The Small RNA Component of Arabidopsis thaliana Phloem Sap and Its Response to Iron Deficiency.

In order to discover sRNA that might function during iron deficiency stress, RNA was prepared from phloem exudates of Arabidopsis thaliana, and used for RNA-seq. Bioanalyzer results indicate that abundant RNA from phloem is small in size-less than 200 nt. Moreover, typical rRNA bands were not observed. Sequencing of eight independent phloem RNA samples indicated that tRNA-derived fragments, specifically 5' tRFs and 5' tRNA halves, are highly abundant in phloem sap, comprising about 46% of all reads. In addition, a set of miRNAs that are present in phloem sap was defined, and several miRNAs and sRNAs were identified that are differentially expressed during iron deficiency.

TP53 gain-of-function mutation modulates the immunosuppressive microenvironment in non-HPV-associated oral squamous cell carcinoma.

BACKGROUND: TP53, the most mutated gene in solid cancers, has a profound impact on most hallmarks of cancer. Somatic TP53 mutations occur in high frequencies in head and neck cancers, including oral squamous cell carcinoma (OSCC). Our study aims to understand the role of TP53 gain-of-function mutation in modulating the tumor immune microenvironment (TIME) in OSCC. METHODS: Short hairpin RNA knockdown of mutant p53R172H in syngeneic oral tumors demonstrated changes in tumor growth between immunocompetent and immunodeficient mice. HTG EdgeSeq targeted messenger RNA sequencing was used to analyze cytokine and immune cell markers in tumors with inactivated mutant p53R172H. Flow cytometry and multiplex immunofluorescence (mIF) confirmed the role of mutant p53R172H in the TIME. The gene expression of patients with OSCC was analyzed by CIBERSORT and mIF was used to validate the immune landscape at the protein level. RESULTS: Mutant p53R172H contributes to a cytokine transcriptome network that inhibits the infiltration of cytotoxic CD8+ T cells and promotes intratumoral recruitment of regulatory T cells and M2 macrophages. Moreover, p53R172H also regulates the spatial distribution of immunocyte populations, and their distribution between central and peripheral intratumoral locations. Interestingly, p53R172H-mutated tumors are infiltrated with CD8+ and CD4+ T cells expressing programmed cell death protein 1, and these tumors responded to immune checkpoint inhibitor and stimulator of interferon gene 1 agonist therapy. CIBERSORT analysis of human OSCC samples revealed associations between immune cell populations and the TP53R175H mutation, which paralleled the findings from our syngeneic mouse tumor model. CONCLUSIONS: These findings demonstrate that syngeneic tumors bearing the TP53R172H gain-of-function mutation modulate the TIME to evade tumor immunity, leading to tumor progression and decreased survival.

Factores de riesgo asociados a ingreso a Unidad de Cuidados Intensivos en pacientes con COVID-19 en hospitales colombianos, estudio de cohorte

Introducción: Los pacientes hospitalizados con COVID-19 presentan un espectro clínico variable y su gravedad puede ser predicha por la presencia de factores de riesgo. Objetivo: Determinar los factores asociados al ingreso a UCI en pacientes internados por COVID-19 en Colombia. Pacientes y Métodos: Estudio de cohorte multicéntrico, retrospectivo, en pacientes adultos hospitalizados por COVID-19 en Colombia, desde marzo de 2020 a enero de 2021. Se describieron las características de los pacientes y se establecieron predictores de ingreso a la UCI mediante un modelo de regresión logística. Resultados: Se incluyeron 1.160 pacientes, edad media de 55 años, 59,7% fueron hombres y 426 pacientes (36,7%) ingresaron a UCI. Los factores asociados al ingreso a UCI fueron edad (OR 1,25; IC 95%: 1,14-1,37), sobrepeso (OR 2,82; IC 95%: 1,98-4,02) y obesidad (OR 2,97; IC 95%: 2,03-4,37), antecedente de cardiopatía valvular (OR 6,46; IC 95%: 1,84-27,48), hipotensión arterial al ingreso (OR 2,35; IC 95%: 1,40-3,97), SIRS (OR 2,03; IC 95%: 1,50-2,74), disnea (OR 1,52; IC 95%: 1,09-2.14), requerimiento de oxígeno (OR 2,64; IC 95%: 1,67-4,30), neutrofilia (OR1,09; IC 95%: 1,05-1,13), elevación de dímero D (OR 1,09; IC 95%: 1,03-1,18), compromiso multilobar (OR 2,19; IC 95%: 1,58-3,07) y consolidación pulmonar (OR1,52; IC 95%: 1,13-2,04). La mortalidad intrahospitalaria fue de 14,4% (166 pacientes), 2,3% entre los que no ingresaron a la UCI y 35,2% entre los que sí lo hicieron. Conclusión: El 36,7% de pacientes hospitalizados por COVID-19 ingresó a UCI, identificándose predictores clínicos y de laboratorio asociados con este desenlace. La elaboración de modelos predictores con estos parámetros podría mejorar el pronóstico de los pacientes con COVID-19 que se hospitalizan.

