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Array CGH Demonstrates Characteristic Aberration Signatures in Human Papillary Thyroid Carcinomas Governed by RET/PTC

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Oncogene (2008) 27, 4592–4602 & 2008 Macmillan Publishers Limited All rights reserved 0950-9232/08 $30.00 www.nature.com/onc ORIGINAL ARTICLE Array CGH demonstrates characteristic aberration signatures in human papillary thyroid carcinomas governed by RET/PTC K Unger1,2,9, E Malisch1,9, G Thomas2, H Braselmann1, A Walch3, G Jackl4, P Lewis5, E Lengfelder6, T Bogdanova7, J Wienberg8 and H Zitzelsberger1 1Institut fu¨r Molekulare Strahlenbiologie, Helmholtz Zentrum Mu¨nchen—Deutsches Forschungszentrum fu¨r Gesundheit und Umwelt GmbH, Germany; 2Department of Histopathology, Hammersmith Hospital, London, UK; 3Institut fu¨r Pathologie, Helmholtz Zentrum Mu¨nchen—Deutsches Forschungszentrum fu¨r Gesundheit und Umwelt GmbH, Germany; 4Institut fu¨r Strahlenbiologie, Helmholtz Zentrum Mu¨nchen—Deutsches Forschungszentrum fu¨r Gesundheit und Umwelt GmbH, Germany; 5Swansea Medical School, Swansea University, Singleton Park, Swansea, UK; 6Strahlenbiologisches Institut, Ludwig Maximilians Universita¨t, Mu¨nchen, Germany; 7Institute of Endocrinology and Metabolism, Academy of Medical Sciences of the Ukraine, Kiev, Ukraine and 8Department Biologie II, Anthropologie und Humangenetik, Ludwig Maximilians Universita¨t, Mu¨nchen, Germany The aim of this study is to investigate additional genetic Introduction alterations in papillary thyroid carcinomas (PTCs) with known RET/PTC rearrangements. We applied array- A frequent genetic alteration in papillary thyroid based comparative genomic hybridization (array CGH) to carcinomas (PTCs) is rearrangement of the RET 33 PTC (20 PTC from adults, 13 post-Chernobyl PTC proto-oncogene, which has been assigned to chromoso- from children) with known RET/PTC status. Principal mal band 10q11.2 (Grieco et al., 1990; Pierotti et al., component analysis and hierarchical cluster analysis 1992). RET/PTC oncogenic activation is the result of identified cases with similar aberration patterns. Signifi- chromosomal rearrangements, which fuse the RET cant deviations between tumour-groups were obtained by tyrosine kinase (RET-TK) domain to the 50-terminal statistical testing (Fisher’s exact test in combination with region of heterologous genes. The rearrangements are a Benjamini–Hochberg FDR-controlling procedure). FISH marker for PTCs as their very name RET/PTC implies. analysis on FFPE sections was applied to validate the At least 16 chimeric mRNAs involving 11 different array CGH data. Deletions were found more frequently in genes have been reported (reviewed in Santoro et al., RET/PTC-positive and RET/PTC-negative tumours than 2004) of which RET/PTC1 (RET rearrangement with amplifications. Specific aberration signatures were identi- H4) and RET/PTC3 (RET rearrangement with RFG/ fied that discriminated between RET/PTC-positive and ELE1) are by far the most common (Santoro et al., RET/PTC-negative cases (aberrations on chromosomes 2004). The incidence of RET/PTC in radiation-induced 1p, 3q, 4p, 7p, 9p/q, 10q, 12q, 13q and 21q). In addition, childhood PTCs is in the range of 50–70% (Klugbauer childhood and adult RET/PTC-positive cases differ et al., 1995; Smida et al., 1999; Thomas et al., 1999; significantly for a deletion on the distal part of Rabes et al., 2000), whereas in sporadic papillary chromosome 1p. There are additional alterations in carcinomas in adults the incidence is somewhat lower RET/PTC-positive tumours, which may act as modifiers (5–30%) (Jhiang and Mazzaferri, 1994). However, the of RET activation. In contrast, alterations in RET/ identification of RET/PTC in other common thyroid PTC-negative tumours indicate alternative routes of tumour histotypes such as oncocytic adenomas and tumour development. The data presented serve as a carcinomas (Cheung et al., 2000), and even in hyper- starting point for further studies on gene expression and plastic thyroid nodules (Ishizaka et al., 1991; Elisei et al., function of genes identified in this study. 