Systems level expression correlation of Ras GTPase regulators

Background: Proteins of the ubiquitously expressed core proteome are quantitatively correlated across multiple eukaryotic species. In addition, it was found that many protein paralogues exhibit expression anticorrelation, suggesting that the total level of protein with a given functionality must be kept constant. Methods: We performed Spearman’s rank correlation analyses of gene expression levels for the RAS GTPase subfamily and their regulatory GEF and GAP proteins across tissues and across individuals for each tissue. A large set of published data for normal tissues from a wide range of species, human cancer tissues and human cell lines was analysed. Results: We show that although the multidomain regulatory proteins of Ras GTPases exhibit considerable tissue and individual gene expression variability, their total amounts are balanced in normal tissues. In a given tissue, the sum of activating (GEFs) and deactivating (GAPs) domains of Ras GTPases can vary considerably, but each person has balanced GEF and GAP levels. This balance is impaired in cell lines and in cancer tissues for some individuals. Conclusions: Our results are relevant for critical considerations of knock out experiments, where functionally related homologs may compensate for the down regulation of a protein

Post-transcriptional determinants of RAS protein abundance

The RAS oncogenes KRAS, NRAS and HRAS are mutated in one third of human cancers where they exhibit different mutation patterns. A potential factor contributing to this mutation bias is the variation of RAS expression levels. Here, I investigate some of the determinants of RAS protein abundance. First, I examine whether codon bias among RAS genes and within other cancer gene families plays a role in cell context-specific expression. I further describe a tRNA expression program that favors oncogene translation in proliferating cells. Second, I investigate why oncogenic RAS mutants exhibit a higher protein abundance than the RAS wild type. In this context, I study the underlying mechanisms leading to this variation and more specifically how protein-protein interactions between RAS and its downstream binding partners change the protein turnover of RAS and therefore, its protein abundance. Overall, this thesis provides insight into the possible relevance of RAS protein synthesis and protein degradation as determinants of RAS mutation patterns in human cancers.Els oncogens KRAS, NRAS i HRAS estan mutats en un terç dels càncers en humans on hi exhibeixen patrons de mutació diferents. Un possible factor que contribueix a aquest biaix de mutació és la variació dels nivells d'expressió de RAS. En aquesta tesi investigo els elements determinants de l'abundància de la proteïna RAS. Primer, examino si el biaix de codó entre els gens RAS i entre gens d'altres famílies implicades en càncer contribueix a les diferències d'expressió, en funció del context cel·lular. Així mateix, descric un programa d'expressió de tRNA que facilita la traducció d'oncogens en cèl·lules proliferatives. En segon lloc, investigo per què mutants oncogènics de RAS tenen una abundància de proteïna més elevada que la RAS salvatge. Així mateix, estudio els mecanismes subjacents responsables d'aquesta variació i més concretament el paper de les interaccions de RAS amb altres proteïnes en la regulació de la seva abundància. Així doncs, aquesta tesi estudia la possible rellevància dels mecanismes de síntesi i degradació de la proteïna RAS en els patrons de mutació en càncer

Post-transcriptional determinants of RAS protein abundance

The RAS oncogenes KRAS, NRAS and HRAS are mutated in one third of human cancers where they exhibit different mutation patterns. A potential factor contributing to this mutation bias is the variation of RAS expression levels. Here, I investigate some of the determinants of RAS protein abundance. First, I examine whether codon bias among RAS genes and within other cancer gene families plays a role in cell context-specific expression. I further describe a tRNA expression program that favors oncogene translation in proliferating cells. Second, I investigate why oncogenic RAS mutants exhibit a higher protein abundance than the RAS wild type. In this context, I study the underlying mechanisms leading to this variation and more specifically how protein-protein interactions between RAS and its downstream binding partners change the protein turnover of RAS and therefore, its protein abundance. Overall, this thesis provides insight into the possible relevance of RAS protein synthesis and protein degradation as determinants of RAS mutation patterns in human cancers.Els oncogens KRAS, NRAS i HRAS estan mutats en un terç dels càncers en humans on hi exhibeixen patrons de mutació diferents. Un possible factor que contribueix a aquest biaix de mutació és la variació dels nivells d'expressió de RAS. En aquesta tesi investigo els elements determinants de l'abundància de la proteïna RAS. Primer, examino si el biaix de codó entre els gens RAS i entre gens d'altres famílies implicades en càncer contribueix a les diferències d'expressió, en funció del context cel·lular. Així mateix, descric un programa d'expressió de tRNA que facilita la traducció d'oncogens en cèl·lules proliferatives. En segon lloc, investigo per què mutants oncogènics de RAS tenen una abundància de proteïna més elevada que la RAS salvatge. Així mateix, estudio els mecanismes subjacents responsables d'aquesta variació i més concretament el paper de les interaccions de RAS amb altres proteïnes en la regulació de la seva abundància. Així doncs, aquesta tesi estudia la possible rellevància dels mecanismes de síntesi i degradació de la proteïna RAS en els patrons de mutació en càncer

Translational efficiency across healthy and tumor tissues is proliferation-related

