Przybyla, L. & Gilbert, L. A. A new era in functional genomics screens. Nat. Rev. Genet. 23, 89–103 (2021).
Article
PubMed
Google Scholar
Findlay, G. M. Linking genome variants to disease: scalable approaches to test the functional impact of human mutations. Hum. Mol. Genet. 30, R187–R197 (2021).
Article
CAS
PubMed
PubMed Central
Google Scholar
Findlay, G. M. et al. Accurate classification of BRCA1 variants with saturation genome editing. Nature 562, 217–222 (2018).
Article
CAS
PubMed
PubMed Central
Google Scholar
Tewhey, R. et al. Direct identification of hundreds of expression-modulating variants using a multiplexed reporter assay. Cell 165, 1519–1529 (2016).
Article
CAS
PubMed
PubMed Central
Google Scholar
van Arensbergen, J. et al. High-throughput identification of human SNPs affecting regulatory element activity. Nat. Genet. 51, 1160–1169 (2019).
Article
PubMed
PubMed Central
Google Scholar
Doench, J. G. Am I ready for CRISPR? A user’s guide to genetic screens. Nat. Rev. Genet. 19, 67–80 (2018).
Article
CAS
PubMed
Google Scholar
Fowler, D. M. & Fields, S. Deep mutational scanning: a new style of protein science. Nat. Methods 11, 801–807 (2014).
Article
CAS
PubMed
PubMed Central
Google Scholar
Replogle, J. M. et al. Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing. Nat. Biotechnol. 38, 954–961 (2020).
Article
CAS
PubMed
PubMed Central
Google Scholar
Adamson, B. et al. A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response. Cell 167, 1867–1882 (2016).
Article
CAS
PubMed
PubMed Central
Google Scholar
Dixit, A. et al. Perturb-seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens. Cell 167, 1853–1866 (2016).
Article
CAS
PubMed
PubMed Central
Google Scholar
Datlinger, P. et al. Pooled CRISPR screening with single-cell transcriptome readout. Nat. Methods 14, 297–301 (2017).
Article
CAS
PubMed
PubMed Central
Google Scholar
Kim, H. S. et al. Direct measurement of engineered cancer mutations and their transcriptional phenotypes in single cells. Nat. Biotechnol. https://doi.org/10.1038/s41587-023-01949-8 (2023).
Ursu, O. et al. Massively parallel phenotyping of coding variants in cancer with Perturb-seq. Nat. Biotechnol. 40, 896–905 (2022).
Article
CAS
PubMed
Google Scholar
Pierce, S. E., Granja, J. M. & Greenleaf, W. J. High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer. Nat. Commun. 12, 2969 (2021).
Article
CAS
PubMed
PubMed Central
Google Scholar
Mertens, F., Johansson, B., Fioretos, T. & Mitelman, F. The emerging complexity of gene fusions in cancer. Nat. Rev. Cancer 15, 371–381 (2015).
Article
CAS
PubMed
Google Scholar
Mertens, F., Antonescu, C. R. & Mitelman, F. Gene fusions in soft tissue tumors: recurrent and overlapping pathogenetic themes. Genes Chromosomes Cancer 55, 291–310 (2016).
Article
CAS
PubMed
Google Scholar
Gryder, B. E. et al. PAX3–FOXO1 establishes myogenic super enhancers and confers BET bromodomain vulnerability. Cancer Discov. 7, 884–899 (2017).
Article
CAS
PubMed
PubMed Central
Google Scholar
Riggi, N. et al. EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma. Cancer Cell 26, 668–681 (2014).
Article
CAS
PubMed
PubMed Central
Google Scholar
Boulay, G. et al. Cancer-specific retargeting of BAF complexes by a prion-like domain. Cell 171, 163–178 (2017).
Article
CAS
PubMed
PubMed Central
Google Scholar
Jang, Y. E. et al. ChimerDB 4.0: an updated and expanded database of fusion genes. Nucleic Acids Res. 48, D817–D824 (2020).
