Clinical application of a contingent screening strategy for trisomies with cell-free DNA: a pilot study

Cell-free DNA; Contingent screening; Fetal trisomyADN libre de células; Cribado contingente; Trisomia fetalADN lliure de cèl·lules; Cribratge contingent; Trisomia fetalBACKGROUND: Different strategies have been designed for clinical implementation of cell-free DNA (cfDNA) testing. We aimed to evaluate the performance of a contingent strategy based on conventional screening and offering cfDNA to the intermediate-risk group, for the screening for trisomies 21, 18 and 13. Secondary objectives were to assess the uptake of cfDNA in women with intermediate-risk, to evaluate the performance of cfDNA testing, and the preferences of pregnant women with intermediate risk. METHODS: Prospective observational pilot study between February 2016 and March 2017. Singleton pregnancies with a known outcome were included in the study. At the conventional screening (first trimester combined test or second trimester quadruple test) women were classified in high (risk ≥1:250) or low risk (< 1:250). For the study, a contingent strategy was applied: following the conventional screening women were classified into three groups: high risk (risk ≥1:10 or nuchal translucency ≥3 mm), intermediate-risk (risk 1:11 to 1:1500) and low risk (< 1:1500), and a cfDNA test was offered to those at the intermediate risk. RESULTS: For the analysis, 2639 women were included, 2422 (91.8%) had a first trimester combined test and 217 (8.2%) a second trimester quadruple test. There were 5 cases of trisomy 21, 4 of trisomy 18 and none of trisomy 13. For the contingent strategy, the detection rate and false positive rates were 88.9% (8/9) and 1.3% (35/2630), respectively. For the conventional strategy, the detection rate and false positive rates were 66.7% (6/9) and 5.3% (140/2630), respectively. The cfDNA test had a detection rate for trisomy 21 of 100% (3 out of 3), and a false positive rate of 0.2% (1/466). In a survey, 81.8% (374/457) of women in the intermediate-risk group would choose cfDNA testing as the second line test, mainly due to the lack of risk for the fetus. CONCLUSION: A contingent screening strategy for trisomies 21, 18 and 13, based on conventional screening, and offering a cfDNA test to women with a risk between 1:11 to 1:1500, reduced the false positive rate and increased the detection rate for these trisomies. Moreover, this strategy is well accepted by women.The study was financially supported by Ariosa Diagnostics, Inc. San Jose, CA, US

Ready to migrate? Reading cellular signs of migration in an epithelial to mesenchymal transition model

The epithelial to mesenchymal transition (EMT) is a cellular program that drives de-differentiation of cells in both physiological and pathological processes. One of the characteristics of cells describing an EMT is the (re)acquisition of a motility capacity that allows them to migrate through the original tissue as well as to other sites in the organism. The molecular mechanisms that control the EMT are rapidly emerging and here we add to the idea that the adaptation required for cells to commit to the EMT includes adjustments of the translation machinery and metabolic pathways to cope with a high demand of extracellular components.Este trabajo fue financiado parcialmente por el Fondo Clemente Estable (ANII) y PEDECIBA, Uruguay

Recurrent dissemination of SARS-CoV-2 through the Uruguayan–Brazilian border

Uruguay is one of the few countries in the Americas that successfully contained the coronavirus disease 19 (COVID-19) epidemic during the first half of 2020. Nevertheless, the intensive human mobility across the dry border with Brazil is a major challenge for public health authorities. We aimed to investigate the origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains detected in Uruguayan localities bordering Brazil as well as to measure the viral flux across this ∼1,100 km uninterrupted dry frontier. Using complete SARS-CoV-2 genomes from the Uruguayan–Brazilian bordering region and phylogeographic analyses, we inferred the virus dissemination frequency between Brazil and Uruguay and characterized local outbreak dynamics during the first months (May–July) of the pandemic. Phylogenetic analyses revealed multiple introductions of SARS-CoV-2 Brazilian lineages B.1.1.28 and B.1.1.33 into Uruguayan localities at the bordering region. The most probable sources of viral strains introduced to Uruguay were the Southeast Brazilian region and the state of Rio Grande do Sul. Some of the viral strains introduced in Uruguayan border localities between early May and mid-July were able to locally spread and originated the first outbreaks detected outside the metropolitan region. The viral lineages responsible for Uruguayan urban outbreaks were defined by a set of between four and 11 mutations (synonymous and non-synonymous) with respect to the ancestral B.1.1.28 and B.1.1.33 viruses that arose in Brazil, supporting the notion of a rapid genetic differentiation between SARS-CoV-2 subpopulations spreading in South America. Although Uruguayan borders have remained essentially closed to non-Uruguayan citizens, the inevitable flow of people across the dry border with Brazil allowed the repeated entry of the virus into Uruguay and the subsequent emergence of local outbreaks in Uruguayan border localities. Implementation of coordinated bi-national surveillance systems is crucial to achieve an efficient control of the SARS-CoV-2 spread across this kind of highly permeable borderland regions around the world

Emergence and spread of a B.1.1.28-derived P.6 lineage with Q675H and Q677H spike mutations in Uruguay

