Correlation between cardiovascular disease biomarkers and biochemical and physical milieu in complex vascular environments

La progressió de l'aterosclerosi i la trombosi en pacients amb risc de malaltia cardiovascular depèn en gran mesura de l'entorn únic a nivell físic i bioquímic cada individu. Característiques tals com l'arquitectura de la vasculatura, la composició bioquímica de la sang o el tipus de tractament defineixen el resultat de les intervencions cardiovasculars. La col•locació d'un stent o d'un bypass busca recuperar la permeabilitat del vas, però es veu limitada per la restenosis i la trombosi. El disseny de models multi-escala específics per a cada pacient pot ajudar a entendre la progressió d'aquests esdeveniments en tenir la capacitat per integrar les respostes cel•lulars microscòpiques en el context del flux macroscòpic i de les condicions estructurals. Aquests models poden proporcionar informació sobre com mitigar respostes adverses en funció de cada individu. Emprant mètodes in silico i in vitro prèviament validats, s'ha desenvolupat una plataforma de replicació arterial per reproduir bifurcacions vasculars coronàries i caròtides derivades d'imatges clíniques que s'han fet servir per generar arxius computacionals per a anàlisi in silico per una banda i per fabricar models arterials polimèrics biocompatibles per a anàlisis in vitro de l’altra. En paral•lel amb les simulacions de flux, els models físics van ser sembrats amb cèl•lules vasculars centrals en l'hemostàsia i la resposta a les lesions. Els models vasculars van ser exposats a fluxos fisiològics rellevants i a entorns urèmics, inflamatoris o anti-proliferatius. Després de la caracterització funcional dels models, el progrés de l'aterosclerosi i la trombosi es va quantificar a nivell local i es va correlacionar amb les característiques biològiques, químiques i físiques de l'entorn cel•lular. La quantitat de recirculació i la presència d'agents inflamatoris, productes químics anti proliferatius i de sèrum i soluts urèmics van ser crítics per a l'activació dels biomarcadors d'evolució d'aterosclerosi i trombosi . Plataformes integrades tals com la descrita en aquesta tesi podrien ser molt útils en una varietat de camps de la biomedicina. La plataforma pot ajudar els investigadors a respondre una sèrie de qüestions biològiques clínicament rellevants i té la capacitat de produir empelts vasculars bioimplantables en un futur pròxim.La progresión de la aterosclerosis y la trombosis en pacientes con riesgo de enfermedad cardiovascular depende en gran medida del entorno único a nivel físico y bioquímico de cada individuo. Características tales como la arquitectura de la vasculatura, composición bioquímica de la sangre o el tipo de tratamiento definen el resultado de las intervenciones cardiovasculares. La colocación de un stent o de un bypass busca recuperar la permeabilidad del vaso, pero se ve limitada por la restenosis y la trombosis. El diseño de modelos multi-escala específicos para cada paciente puede ayudar a entender la progresión de estos eventos al tener capacidad para integrar las respuestas celulares microscópicas en el contexto del flujo macroscópico y de las condiciones estructurales. Dichos modelos pueden proporcionar información sobre cómo mitigar respuestas adversas en función de cada individuo. Usando métodos in silico e in vitro previamente validados se ha desarrollado una plataforma de replicación arterial para reproducir bifurcaciones vasculares coronarias y carótidas derivadas de imágenes clínicas, que se han usado para generar archivos computacionales para análisis in silico por un lado y para fabricar modelos arteriales poliméricos biocompatibles para análisis in vitro por otro. En paralelo con las simulaciones de flujo, los modelos físicos fueron sembrados con células vasculares centrales en la hemostasia y la respuesta a las lesiones. Los modelos vasculares fueron expuestos a flujos fisiológicos relevantes y a entornos urémicos, inflamatorios o anti proliferativos. Tras la caracterización funcional de los modelos, el progreso de la aterosclerosis y la trombosis se cuantificó a nivel local y se correlacionó con las características biológicas, químicas y físicas del entorno celular. La cantidad de recirculación y la presencia de agentes inflamatorios, productos químicos anti proliferativos y de suero y solutos urémicos fueron críticos para la activación de los biomarcadores de evolución de aterosclerosis y trombosis. Plataformas integradas tales como la descrita en esta tesis podrían ser muy útiles en una variedad de campos de la biomedicina. La plataforma puede ayudar a los investigadores a responder una serie de cuestiones biológicas clínicamente relevantes y tiene la capacidad de producir injertos vasculares bioimplantables en un futuro próximo.Progression of atherosclerosis and thrombosis in patients at risk of cardiovascular disease depend heavily upon the unique physical and biochemical environment of each individual. Characteristics such as vessel architecture, biochemical composition of blood or type of treatment define the outcome of cardiovascular interventions. Stent placement and graft positioning seek to recover vessel patency, yet are limited by restenosis and thrombosis. Composite, patient-specific, multi-scale models able to integrate microscopic cellular responses in the context of relevant macroscopic flow and structural conditions may help understand the progression of these events, providing insight into how to mitigate adverse responses in specific settings and individuals. Based on previously validated in silico and in vitro methods, an arterial replication platform was developed. Vascular architectures from coronary and carotid bifurcations were derived from clinical imaging and used to generate conjoint computational meshing for in silico analysis and polymeric, biocompatible scaffolds for in vitro models. In parallel with three dimensional flow simulations, the geometrically-realistic constructs were seeded with vascular cells critical to vessel hemostasis and response to injury and exposed to relevant, physiologic flows and uremic, inflammatory or anti-proliferative conditions. Following functional characterization, in vitro surrogates of atherosclerotic and thrombogenic progression were locally quantified and correlated with the biological, chemical and physical characteristics of the cellular environment. The extent of recirculation and the presence of inflammatory agents, anti-proliferative chemicals and uremic serum and solutes were critical to the activation of atherosclerosis and thrombosis progression biomarkers. Integrated frameworks such as the one described in this thesis could be very useful in a range of biomedical fields. The platform may help researchers to answer an array of biological and clinically relevant questions and holds the capacity to cast bioimplantable vascular grafts in a close future

