Abstract 1417: Investigating the functional impacts of single-nucleotide variants in anaplastic large cell lymphoma
Authors: Hugo Larose, Shahid A. Mian, Edem Nuglozeh, Feroze M. Fazaludeen, Ahmed M. Elmouna, Ibraheem Ashankyty, Ming-Qing Du, Gerald Hofler, Sarka Pospisilova, Wilhem Woessmann, Christine Damm-Welk, Alina Fedorova, Laurence Lamant, Michaela Schlederer, Olaf Merkel, Lukas Kenner, Suzanne D. Turner
Journal: Cancer Research (2018)

Abstract In order to understand the biology of Anaplastic Large Cell Lymphoma (ALCL) and to develop biomarkers, we performed Whole-Exome Sequencing (WES) of DNA extracted from patient tumor samples (of at least 90% tumor cell content; n=31), and are exploring the functional implications of the mutations detected. Bioinformatics processing involved variant calling using software Pindel1 and CaVeman, while annotation was done using Annovar2. Single nucleotide polymorphisms (SNPs) and single nucleotide variants (SNVs) with an allele frequency in excedent of 0.1% (as determined by the dbSNP database, build 150), and variants not predicted to be damaging (ie with a low variant effect prediction - VEP - score) were filtered out. Pathway analysis using the Panther database3 revealed that our variants were enriched in genes of the Wnt signalling pathway and of the signalling pathway of the Nicotinic acetylcholine receptor. 54 of our hits, single nucleotide variants or Insertions/Deletions (Indels) were identified as being common to at least 20% of all our sequenced samples. In 8.6% of patient samples (n=71) and 1 of 4 ALCL cell lines, a novel SNV in Notch1 was detected and investigated further for its functional consequences. Inhibition of Notch1 with several Gamma-Secretase Inhibitors or shRNA led to a significant decrease in cell growth concomitant with an increase in cell death. Furthermore, co-treatment with the ALK/cMet/ROS inhibitor Crizotinib together with Notch inhibitors led to additive effects on cell death. Our genomics study indicates an important role for Notch1 in the biology of ALCL, although the exact functional implications of the SNV detected is as yet unclear. References 1 Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 2009; 25: 2865-2871. 2 Wang K, Li M, Hakonarson H. ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 2010; 38: 1-7. 3 Mi H, Huang X, Muruganujan A, Tang H, Mills C, Kang D et al. PANTHER version 11: Expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements. Nucleic Acids Res 2017; 45: D183-D189. Citation Format: Hugo Larose, Shahid A. Mian, Edem Nuglozeh, Feroze M. Fazaludeen, Ahmed M. Elmouna, Ibraheem Ashankyty, Ming-Qing Du, Gerald Hofler, Sarka Pospisilova, Wilhem Woessmann, Christine Damm-Welk, Alina Fedorova, Laurence Lamant, Michaela Schlederer, Olaf Merkel, Lukas Kenner, Suzanne D. Turner. Investigating the functional impacts of single-nucleotide variants in anaplastic large cell lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1417.