2001) and Hashimoto’s thyroiditis (Rhoden et al., 2006), Oncogene (2008) 27, 4592–4602; doi:10.1038/onc.2008.99; seems to challenge the validity of RET/PTC as a tumour published online 14 April 2008 marker and its specificity for PTC. Moreover, it has been recently shown that the level of RET/PTC Keywords: papillary thyroid carcinoma; array CGH; expression in papillary carcinoma is highly variable, RET/PTC; candidate genes; tumour development; suggesting that the distribution of RET/PTC within one aberration signature tumour may not be homogenous (Rhoden et al., 2004; Unger et al., 2004). This is also supported by recent fluorescence in situ hybridization (FISH) studies by ourselves and others (Unger et al., 2004; Ciampi and Correspondence: Dr H Zitzelsberger, Helmholtz Zentrum Mu¨ nchen, Nikiforov, 2007). Institute for Molecular Radiobiology, Ingolsta¨ dter-Landstrae1, To investigate whether other genes are involved in Neuherberg D-85764, Germany. thyroid carcinogenesis, we have studied a series of PTCs E-mail: [email protected] 9These authors contributed equally to this study. by array-based comparative genomic hybridization Received 19 July 2007; revised 29 November 2007; accepted 29 February (array CGH). Array CGH represents an approach using 2008; published online 14 April 2008 mapped sequences arrayed onto glass slides instead of Array CGH on PTC K Unger et al 4593 metaphase chromosomes that are used in conventional Results CGH as hybridization targets. This generates a higher resolution dependent on the insert size and density of We analysed 33 post-Chernobyl PTCs from adults and the mapped sequences. In this study, we used bacterial children for chromosomal changes by array CGH. The artificial chromosome (BAC)-arrays (B3400 clones) tumours were also characterized for the presence of RET/ that allow the examination of the entire genome for PTC rearrangements on a single-cell level by FISH. The chromosomal copy number changes (DNA gains and RET/PTC status of each tumour and the patient’s losses) with a resolution of 1 Mb. A striking advantage demographic and clinical data are summarized in Table 1. of this technology is its use on archival paraffin- embedded material (van Beers et al., 2006). In this study on PTC, array CGH was used to Chromosomal imbalances, hierarchical cluster analysis investigate chromosomal changes in 33 papillary thyroid and principal component analysis post-Chernobyl adult and childhood PTC. In all cases, In general, DNA losses occurred more frequently than the tumours have been pre-characterized in terms of DNA gains. The most frequent imbalances (in more RET/PTC rearrangements. than 30% of tumours) were losses on chromosomes The aim of this study was to determine differences in 1, 6, 7, 9, 10, 11, 12, 13, 16, 19, 20, 22 and gains on chromosomal aberration patterns between RET/PTC- chromosomes 10, 12, 19, 20, 21 (Figure 1). Hierarchical positive and -negative PTC. The identification of char- cluster analysis (HCA) employing the correlations acteristic alteration signatures in different tumour groups between the array CGH profiles segregated significantly (adult, childhood, RET/PTC-positive, RET/PTC-nega- nine adult RET/PTC-negative cases from all other cases tive) enabled a subsequent characterization of candidate (Fisher’s exact test, Po0.05; Figure 2). The patterns of genes that may either cooperate with or substitute for array CGH differences observed using HCA RET/PTC in papillary thyroid carcinogenesis. were confirmed using principal component analysis Table 1 Patient data and RET/PTC status Case no. Gender/age (years) Histology Histological variant RET/PTC statusa BRAF T1796A mutationb 1 F/35 PTC, pT4aN1aM0 Papillary RET/PTC1 + 2 F/32 PTC, pT4bN1aM0 