A post-transcriptional program of chemoresistance by AU-rich elements and TTP in quiescent leukemic cells

Sooncheol Lee,Syed I A Bukhari,David T Myers,Dongjun Lee,Myriam Boukhali,Ruslan I Sadreyev ,Radhika Raheja,Maria Antonietta Mazzola ,Adam Langenbucher,Christopher Tiedje,Ipsita Dey‐Guha ,Jennifer Lombardi‐Story ,Min‐Kyung Choo ,Nicholas J Haradhvala,Douglas S Micalizzi ,Shyamala Maheswaran,Wilhelm Haas,Daniel A Haber,Yasutaka Kato,David B Sykes ,Benjamin Nicholson ,Michael S Lawrence,Roopali Gandhi,Manuel D Díaz-Muñoz ,Fei Ji,David A Sweetser,Samuel S Truesdell,Shobha Vasudevan

doi:10.1186/s13059-020-1936-4

Abstract

BackgroundQuiescence (G0) is a transient, cell cycle-arrested state. By entering G0, cancer cells survive unfavorable conditions such as chemotherapy and cause relapse. While G0 cells have been studied at the transcriptome level, how post-transcriptional regulation contributes to their chemoresistance remains unknown.ResultsWe induce chemoresistant and G0 leukemic cells by serum starvation or chemotherapy treatment. To study post-transcriptional regulation in G0 leukemic cells, we systematically analyzed their transcriptome, translatome, and proteome. We find that our resistant G0 cells recapitulate gene expression profiles of in vivo chemoresistant leukemic and G0 models. In G0 cells, canonical translation initiation is inhibited; yet we find that inflammatory genes are highly translated, indicating alternative post-transcriptional regulation. Importantly, AU-rich elements (AREs) are significantly enriched in the upregulated G0 translatome and transcriptome. Mechanistically, we find the stress-responsive p38 MAPK-MK2 signaling pathway stabilizes ARE mRNAs by phosphorylation and inactivation of mRNA decay factor, Tristetraprolin (TTP) in G0. This permits expression of ARE mRNAs that promote chemoresistance. Conversely, inhibition of TTP phosphorylation by p38 MAPK inhibitors and non-phosphorylatable TTP mutant decreases ARE-bearing TNFα and DUSP1 mRNAs and sensitizes leukemic cells to chemotherapy. Furthermore, co-inhibiting p38 MAPK and TNFα prior to or along with chemotherapy substantially reduces chemoresistance in primary leukemic cells ex vivo and in vivo.ConclusionsThese studies uncover post-transcriptional regulation underlying chemoresistance in leukemia. Our data reveal the p38 MAPK-MK2-TTP axis as a key regulator of expression of ARE-bearing mRNAs that promote chemoresistance. By disrupting this pathway, we develop an effective combination therapy against chemosurvival.

Highlights

Quiescence (G0) is a transient, cell cycle-arrested state
We find that serum starvation-induced G0 SS cells show resistance to AraC chemotherapy
We find that AraC-surviving THP1 cells are transiently arrested, like SS cells (Fig. 1b and Additional file 1: Figure S1B); both AraCS and SS cells survive chemotherapy (Fig. 1c)

Summary

Introduction

Quiescence (G0) is a transient, cell cycle-arrested state. By entering G0, cancer cells survive unfavorable conditions such as chemotherapy and cause relapse. Quiescent (G0) cells are an assortment of reversibly arrested cells, including dormant stem cells, which are found as a clinically relevant subpopulation in cancers [1,2,3,4] Such cells are anti-proliferative, anti-differentiation, and anti-apoptotic and show distinct properties including resistance to harsh conditions [1, 2, 5,6,7,8,9,10]. Our previous data demonstrated that translation mechanisms are distinct in G0 leukemic cells, with decreased canonical translation mechanisms and increase in alternative mechanisms that involve non-canonical translation initiation factors [13] and 3′UTR-mediated specific mRNA translation [14] These data suggest that alternate post-transcriptional mechanisms in G0 cancer cells may regulate a distinct translatome to mediate their resistance. Translated genes in G0, the post-transcriptional mechanisms involved, and outcomes on cancer persistence remain to be investigated

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