Uruguay controlled the viral dissemination during the first nine months of the SARS-CoV-2 pandemic. Unfortunately, towards the end of 2020, the number of daily new cases exponentially increased. Herein, we analyzed the country-wide genetic diversity of SARS-CoV-2 between November 2020 and April 2021. We identified that the most prevalent viral variant during the first epidemic wave in Uruguay (December 2020–February 2021) was a B.1.1.28 sublineage carrying Spike mutations Q675H + Q677H, now designated as P.6, followed by lineages P.2 and P.7. P.6 probably arose around November 2020, in Montevideo, Uruguay’s capital department, and rapidly spread to other departments, with evidence of further local transmission clusters; it also spread sporadically to the USA and Spain. The more efficient dissemination of lineage P.6 with respect to P.2 and P.7 and the presence of mutations (Q675H and Q677H) in the proximity of the key cleavage site at the S1/S2 boundary suggest that P.6 may be more transmissible than other lineages co-circulating in Uruguay. Although P.6 was replaced by the variant of concern (VOC) P.1 as the predominant lineage in Uruguay since April 2021, the monitoring of the concurrent emergence of Q675H + Q677H in VOCs should be of worldwide interest

Real-Time genomic surveillance for SARS-CoV-2 variants of concern, Uruguay

We developed a genomic surveillance program for realtime monitoring of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) in Uruguay. We report on a PCR method for SARSCoV- 2 VOCs, the surveillance workflow, and multiple independent introductions and community transmission of the SARS-CoV-2 P.1 VOC in Uruguay

Silent Polymorphisms: Can the tRNA Population Explain Changes in Protein Properties?

Silent mutations are being intensively studied. We previously showed that the estrogen receptor alpha Ala87’s synonymous polymorphism affects its functional properties. Whereas a link has been clearly established between the effect of silent mutations, tRNA abundance and protein folding in prokaryotes, this connection remains controversial in eukaryotic systems. Although a synonymous polymorphism can affect mRNA structure or the interaction with specific ligands, it seems that the relative frequencies of isoacceptor tRNAs could play a key role in the protein-folding process, possibly through modulation of translation kinetics. Conformational changes could be subtle but enough to cause alterations in solubility, proteolysis profiles, functional parameters or intracellular targeting. Interestingly, recent advances describe dramatic changes in the tRNA population associated with proliferation, differentiation or response to chemical, physical or biological stress. In addition, several reports reveal changes in tRNAs’ posttranscriptional modifications in different physiological or pathological conditions. In consequence, since changes in the cell state imply quantitative and/or qualitative changes in the tRNA pool, they could increase the likelihood of protein conformational variants, related to a particular codon usage during translation, with consequences of diverse significance. These observations emphasize the importance of genetic code flexibility in the co-translational protein-folding process

Silent Polymorphisms: Can the tRNA Population Explain Changes in Protein Properties?

International audienceSilent mutations are being intensively studied. We previously showed that the estrogen receptor alpha Ala87's synonymous polymorphism affects its functional properties. Whereas a link has been clearly established between the effect of silent mutations, tRNA abundance and protein folding in prokaryotes, this connection remains controversial in eukaryotic systems. Although a synonymous polymorphism can affect mRNA structure or the interaction with specific ligands, it seems that the relative frequencies of isoacceptor tRNAs could play a key role in the protein-folding process, possibly through modulation of translation kinetics. Conformational changes could be subtle but enough to cause alterations in solubility, proteolysis profiles, functional parameters or intracellular targeting. Interestingly, recent advances describe dramatic changes in the tRNA population associated with proliferation, differentiation or response to chemical, physical or biological stress. In addition, several reports reveal changes in tRNAs' posttranscriptional modifications in different physiological or pathological conditions. In consequence, since changes in the cell state imply quantitative and/or qualitative changes in the tRNA pool, they could increase the likelihood of protein conformational variants, related to a particular codon usage during translation, with consequences of diverse significance. These observations emphasize the importance of genetic code flexibility in the co-translational protein-folding process

Translational selection on codon usage in the genus Aspergillus.

International audienceAspergillus is a genus of mold fungi that includes more than 200 described species. Many members of the group are relevant pathogens and other species are economically important. Only one species has been analyzed for codon usage, and this was performed with a small number of genes. In this paper, we report the codon usage patterns of eight completely sequenced genomes which belong to this genus. The results suggest that selection for translational efficiency and accuracy are the major factors shaping codon usage in all of the species studied so far, and therefore they were active in the last common ancestor of the group. Composition and molecular distances analyses show that highly expressed genes evolve slower at synonymous sites. We identified a conserved core of translationally optimal codons and study the tRNA gene pool in each genome. We found that the great majority of preferred triplets match the respective cognate tRNA with more copies in the respective genome. We discuss the possible scenarios that can explain the observed differences among the species analyzed. Finally we highlight the biotechnological application of this research regarding heterologous protein expression

The transcriptional activities and cellular localization of the human estrogen receptor alpha are affected by the synonymous Ala87 mutation.

International audience: Until recently, synonymous mutations (which do not change amino acids) have been much neglected. Some evidence suggests that this kind of mutations could affect mRNA secondary structure or stability, translation kinetics and protein structure. To explore deeper the role of synonymous mutations, we studied their consequence on the functional activity of the estrogen receptor alpha (ERα). The ERα is a ligand-inducible transcription factor that orchestrates pleiotropic cellular effects, at both genomic and non-genomic levels in response to estrogens. In this work we analyzed in transient transfection experiments, the activity of ERα carrying the synonymous mutation Ala87, a polymorphism involving about 5-10% of the population. In comparison to the wild type receptor, our results show that ERαA87 mutation reduces the transactivation efficiency of ERα on an ERE reporter gene while its expression level remains similar. This mutation enhances 4-OHT-induced transactivation of ERα on an AP1 reporter gene. Finally, the mutation affects the subcellular localization of ERα in a cell type specific manner. It enhances the cytoplasmic location of ERα without significant changes in non-genomic effects of E2. The functional alteration of the ERαA87 determined in this work highlights the relevance of synonymous mutations for biomedical and pharmacological points of view