Differential Expression of NEK Kinase Family Members in Esophageal Adenocarcinoma and Barrett’s Esophagus

SIMPLE SUMMARY: In the present study, we analyzed gene expression of NEK family members (NEK1-NEK11) in esophageal adenocarcinoma (EAC) and its precancerous condition, Barrett’s esophagus (BE), from the TCGA database and eight GEO datasets using a bioinformatics approach. We analyzed genomic alterations of NEKs in EAC samples using cBioPortal For Cancer Genomics and explored the clinical significance of NEKs expression on patients’ survival using the Kaplan–Meier Plotter. We validated the findings using qRT-PCR, Western blotting, immunohistochemistry, and immunofluorescence in cell lines from esophagus and primary EAC tissue samples. Our data indicate that upregulation of several NEKs, such as NEK2, NEK3, and NEK7, may be important in EAC. ABSTRACT: The incidence of esophageal adenocarcinoma (EAC) has risen rapidly during the past four decades, making it the most common type of esophageal cancer in the USA and Western countries. The NEK (Never in mitosis A (NIMA) related kinase) gene family is a group of serine/threonine kinases with 11 members. Aberrant expression of NEKs has been recently found in a variety of human cancers and plays important roles in tumorigenesis, progression, and drug-resistance. However, the expression of the NEKs in EAC and its precancerous condition (Barrett’s esophagus, BE) has not been investigated. In the present study, we first analyzed the TCGA and 9 GEO databases (a total of 10 databases in which 8 contain EAC and 6 contain BE) using bioinformatic approaches for NEKs expression in EAC and BE. We identified that several NEK members, such as NEK2 (7/8), NEK3 (6/8), and NEK6 (6/8), were significantly upregulated in EAC as compared to normal esophagus samples. Alternatively, NEK1 was downregulated in EAC as compared to the normal esophagus. On the contrary, genomic alterations of these NEKs are not frequent in EAC. We validated the above findings using qRT-PCR and the protein expression of NEKs in EAC cell lines using Western blotting and in primary EAC tissues using immunohistochemistry and immunofluorescence. Our data suggest that frequent upregulation of NEK2, NEK3, and NEK7 may be important in EAC.