Les marqueurs du vivant : génétique et big data

Comment imaginer une pratique scientifique qui résiste aux impératifs de la croissance, du big data et de l'innovation perpétuelle ? Deux chercheuses en génétique des populations réfléchissent ici aux évolutions récentes de leur discipline et à ses devenirs possibles

Infection‐driven activation of transglutaminase 2 boosts glucose uptake and hexosamine biosynthesis in epithelial cells

DATA AVAILABILITYThe mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD017117.International audienceTransglutaminase 2 (TG2) is a ubiquitously expressed enzyme with transamidating activity. We report here that both expression and activity of TG2 are enhanced in mammalian epithelial cells infected with the obligate intracellular bacteria Chlamydia trachomatis. Genetic or pharmacological inhibition of TG2 impairs bacterial development. We show that TG2 increases glucose import by up-regulating the transcription of the glucose transporter genes GLUT-1 and GLUT-3. Furthermore, TG2 activation drives one specific glucose-dependent pathway in the host, i.e., hexosamine biosynthesis. Mechanistically, we identify the glucosamine:fructose-6-phosphate amidotransferase (GFPT) among the substrates of TG2. GFPT modification by TG2 increases its enzymatic activity, resulting in higher levels of UDP-N-acetylglucosamine biosynthesis and protein O-GlcNAcylation. The correlation between TG2 transamidating activity and O-GlcNAcylation is disrupted in infected cells because host hexosamine biosynthesis is being exploited by the bacteria, in particular to assist their division. In conclusion, our work establishes TG2 as a key player in controlling glucose-derived metabolic pathways in mammalian cells, themselves hijacked by C. trachomatis to sustain their own metabolic needs

Preoperative chemoradiation with paclitaxel-carboplatin or with fluorouracil-oxaliplatin-folinic acid (FOLFOX) for resectable esophageal and junctional cancer: the PROTECT-1402, randomized phase 2 trial.

BACKGROUND: Often curative treatment for locally advanced resectable esophageal or gastro-esophageal junctional cancer consists of concurrent neoadjuvant radiotherapy and chemotherapy followed by surgery. Currently, one of the most commonly used chemotherapy regimens in this setting is a combination of a fluoropyrimidin and of a platinum analogue. Due to the promising results of the recent CROSS trial, another regimen combining paclitaxel and carboplatin is also widely used by European and American centers. No clinical study has shown the superiority of one treatment over the other. The objective of this Phase II study is to clarify clinical practice by comparing these two chemotherapy treatments. Our aim is to evaluate, in operable esophageal and gastro-esophageal junctional cancer, the complete resection rate and severe postoperative morbidity rate associated with these two neoadjuvant chemotherapeutic regimens (carboplatin-paclitaxel or fluorouracil-oxaliplatin-folinic acid) when each is combined with the radiation regime utilized in the CROSS trial. METHODS/DESIGN: PROTECT is a prospective, randomized, multicenter, open arms, phase II trial. Eligible patients will have a histologically confirmed adenocarcinoma or squamous cell carcinoma and be treated with neoadjuvant radiochemotherapy followed by surgery for stage IIB or stage III resectable esophageal cancer. A total of 106 patients will be randomized to receive either 3 cycles of FOLFOX combined to concurrent radiotherapy (41.4 Grays) or carboplatin and paclitaxel with the same radiation regimen, using a 1:1 allocation ratio. DISCUSSION: This ongoing trial offers the unique opportunity to compare two standards of chemotherapy delivered with a common regimen of preoperative radiation, in the setting of operable locally advanced esophageal or gastro-esophageal junctional tumors. TRIAL REGISTRATION: NCT02359968 (ClinicalTrials.gov) (registration date: 9 FEB 2015), EudraCT: 2014-000649-62 (registration date: 10 FEB 2014)

Population structure and genetic bottleneck in sweet cherry estimated with SSRs and the gametophytic self-incompatibility locus

<p>Abstract</p> <p>Background</p> <p>Domestication and breeding involve the selection of particular phenotypes, limiting the genomic diversity of the population and creating a bottleneck. These effects can be precisely estimated when the location of domestication is established. Few analyses have focused on understanding the genetic consequences of domestication and breeding in fruit trees. In this study, we aimed to analyse genetic structure and changes in the diversity in sweet cherry <it>Prunus avium </it>L.</p> <p>Results</p> <p>Three subgroups were detected in sweet cherry, with one group of landraces genetically very close to the analysed wild cherry population. A limited number of SSR markers displayed deviations from the frequencies expected under neutrality. After the removal of these markers from the analysis, a very limited bottleneck was detected between wild cherries and sweet cherry landraces, with a much more pronounced bottleneck between sweet cherry landraces and modern sweet cherry varieties. The loss of diversity between wild cherries and sweet cherry landraces at the <it>S</it>-locus was more significant than that for microsatellites. Particularly high levels of differentiation were observed for some <it>S</it>-alleles.</p> <p>Conclusions</p> <p>Several domestication events may have happened in sweet cherry or/and intense gene flow from local wild cherry was probably maintained along the evolutionary history of the species. A marked bottleneck due to breeding was detected, with all markers, in the modern sweet cherry gene pool. The microsatellites did not detect the bottleneck due to domestication in the analysed sample. The vegetative propagation specific to some fruit trees may account for the differences in diversity observed at the <it>S</it>-locus. Our study provides insights into domestication events of cherry, however, requires confirmation on a larger sampling scheme for both sweet cherry landraces and wild cherry.</p

High-quality SNPs from genic regions highlight introgression patterns among European white oaks (Quercus petraea and Q. robur)

