Abstract 3482: Single-cell transcriptome analysis reveals that PLK4 signature genes are highly associated with cancer proliferation and hotspot mutations in non-small cell lung cancer (NSCLC)
Authors: Kim Youngtaek , Hwang Joon Yeon , Park YoungJoon , Kim Dong Kwon , Na Kwangmin , Lee Seul , Baek Sujeong , Kang Seong-san , Yang Seung Min , Kim Mi Hyun , Han Heekyung , Lee Chai Young , Han Yu Jin , Hong Min Hee , Lee Jii Bum , Lim Sun Min , Pyo Kyoung-Ho , Cho Byoung Chul 
Published: March 2024

Background: Polo-like kinase 4 (PLK4) is a member of the polo-like kinase family known for its precise regulation during the cell cycle and its key role in centriole duplication, which is essential for proper cell division. Dysregulation of PLK4 is associated with abnormal centriole number, genomic instability and cancer development. In our previous study, we proposed PLK4 as a potential therapeutic target and biomarker for LUAD patients with TP53 mutations by bulk RNA-seq analysis and confirmed its association with drug resistance. In this study, we analyzed the expression of PLK4 and its association with cell cycle at the cellular level by scRNA-seq in NSCLC data.

Methods: In a previous study, we analyzed NSCLC data from The Cancer Genome Atlas (TCGA) database using the UCSC Xena data portal. In this study, we analyzed E-MTAB-6653 dataset from the single cell expression atlas(https://www.ebi.ac.uk/gxa/sc/home).

Results: In the previous study, we demonstrated that PLK4 expression is higher in primary tumors compared to normal tissues in NSCLC. Higher PLK4 expression in patients is associated with an unfavorable prognosis. Using genes highly correlated with PLK4, we confirmed a significant association between PLK4 and TP53 mutation by statistical analysis. Using the Drug Gene Interaction database, we observed an association between the drug resistance-related genes PBK and BIRC5 with PLK4, and these genes were also correlated with TP53 mutation. In this study, we investigated the association between PLK4 and the cell cycle using single cell RNA-seq. First, we performed data pre-processing to selectively isolate NSCLC cells. Using a set of 87 PLK4 signature genes obtained from previous research, we stratified the samples into PLK4 high and low groups based on the expression of these genes. We then analyzed cell cycle related genes in both groups and observed a higher expression of G2/M phase related genes in the PLK4 high group compared to the PLK4 low group. We also examined the expression of PLK4 signature genes based on pathological differences and found higher expression in tumor tissue compared to normal tissue. There was also an increasing expression gradient from the tumor margin to the tumor core. Finally, using Gene Ontology analysis of both groups, we confirmed the upregulation of genes associated with transcription and translation, as indicated by the GO terms obtained.

Conclusion: In a previous study, the association between PLK4 expression, TP53 mutation and drug resistance was identified by bulk RNA-seq. In the current study, we used single cell RNA-seq to verify the correlation between PLK4 and cell cycle in NSCLC. In addition, we observed that the expression of PLK4 signature genes increased towards the tumor core based on pathological differences.

Citation Format: Youngtaek Kim, Joon Yeon Hwang, YoungJoon Park, Dong Kwon Kim, Kwangmin Na, Seul Lee, Sujeong Baek, Seong-san Kang, Seung Min Yang, Mi Hyun Kim, Heekyung Han, Chai Young Lee, Yu Jin Han, Min Hee Hong, Jii Bum Lee, Sun Min Lim, Kyoung-Ho Pyo, Byoung Chul Cho. Single-cell transcriptome analysis reveals that PLK4 signature genes are highly associated with cancer proliferation and hotspot mutations in non-small cell lung cancer (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3482.