MESH1 knockdown triggers proliferation arrest through TAZ repression

Tianai Sun,Jianli Wu,Chao-Chieh Lin,Si’Ana Coggins,Jen-Tsan Chi,Everardo Macias,Yasaman Setayeshpour,Yang Zhang,Pei Zhou,Chien-Kuang Cornelia Ding,Caitlin Shepard,Yuning Zhang,Raluca Gordân,Baek Kim

doi:10.1038/s41419-022-04663-6

Tianai Sun, Jianli Wu + Show 12 more

Open Access

https://doi.org/10.1038/s41419-022-04663-6

Copy DOI

Abstract

All organisms are constantly exposed to various stresses, necessitating adaptive strategies for survival. In bacteria, the main stress-coping mechanism is the stringent response triggered by the accumulation of “alarmone” (p)ppGpp to arrest proliferation and reprogram transcriptome. While mammalian genomes encode MESH1—the homolog of the (p)ppGpp hydrolase SpoT, current knowledge about its function remains limited. We found MESH1 expression tended to be higher in tumors and associated with poor patient outcomes. Consistently, MESH1 knockdown robustly inhibited proliferation, depleted dNTPs, reduced tumor sphere formation, and retarded xenograft growth. These antitumor phenotypes associated with MESH1 knockdown were accompanied by a significantly altered transcriptome, including the repressed expression of TAZ, a HIPPO coactivator, and proliferative gene. Importantly, TAZ restoration mitigated many anti-growth phenotypes of MESH1 knockdown, including proliferation arrest, reduced sphere formation, tumor growth inhibition, dNTP depletion, and transcriptional changes. Furthermore, TAZ repression was associated with the histone hypo-acetylation at TAZ regulatory loci due to the induction of epigenetic repressors HDAC5 and AHRR. Together, MESH1 knockdown in human cells altered the genome-wide transcriptional patterns and arrested proliferation that mimicked the bacterial stringent response through the epigenetic repression of TAZ expression.

Highlights

Our results indicate that MESH1 knockdown in human cells triggers proliferation arrest through epigenetically repressing TAZ transcription, and may hold antitumor therapeutic potential
Significantly reduced the cell number of non-small cell lung cancer (H1975) (Fig. 1a) under different serum levels tested by crystal violet staining. We expanded this finding in a broader panel of cancer cell lines, including renal cell carcinoma (RCC4, 786-O), breast cancer (BT20, BT474, MCF-7), chondrosarcoma (SW-1353), and fibrosarcoma (HT-1080), and noticed a consistent cell number reduction by MESH1 knockdown (Supplementary Fig. 1d)
Since AHR has been reported to bind at TAZ regulatory regions and promote TAZ transcription [26, 29], we investigated the potential that HDAC5 and AHRR could repress TAZ expression by inhibiting the binding of AHR to TAZ regulatory regions

Summary

Introduction

Most solid tumor cells experience hypoxia [1, 2], lactic acidosis [3, 4], and nutrient deprivations [5–9], necessitating stress responses to ensure survival and homeostasis. The main stress mechanism is “stringent response” mediated by elevated alarmone (p)ppGpp via synthesis by its synthetase (RelA), or inhibited degradation by its hydrolase (SpoT). While a similar stress response has not been reported in metazoan, metazoan genomes encode MESH1 (Metazoan SpoT Homolog 1, named HDDC3). A previous study [13] described the conserved structures of Drosophila and human MESH1 and their in vitro enzymatic activities to degrade (p)ppGpp. Genetic depletion of Drosophila MESH1 enhanced stress survival and triggered transcriptional responses bearing significant similarities to bacterial stringent response [13]. We have shown that MESH1 is a cytosolic NADPH phosphatase and MESH1 knockdown protected cancer cells against ferroptosis [14] and triggered integrative stresses response. Much remains unknown about the phenotypic responses to MESH1 knockdown

Objectives

Methods

Results

Conclusion