Abstract 3050: Comprehensive coding and non coding transcript based characterization of Indian medulloblastoma
Authors: Neetu Singh, Nawazish Alam, Dinesh K. Sahu, Ratnesh K. Tripathi, Mayank Jain, Pratap Shankar, Hari Shyam, Archana Mishra, Anil Kumar, Uma S. Singh, Anil Chandra, Chhitij Srivastava, Bal K. Ojha, Devendra K. Gupta, Ravi Kant, Bipin Puri
Journal: Cancer Research (2021)

Abstract Medulloblastoma is the most common malignant pediatric brain tumor with a high mortality rate. A comprehensive protein-coding and regulatory transcriptomics is needed to understand four major molecular subgroups. Molecularly sub-classified 22 histo-pathologically characterized Medulloblastoma (MB) into group4-MB (G4), group3-MB (G3), Wnt-MB and SHH-MB two approved methods were used Molecular Inversion Probe based Array (Oncoscan Array) and transcript-probe-based Nanostring assay. For 2-control, normal tissue extracted while reaching tumor was utilized. Out of 22, 12 samples (10 MB and 2 controls) including all sub-groups of MB was considered for long and short read sequencing. Assembly was done through PacBio and ToFU pipeline to obtain consensus transcripts. Sqanti was used to assess the quality of data and the pre-processing pipeline using 47 unique descriptors. All the above samples were aligned to human reference genome and differential expression level matrix was created between tumor and control samples. Using standard settings (minimum fold change 2.0 and p value correction was through Bonferroni and cut off p value was 0.05) heat map was generated between control and experimental samples. Using standard t-test each subtype was compared with control as well as subtypes were also compared among themselves. Novel-Canonical (NC) junctions were identified in Novel in catalogue {NIC (1-5%)}, Novel not in catalogue {NNC (25%)}, Antigenic and Intergenic transcripts. Novel-Non-Canonical junctions was not observed among the structurally classified transcripts. Also identified sub-group specific 6 fusion transcripts. Novel Antisense (AS) transcripts were also identified: CROCC, TOM1, STON2 and AK5 were WNT-specific; CENPX and EZR were common between SHH and G-3; while ZNF391 and ZNF 865 were specific to G-3 and COL18A1 and ZC3HAV1L to G-4. Differential Analysis among all subtypes of MB versus control was analyzed, we identified TTR, PDLIM3 and SFRP1 significantly up-regulated transcripts in SHH compared to both G-3/4. NRL was specifically increased in G-3 compared to SHH and G-4. While NNAT was up-regulated in G-4 compared to SHH and G-3. Have created a customized Nanostring based panel in which 35 differentially expressed transcripts, 30 AS and previously reported 22 transcripts. This panel can comprehensively and specifically characterize Indian MB and can also be used for future clinical trials and personalized medicine. Antisense transcripts and fusion transcripts can be used as target for developing small molecules. Citation Format: Neetu Singh, Nawazish Alam, Dinesh K. Sahu, Ratnesh K. Tripathi, Mayank Jain, Pratap Shankar, Hari Shyam, Archana Mishra, Anil Kumar, Uma S. Singh, Anil Chandra, Chhitij Srivastava, Bal K. Ojha, Devendra K. Gupta, Ravi Kant, Bipin Puri. Comprehensive coding and non coding transcript based characterization of Indian medulloblastoma [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 3050.