Different tissues express genes with particular codon usage and anticodon tRNA repertoires. However, the codon-anticodon co-adaptation in humans is not completely understood, nor is its effect on tissue-specific protein levels. Here, we first validated the accuracy of small RNA-seq for tRNA quantification across five human cell lines. We then analyzed the tRNA abundance of more than 8,000 tumor samples from TCGA, together with their paired mRNA-seq and proteomics data, to determine the Supply-to-Demand Adaptation. We thereby elucidate that the dynamic adaptation of the tRNA pool is largely related to the proliferative state across tissues. The distribution of such tRNA pools over the whole cellular translatome affects the subsequent translational efficiency, which functionally determines a condition-specific expression program both in healthy and tumor states. Furthermore, the aberrant translational efficiency of some codons in cancer, exemplified by ProCCA and GlyGGT, is associated with poor patient survival. The regulation of these tRNA profiles is partly explained by the tRNA gene copy numbers and their promoter DNA methylation.We acknowledge the support of the Spanish Ministry of Science and Innovation (MICINN), “Centro de Excelencia Severo Ochoa”, the CERCA Programme/Generalitat de Catalunya, and the Spanish Ministry of Science and Innovation (MICINN) to the EMBL partnership. The work of X.H. has been supported by a PhD fellowship from the Fundación Ramón Arece

An intermediate along the recovery stroke of myosin VI revealed by X-ray crystallography and molecular dynamics

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Using protein-per-mRNA differences among human tissues in codon optimization

Background: Codon usage and nucleotide composition of coding sequences have profound effects on protein expression. However, while it is recognized that different tissues have distinct tRNA profiles and codon usages in their transcriptomes, the effect of tissue-specific codon optimality on protein synthesis remains elusive. Results: We leverage existing state-of-the-art transcriptomics and proteomics datasets from the GTEx project and the Human Protein Atlas to compute the protein-to-mRNA ratios of 36 human tissues. Using this as a proxy of translational efficiency, we build a machine learning model that identifies codons enriched or depleted in specific tissues. We detect two clusters of tissues with an opposite pattern of codon preferences. We then use these identified patterns for the development of CUSTOM, a codon optimizer algorithm which suggests a synonymous codon design in order to optimize protein production in a tissue-specific manner. In human cell-line models, we provide evidence that codon optimization should take into account particularities of the translational machinery of the tissues in which the target proteins are expressed and that our approach can design genes with tissue-optimized expression profiles. Conclusions: We provide proof-of-concept evidence that codon preferences exist in tissue-specific protein synthesis and demonstrate its application to synthetic gene design. We show that CUSTOM can be of benefit in biological and biotechnological applications, such as in the design of tissue-targeted therapies and vaccines.We acknowledge the support of the Spanish Ministry of Science and Innovation (MICINN) (PGC2018-101271-B-I00 Plan Estatal), ‘Centro de Excelencia Severo Ochoa’, and the CERCA Programme/Generalitat de Catalunya. The work of X.H. has been supported by a PhD fellowship from the Fundación Ramón Areces. The work leading to this manuscript was supported by Fondazione AIRC, grant reference number MFAG 21791, and partially supported by the Italian Ministry of Health with Ricerca Corrente and 5x1000 funds

Mutation bias within oncogene families is related to proliferation-specific codon usage

It is well known that in cancer gene families some members are more frequently mutated in tumor samples than their family counterparts. A paradigmatic case of this phenomenon is KRAS from the RAS family. Different explanations have been proposed ranging from differential interaction with other proteins to preferential expression or localization. Interestingly, it has been described that despite the high amino acid identity between RAS family members, KRAS employs an intriguing differential codon usage. Here, we found that this phenomenon is not exclusive to the RAS family. Indeed, in the RAS family and other oncogene families with two or three members, the most prevalently mutated gene in tumor samples employs a differential codon usage that is characteristic of genes involved in proliferation. Prompted by these observations, we chose the RAS family to experimentally demonstrate that the translation efficiency of oncogenes that are preferentially mutated in tumor samples is increased in proliferative cells compared to quiescent cells. These results were further validated by assessing the translation efficiency of KRAS in cell lines that differ in their tRNA expression profile. These differences are related to the cell division rate of the studied cells and thus suggest an important role in context-specific oncogene expression regulation. Altogether, our study demonstrates that dynamic translation programs contribute to shaping the expression profiles of oncogenes. Therefore, we propose this codon bias as a regulatory layer to control cell context-specific expression and explain the differential prevalence of mutations in certain members of oncogene families.The work of X.H.-A. has been supported by a PhD fellowship from the Fundación Ramón Areces. We acknowledge the support of the Spanish Ministry of Science and Innovation to the European Molecular Biology Laboratory partnership, the Centro de Excelencia Severo Ochoa and the Centres de Recerca de Catalunya Programme/Generalitat de Cataluny

Tuneable endogenous mammalian target complementation via multiplexed plasmid-based recombineering

Includes supplementary materials for the online appendix.Understanding the quantitative functional consequences of human disease mutations requires silencing of endogenous genes and expression of mutants at close to physiological levels. Changing protein levels above or below these levels is also important for system perturbation and modelling. Fast design optimization demands flexible interchangeable cassettes for endogenous gene silencing and tuneable expression. Here, we introduce ‘TEMTAC’, a multigene recombineering and delivery system for simultaneous siRNA-based knockdown and regulated mutant (or other variant) expression with different dynamic ranges. We show its applicability by confirming known phenotypic effects for selected mutations for BRAF, HRAS and SHP2.We thank all members of our laboratories for their contributions and helpful discussions. We thank the CRG Genomics Unit and the Biomolecular Screening & Protein Technologies Unit. We acknowledge help in the quantifications of the Western blots by Dina Cramer and assistance in RNA sequencing analysis by Javier Delgado. Armelle Yart provided the HEK293 cells stably expressing GH receptor. This work was funded by the European Commission (EC) Framework programme (FP) 7 projects PRIMES (contract nr. 278568), ComplexINC (contract nr. 279039) and SynSignal (contract nr. 613879). LS is supported by the Spanish Ministerio de Economía y Competitividad, Plan Nacional BIO2012-39754 and the European Fund for Economic and Regional Development. We are particularly grateful for the support of the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017′ (SEV-2012-0208)