Somatic Functional Deletions of Upstream Open Reading Frame-Associated Initiation and Termination Codons in Human Cancer.

Lara Jürgens,Christoph Schliemann,Felix Manske,Oliver Klaas,Victoria Shabardina,Wojciech Makalowski,Lea Flötotto,Elvira Hubert,Tabea Kischka,Klaus Wethmar

doi:10.3390/biomedicines9060618

Abstract

Upstream open reading frame (uORF)-mediated translational control has emerged as an important regulatory mechanism in human health and disease. However, a systematic search for cancer-associated somatic uORF mutations has not been performed. Here, we analyzed the genetic variability at canonical (uAUG) and alternative translational initiation sites (aTISs), as well as the associated upstream termination codons (uStops) in 3394 whole-exome-sequencing datasets from patient samples of breast, colon, lung, prostate, and skin cancer and of acute myeloid leukemia, provided by The Cancer Genome Atlas research network. We found that 66.5% of patient samples were affected by at least one of 5277 recurrent uORF-associated somatic single nucleotide variants altering 446 uAUG, 347 uStop, and 4733 aTIS codons. While twelve uORF variants were detected in all entities, 17 variants occurred in all five types of solid cancer analyzed here. Highest frequencies of individual somatic variants in the TLSs of NBPF20 and CHCHD2 reached 10.1% among LAML and 8.1% among skin cancer patients, respectively. Functional evaluation by dual luciferase reporter assays identified 19 uORF variants causing significant translational deregulation of the associated main coding sequence, ranging from 1.73-fold induction for an AUG.1 > UUG variant in SETD4 to 0.006-fold repression for a CUG.6 > GUG variant in HLA-DRB1. These data suggest that somatic uORF mutations are highly prevalent in human malignancies and that defective translational regulation of protein expression may contribute to the onset or progression of cancer.

Highlights

IntroductionRibosome profiling and recent mass spectrometric analyses uncovered high translational activity outside of previously annotated protein coding sequences (CDSs) [1,2]
Ribosome profiling and recent mass spectrometric analyses uncovered high translational activity outside of previously annotated protein coding sequences (CDSs) [1,2].A large fraction of such ectopic translational events mapped to upstream open reading frames initiated by canonical or alternative translational initiation sites [3,4,5,6]
To determine the read coverage in whole-exome sequencing (WES) datasets provided by the Cancer Genome Atlas, we first localized all Upstream open reading frame (uORF)-associated canonical and alternative initiation sites plus all uORF-related upstream termination codons in the current human genome assembly

Summary

Introduction

Ribosome profiling and recent mass spectrometric analyses uncovered high translational activity outside of previously annotated protein coding sequences (CDSs) [1,2]. A large fraction of such ectopic translational events mapped to upstream open reading frames (uORFs) initiated by canonical (uAUG) or alternative translational initiation sites (aTISs) [3,4,5,6]. While more than half of all human 50 -transcript leader sequences (TLSs) contain uAUG codons [6], virtually all eukaryotic TLSs contain aTISs, differing in one base from the classical AUG triplet [1,5,7,8,9]. The 43S pre-initiation complex scans the mRNA in 50 - to 30 -direction and initiates translation at the first start codon suitable for ribosomal initiation [5,11].

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Conclusion