Polycomb regulation is coupled to cell cycle transition in pluripotent stem cells

When self-renewing pluripotent cells receive a differentiation signal, ongoing cell duplication needs to be coordinated with entry into a differentiation program. Accordingly, transcriptional activation of lineage specifier genes and cell differentiation is confined to the G1 phase of the cell cycle by unknown mechanisms. We found that Polycomb repressive complex 2 (PRC2) subunits are differentially recruited to lineage specifier gene promoters across cell cycle in mouse embryonic stem cells (mESCs). Jarid2 and the catalytic subunit Ezh2 are markedly accumulated at target promoters during S and G2 phases, while the transcriptionally activating subunits EPOP and EloB are enriched during G1 phase. Fluctuations in the recruitment of PRC2 subunits promote changes in RNA synthesis and RNA polymerase II binding that are compromised in Jarid2 −/− mESCs. Overall, we show that differential recruitment of PRC2 subunits across cell cycle enables the establishment of a chromatin state that facilitates the induction of cell differentiation in G1 phase.This study was supported by the Spanish Ministry of Economy and Competitiveness (SAF2013-40891-R and BFU2016-75233-P) and the Andalusian Regional Government (PC-0246-2017). D.L. is a Ramón y Cajal researcher of the Spanish Ministry of Economy and Competitiveness (RYC-2012-10019)

Exploring the interplay between climate, population immunity and SARS-CoV-2 transmission dynamics in Mediterranean countries

The relationship between SARS-CoV-2 transmission and environmental factors has been analyzed in numerous studies since the outbreak of the pandemic, resulting in heterogeneous results and conclusions. This may be due to differences in methodology, considered variables, confounding factors, studied periods and/or lack of adequate data. Furthermore, previous works have reported that the lack of population immunity is the fundamental driver in transmission dynamics and can mask the potential impact of environmental variables. In this study, we aimed to investigate the association between climate variables and COVID-19 transmission considering the influence of population immunity. We analyzed two different periods characterized by the absence of vaccination (low population immunity) and a high degree of vaccination (high level of population immunity), respectively. Although this study has some limitations, such us the restriction to a specific climatic zone and the omission of other environmental factors, our results indicate that transmission of SARSCoV-2 may increase independently of temperature and specific humidity in periods with low levels of population immunity while a negative association is found under conditions with higher levels of population immunity in the analyzed regions

