Abstract 3028: Integrative genomics reveals lncRNAs associated with pediatric cancer
Authors: Apexa Modi, Gonzalo Lopez, Karina L. Conkrite, Tsz Ching Leung, Sathvik Ramanan, Daphne Cheung, Chun Su, Matthew E. Johnson, Elisabetta Manduchi, Samantha Gadd, Jinghui Zhang, Malcolm A. Smith, Jaime M. Guidry Auvil, Daniela S. Gerhard, Soheil Meshinchi, Elizabeth J. Perlman, Stephen P. Hunger, John M. Maris, Andrew D. Wells, Struan F. Grant, Sharon J. Diskin
Journal: Cancer Research (2021)

Abstract Background: Long non-coding RNAs (lncRNAs) have emerged as key components of transcriptional and post-transcriptional gene regulation. Dysregulation of lncRNA expression has been widely observed in cancer and several lncRNAs are known to influence tumor initiation and progression. Despite this, the lncRNA landscape and regulatory networks across pediatric cancers remain relatively uncharted. Methods: To characterize the lncRNA landscape of pediatric cancers, we first curated RNA sequencing data for 1,044 pediatric leukemia and solid tumors from the Therapeutically Applicable Research To Generate Effective Treatments (TARGET) project to identify known and novel expressed lncRNAs. This data set included: 280 acute myeloid leukemia (AML), 190 acute B-cell leukemia (B-ALL), 244 acute T-cell leukemia (T-ALL), 121 Wilm's tumor (WT), 48 rhabdoid tumors (RT), and 161 neuroblastoma (NBL). Histotype-specific expression was assessed using the tau score. Whole genome sequencing (WGS) from 826 matched normal-tumor pairs was integrated to identify somatic copy number alterations (SCNAs) disrupting lncRNA expression. To further implicate cancer-relevant drivers of lncRNA expression, we used a unique combination of epigenetic data in pediatric cell lines, including ChIP-sequencing for cancer-specific transcription factors and genome-scale chromatin capture data. A global analysis of lncRNA function was performed using the lncMod method, in which expression data is modelled to identify lncRNA modulators that perturb transcription factor regulation of target genes. Functional prioritization of lncRNAs was obtained through integration of analyses per cancer. Biochemical assays in human-derived cell line models were utilized to validate the function of the top prioritized lncRNA in NBL. Results: We report a total of 2,657 robustly expressed lncRNAs across six pediatric cancers, including 1,142 lncRNAs exhibiting histotype-specific expression. SCNAs contributed to lncRNA dysregulation at a proportion comparable to protein coding genes. There were 207 (28%) lncRNAs in regions with SCNA that had significant expression dysregulation. LncMod analysis across the cancers revealed context-specific transcriptional gene networks per dysregulated lncRNA and enrichment for proliferation, metabolic, and DNA damage hallmarks. We further identified 547 cancer-associated lncRNAs in NBL based on upstream regulation via oncogenic transcription factors. The top-prioritized lncRNA, TBX2-AS1, was predicted to impact proliferation in NBL. Silencing of TBX2-AS1 using siRNAs achieved &amp;gt;90% knockdown in NBL cells and resulted in 46.6% decreased cell growth (p = 8.1 x 10-4). Conclusion: This study defines the lncRNA landscape across six pediatric cancers and provides a detailed catalog of how lncRNAs impact regulatory gene networks. These data serve as a robust resource for future hypothesis-driven mechanistic studies. Citation Format: Apexa Modi, Gonzalo Lopez, Karina L. Conkrite, Tsz Ching Leung, Sathvik Ramanan, Daphne Cheung, Chun Su, Matthew E. Johnson, Elisabetta Manduchi, Samantha Gadd, Jinghui Zhang, Malcolm A. Smith, Jaime M. Guidry Auvil, Daniela S. Gerhard, Soheil Meshinchi, Elizabeth J. Perlman, Stephen P. Hunger, John M. Maris, Andrew D. Wells, Struan F. Grant, Sharon J. Diskin. Integrative genomics reveals lncRNAs associated with pediatric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 3028.