International audienceIn the post-genomics era, non-model species like most Fagaceae still lack operational diversity resources for population genomics studies. Sequence data were produced from over 800 gene fragments covering ~530 kb across the genic partition of European oaks, in a discovery panel of 25 individuals from western and central Europe (11 Quercus petraea, 13 Q. robur, one Q. ilex as an outgroup). Regions targeted represented broad functional categories potentially involved in species ecological preferences, and a random set of genes. Using a high-quality dedicated pipeline, we provide a detailed characterization of these genic regions, which included over 14500 polymorphisms, with ~12500 SNPs −218 being triallelic-, over 1500 insertion-deletions, and ~200 novel di- and tri-nucleotide SSR loci. This catalog also provides various summary statistics within and among species, gene ontology information, and standard formats to assist loci choice for genotyping projects. The distribution of nucleotide diversity (θπ) and differentiation (FST) across genic regions are also described for the first time in those species, with a mean n θπ close to ~0.0049 in Q. petraea and to ~0.0045 in Q. robur across random regions, and a mean FST ~0.13 across SNPs. The magnitude of diversity across genes is within the range estimated for long-term perennial outcrossers, and can be considered relatively high in the plant kingdom, with an estimate across the genome of 41 to 51 million SNPs expected in both species. Individuals with typical species morphology were more easily assigned to their corresponding genetic cluster for Q. robur than for Q. petraea, revealing higher or more recent introgression in Q. petraea and a stronger species integration in Q. robur in this particular discovery panel. We also observed robust patterns of a slightly but significantly higher diversity in Q. petraea, across a random gene set and in the abiotic stress functional category, and a heterogeneous landscape of both diversity and differentiation. To explain these patterns, we discuss an alternative and non-exclusive hypothesis of stronger selective constraints in Q. robur, the most pioneering species in oak forest stand dynamics, additionally to the recognized and documented introgression history in both species despite their strong reproductive barriers. The quality of the data provided here and their representativity in terms of species genomic diversity make them useful for possible applications in medium-scale landscape and molecular ecology projects. Moreover, they can serve as reference resources for validation purposes in larger-scale resequencing projects. This type of project is preferentially recommended in oaks in contrast to SNP array development, given the large nucleotide variation and the low levels of linkage disequilibrium revealed

Symptom-based stratification of patients with primary Sjögren's syndrome: multi-dimensional characterisation of international observational cohorts and reanalyses of randomised clinical trials

Background Heterogeneity is a major obstacle to developing effective treatments for patients with primary Sjögren's syndrome. We aimed to develop a robust method for stratification, exploiting heterogeneity in patient-reported symptoms, and to relate these differences to pathobiology and therapeutic response. Methods We did hierarchical cluster analysis using five common symptoms associated with primary Sjögren's syndrome (pain, fatigue, dryness, anxiety, and depression), followed by multinomial logistic regression to identify subgroups in the UK Primary Sjögren's Syndrome Registry (UKPSSR). We assessed clinical and biological differences between these subgroups, including transcriptional differences in peripheral blood. Patients from two independent validation cohorts in Norway and France were used to confirm patient stratification. Data from two phase 3 clinical trials were similarly stratified to assess the differences between subgroups in treatment response to hydroxychloroquine and rituximab. Findings In the UKPSSR cohort (n=608), we identified four subgroups: Low symptom burden (LSB), high symptom burden (HSB), dryness dominant with fatigue (DDF), and pain dominant with fatigue (PDF). Significant differences in peripheral blood lymphocyte counts, anti-SSA and anti-SSB antibody positivity, as well as serum IgG, κ-free light chain, β2-microglobulin, and CXCL13 concentrations were observed between these subgroups, along with differentially expressed transcriptomic modules in peripheral blood. Similar findings were observed in the independent validation cohorts (n=396). Reanalysis of trial data stratifying patients into these subgroups suggested a treatment effect with hydroxychloroquine in the HSB subgroup and with rituximab in the DDF subgroup compared with placebo. Interpretation Stratification on the basis of patient-reported symptoms of patients with primary Sjögren's syndrome revealed distinct pathobiological endotypes with distinct responses to immunomodulatory treatments. Our data have important implications for clinical management, trial design, and therapeutic development. Similar stratification approaches might be useful for patients with other chronic immune-mediated diseases. Funding UK Medical Research Council, British Sjogren's Syndrome Association, French Ministry of Health, Arthritis Research UK, Foundation for Research in Rheumatology

Using automated sanding to homogeneously break seed dormancy in black locust (Robinia pseudoacacia L., Fabaceae)

Physical dormancy of Robinia pseudoacacia seeds makes it a challenge for scientists and forest managers to obtain a homogeneous germination for larger seed samples. Water imbibition of the seeds can be achieved through manual piercing of the seed coat, but this method remains time consuming and heterogeneous. We tested several ecologically friendly methods to break seed dormancy, including manual pin puncture, water soaking, oven dry-heating (two temperatures) and sanding. Sanding was performed using an automatic grinder to control shaking duration (three durations) and get a homogeneous scraping of the coat. All methods, except dry-heating, resulted in successful dormancy breaking; water soaking was the least efficient method, attaining 57% germination. Sanding proved to be as efficient as puncturing (97%) but long duration sanding (10 or 15 min) could damage cotyledons, which would impede further development of the plant. Short-time sanding (5 min) proved to be the best method to reach high total germination and healthy (undamaged cotyledon) seedlings, and was successfully applied to 500 seeds. The reference puncture method and the automatic sanding were also tested on seeds of nine Fabaceae species and proved to be efficient for some species. Automated sanding can thus be used as a standard to break physical dormancy of black locust or other Fabaceae seeds to allow further comparative studies of plant populations or genotypes