Scoring personalized molecular portraits identify Systemic Lupus Erythematosus subtypes and predict individualized drug responses, symptomatology and disease progression

Objectives Systemic Lupus Erythematosus is a complex autoimmune disease that leads to significant worsening of quality of life and mortality. Flares appear unpredictably during the disease course and therapies used are often only partially effective. These challenges are mainly due to the molecular heterogeneity of the disease, and in this context, personalized medicine-based approaches offer major promise. With this work we intended to advance in that direction by developing MyPROSLE, an omic-based analytical workflow for measuring the molecular portrait of individual patients to support clinicians in their therapeutic decisions. Methods Immunological gene-modules were used to represent the transcriptome of the patients. A dysregulation score for each gene-module was calculated at the patient level based on averaged z-scores. Almost 6100 Lupus and 750 healthy samples were used to analyze the association among dysregulation scores, clinical manifestations, prognosis, flare and remission events and response to Tabalumab. Machine learning-based classification models were built to predict around 100 different clinical parameters based on personalized dysregulation scores. Results MyPROSLE allows to molecularly summarize patients in 206 gene-modules, clustered into nine main lupus signatures. The combination of these modules revealed highly differentiated pathological mechanisms. We found that the dysregulation of certain gene-modules is strongly associated with specific clinical manifestations, the occurrence of relapses or the presence of long-term remission and drug response. Therefore, MyPROSLE may be used to accurately predict these clinical outcomes. Conclusions MyPROSLE (https://myprosle.genyo.es) allows molecular characterization of individual Lupus patients and it extracts key molecular information to support more precise therapeutic decisions.PID2020-119032RB-I00 supported by MCIN/AEI/10.13039/501100011033FEDER and the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 831434 (3TR)European Union’s Horizon 2020EFPIAFEDER/Junta de Andalucía-Consejer’a de Transformación Económica, Industria, Conocimiento y Universidades (grants P20_00335 and B-CTS-40-UGR20)‘Consejería de Transformación Económica, Industria, Conocimiento y Universidades’ (CTEICU)European Union through the European Social Fund (ESF) named ‘Andalucía se mueve con Europa”Andalusian ESF Operational Program 2014–2020ISCIII CD18/00149Ministerio de Universidades (Spain’s Government) and the European Union – NextGenerationE

DREIMT: a drug repositioning database and prioritization tool for immunomodulation

Motivation Drug immunomodulation modifies the response of the immune system and can be therapeutically exploited in pathologies such as cancer and autoimmune diseases. Results DREIMT is a new hypothesis-generation web tool, which performs drug prioritization analysis for immunomodulation. DREIMT provides significant immunomodulatory drugs targeting up to 70 immune cells subtypes through a curated database that integrates 4960 drug profiles and ∼2600 immune gene expression signatures. The tool also suggests potential immunomodulatory drugs targeting user-supplied gene expression signatures. Final output includes drug–signature association scores, FDRs and downloadable plots and results tables. Availabilityand implementation http://www.dreimt.org. Supplementary information Supplementary data are available at Bioinformatics online.Agencia Estatal de Investigación | Ref. RTI2018-097596-B-I00Instituto de Salud Carlos IIIComunidad de Madrid | Ref. PEJD-2019-PRE/BMD-15732Xunta de Galicia | Ref. ED431C2018/55-GRCJunta de Andalucía | Ref. PI-0173-201

Optimization of the Combustion System of a Medium Duty Direct Injection Diesel Engine by Combining CFD modeling with Experimental Validation