Follicular RET/PTC1 À 3 M/32 PTC, pT4aN1aM0 Papillary RET/PTC1 À 4 F/42 PTC, pT4bN1aM0 Mixed RET/PTC3 À 5 F/37 PTC, pT4aN1aM0 Papillary RET/PTC1 À 6 M/31 PTC, pT4bN1M0 Papillary RET/PTC3 À 7 M/21 PTC, pT4bN1bM0 Papillary RET/PTC3 À 8 F/26 PTC, pT4bN1bM0 Papillary RET/PTC3 À 9 F/28 PTC, pT4bN2bM0 Papillary RET/PTC-positive À 10 F/36 PTC, pT4N1bM0 Solid RET/PTC1 À 11 F/35 PTC, pT4bN0M0 Papillary RET/PTC-negative À 12 F/32 PTC, pT2aN0M0 Solid RET/PTC-positive À 13 F/32 PTC, pT3N0M0 Papillary RET/PTC-negative À 14 F/42 PTC, pT4aN1aM0 Papillary RET/PTC-negative + 15 F/37 PTC, pT4bN1bM0 Papillary RET/PTC-negative À 16 F/31 PTC, pT4aN1bM0 Papillary RET/PTC-negative À 17 F/21 PTC, pT4aN1bM0 Papillary RET/PTC-negative + 18 M/26 PTC, pT3aN1aM0 Papillary RET/PTC-negative À 19 F/28 PTC, pT4aN1aM0 Papillary RET/PTC-negative À 20 F/36 PTC, pT4aN1aM0 Papillary RET/PTC-negative À 21 M/8 PTC, pT4N2M0 Follicular-solid RET/PTC3 À 22 M/10 PTC, pT4N2M1 Follicular-solid RET/PTC1 À 23 F/15 PTC, pT4N2M0 Follicular-solid RET/PTC3 À 24 F/11 PTC, pT4N2M1 Follicular-solid RET/PTC1 À 25 F/15 PTC, pT4N2M1 Follicular-solid RET/PTC3 À 26 F/14 PTC, pT4N2M1 Follicular-solid RET/PTC3 À 27 F/11 PTC, pT4N1b,M0 Solid RET/PTC3 À 28 M/13 PTC, pT4N2M1 Follicular-solid RET/PTC-negative À 29 M/10 PTC, pT4N1M0 Follicular-solid RET/PTC-negative À 30 F/14 PTC, pT4N0M0 Follicular-solid RET/PTC-positive À 31 F/10 PTC, pT4N1M1 Follicular-solid RET/PTC-negative À 32 F/10 PTC, pT4N1M1 Follicular-solid RET/PTC-positive À 33 M/10 PTC, pT4N0M0 Follicular-solid RET/PTC-positive À Abbreviations: F, female; M, male; RET/PTC-negative, no indication for elevated RET tyrosine kinase (TK) expression or specific RET rearrangement; RET/PTC-positive, elevated expression of TK domain in comparison to extracellular domain, measured by reverse transcription– PCR; PTC, papillary thyroid carcinoma; +, mutation present; À, mutation absent. aAs previously published in Smida et al., 1999 and Unger et al., 2006. bBRAF mutation analysed according to Powell et al., 2005. Oncogene Array CGH on PTC K Unger et al 4594 Comparison of tumour groups On the basis of the results from the cluster analysis, we grouped tumours into RET/PTC-positive from adults, RET/PTC-positive from children and RET/PTC- negative tumours from adults and analysed them for significant differences.
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    bioRxiv preprint doi: https://doi.org/10.1101/2020.05.08.084418; this version posted May 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Proteomic Analysis Uncovers Measles Virus Protein C Interaction with p65/iASPP/p53 Protein Complex Alice Meignié1,2*, Chantal Combredet1*, Marc Santolini 3,4, István A. Kovács4,5,6, Thibaut Douché7, Quentin Giai Gianetto 7,8, Hyeju Eun9, Mariette Matondo7, Yves Jacob10, Regis Grailhe9, Frédéric Tangy1**, and Anastassia V. Komarova1, 10** 1 Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, CNRS UMR-3569, 75015 Paris, France 2 Université Paris Diderot, Sorbonne Paris Cité, Paris, France 3 Center for Research and Interdisciplinarity (CRI), Université de Paris, INSERM U1284 4 Network Science Institute and Department of Physics, Northeastern University, Boston, MA 02115, USA 5 Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208-3109, USA 6 Department of Network and Data Science, Central European University, Budapest, H-1051, Hungary 7 Proteomics platform, Mass Spectrometry for Biology Unit (MSBio), Institut Pasteur, CNRS USR 2000, Paris, France. 8 Bioinformatics and Biostatistics Hub, Computational Biology Department, Institut Pasteur, CNRS USR3756, Paris, France 9 Technology Development Platform, Institut Pasteur Korea, Seongnam-si, Republic of Korea 10 Laboratory of Molecular Genetics of RNA Viruses, Institut Pasteur, CNRS UMR-3569,
  • Supplementary Table 1: Adhesion Genes Data Set

    Supplementary Table 1: Adhesion Genes Data Set

    Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like,