NEK1 deficiency affects mitochondrial functions and the transcriptome of key DNA repair pathways

Abstract

Previous studies have indicated important roles for NIMA-related kinase 1 (NEK1) in modulating DNA damage checkpoints and DNA repair capacity. To broadly assess the contributions of NEK1 to genotoxic stress and mitochondrial functions, we characterized several relevant phenotypes of NEK1 CRISPR knockout (KO) and WT HAP1 cells. Our studies revealed that NEK1 KO cells resulted in increased apoptosis and hypersensitivity to the alkylator methyl methanesulfonate, the radiomimetic bleomycin, and UVC light, yet increased resistance to the crosslinker cisplatin. Mitochondrial functionalities were also altered in NEK1 KO cells, with phenotypes of reduced mitophagy, increased total mitochondria, elevated levels of reactive oxygen species, impaired complex I activity, and higher amounts of mitochondrial DNA damage. RNA-seq transcriptome analysis coupled with qRT-PCR studies comparing NEK1 KO cells with NEK1 overexpressing cells revealed that the expression of genes involved in DNA repair pathways, such as base excision repair, nucleotide excision repair, and double-strand break repair, are altered in a way that might influence genotoxin resistance. Together, our studies underline and further support that NEK1 serves as a hub signaling kinase in response to DNA damage, modulating DNA repair capacity, mitochondrial activity and cell fate determination.

Identification of biological pathways and processes regulated by NEK5 in breast epithelial cells via an integrated proteomic approach

“…Finally, other NEK family members are associated with mitochondrial homeostasis and dynamics. NEK1 deficiency is related to abnormal mitochondrial functions and elevated ROS levels [ 60 ] while NEK4 deficiency leads to altered mitochondrial morphology and reduced mitochondrial respiration [ 61 ]. Consequently, there is overlap in the NEK5-associated pathways identified and those linked to other family members, indicating that that this kinase family must regulate critical biological processes in a concerted and integrated manner.…”

Nek4 regulates mitochondrial respiration and morphology

“…Nek4 has been previously detected in mitochondrial fractions, and it has been proposed that it may interact with several mitochondrial proteins [10]. Based on this observation, and that other members of the Nek family show effects on mitochondria [13][14][15][16][17][18][19], we decided to investigate the effects of Nek4 on mitochondrial respiration. Nek4.1 Flag expressing cells showed an increase in basal or in ATP-coupled respiration (Fig.…”

“…For some Nek family members, a role in mitochondria has already been shown [13][14][15][16][17][18][19], and for Nek1, a mitochondrial substrate, VDAC, was characterized [13]. As different members of the Nek family often show different and sometimes even opposite functions, we decided to investigate the role of Nek4 in this organelle, too.…”

In Mitosis You Are Not: The NIMA Family of Kinases in Aspergillus, Yeast, and Mammals

“…Nek1 also contributes to mitochondrial functions. Nek1 deficiency can alter mitochondrial functions as it is associated with phenotypes of reduced mitophagy, increased number of mitochondria, and increased mitochondrial reactive oxygen species (ROS) [ 59 ]. Studies found that the activation of Nek1 by TLK1 contributes to the stability of Voltage Dependent Anion Channel 1 (VDAC1) and thus to mitochondrial permeability and integrity [ 60 ].…”