Background: Hospitalized patients with COVID-19 present a variable clinical spectrum and its severity might be predicted by the presence of risk factors. Aim: To determine the factors associated with ICU admission in patients hospitalized for COVID-19 in Colombia. Method: Retrospective multicenter cohort study, in adult patients hospitalized for COVID-19 in Colombia, from March 2020 to January 2021. Population characteristics were described and ICU admission predictors were established using a logistic regression model. Results: 1,160 patients were included, mean age 55 years, 59.7% were men and 426 patients (36.7%) were admitted to the ICU. The associated factors were age (OR 1.25, 95% CI: 1.14-1.37), overweight (OR 2.82, 95% CI: 1.98-4.02) and obesity (OR 2.97, 95% CI: 2.03-4.37), valvular heart disease (OR 6.46, 95% CI: 1.84-27.48) hypotension at admission (OR 2.35, 95% CI: 1.40-3, 97), SIRS (OR 2.03, 95% CI: 1.50-2.74), dyspnea (OR 1.52, 95% CI: 1.09-2.14), oxygen requirement (OR 2.64, 95% CI: 1.67-4.30), neutrophilia (OR 1.09, 95% CI: 1.05-1.13), elevated D-dimer (OR 1.09, 95% CI: 1.03-1.18), multilobar lung involvement (OR 2.19, 95% CI: 1.58-3.07) and pulmonary consolidation (OR 1.52, 95% CI: 1.13-2.04). In-hospital mortality was 14.4% (166 patients), 2.3% among those that did not enter to the ICU and 35.2% among those who did. Conclusion: 36.7% of patients hospitalized for COVID-19 were admitted to the ICU. We identified clinical predictors associated with this outcome. Predictive models using these parameters could improve the prognostic of those patients with COVID-19 that are hospitalized.

Event-related (de)synchronization and potential in whole vs. part sensorimotor learning.

Background: There are different ways to learn a sensorimotor task. This research focuses on whole versus part learning in a complex video game that involves sensorimotor adaptations and skill learning. The primary aim of this research is to compare the changes in (1) event-related potentials (ERP) and (2) Alpha and Beta event-related desynchronization/synchronization [ERD(S)] of EEG between whole and part practice protocols. Materials and methods: 18 Healthy young participants practiced for 5 days a video game with distorted kinematic (advancing skill) and dynamic features (shooting skill) to test the ability to combine sensorimotor skill components learned modularly (part learning, 9 participants) or combined (whole practice, 9 participants). We examined ERP and ERD(S) in EEG channels in the baseline test (day 1) and the retention test (day 5), dissociating epochs with advancing or shooting. We focus the analysis on the main activity of ERP or ERD(S) in different time windows. Results: In the advancing epochs (distorted kinematic), both groups showed a decrease in time for ERP and an increase in Beta ERD activity in central and posterior channels. In the shooting epochs (distorted dynamic), the Whole group showed a decrease in time for ERPs in anterior and central-posterior channels. Additionally, the shooting ERS in the Beta band decreases within sessions in central channels, particularly for the Part group. Conclusion: Neural correlates of kinematic and dynamic control [ERP and ERD(S)] were modulated by sensorimotor learning, which reflects the effect of the type of practice on the execution and the evaluation of the action. These results can be linked with our previous report, where the simultaneous practice of kinematic and dynamic distortions takes advantage of the motor performance on retention tests, indicating a more automatic control for the whole practice group.

Age-dependent association of clonal hematopoiesis with COVID-19 mortality in patients over 60 years.

