Translatome analysis reveals altered serine and glycine metabolism in T-cell acute lymphoblastic leukemia cells

Kim R Kampen,Tiziana Girardi,David Cassiman,Mark Fiers,Jan Cools,Jonathan Royaert,Fabricio Loayza-Puch,Joyce Op De Beeck,Benno Verbelen,Stijn Vereecke,Reuven Agami,Sergey O Sulima,Mélanie Planque,Laura Fancello,Gianmarco Rinaldi,Kim De Keersmaecker,Sarah-Maria Fendt,Jelle Verbeeck,Pieter Vermeersch

doi:10.1038/s41467-019-10508-2

Abstract

Somatic ribosomal protein mutations have recently been described in cancer, yet their impact on cellular transcription and translation remains poorly understood. Here, we integrate mRNA sequencing, ribosome footprinting, polysomal RNA sequencing and mass spectrometry datasets from a mouse lymphoid cell model to characterize the T-cell acute lymphoblastic leukemia (T-ALL) associated ribosomal RPL10 R98S mutation. Surprisingly, RPL10 R98S induces changes in protein levels primarily through transcriptional rather than translation efficiency changes. Phosphoserine phosphatase (PSPH), encoding a key serine biosynthesis enzyme, was the only gene with elevated transcription and translation leading to protein overexpression. PSPH upregulation is a general phenomenon in T-ALL patient samples, associated with elevated serine and glycine levels in xenograft mice. Reduction of PSPH expression suppresses proliferation of T-ALL cell lines and their capacity to expand in mice. We identify ribosomal mutation driven induction of serine biosynthesis and provide evidence supporting dependence of T-ALL cells on PSPH.

Highlights

Somatic ribosomal protein mutations have recently been described in cancer, yet their impact on cellular transcription and translation remains poorly understood
Psph, which encodes a key enzyme in serine biosynthesis, is consistently upregulated at both transcriptional and translational levels in RPL10 R98S cells, and is one of the strongest upregulated proteins associated with this mutation
In order to better delineate the causes of detected protein changes in RPL10 R98S cells, we generated a ribosome footprinting dataset together with an mRNAsequencing dataset of the same cells in this study

Summary

Introduction

Somatic ribosomal protein mutations have recently been described in cancer, yet their impact on cellular transcription and translation remains poorly understood. We recently performed quantitative mass spectrometry on an isogenic lymphoid Ba/F3 B-cell model expressing the WT or R98S mutant allele of RPL1011 This allowed to compare expression levels of the 5557 most abundant proteins and revealed an upregulation of 178 (3%) and a downregulation of 68 (1%) proteins in the R98S cells (p < 0.01). It is unclear to what extent previously detected quantitative proteomics changes were caused by RPL10 R98S-associated transcriptional, translational, and post-translational modulation For this purpose, we perform mRNA sequencing and sequencing of ribosome-associated RNA (ribosome footprinting or RPF-seq)[13] using the same isogenic Ba/F3 cell model, and integrate these datasets with our previously described quantitative proteomics and polysomal RNA sequencing datasets[11]. Psph, which encodes a key enzyme in serine biosynthesis, is consistently upregulated at both transcriptional and translational levels in RPL10 R98S cells, and is one of the strongest upregulated proteins associated with this mutation. Our results support dependence of T-ALL cells on the serine biosynthesis enzyme PSPH

Methods

Results

Conclusion