Traitement des données scRNA-seq issues de la technologie Drop-Seq : application à l’étude des réseaux transcriptionnels dans le cancer du sein

Les technologies récentes de séquençage de l’ARN de cellules uniques (scRNA-seq, pour single cell RNA-seq) ont permis de quantifier le niveau d’expression des gènes au niveau de la cellules, alors que les technologies standards de séquençage de l’ARN (RNA-seq, ou bulk RNA-seq) ne permettaient de quantifier que l’expression moyenne des gènes dans un échantillon de cellules. Cette résolution supérieure a permis des avancées majeures dans le domaine de la recherche biomédicale, mais a également posé de nouveaux défis, notamment computationnels. Les données qui découlent des technologies de scRNA-seq sont en effet complexes et plus bruitées que les données de bulk RNA-seq. En outre, les technologies sont nombreuses et leur nombre explose, nécessitant chacune un prétraitement plus ou moins différent. De plus en plus de méthodes sont ainsi développées, mais il n’existe pas encore de norme établie (gold standard) pour le prétraitement et l’analyse de ces données. Le laboratoire du Dr. Mader a récemment fait l’acquisition de la technologie Drop-Seq (une technologie haut débit de scRNA-seq), nécessitant une expertise nouvelle pour le traitement des données qui en découlent. Dans ce mémoire, différentes étapes du prétraitement des données issues de la technologie Drop-Seq sont donc passées en revue et le fonctionnement de certains outils dédiés à cet effet est étudié, permettant d’établir des lignes directrices pour de futures expériences au sein du laboratoire du Dr. Mader. Cette étude est menée sur les premiers jeux de données générés avec la technologie Drop-Seq du laboratoire, issus de lignées cellulaires du cancer du sein. Les méthodes d’analyses, moins spécifiques à la technologie, ne sont pas étudiées dans ce mémoire, mais une analyse exploratoire des jeux de données du laboratoire pose les bases pour une analyse plus poussée.Recent single cell RNA sequencing technologies (scRNA-seq) have enabled the quantification of gene expression levels at the cellular level, while standard RNA sequencing technologies (RNA-seq, or bulk RNA-seq) have only been able to quantify the average gene expression in a sample of cells. This higher resolution has allowed major advances in biomedical research, but has also raised new challenges, in particular computational ones. The data derived from scRNA-seq technologies are indeed complex and noisier than bulk RNA-seq data. In addition, the number of scRNA-seq technologies is exploding, each of them requiring a rather different pre-processing. More and more methods are thus being developed, but there is still no gold standard for the preprocessing and analysis of these data. Dr. Mader’s laboratory has recently invested in the Drop-Seq technology (a high-throughput scRNAseq technology), requiring new expertise for the processing of the resulting data. In this thesis, different steps for the pre-processing of Drop-Seq data are reviewed and the behavior of some of the dedicated tools are studied, allowing to establish guidelines for future experiments in Dr. Mader’s laboratory. This study is conducted on the first data sets generated with the Drop-Seq technology of the laboratory, derived from breast cancer cell lines. Analytical methods, less specific to the technology, are not investigated in this thesis, but an exploratory analysis of the lab’s datasets lays the foundation for further analysis

Construing Worst Experiences of the COVID-19 Pandemic in the USA: A Thematic Analysis

© 2022 The Authors. This is an Open Access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License (http://creativecommons.org/licenses/by-nc-nd/4.0/.The COVID-19 pandemic has not only resulted in millions of deaths but, together with the strategies imposed to contain the spread of the disease, it has had significant psychological and social effects. This paper considers these effects in residents of the USA, the country that has reported the highest number of deaths from COVID-19. Between April and May, 2020, responses were obtained to an on-line survey, which included asking participants, recruited by snowball sampling, to describe their worst experience of the pandemic. The responses of 741 participants, primarily female and Caucasian, were subjected to a thematic content analysis which used a primarily deductive approach in which these responses were viewed in terms of transitions in construing. The transition themes identified were anxiety; threat; loss of role; sadness; contempt; and stress. Various subthemes were also identified. The study provided further evidence of the utility of a personal construct framework in conceptualizing experiences associated with illness and the risk of this. Implications of its findings are considered at both an individual and a societal level.Peer reviewedFinal Published versio

Ability to remotely monitor atrial high-rate episodes using a single-chamber implantable cardioverter-defibrillator with a floating atrial sensing dipole