Clonal hematopoiesis, especially that of indeterminate potential (CHIP), has been associated with age-related diseases, such as those contributing to a more severe COVID-19. Four studies have attempted to associate CHIP with COVID-19 severity without conclusive findings. In the present work, we explore the association between CHIP and COVID-19 mortality. Genomic DNA extracted from peripheral blood of COVID-19 patients (n = 241 deceased, n = 239 survivors) was sequenced with the Myeloid Solutions™ panel of SOPHiA Genetics. The association between clonality and age and clonality and mortality was studied using logistic regression models adjusted for sex, ethnicity, and comorbidities. The association with mortality was performed with patients stratified into four groups of age according to the quartiles of the distribution: 60-74 years, 75-84 years, 85-91 years, and 92-101 years. Clonality was found in 38% of the cohort. The presence of CHIP variants, but not the number, significantly increased with age in the entire cohort of COVID-19 patients, as well as in the group of survivors (p < 0.001). When patients were stratified by age and the analysis adjusted, CHIP classified as pathogenic/likely pathogenic was significantly more represented in deceased patients compared with survivors in the group of 75-84 years (34.6% vs 13.7%, p = 0.020). We confirmed the well-established linear relationship between age and clonality in the cohort of COVID-19 patients and found a significant association between pathogenic/likely pathogenic CHIP and mortality in patients from 75 to 84 years that needs to be further validated.

Clinical description, molecular delineation and genotype-phenotype correlation in 340 patients with KBG syndrome: addition of 67 new patients.

BACKGROUND: KBG syndrome is a highly variable neurodevelopmental disorder and clinical diagnostic criteria have changed as new patients have been reported. Both loss-of-function sequence variants and large deletions (copy number variations, CNVs) involving ANKRD11 cause KBG syndrome, but no genotype-phenotype correlation has been reported. METHODS: 67 patients with KBG syndrome were assessed using a custom phenotypical questionnaire. Manifestations present in >50% of the patients and a 'phenotypical score' were used to perform a genotype-phenotype correlation in 340 patients from our cohort and the literature. RESULTS: Neurodevelopmental delay, macrodontia, triangular face, characteristic ears, nose and eyebrows were the most prevalentf (eatures. 82.8% of the patients had at least one of seven main comorbidities: hearing loss and/or otitis media, visual problems, cryptorchidism, cardiopathy, feeding difficulties and/or seizures. Associations found included a higher phenotypical score in patients with sequence variants compared with CNVs and a higher frequency of triangular face (71.1% vs 42.5% in CNVs). Short stature was more frequent in patients with exon 9 variants (62.5% inside vs 27.8% outside exon 9), and the prevalence of intellectual disability/attention deficit hyperactivity disorder/autism spectrum disorder was lower in patients with the c.1903_1907del variant (70.4% vs 89.4% other variants). Presence of macrodontia and comorbidities were associated with larger deletion sizes and hand anomalies with smaller deletions. CONCLUSION: We present a detailed phenotypical description of KBG syndrome in the largest series reported to date of 67 patients, provide evidence of a genotype-phenotype correlation between some KBG features and specific ANKRD11 variants in 340 patients, and propose updated clinical diagnostic criteria based on our findings.

Androgen receptor polyQ alleles and COVID-19 severity in men: A replication study.

BACKGROUND: Ample evidence indicates a sex-related difference in severity of COVID-19, with less favorable outcomes observed in men. Genetic factors have been proposed as candidates to explain this difference. The polyglutamine (polyQ) polymorphism in the androgen receptor gene has been recently described as a genetic biomarker of COVID-19 severity. OBJECTIVE: To test the association between the androgen receptor polyQ polymorphism and COVID-19 severity in a large cohort of COVID-19 male patients. MATERIALS AND METHODS: This study included 1136 male patients infected with SARS-CoV-2 as confirmed by positive PCR. Patients were retrospectively and prospectively enrolled from March to November 2020. Patients were classified according to their severity into three categories: oligosymptomatic, hospitalized and severe patients requiring ventilatory support. The number of CAG repeats (polyQ polymorphism) at the androgen receptor was obtained by PCR and patients were classified as either short (<23 repeats) or long (≥23 repeats) allele carriers. The association between polyQ alleles (short or long) and COVID-19 severity was assessed by Chi-squared (Chi2 ) and logistic regression analysis. RESULTS: The mean number of polyQ CAG repeats was 22 (±3). Patients were classified as oligosymptomatic (15.5%), hospitalized (63.2%), and severe patients (21.3%) requiring substantial respiratory support. PolyQ alleles distribution did not show significant differences between severity classes in our cohort (Chi2 test p > 0.05). Similar results were observed after adjusting by known risk factors such as age, comorbidities, and ethnicity (multivariate logistic regression analysis). DISCUSSION: Androgen sensitivity may be a critical factor in COVID-19 disease severity. However, we did not find an association between the polyQ polymorphism and the COVID-19 severity. Additional studies are needed to clarify the mechanism underlying the association between androgens and COVID-19 outcome. CONCLUSIONS: The results obtained in our study do not support the role of this polymorphism as biomarker of COVID-19 severity.

