Abstract 3396: Characterization of oral squamous cell carcinoma transcriptome through long read sequencing technology
Authors: Singh Neetu , Sahu Dinesh Kumar , Tripathi Ratnesh Kumar , Mishra Archana , Singh Satyendra Kumar , Chowdhry Rebecca , Gupta Sameer , Mehrotra Divya , Agarwal Preeti , Goel Madhu Mati , Singh Sudhir , Chaturvedi Arun , Mishra Akshay , Agarwal Satya Prakash , Bajpai Manish , Kant Ravi , Bhatt Madan Lal 
Published: August 2018

Abstract
Large and increasing public-databases of oral squamous cell carcinoma (OSCC) transcriptome sequencing data has been generated through next-generation which has limitation for novel full-length transcript isoforms. Hence, our objective was to identify differential specific OSCC-related novel full length transcript isoforms, long noncoding RNA and fusion genes compared to non-matched oral-cavity control samples through PacBio-RSII platform. The OSCC, patients from different anatomical sites (gingivobuccal region, retro-molar trigone and lower gum) were processed through human transcriptome array 2.0 (HTA2.0). Heatmap generated expression patterns showed two distinct subgroups against control. Both tumor and control samples were individually run on Oncoscan array. On aggregate analysis significant copy number gain of Ch 7p11.2 EGFR gene; and Ch11q13.3-13.4 (FGF19, FGF4, FGF3, LOC101928443, ANO1-AS2, ANO1, FADD, MIR548K, PPFIA1, CTTN, SHANK2) were identified. Based on HTA2.0 and Oncoscan array we pooled six oral cancer and three oral control samples for Isoseq analysis. Differentially expressed full length transcripts between OC and OT were generated through GFOLD and were processed through Reactome Pathway. On considering more than 20 transcript-entities, Metabolism of RNA (22), Developmental Biology (25), Cytokine Signaling (25), Innate Immune System (25), Metabolism of proteins (31), Immune System (35), Metabolism (29), and Signal Transduction (21) pathways were identified. Differential regulation was also validated through HTA2.0. The identified high quality full length transcripts were annotated and classified through Blast2Go in different sub-group under Biological-Process, Cellular-Process and Molecular-function in Level 2. Out of these most highly up-regulated were Type I-Keratins (KRT)-KRT17, -KRT16, -KRT14 and Type-II keratins-KRT6A and -KRT6B showing involvement of formation of cornified envelope, Keratinization, Cell-cell communication, Type I hemi-desmosome assembly and developmental biology pathways. Long non-coding RNA-NMD candidates ARL2-SNX15, RAB4B-EGLN2, SENP3-EIF4A1 and fusion genes-ACTA2–ACTB, ACTB–ACTC1, ACTB–ACTG2, CALML3–CALM3, CKM–CKB, ENO1–ENO3, IGKV1-27–IGKV3-15, IGKV4-1–IGKJ1, IGKV4-1–IGKJ2, IGKV4-1–IGKJ3, IGKV4-1–IGKJ4, KRT6B–KRT6A were also differentially expressed. Additionally, 457 novel full length transcript isoforms including 289 from OC and 168 from OT datasets were identified. Hence, differentially regulated-KRT17, KRT16, KRT14, KRT6A, KRT 6B; long non-coding RNA and identified fusion genes and full length novel transcript isofoms may be the characteristic of these tumors after validation in histo-pathologically characterized FFPE-Keratinized OSCC and may also prove as early detection marker for Keratinized OSCC if identified in pre-neoplastic conditions.
Citation Format: Neetu Singh, Dinesh Kumar Sahu, Ratnesh Kumar Tripathi, Archana Mishra, Satyendra Kumar Singh, Rebecca Chowdhry, Sameer Gupta, Divya Mehrotra, Preeti Agarwal, Madhu Mati Goel, Sudhir Singh, Arun Chaturvedi, Akshay Mishra, Satya Prakash Agarwal, Manish Bajpai, Ravi Kant, Madan Lal Bhatt. Characterization of oral squamous cell carcinoma transcriptome through long read sequencing technology [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 3396.