The use of sequencing technologies for enhanced understanding of molecular determinants in renal diseases

Les maladies rénales ont un impact important sur l'économie de tout système de santé dans le monde. En outre, le nombre de patients augmente régulièrement au cours des dernières décennies avec une prévalence de plus de 500 000 nouveaux cas de maladie rénale en phase terminale (ESRD) dans le monde entier chaque année. L'ESRD est l'étape finale de la maladie rénale chronique (CKD) qui a comme principales causes le diabète et l'hypertension, ainsi que la glomérulonéphrite, urolithiasis, la polykystose rénale autosomique dominante (ADPKD) et la progression de la lésion rénale aiguë (LRA), entre autres. Cependant, dans de nombreux cas, les mécanismes de ces maladies affectant le rein et sa fonction sont mal connus ou difficiles à diagnostiquer. Dans le cadre de cette étude, nous avons utilisé des technologies plus récentes, des méthodologies et des approches d'analyse de données pour jeter un peu de lumière dans les pathomécanismes de la CKD et de l'AKI. En outre, l'amélioration potentielle de la valeur diagnostique des tests diagnostiques déjà existants (par exemple ADPKD). Au cours des dernières années, les progrès dans les technologies de séquençage de l'ADN ont révolutionné le domaine de la recherche clinique et du diagnostic. Le séquençage à haut débit tel que le séquençage de prochaine génération (NG) est utilisé en raison de sa haute qualité et de précision lors que l'analyse des échantillons d'ADN. D'autres technologies de séquençage ont également montré leur valeur, comme le séquençage à longue lecture qui est utilisé en raison de ses longues lectures de séquençage et de la précision de résolution de séquençages de faible complexité, telles que les régions répétitives ou des régions de GC-pourcentage élevé. Dans le cadre de cette thèse, nous avons utilisé plusieurs méthodes de pointe de séquençage appliquées à la recherche clinique sur la maladie rénale afin de: 1. Améliorer la valeur diagnostique des tests diagnostiques déjà existants pour l'ADPKD. ADPKD est une maladie héréditaire qui représente de 5% à 10% de l'ESRD. Cependant, le criblage du principal gène ADPKD PKD1 est difficile en raison de sa structure multi-exon, de son hétérogénéité allélique et de son homologie élevée avec six pseudogènes PKD1, ainsi que d'une teneur en GC extrêmement élevée. En utilisant le séquençage direct à longue lecture, nous avons montré que le diagnostic ADPKD sans interférence des séquences homologues PKD1 est possible. 2. Caractériser le profil d'expression de l'IRA et des mécanismes sous-jacents en utilisant le séquençage de l'ARN. Les patients qui subissent une chirurgie majeure peuvent développer une IRA qui a été associée à un risque de mortalité plus élevé et une fonctionnalité rénale réduite, et un risque élevé de progression de la CKD. Certaines preuves indiquent que le système tubulaire est au milieu de cette pathophysiologie et de la récupération ultérieure. Cependant, les facteurs impliqués dans cette reprise sont encore mal compris. Dans ce contexte, nous avons caractérisé les profils d'expression de l'ARN messager rénal d'AKI dans des constructions de type sauvage et knock-out Gdf15. Gdf15 a été identifié comme étant associé à des lésions tubulaires inférieures suggérant un rôle protecteur du rein. Nous avons identifié 89 facteurs de transcription qui sont potentiellement moteurs des mécanismes de réponse dans l'IRA, ainsi que d'autres facteurs de transcription 13 éventuellement liés avec les mécanismes de protection de Gdf15. 3. Évaluer les limites pratiques du séquençage de l'ARN pour caractériser les maladies glomérulaires pour la CKD. L'analyse des biopsies rénales est très informative pour déterminer le stade de la maladie glomérulaire du patient et les taux de progression. Cependant, les biopsies congelées fraîches sont limitées ou inexistantes par rapport aux biopsies rénales fixées au formol et à la paraffine (FFPE) plus abondantes. Les tissus FFPE peuvent être facilement stockés pendant de longues périodes, ce qui permet de disposer d'importantes archives d'échantillons avec de nombreuses années de collecte de données cliniques et de suivi. Nous avons montré que la caractérisation des profils d'expression de la maladie glomérulaire par séquençage d'ARN à partir d'échantillons de FFPE est possible. Cependant, nos données suggèrent que le nombre requis de glomérules dans les coupes transversales peut être supérieur au nombre de glomérules présents dans une biopsie rénale habituelle. Enfin, nous avons développé l'impact futur des résultats obtenus dans le cadre de la recherche clinique et leur valeur pour la compréhension ou le diagnostic des maladies rénales.Renal diseases have a high impact on the economy of any health care system worldwide. In addition, patient numbers are steadily increasing over the past decades with a prevalence of over 500.000 new end stage renal disease (ESRD) worldwide cases every year. ESRD is the final stage of chronic kidney disease (CKD) that has as the leading causes diabetes and hypertension, as well as glomerulonephritis, urolithiasis, autosomal dominant polycystic kidney disease (ADPKD), and progression of acute kidney injury (AKI), among others. However, in many cases, the mechanisms of these diseases affecting kidney and its function are poorly understood, or difficult to diagnose. Within this study, we used newer technologies, methodologies, and data analysis approaches to throw some light into the pathomechanisms of CKD and AKI. Moreover, potentially improving the diagnostic value for already existing diagnostic assays (e.g. ADPKD). In the past years, advances in DNA sequencing technologies have revolutionized the field of clinical research and diagnostics. High throughput sequencing such as next-generation sequencing (NGs) is being used because of its high quality and accuracy when analysing DNA samples. Other sequencing technologies have also shown their value such as long-read sequencing which is used because of its longer sequencing reads and accuracy resolving low-complexity sequences, such as repetitive regions or high GC-percent regions. Within the scope of this thesis we used several cutting-edge sequencing approaches applied to renal disease's clinical research to: 1. Improve the diagnostic value of already existing diagnostic assays for ADPKD. ADPKD is an inherited disease that accounts for 5% to 10% of ESRD. However, the screening of the main ADPKD gene PKD1 is challenging because of its multi-exon structure, allelic heterogeneity, and high homology with six PKD1 pseudogenes, as well as extremely high GC content. Using direct long-read sequencing we showed that ADPKD diagnostics without interference of PKD1 homologous sequences is possible. 2. Characterize the expression profile of AKI and the underlying mechanisms using RNA sequencing. Patients undergoing major surgery may develop AKI which has been associated with higher mortality risk and reduced renal functionality, and high risk of progression of CKD. Some evidences pointed out to the tubular system being at the middle of this pathophysiology and further recovery. However, the factors involved in this recovery are still poorly understood. In this context, we characterized renal messenger RNA expression profiles of AKI in wild type and Gdf15 knock out constructs. Gdf15 was identified to be associated with lower tubular damage suggesting a protective role of the kidney. We identified 89 transcription factors that are potentially driving the response mechanisms in AKI, as well as other 13 transcription factors possibly linked with the protective mechanisms of Gdf15. 3. Evaluate the practical boundaries of RNA sequencing to characterize glomerular diseases for CKD. The analysis of renal biopsies is very informative to determine patient's glomerular disease stage and progression rates. However, fresh frozen biopsies are limited or non-existent compared to the more abundant formalin-fixed, paraffin-embedded (FFPE) renal biopsies. FFPE tissue can be easily stored for long periods of time, allowing large sample archives with many years of clinical data collection and follow-up. We showed that characterizing glomerular disease expression profiles by RNA sequencing from FFPE samples is possible. However, our data suggests that the required number of glomeruli in cross sections may be higher than the number glomeruli present in a usual renal biopsy. Finally, we elaborated about the future impact of the results obtained in the context of clinical research, and their value for the understanding or diagnostics of renal diseases

