Suppression of m6A mRNA modification by DNA hypermethylated ALKBH5 aggravates the oncological behavior of KRAS mutation/LKB1 loss lung cancer

Donghong Zhang,Shidong Xu,Ping Song,Jinfeng Ning,Ganesh Satyanarayana,Ming-Hui Zou,Xiaoxu Zheng,Imoh Okon

doi:10.1038/s41419-021-03793-7

Abstract

Oncogenic KRAS mutations combined with the loss of the LKB1 tumor-suppressor gene (KL) are strongly associated with aggressive forms of lung cancer. N6-methyladenosine (m6A) in mRNA is a crucial epigenetic modification that controls cancer self-renewal and progression. However, the regulation and role of m6A modification in this cancer are unclear. We found that decreased m6A levels correlated with the disease progression and poor survival for KL patients. The correlation was mediated by a special increase in ALKBH5 (AlkB family member 5) levels, an m6A demethylase. ALKBH5 gain- or loss-of function could effectively reverse LKB1 regulated cell proliferation, colony formation, and migration of KRAS-mutated lung cancer cells. Mechanistically, LKB1 loss upregulated ALKBH5 expression by DNA hypermethylation of the CTCF-binding motif on the ALKBH5 promoter, which inhibited CTCF binding but enhanced histone modifications, including H3K4me3, H3K9ac, and H3K27ac. This effect could successfully be rescued by LKB1 expression. ALKBH5 demethylation of m6A stabilized oncogenic drivers, such as SOX2, SMAD7, and MYC, through a pathway dependent on YTHDF2, an m6A reader protein. The above findings were confirmed in clinical KRAS-mutated lung cancer patients. We conclude that loss of LKB1 promotes ALKBH5 transcription by a DNA methylation mechanism, reduces m6A modification, and increases the stability of m6A target oncogenes, thus contributing to aggressive phenotypes of KRAS-mutated lung cancer.

Highlights

Recent global cancer statistics confirm that lung cancer is a commonly diagnosed malignancy and a leading cause of cancer-related deaths in both men and women[1]
The lowest of m6A level was found in KL tumor tissues when compared to wild type (WT), KRAS Wt; LKB1 Loss (L), or KRAS Mut; LKB1 Wt (K) tumor tissues (Fig. 1A, B)
We found lower m6A level in K specimens that were null for thyroid transcription factor 1 (TTF1), a positive prognostic feature (Fig. 1D)[23]

Summary

Introduction

Recent global cancer statistics confirm that lung cancer is a commonly diagnosed malignancy and a leading cause of cancer-related deaths in both men and women[1]. 10% of NSCLC cases involve concurrent KRAS mutation and LKB1 loss (KL)[2,3,4]. These cases are often more aggressive in terms of metastatic spread and drug resistance[5,6,7,8,9] than those with neither mutation nor loss. Epigenetic modifications, including DNA/RNA methylation and histone methylation/ acetylation, have important roles in carcinogenesis[10]. KL cancer cells have higher levels of S-adenylmethionine (SAM) synthesis and DNA methylation[11]. Elevated SAM levels may fuel RNA methylation[12], suggesting that KL-mutations mediate a distinct form of epigenetic dysregulation.

Methods

Results

Conclusion