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      MYCN induces cell-specific tumorigenic growth in RB1-proficient human retinal organoid and chicken retina models of retinoblastoma

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          Abstract

          Retinoblastoma is a rare, intraocular paediatric cancer that originates in the neural retina and is most frequently caused by bi-allelic loss of RB1 gene function. Other oncogenic mutations, such as amplification and increased expression of the MYCN gene, have been found even with proficient RB1 function. In this study, we investigated whether MYCN over-expression can drive carcinogenesis independently of RB1 loss-of-function mutations. The aim was to elucidate the events that result in carcinogenesis and identify the cancer cell-of-origin. We used the chicken retina, a well-established model for studying retinal neurogenesis, and established human embryonic stem cell-derived retinal organoids as model systems. We over-expressed MYCN by electroporation of piggyBac genome-integrating expression vectors. We found that over-expression of MYCN induced tumorigenic growth with high frequency in RB1-proficient chicken retinas and human organoids. In both systems, the tumorigenic cells expressed markers for undifferentiated cone photoreceptor/horizontal cell progenitors. The over-expression resulted in metastatic retinoblastoma within 7–9 weeks in chicken. Cells expressing MYCN could be grown in vitro and, when orthotopically injected, formed tumours that infiltrated the sclera and optic nerve and expressed markers for cone progenitors. Investigation of the tumour cell phenotype determined that the potential for neoplastic growth was embryonic stage-dependent and featured a cell-specific resistance to apoptosis in the cone/horizontal cell lineage, but not in ganglion or amacrine cells. We conclude that MYCN over-expression is sufficient to drive tumorigenesis and that a cell-specific resistance to apoptosis in the cone/horizontal cell lineage mediates the cancer phenotype.

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          clusterProfiler: an R package for comparing biological themes among gene clusters.

          Increasing quantitative data generated from transcriptomics and proteomics require integrative strategies for analysis. Here, we present an R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters. The analysis module and visualization module were combined into a reusable workflow. Currently, clusterProfiler supports three species, including humans, mice, and yeast. Methods provided in this package can be easily extended to other species and ontologies. The clusterProfiler package is released under Artistic-2.0 License within Bioconductor project. The source code and vignette are freely available at http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html.
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            featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.

            Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to each genomic feature, for example to each exon or each gene. The process of counting reads is called read summarization. Read summarization is required for a great variety of genomic analyses but has so far received relatively little attention in the literature. We present featureCounts, a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments. featureCounts implements highly efficient chromosome hashing and feature blocking techniques. It is considerably faster than existing methods (by an order of magnitude for gene-level summarization) and requires far less computer memory. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications. featureCounts is available under GNU General Public License as part of the Subread (http://subread.sourceforge.net) or Rsubread (http://www.bioconductor.org) software packages.
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              A series of normal stages in the development of the chick embryo

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                Author and article information

                Contributors
                finn.hallbook@igp.uu.se
                Journal
                Oncogenesis
                Oncogenesis
                Oncogenesis
                Nature Publishing Group UK (London )
                2157-9024
                21 June 2022
                21 June 2022
                December 2022
                : 11
                : 1
                : 34
                Affiliations
                [1 ]GRID grid.8993.b, ISNI 0000 0004 1936 9457, Department of Immunology, Genetics, and Pathology, , Uppsala University, ; Uppsala, Sweden
                [2 ]GRID grid.8993.b, ISNI 0000 0004 1936 9457, National Bioinformatics Infrastructure Sweden, Uppsala University, SciLifeLab, , Department of Medical Biochemistry and Microbiology, ; Uppsala, Sweden
                [3 ]GRID grid.4714.6, ISNI 0000 0004 1937 0626, St. Erik Eye Hospital, Department of Clinical Neuroscience, , Karolinska Institute, ; Stockholm, Sweden
                Author information
                http://orcid.org/0000-0002-1459-0377
                http://orcid.org/0000-0002-6959-8376
                http://orcid.org/0000-0002-3687-9745
                http://orcid.org/0000-0001-7552-187X
                Article
                409
                10.1038/s41389-022-00409-3
                9213451
                35013097
                ed34b7a0-8995-46ec-a65e-cf118c24ff76
                © The Author(s) 2022

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 10 March 2022
                : 3 June 2022
                : 7 June 2022
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100006313, Barncancerfonden (Swedish Childhood Cancer Foundation);
                Award ID: PR2019-0068, PR2017-0105
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100004359, Vetenskapsrådet (Swedish Research Council);
                Award ID: 2016-01641
                Award Recipient :
                Funded by: The Eye fund, 2020-055 The Brain fund, FO2020-0291, FO2019-0151
                Categories
                Article
                Custom metadata
                © The Author(s) 2022

                Oncology & Radiotherapy
                cancer models,embryonal neoplasms,paediatric cancer,cns cancer
                Oncology & Radiotherapy
                cancer models, embryonal neoplasms, paediatric cancer, cns cancer

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