Minimal information for studies of extracellular vesicles 2018 (MISEV2018):a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles (“MISEV”) guidelines for the field in 2014. We now update these “MISEV2014” guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points

QCloud2: an improved cloud-based quality-control system for mass-spectrometry-based proteomics laboratories

QCloud is a cloud-based system to support proteomics laboratories in daily quality assessment using a user-friendly interface, easy setup, and automated data processing. Since its release, QCloud has facilitated automated quality control for proteomics experiments in many laboratories. QCloud provides a quick and effortless evaluation of instrument performance that helps to overcome many analytical challenges derived from clinical and translational research. Here we present an improved version of the system, QCloud2. This new version includes enhancements in the scalability and reproducibility of the quality-control pipelines, and it features an improved front end for data visualization, user management, and chart annotation. The QCloud2 system also includes programmatic access and a standalone local version.The CRG/UPF Proteomics Unit is part of the Spanish Infrastructure for Omics Technologies (ICTS OmicsTech), and it is a member of the ProteoRed PRB3 consortium, which is supported by grant PT17/0019 of the PE I+D+i 2013−2016 from the Instituto de Salud Carlos III (ISCIII), ERDF, and “Secretaria d’Universitats i Recerca del Departament d’Econòmia i Coneixement de la Generalitat de Catalunya” (2017SGR595). This project was supported by EPIC-XS, project number 823839, funded by the Horizon 2020 Programme of the European Union. We also acknowledge support of the Spanish Ministry of Science and Innovation to the EMBL partnership, the Centro de Excelencia Severo Ochoa and the CERCA Programme from Generalitat de Cataluny