Aims To allow timely initiation of anticoagulation therapy for the prevention of stroke, the European guidelines on atrial fibrillation (AF) recommend remote monitoring (RM) of device-detected atrial high-rate episodes (AHREs) and progression of arrhythmia duration along pre-specified strata (6 min…&lt;1 h, 1 h…&lt;24 h, ≥ 24 h). We used the MATRIX registry data to assess the capability of a single-lead implantable cardioverter-defibrillator (ICD) with atrial sensing dipole (DX ICD system) to follow this recommendation in patients with standard indication for single-chamber ICD. Methods In 1841 DX ICD patients with daily automatic RM transmissions, electrograms of first device-detected AHREs per patient in and results each duration stratum were adjudicated, and the corresponding positive predictive values (PPVs) for the detections to be true atrial arrhythmia were calculated. Moreover, the incidence and progression of new-onset AF was assessed in 1451 patients with no AF history. A total of 610 AHREs ≥6 min were adjudicated. The PPV was 95.1% (271 of 285) for episodes 6min…&lt;1 h, 99.6% (253/254) for episodes 1 h…&lt;24 h, 100% (71/71) for episodes ≥24 h, or 97.5% for all episodes (595/ 610). The incidence of new-onset AF was 8.2% (119/1451), and in 31.1% of them (37/119), new-onset AF progressed to a higher duration stratum. Nearly 80% of new-onset AF patients had high CHA 2DS 2-VASc stroke risk, and 70% were not on anticoagulation therapy. Age was the only significant predictor of new-onset AF. Conclusion A 99.7% detection accuracy for AHRE ≥1 h in patients with DX ICD systems in combination with daily RM allows a reliable guideline-recommended screening for subclinical AF and monitoring of AF-duration progression.</p

PUF60 variants cause a syndrome of ID, short stature, microcephaly, coloboma, craniofacial, cardiac, renal and spinal features.

PUF60 encodes a nucleic acid-binding protein, a component of multimeric complexes regulating RNA splicing and transcription. In 2013, patients with microdeletions of chromosome 8q24.3 including PUF60 were found to have developmental delay, microcephaly, craniofacial, renal and cardiac defects. Very similar phenotypes have been described in six patients with variants in PUF60, suggesting that it underlies the syndrome. We report 12 additional patients with PUF60 variants who were ascertained using exome sequencing: six through the Deciphering Developmental Disorders Study and six through similar projects. Detailed phenotypic analysis of all patients was undertaken. All 12 patients had de novo heterozygous PUF60 variants on exome analysis, each confirmed by Sanger sequencing: four frameshift variants resulting in premature stop codons, three missense variants that clustered within the RNA recognition motif of PUF60 and five essential splice-site (ESS) variant. Analysis of cDNA from a fibroblast cell line derived from one of the patients with an ESS variants revealed aberrant splicing. The consistent feature was developmental delay and most patients had short stature. The phenotypic variability was striking; however, we observed similarities including spinal segmentation anomalies, congenital heart disease, ocular colobomata, hand anomalies and (in two patients) unilateral renal agenesis/horseshoe kidney. Characteristic facial features included micrognathia, a thin upper lip and long philtrum, narrow almond-shaped palpebral fissures, synophrys, flared eyebrows and facial hypertrichosis. Heterozygote loss-of-function variants in PUF60 cause a phenotype comprising growth/developmental delay and craniofacial, cardiac, renal, ocular and spinal anomalies, adding to disorders of human development resulting from aberrant RNA processing/spliceosomal function

Finger creases lend a hand in Kabuki syndrome.

International audienceKabuki syndrome (KS) is a rare syndrome associating malformations with intellectual deficiency and numerous visceral, orthopedic, endocrinological, immune and autoimmune complications. The early establishment of a diagnostic of KS leads to better care of the patients and therefore prevents complications such as perception deafness, severe complications of auto-immune diseases or obesity. However, the diagnosis of KS remains difficult because based on the appreciation of facial features combined with other highly variable features. We describe a novel sign, namely the attenuation and/or congenital absence of the IPD crease of the third and fourth fingers associated with limitation of flexion of the corresponding joints, which seems to be specific of KS and could help the clinician to diagnose KS

A cross-sectional study to assess job strain of emergency healthcare workers by Karasek questionnaire: The SEEK study

