Hilz et al. · 2025 · Science Advances
  90. Chromatin organization modulates the origin of heritable structural variations in human genome
    Tanmoy Roychowdhury, Alexej S. Abyzov · 2019 · Nucleic Acids Research
  91. Balanced SET levels favor the correct enhancer repertoire during cell fate acquisition
    Mattia Zaghi, Federica Banfi, Luca Massimino, Monica Volpin, Edoardo Niccolò Bellini, Simone Brusco, Ivan Merelli A, Cristiana Barone, Michela Bruni, Linda Bossini et al. · 2023 · Nature Communications
  92. LINC01296 promotes neuroblastoma tumorigenesis via the NCL-SOX11 regulatory complex
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  93. Cross-species enhancer prediction using machine learning
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  94. Spatial and clonality-resolved 3D cancer genome alterations reveal enhancer-hijacking as a potential prognostic marker for colorectal cancer
    Kyukwang Kim, Mooyoung Kim, Andrew Lee, Sang‐Hyun Song, Jun‐Kyu Kang, Junghyun Eom, Gyeong Hoon Kang, Jeong Mo Bae, Sunwoo Min, Yeon Soo Kim et al. · 2023 · Cell Reports
  95. Molecular basis for SOX2-dependent regulation of super-enhancer activity
    Wanki Yoo, Yi Wei Song, Jihyun Kim, Jihye Ahn, Jaehoon Kim, Yongdae Shin, Je‐Kyung Ryu, Kyeong Kyu Kim · 2023 · Nucleic Acids Research
  96. Super-enhancer omics in stem cell
    Hongying Ma, Jian Qu, Zicheng Pang, Jian Luo, Min Yan, Wei-Xin Xu, Haihui Zhuang, Linxin Liu, Qiang Qu · 2024 · Molecular Cancer
  97. Defining the regulatory logic of breast cancer using single-cell epigenetic and transcriptome profiling
    Matthew J. Regner, Susana García‐Recio, Aatish Thennavan, Kamila Wiśniewska, Raúl Méndez-Giráldez, Brooke Felsheim, Philip M. Spanheimer, Joel S. Parker, Charles M. Perou, Hector L. Franco · 2025 · Cell Genomics
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    Patricia Sanmartín-Salinas, M. Val Toledo-Lobo, Fernando Noguerales-Fraguas, M.E. Fernández-Contreras, Luis G. Guijarro · 2017 · Journal of Molecular Histology
  99. InTAD: chromosome conformation guided analysis of enhancer target genes
    Konstantin Okonechnikov, Serap Erkek, Jan O. Korbel, Stefan Michael Pfister, Lukas Chávez · 2019 · BMC Bioinformatics
  100. Long Noncoding RNA LINC00173 Promotes the Malignancy of Melanoma by Promoting the Expression of IRS4 Through Competitive Binding to microRNA-493
    Fan Yang, Pengzhen Lei, Weihui Zeng, Jianwu Gao, Na Wu · 2020 · Cancer Management and Research · Retracted