The genomic history of the Iberian Peninsula over the past 8000 years

We assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula. We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming. We reveal sporadic contacts between Iberia and North Africa by ~2500 BCE and, by ~2000 BCE, the replacement of 40% of Iberia’s ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry. We show that, in the Iron Age, Steppe ancestry had spread not only into Indo-European–speaking regions but also into non-Indo-European–speaking ones, and we reveal that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia. Additionally, we document how, beginning at least in the Roman period, the ancestry of the peninsula was transformed by gene flow from North Africa and the eastern Mediterranean.J.M.F., F.J.L.-C., J.I.M., F.X.O., J.D., and M.S.B. were supported by HAR2017-86509-P, HAR2017-87695-P, and SGR2017-11 from the Generalitat de Catalunya, AGAUR agency. C.L.-F. was supported by Obra Social La Caixa and by FEDER-MINECO (BFU2015- 64699-P). L.B.d.L.E. was supported by REDISCO-HAR2017-88035-P (Plan Nacional I+D+I, MINECO). C.L., P.R., and C.Bl. were supported by MINECO (HAR2016-77600-P). A.Esp., J.V.-V., G.D., and D.C.S.-G. were supported by MINECO (HAR2009-10105 and HAR2013-43851-P). D.J.K. and B.J.C. were supported by NSF BCS-1460367. K.T.L., A.W., and J.M. were supported by NSF BCS-1153568. J.F.-E. and J.A.M.-A. were supported by IT622-13 Gobierno Vasco, Diputación Foral de Álava, and Diputación Foral de Gipuzkoa. We acknowledge support from the Portuguese Foundation for Science and Technology (PTDC/EPH-ARQ/4164/2014) and the FEDER-COMPETE 2020 project 016899. P.S. was supported by the FCT Investigator Program (IF/01641/2013), FCT IP, and ERDF (COMPETE2020 – POCI). M.Si. and K.D. were supported by a Leverhulme Trust Doctoral Scholarship awarded to M.B.R. and M.P. D.R. was supported by an Allen Discovery Center grant from the Paul Allen Foundation, NIH grant GM100233, and the Howard Hughes Medical Institute. V.V.-M. and W.H. were supported by the Max Planck Society

The genomic history of the Iberian Peninsula over the past 8000 years

We assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula. We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming. We reveal sporadic contacts between Iberia and North Africa by ~2500 BCE and, by ~2000 BCE, the replacement of 40% of Iberia's ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry. We show that, in the Iron Age, Steppe ancestry had spread not only into Indo-European-speaking regions but also into non-Indo-European-speaking ones, and we reveal that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia. Additionally, we document how, beginning at least in the Roman period, the ancestry of the peninsula was transformed by gene flow from North Africa and the eastern Mediterranean.J.M.F., F.J.L.-C., J.I.M., F.X.O., J.D., and M.S.B. were supported by HAR2017-86509-P, HAR2017-87695-P, and SGR2017-11 from the Generalitat de Catalunya, AGAUR agency. C.L.-F. was supported by Obra Social La Caixa and by FEDER-MINECO (BFU2015- 64699-P). L.B.d.L.E. was supported by REDISCO-HAR2017-88035-P (Plan Nacional I+D+I, MINECO). C.L., P.R., and C.Bl. were supported by MINECO (HAR2016-77600-P). A.Esp., J.V.-V., G.D., and D.C.S.-G. were supported by MINECO (HAR2009-10105 and HAR2013-43851-P). D.J.K. and B.J.C. were supported by NSF BCS-1460367. K.T.L., A.W., and J.M. were supported by NSF BCS-1153568. J.F.-E. and J.A.M.-A. were supported by IT622-13 Gobierno Vasco, Diputación Foral de Álava, and Diputación Foral de Gipuzkoa. We acknowledge support from the Portuguese Foundation for Science and Technology (PTDC/EPH-ARQ/4164/2014) and the FEDER-COMPETE 2020 project 016899. P.S. was supported by the FCT Investigator Program (IF/01641/2013), FCT IP, and ERDF (COMPETE2020 – POCI). M.Si. and K.D. were supported by a Leverhulme Trust Doctoral Scholarship awarded to M.B.R. and M.P. D.R. was supported by an Allen Discovery Center grant from the Paul Allen Foundation, NIH grant GM100233, and the Howard Hughes Medical Institute. V.V.-M. and W.H. were supported by the Max Planck Society