The research in the field of internal combustion engines is currently driven by the needs of decreasing fuel consumption and CO2 emissions, while fulfilling the increasingly stringent pollutant emissions regulations. In this framework, this research work focuses on describing a methodology for optimizing the combustion system of compression ignition (CI) engines, by combining computational fluid dynamics (CFD) modeling, and the statistical Design of Experiments (DOE) technique known as Response Surface Method (RSM). As a key aspect, in addition to the definition of the optimum set of values for the input parameters, this methodology is extremely useful to gain knowledge on the cause/effect relationships between the input and output parameters under investigation. This methodology is applied in two sequential studies to the optimization of the combustion system of a 4-cylinder 4-stroke Medium Duty Direct Injection (DI) CI engine, minimizing the fuel consumption while fulfilling the emission limits in terms of NOx and soot. The first study targeted four optimization parameters related to the engine hardware including piston bowl geometry, injector nozzle configuration and mean swirl number (MSN) induced by the intake manifold design. After the analysis of the results, the second study extended to six parameters, limiting the optimization of the engine hardware to the bowl geometry, but including the key air management and injection settings. For both studies, the simulation plans were defined following a Central Composite Design (CCD), providing 25 and 77 simulations respectively. The results confirmed the limited benefits, in terms of fuel consumption, around 2%, with constant NOx emission achieved when optimizing the engine hardware, while keeping air management and injection settings. Thus, including air management and injection settings in the optimization is mandatory to significantly decrease the fuel consumption, by around 5%, while keeping the emission limits.Benajes Calvo, JV.; Novella Rosa, R.; Pastor Enguídanos, JM.; Hernández-López, A.; Hasegawa, M.; Tsuji, N.; Emi, M.... (2016). Optimization of the Combustion System of a Medium Duty Direct Injection Diesel Engine by Combining CFD modeling with Experimental Validation. Energy Conversion and Management. 110:212-229. doi:10.1016/j.enconman.2015.12.010S21222911

The molecular clock protein Bmal1 regulates cell differentiation in mouse embryonic stem cells

Mammals optimize their physiology to the light–dark cycle by synchronization of the master circadian clock in the brain with peripheral clocks in the rest of the tissues of the body. Circadian oscillations rely on a negative feedback loop exerted by the molecular clock that is composed by transcriptional activators Bmal1 and Clock, and their negative regulators Period and Cryptochrome. Components of the molecular clock are expressed during early development, but onset of robust circadian oscillations is only detected later during embryogenesis. Here, we have used na¨ıve pluripotent mouse embryonic stem cells (mESCs) to study the role of Bmal1 during early development. We found that, compared to wild-type cells, Bmal12/2 mESCs express higher levels of Nanog protein and altered expression of pluripotencyassociated signalling pathways. Importantly, Bmal12/2 mESCs display deficient multi-lineage cell differentiation capacity during the formation of teratomas and gastrula-like organoids. Overall, we reveal that Bmal1 regulates pluripotent cell differentiation and propose that the molecular clock is an hitherto unrecognized regulator of mammalian development.Ramon y Cajal grant of the Spanish ministry of economy and competitiveness RYC2012-10019Spanish ministry of economy and competitiveness BFU2016-75233-PAndalusian regional government PC-0246-2017Fundacion Progreso y Salud (FPS)Instituto de Salud Carlos III European Union (EU) CPII17/00032 PI17/01574University of Granad

Changes in PRC1 activity during interphase modulate lineage transition in pluripotent cells