CAS
PubMed
Google Scholar
Sweeney, N. P. & Vink, C. A. The impact of lentiviral vector genome size and producer cell genomic to gag-pol mRNA ratios on packaging efficiency and titre. Mol. Ther. Methods Clin. Dev. 21, 574–584 (2021).
Article
CAS
PubMed
PubMed Central
Google Scholar
Milone, M. C. & O’Doherty, U. Clinical use of lentiviral vectors. Leukemia 32, 1529–1541 (2018).
Article
CAS
PubMed
PubMed Central
Google Scholar
Xie, S., Cooley, A., Armendariz, D., Zhou, P. & Hon, G. C. Frequent sgRNA-barcode recombination in single-cell perturbation assays. PLoS ONE 13, e0198635 (2018).
Article
PubMed
PubMed Central
Google Scholar
Adamson, B., Norman, T. M., Jost, M. & Weissman, J. S. Approaches to maximize sgRNA-barcode coupling in Perturb-seq screens. Preprint at bioRxiv https://doi.org/10.1101/298349 (2018).
Feldman, D., Singh, A., Garrity, A. J. & Blainey, P. C. Lentiviral co-packaging mitigates the effects of intermolecular recombination and multiple integrations in pooled genetic screens. Preprint at bioRxiv https://doi.org/10.1101/262121 (2018).
Parekh, U. et al. Mapping cellular reprogramming via pooled overexpression screens with paired fitness and single-cell RNA-sequencing readout. Cell Syst. 7, 548–555 (2018).
Article
CAS
PubMed
PubMed Central
Google Scholar
Hill, A. J. et al. On the design of CRISPR-based single-cell molecular screens. Nat. Methods 15, 271–274 (2018).
Article
CAS
PubMed
PubMed Central
Google Scholar
Matreyek, K. A., Stephany, J. J., Chiasson, M. A., Hasle, N. & Fowler, D. M. An improved platform for functional assessment of large protein libraries in mammalian cells. Nucleic Acids Res. 48, e1 (2020).
CAS
PubMed
Google Scholar
Sánchez-Molina, S. et al. RING1B recruits EWSR1-FLI1 and cooperates in the remodeling of chromatin necessary for Ewing sarcoma tumorigenesis. Sci. Adv. 6, eaba3058 (2020).
Article
PubMed
PubMed Central
Google Scholar
Deng, Q. et al. Oncofusion-driven de novo enhancer assembly promotes malignancy in Ewing sarcoma via aberrant expression of the stereociliary protein LOXHD1. Cell Rep. 39, 110971 (2022).
Article
CAS
PubMed
PubMed Central
Google Scholar
Manceau, L. et al. Divergent transcriptional and transforming properties of PAX3-FOXO1 and PAX7-FOXO1 paralogs. PLoS Genet. 18, e1009782 (2022).
Article
CAS
PubMed
PubMed Central
Google Scholar
Orth, M. F. et al. Systematic multi-omics cell line profiling uncovers principles of Ewing sarcoma fusion oncogene-mediated gene regulation. Cell Rep. 41, 111761 (2022).
Article
CAS
PubMed
PubMed Central
Google Scholar
Tate, J. G. et al. COSMIC: the Catalogue Of Somatic Mutations In Cancer. Nucleic Acids Res. 47, D941–D947 (2019).
Article
CAS
PubMed
Google Scholar
Granja, J. M. et al. ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis. Nat. Genet. 53, 403–411 (2021).
Article
CAS
PubMed
PubMed Central
Google Scholar
Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587 (2021).
Article
CAS
PubMed
PubMed Central
Google Scholar
Jost, M. et al. Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs. Nat. Biotechnol. 38, 355–364 (2020).
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang, Y. et al. Model-based analysis of ChIP-seq (MACS). Genome Biol. 9, R137 (2008).