Contemporary use of cefazolin for MSSA infective endocarditis: analysis of a national prospective cohort

Objectives: This study aimed to assess the real use of cefazolin for methicillin-susceptible Staphylococcus aureus (MSSA) infective endocarditis (IE) in the Spanish National Endocarditis Database (GAMES) and to compare it with antistaphylococcal penicillin (ASP). Methods: Prospective cohort study with retrospective analysis of a cohort of MSSA IE treated with cloxacillin and/or cefazolin. Outcomes assessed were relapse; intra-hospital, overall, and endocarditis-related mortality; and adverse events. Risk of renal toxicity with each treatment was evaluated separately. Results: We included 631 IE episodes caused by MSSA treated with cloxacillin and/or cefazolin. Antibiotic treatment was cloxacillin, cefazolin, or both in 537 (85%), 57 (9%), and 37 (6%) episodes, respectively. Patients treated with cefazolin had significantly higher rates of comorbidities (median Charlson Index 7, P <0.01) and previous renal failure (57.9%, P <0.01). Patients treated with cloxacillin presented higher rates of septic shock (25%, P = 0.033) and new-onset or worsening renal failure (47.3%, P = 0.024) with significantly higher rates of in-hospital mortality (38.5%, P = 0.017). One-year IE-related mortality and rate of relapses were similar between treatment groups. None of the treatments were identified as risk or protective factors. Conclusion: Our results suggest that cefazolin is a valuable option for the treatment of MSSA IE, without differences in 1-year mortality or relapses compared with cloxacillin, and might be considered equally effective

Subcutaneous anti-COVID-19 hyperimmune immunoglobulin for prevention of disease in asymptomatic individuals with SARS-CoV-2 infection: a double-blind, placebo-controlled, randomised clinical trialResearch in context

Summary: Background: Anti-COVID-19 hyperimmune immunoglobulin (hIG) can provide standardized and controlled antibody content. Data from controlled clinical trials using hIG for the prevention or treatment of COVID-19 outpatients have not been reported. We assessed the safety and efficacy of subcutaneous anti-COVID-19 hyperimmune immunoglobulin 20% (C19-IG20%) compared to placebo in preventing development of symptomatic COVID-19 in asymptomatic individuals with SARS-CoV-2 infection. Methods: We did a multicentre, randomized, double-blind, placebo-controlled trial, in asymptomatic unvaccinated adults (≥18 years of age) with confirmed SARS-CoV-2 infection within 5 days between April 28 and December 27, 2021. Participants were randomly assigned (1:1:1) to receive a blinded subcutaneous infusion of 10 mL with 1 g or 2 g of C19-IG20%, or an equivalent volume of saline as placebo. The primary endpoint was the proportion of participants who remained asymptomatic through day 14 after infusion. Secondary endpoints included the proportion of individuals who required oxygen supplementation, any medically attended visit, hospitalisation, or ICU, and viral load reduction and viral clearance in nasopharyngeal swabs. Safety was assessed as the proportion of patients with adverse events. The trial was terminated early due to a lack of potential benefit in the target population in a planned interim analysis conducted in December 2021. ClinicalTrials.gov registry: NCT04847141. Findings: 461 individuals (mean age 39.6 years [SD 12.8]) were randomized and received the intervention within a mean of 3.1 (SD 1.27) days from a positive SARS-CoV-2 test. In the prespecified modified intention-to-treat analysis that included only participants who received a subcutaneous infusion, the primary outcome occurred in 59.9% (91/152) of participants receiving 1 g C19-IG20%, 64.7% (99/153) receiving 2 g, and 63.5% (99/156) receiving placebo (difference in proportions 1 g C19-IG20% vs. placebo, −3.6%; 95% CI -14.6% to 7.3%, p = 0.53; 2 g C19-IG20% vs placebo, 1.1%; −9.6% to 11.9%, p = 0.85). None of the secondary clinical efficacy endpoints or virological endpoints were significantly different between study groups. Adverse event rate was similar between groups, and no severe or life-threatening adverse events related to investigational product infusion were reported. Interpretation: Our findings suggested that administration of subcutaneous human hyperimmune immunoglobulin C19-IG20% to asymptomatic individuals with SARS-CoV-2 infection was safe but did not prevent development of symptomatic COVID-19. Funding: Grifols

Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles ("MISEV") guidelines for the field in 2014. We now update these "MISEV2014" guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points