We thank the core facilities at GENYO for excellent technical support. We also thank the genomics unit at the CRG for assistance with RNA-seq and ChIP-seq experiments. The Landeira lab is supported by the Spanish ministry of science and innovation (PID2019-108108-100, EUR2021- 122005), the Andalusian regional government (PIER-0211-2019, PY20_00681) and the University of Granada (A-BIO-6-UGR20) grants. Research in the Klose lab is supported by the Wellcome Trust (209400/ Z/17/Z) and the European Research Council (681440). A.F. was sup- ported by a Sir Henry Wellcome Post-doctoral fellowship (110286/Z/15/ Z). Work in the Rada-Iglesias lab is funded by the Ministerio de Ciencia e Innovación, the Agencia Española de Investigación and the European Regional Development Fund (PGC2018-095301-B-I00 and RED2018- 102553-T); by the European Research Council (862022); and by the European Commission (H2020-MSCA-ITN-2019-860002).The online version contains supplementary material available at https://doi.org/10.1038/s41467-023-35859-9The potential of pluripotent cells to respond to developmental cues and trigger cell differentiation is enhanced during the G1 phase of the cell cycle, but the molecular mechanisms involved are poorly understood. Variations in polycomb activity during interphase progression have been hypothesized to regulate the cell-cycle-phase-dependent transcriptional activation of differentiation genes during lineage transition in pluripotent cells. Here, we show that recruitment of Polycomb Repressive Complex 1 (PRC1) and associated molecular functions, ubiquitination of H2AK119 and three-dimensional chromatin interactions, are enhanced during S and G2 phases compared to the G1 phase. In agreement with the accumulation of PRC1 at target promoters upon G1 phase exit, cells in S and G2 phases show firmer transcriptional repression of developmental regulator genes that is drastically perturbed upon genetic ablation of the PRC1 catalytic subunit RING1B. Importantly, depletion of RING1B during retinoic acid stimu- lation interferes with the preference of mouse embryonic stem cells (mESCs) to induce the transcriptional activation of differentiation genes in G1 phase. We propose that incremental enrolment of polycomb repressive activity during interphase progression reduces the tendency of cells to respond to develop- mental cues during S and G2 phases, facilitating activation of cell differentiation in the G1 phase of the pluripotent cell cycle.Ministry of Science and Innovation, Spain (MICINN) Spanish Government PID2019-108108-100, EUR2021-122005Andalusian regional government PIER-0211-2019, PY20_00681University of Granada A-BIO-6-UGR20Wellcome Trust 209400/Z/17/ZEuropean Research Council (ERC) European Commission 862022Wellcome Trust PGC2018-095301-B-I00Ministry of Science and Innovation, Spain (MICINN) Instituto de Salud Carlos III Spanish GovernmentEuropean Commission RED2018-102553-T, H2020-MSCA-ITN-2019-860002European Commission European Commission Joint Research Centre 681440Agencia Española de Investigación110286/Z/15/

Quality improvement in palliative care services and networks: preliminary results of a benchmarking process in Catalonia

Background: a wide range of palliative care services has been implemented in Catalonia over the past 20 years. Quantitative and qualitative differences in the organization of palliative care services between districts and settings can result in wide variability in the quality of these services, and their accessibility. Methods: we implemented a benchmark methodology to compare dimensions of care and organization, to identify aspects requiring improvement, and to establish indicators to measure progress. The overall aim was to generate a consensus document for submission to the Department of Health (DoH) of the Government of Catalonia. Results: a Steering Committee convoked a meeting in Barcelona (Catalonia, Spain) and representatives (n = 114) of all the 37 districts within our health care remit (rural, urban, intermediate, and metropolitan) and settings of the health care system (hospitals, social health centers, community, and nursing homes) attended and took part in plenary sessions and workshops to define areas that, in their experience, were considered weak. Twenty-one consensus recommendations achieving high levels of consensus were generated for submission to the DoH. These included the formal definition of the model of care and organization of palliative care services at all levels in the region, the implementation of measures for improvement in different settings and scenarios, systems for continuous care, and facilities for the continuing training of health care personnel. These proposals have since been implemented in a trial region and, depending on the outcomes, will be applied throughout our health service. Conclusion: we conclude that benchmark methodology is valuable in acquiring data for use in improving palliative care organization for patients' benefit

Controlling the electrochemical hydrogen generation and storage in graphene oxide by in-situ Raman spectroscopy

Hydrogen, generated from water splitting, is postulated as one of the most promising alternatives to fossil fuels. In this context, direct hydrogen generation by electrolysis and fixation to graphene oxide in an aqueous suspension could overcome storage and distribution problems of gaseous hydrogen. This study presents time-resolved determination of the electrochemical hydrogenation of GO by in-situ Raman spectroscopy, simultaneous to original functional groups elimination. Hydrogenation is found favoured by dynamic modulation of the electrochemical environment compared to fixed applied potentials, with a 160% increase of C-H bond formation. Epoxide groups suppression and generated hydroxide groups point at these epoxide groups being one of the key sites where hydrogenation was possible. FTIR revealed characteristic symmetric and asymmetric stretching vibrations of C-H bonds in CH and CH groups. This shows that hydrogenation is significantly also occurring in defective sites and edges of the graphene basal plane, rather than H-Csp groups as graphane. We also determined a −0.05 V reduction starting potential in alkaline electrolytes and a 150 mV cathodic delay in acid electrolytes. The identified key parameters role, together with observed diverse C-H groups formation, points at future research directions for large-scale hydrogen storage in graphene