WHOLE TRANSCRIPTOME SEQUENCING ANALYSIS OF PATIENTS WITH ESOPHAGEAL SQUAMOUS CELL CARCINOMA FROM KAZAKHSTAN
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Date
2020
Authors
Sharip, A.
Rakhimova, S.
Molkenov, A.
Kozhamkulov, U.
Zhukov, Y.
Omarov, M.
Akilzhanova, A.
Kairov, U.
Journal Title
Journal ISSN
Volume Title
Publisher
International conference "MODERN PERSPECTIVES FOR BIOMEDICAL SCIENCES: FROM BENCH TO BEDSIDE”; National Laboratory Astana
Abstract
Introduction: Esophageal cancer is the sixth most common cancer in Kazakhstan, and usually not detected
until it has progressed to an advanced incurable stage. The predominant histological subtype of
esophageal cancer in Kazakhstan is esophageal squamous cell carcinoma (ESCC). The purpose of the
project was to identify genetic basis of ESCC by analysing differentially expressed genes (DEGs) from
whole transcriptome sequencing of Kazakhstani patients.
Materials and Methods: Tissue samples were obtained from 25 ESCC-affected individuals immediately
after Ivor-Lewis esophagectomy from Multidisciplinary Medical Center. Normal esophageal tissue
sample were extracted from Atlas of RNA sequencing profiles. Whole transcriptome sequencing was prepared
and performed following the TruSeq RNA Protocol. STAR software and DESeq2package have been
used for mapping and identifying differentially expressed genes (DEGs). Functional analysis of DEGs was
performed using various R packages.
Results: The study sized 14 men and 11women, average age of patient 65.5±7.7 years. 88% of the patients
were diagnosed with advanced stages T3-T4. Bioinformatics analysis of tumor and normal esophageal
tissues identified 34 DEGs (adj. p-value <0.05). We found ten significantly upregulated and two
significantly downregulated KEGG pathways (p-value <0.05). Top 300 DEGs were mapped to PPI network
and three modules of closely connected nodes were identified. Functional enrichment analysis of these
modules showed that “module 1” is significantly associated with immune response, “module 2” is linked
with histone functions, and “module 3” is associated with mitotic division and checkpoint.
Conclusion: Most patients diagnosed with late stages T3-T4 with moderate dysplasia, which was the
most common histologic subtype of esophageal cancer in Kazakhstani patients High-throughput sequencing
approach allows the comprehensive understanding of molecular pathways involved in esophageal
carcinogenesis that could improve diagnosis and treatment strategies.
Acknowledgments: Work was supported by grant projects #AP05134722, #AP05135430 and
#AP05136106 from the Committee Science and Ministry of Education and Science at the Republic of
Kazakhstan.
Description
Keywords
Ivor-Lewis esophagectomy, Research Subject Categories::MEDICINE, esophageal squamous cell carcinoma, ESCC, differentially expressed genes, DEGs