Article
PubMed
PubMed Central
Google Scholar
Sunkel, B. D. et al. Evidence of pioneer factor activity of an oncogenic fusion transcription factor. iScience 24, 102867 (2021).
Article
CAS
PubMed
PubMed Central
Google Scholar
AACR Project GENIE Consortium AACR Project GENIE: powering precision medicine through an international consortium. Cancer Discov. 7, 818–831 (2017).
Article
Google Scholar
Chang, W.-I. et al. Molecular targets for novel therapeutics in pediatric fusion-positive non-CNS solid tumors. Front. Pharmacol. 12, 747895 (2022).
Article
PubMed
PubMed Central
Google Scholar
Perry, J. A., Seong, B. K. A. & Stegmaier, K. Biology and therapy of dominant fusion oncoproteins involving transcription factor and chromatin regulators in sarcomas. Annu. Rev. Cancer Biol. 3, 299–321 (2019).
Article
Google Scholar
Möller, E. et al. EWSR1-ATF1 dependent 3D connectivity regulates oncogenic and differentiation programs in clear cell sarcoma. Nat. Commun. 13, 2267 (2022).
Article
PubMed
PubMed Central
Google Scholar
Johnson, K. M. et al. Role for the EWS domain of EWS/FLI in binding GGAA-microsatellites required for Ewing sarcoma anchorage independent growth. Proc. Natl Acad. Sci. USA 114, 9870–9875 (2017).
Article
CAS
PubMed
PubMed Central
Google Scholar
Johnson, K. M., Taslim, C., Saund, R. S. & Lessnick, S. L. Identification of two types of GGAA-microsatellites and their roles in EWS/FLI binding and gene regulation in Ewing sarcoma. PLoS ONE 12, e0186275 (2017).
Article
PubMed
PubMed Central
Google Scholar
Guillon, N. et al. The oncogenic EWS-FLI1 protein binds in vivo GGAA microsatellite sequences with potential transcriptional activation function. PLoS ONE 4, e4932 (2009).
Article
PubMed
PubMed Central
Google Scholar
Li, Z. et al. ETV6-NTRK3 fusion oncogene initiates breast cancer from committed mammary progenitors via activation of AP1 complex. Cancer Cell 12, 542–558 (2007).
Article
CAS
PubMed
PubMed Central
Google Scholar
Przybyl, J. et al. Gene expression profiling of low-grade endometrial stromal sarcoma indicates fusion protein-mediated activation of the Wnt signaling pathway. Gynecol. Oncol. 149, 388–393 (2018).
Article
CAS
PubMed
Google Scholar
Gordon, A. T. et al. A novel and consistent amplicon at 13q31 associated with alveolar rhabdomyosarcoma. Genes Chromosomes Cancer 28, 220–226 (2000).
Article
CAS
PubMed
Google Scholar
Yoon, J. W., Lamm, M., Chandler, C., Iannaccone, P. & Walterhouse, D. Up-regulation of GLI1 in vincristine-resistant rhabdomyosarcoma and Ewing sarcoma. BMC Cancer 20, 511 (2020).
Article
CAS
PubMed
PubMed Central
Google Scholar
Birdsey, G. M. et al. The endothelial transcription factor ERG promotes vascular stability and growth through Wnt/β-catenin signaling. Dev. Cell 32, 82–96 (2015).
Article
CAS
PubMed
PubMed Central
Google Scholar
Brcic, I. et al. Implementation of copy number variations-based diagnostics in morphologically challenging EWSR1/FUS::NFATC2 neoplasms of the bone and soft tissue. Int. J. Mol. Sci. 23, 16196 (2022).
Article
PubMed
PubMed Central
Google Scholar
Deplus, R. et al. TMPRSS2-ERG fusion promotes prostate cancer metastases in bone. Oncotarget 8, 11827–11840 (2016).