BackgroundEmergency healthcare workers (eHCWs) are particularly at risk of stress, but data using the gold standard questionnaire of Karasek are scarce. We assessed the level of stress of eHCWs and aimed to compare it with the general population.MethodsThis is a cross-sectional nationwide study in French Emergency Departments (EDs), using the job-content questionnaire of Karasek, compared with the 25,000 answers in the French general population (controls from the SUMER study). The descriptions of job demand, job control, and social support were described as well as the prevalence of job strain and isostrain. Putative factors were searched using mixed-method analysis.ResultsA total of 166 eHCWs (37.9 ± 10.5 years old, 42% men) from five French EDs were included: 53 emergency physicians and 104 emergency paramedics, compared to 25,000 workers with other occupations. Job demand was highest for physicians (28.3 ± 3.3) and paramedics (25.9 ± 3.8), compared to controls (36.0 ± 7.2; p &lt; 0.001). Job control was the lowest for physicians (61.2 ± 5.8) and paramedics (59.1 ± 6.8), compared to controls (70.4 ± 11.7; p &lt; 0.001). Mean social support did not differ between groups (23.6 ± 3.4 for physicians, 22.6 ± 2.9 for paramedics, and 23.7 ± 3.6 for controls). The prevalence of job strain was massively higher for physicians (95.8%) and paramedics (84.8%), compared to controls (23.9%; p &lt; 0.001), as well as for isostrain (45.1% for physicians, 56.8% for paramedics, and 14.3% for controls, p &lt; 0.001). We did not find any significant impact of sociodemographic characteristics on job control, job demand, or social support.ConclusionEmergency healthcare workers have a dramatic rate of job strain, necessitating urgent promotion of policy to take care of them

A blueprint for integrating scientific approaches and international communities to assess basin-wide ocean ecosystem status

Ocean ecosystems are at the forefront of the climate and biodiversity crises, yet we lack a unified approach to assess their state and inform sustainable policies. This blueprint is designed around research capabilities and cross-sectoral partnerships. We highlight priorities including integrating basin-scale observation, modelling and genomic approaches to understand Atlantic oceanography and ecosystem connectivity; improving ecosystem mapping; identifying potential tipping points in deep and open ocean ecosystems; understanding compound impacts of multiple stressors including warming, acidification and deoxygenation; enhancing spatial and temporal management and protection. We argue that these goals are best achieved through partnerships with policy-makers and community stakeholders, and promoting research groups from the South Atlantic through investment and engagement. Given the high costs of such research (€800k to €1.7M per expedition and €30–40M for a basin-scale programme), international cooperation and funding are integral to supporting science-led policies to conserve ocean ecosystems that transcend jurisdictional borders

10 years of CEMARA database in the AnDDI-Rares network: a unique resource facilitating research and epidemiology in developmental disorders in France

Background : In France, the Ministry of Health has implemented a comprehensive program for rare diseases (RD) that includes an epidemiological program as well as the establishment of expert centers for the clinical care of patients with RD. Since 2007, most of these centers have entered the data for patients with developmental disorders into the CEMARA population-based registry, a national online data repository for all rare diseases. Through the CEMARA web portal, descriptive demographic data, clinical data, and the chronology of medical follow-up can be obtained for each center. We address the interest and ongoing challenges of this national data collection system 10 years after its implementation. Methods : Since 2007, clinicians and researchers have reported the “minimum dataset (MDS)” for each patient presenting to their expert center. We retrospectively analyzed administrative data, demographic data, care organization and diagnoses. Results : Over 10 years, 228,243 RD patients (including healthy carriers and family members for whom experts denied any suspicion of RD) have visited an expert center. Among them, 167,361 were patients affected by a RD (median age 11 years, 54% children, 46% adults, with a balanced sex ratio), and 60,882 were unaffected relatives (median age 37 years). The majority of patients (87%) were seen no more than once a year, and 52% of visits were for a diagnostic procedure. Among the 2,869 recorded rare disorders, 1,907 (66.5%) were recorded in less than 10 patients, 802 (28%) in 10 to 100 patients, 149 (5.2%) in 100 to 1,000 patients, and 11 (0.4%) in > 1,000 patients. Overall, 45.6% of individuals had no diagnosis and 6.7% had an uncertain diagnosis. Children were mainly referred by their pediatrician (46%; n = 55,755 among the 121,136 total children referrals) and adults by a medical specialist (34%; n = 14,053 among the 41,564 total adult referrals). Given the geographical coverage of the centers, the median distance from the patient’s home was 25.1 km (IQR = 6.3 km-64.2 km). Conclusions : CEMARA provides unprecedented support for epidemiological, clinical and therapeutic studies in the field of RD. Researchers can benefit from the national scope of CEMARA data, but also focus on specific diseases or patient subgroups. While this endeavor has been a major collective effort among French RD experts to gather large-scale data into a single database, it provides tremendous potential to improve patient care