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 eighth most common cancer worldwide and sixth in Kazakhstan.
Esophageal squamous cell carcinoma (ESCC) is the predominant histological subtype of esophageal
cancer and diagnosed at late stage. The aim of the project was to identify genetic basis of ESCC by analyzing
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 Oncology Center in Nur-Sultan. Whole transcriptome sequencing
was performed following the TruSeq RNA Protocol. STAR software and DESeq2package have been used
for mapping and defining differentially expressed genes. 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. Analysis of tumor and normal esophageal tissues
identified 7 DEGs, comprising 883 upregulated and 314 downregulated genes (with adjusted p-value
<0.05). We found significant 4 up-regulated and 6 down-regulated KEGG pathways (p-value<0.05). Top
300 DEGs were mapped to PPI network and functional enrichment analysis was performed on identified
three modules of closely connected nodes (genes).
Conclusion: ESCC with moderate dysplasia is the most common histologic subtype of esophageal cancer
in our patients and is characterized by a poor prognosis.High-throughput sequencing approach allows
identifying 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
Research Subject Categories::MEDICINE, esophageal squamous cell carcinoma, ESCC, differentially expressed genes, DEGs