Article
PubMed Central
Google Scholar
Parviz, F. et al. Hepatocyte nuclear factor 4α controls the development of a hepatic epithelium and liver morphogenesis. Nat. Genet. 34, 292–296 (2003).
Article
CAS
PubMed
Google Scholar
Zhang, B. et al. Proteogenomic characterization of human colon and rectal cancer. Nature 513, 382–387 (2014).
Article
CAS
PubMed
PubMed Central
Google Scholar
Weinstein, J. N. et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat. Genet. 45, 1113–1120 (2013).
Article
PubMed
PubMed Central
Google Scholar
Davis, R. B., Kaur, T., Moosa, M. M. & Banerjee, P. R. FUS oncofusion protein condensates recruit mSWI/SNF chromatin remodeler via heterotypic interactions between prion‐like domains. Protein Sci. Publ. Protein Soc. 30, 1454–1466 (2021).
Article
CAS
Google Scholar
Domingo, J. et al. Non-linear transcriptional responses to gradual modulation of transcription factor dosage. Preprint at bioRxiv https://doi.org/10.1101/2024.03.01.582837 (2024).
Backman, J. D. et al. Exome sequencing and analysis of 454,787 UK Biobank participants. Nature 599, 628–634 (2021).
Article
CAS
PubMed
PubMed Central
Google Scholar
Lancaster, A. K., Nutter-Upham, A., Lindquist, S. & King, O. D. PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition. Bioinformatics 30, 2501–2502 (2014).
Article
CAS
PubMed
PubMed Central
Google Scholar
Farag, M., Borcherds, W. M., Bremer, A., Mittag, T. & Pappu, R. V. Phase separation in mixtures of prion-like low complexity domains is driven by the interplay of homotypic and heterotypic interactions. Preprint at bioRxiv https://doi.org/10.1101/2023.03.15.532828 (2023).
Boncella, A. E. et al. Composition-based prediction and rational manipulation of prion-like domain recruitment to stress granules. Proc. Natl Acad. Sci. USA 117, 5826–5835 (2020).
Article
CAS
PubMed
PubMed Central
Google Scholar
Sprunger, M. L. & Jackrel, M. E. Prion-like proteins in phase separation and their link to disease. Biomolecules 11, 1014 (2021).
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang, Y. et al. Dissolution of oncofusion transcription factor condensates for cancer therapy. Nat. Chem. Biol. 19, 1223–1234 (2023).
Article
CAS
PubMed
Google Scholar
Frankish, A. et al. GENCODE 2021. Nucleic Acids Res. 49, D916–D923 (2021).
Article
CAS
PubMed
Google Scholar
Rubin, A. F. et al. A statistical framework for analyzing deep mutational scanning data. Genome Biol. 18, 150 (2017).
Article
PubMed
PubMed Central
Google Scholar
Corces, M. R. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat. Methods 14, 959–962 (2017).
Article
CAS
PubMed
PubMed Central
Google Scholar
Reske, J. J., Wilson, M. R. & Chandler, R. L. ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation. Epigenetics Chromatin 13, 22 (2020).
Article
CAS
PubMed
PubMed Central
Google Scholar
Center for High Throughput Computing (University of Wisconsin–Madison); https://doi.org/10.21231/GNT1-HW21. Accessed September 2021
Frenkel, M., Corban, J. E., Hujoel, M. L. A., Morris, Z. & Raman, S. Large-scale discovery of chromatin dysregulation induced by oncofusions and other protein-coding variants. NCBI https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE243553 (2024).
Frenkel, M., Corban, J. E., Hujoel, M. L. A., Morris, Z. & Raman, S. Oncofusion PROD-ATAC. GitHub https://github.com/mfrenkel16/OncofusionPRODATAC (2024).
Information contained on this page is provided by an independent third-party content provider. This website makes no warranties or representations in connection therewith. If you are affiliated with this page and would like it removed please contact editor @americanfork.business