Novel APOB nonsense variant related to familial hypobetalipoproteinemia and hepatic steatosis: A case report and review.

Hereditary familial hypobetalipoproteinemia (FHBL) is a syndrome caused by variants in the APOB gene, that cause a defect in the secretion and mobilization of liver lipids to peripheral tissues, associated with the synthesis of truncated ApoB100 apolipoproteins. This condition causes significant reduction in total cholesterol (TC), low-density lipoproteins (LDL), very low-density proteins (VLDL) and serum triglyceride levels, with unchanged high-density lipoprotein (HDL) cholesterol levels. Herein we present the case of a middle-aged woman diagnosed with FHBL and hepatic steatosis, heterozygous for c.4698C>A; (p.Tyr1566Ter) variant in APOB. The variant presented herein showed high expressiveness in the two generations of individuals analyzed and has not yet being described in the medical literature. Early diagnosis and screening for associated metabolic comorbidities such as metabolic fatty liver disease and its subsequent progression to fibrosis are the two main goals in the treatment of this condition, in order to prevent medium to long term potential complications.

Mutant p53 drives an immune cold tumor immune microenvironment in oral squamous cell carcinoma.

The critical role of the tumor immune microenvironment (TIME) in determining response to immune checkpoint inhibitor (ICI) therapy underscores the importance of understanding cancer cell-intrinsic mechanisms driving immune-excluded ("cold") TIMEs. One such cold tumor is oral cavity squamous cell carcinoma (OSCC), a tobacco-associated cancer with mutations in the TP53 gene which responds poorly to ICI therapy. Because altered TP53 function promotes tumor progression and plays a potential role in TIME modulation, here we developed a syngeneic OSCC models with defined Trp53 (p53) mutations and characterized their TIMEs and degree of ICI responsiveness. We observed that a carcinogen-induced p53 mutation promoted a cold TIME enriched with immunosuppressive M2 macrophages highly resistant to ICI therapy. p53-mutated cold tumors failed to respond to combination ICI treatment; however, the combination of a programmed cell death protein 1 (PD-1) inhibitor and stimulator of interferon genes (STING) agonist restored responsiveness. These syngeneic OSCC models can be used to gain insights into tumor cell-intrinsic drivers of immune resistance and to develop effective immunotherapeutic approaches for OSCC and other ICI-resistant solid tumors.

SARS-CoV-2 Mutant Spectra at Different Depth Levels Reveal an Overwhelming Abundance of Low Frequency Mutations.

Populations of RNA viruses are composed of complex and dynamic mixtures of variant genomes that are termed mutant spectra or mutant clouds. This applies also to SARS-CoV-2, and mutations that are detected at low frequency in an infected individual can be dominant (represented in the consensus sequence) in subsequent variants of interest or variants of concern. Here we briefly review the main conclusions of our work on mutant spectrum characterization of hepatitis C virus (HCV) and SARS-CoV-2 at the nucleotide and amino acid levels and address the following two new questions derived from previous results: (i) how is the SARS-CoV-2 mutant and deletion spectrum composition in diagnostic samples, when examined at progressively lower cut-off mutant frequency values in ultra-deep sequencing; (ii) how the frequency distribution of minority amino acid substitutions in SARS-CoV-2 compares with that of HCV sampled also from infected patients. The main conclusions are the following: (i) the number of different mutations found at low frequency in SARS-CoV-2 mutant spectra increases dramatically (50- to 100-fold) as the cut-off frequency for mutation detection is lowered from 0.5% to 0.1%, and (ii) that, contrary to HCV, SARS-CoV-2 mutant spectra exhibit a deficit of intermediate frequency amino acid substitutions. The possible origin and implications of mutant spectrum differences among RNA viruses are discussed.

Presence of rare potential pathogenic variants in subjects under 65 years old with very severe or fatal COVID-19.

Rare variants affecting host defense against pathogens could be involved in COVID-19 severity and may help explain fatal outcomes in young and middle-aged patients. Our aim was to report the presence of rare genetic variants in certain genes, by using whole exome sequencing, in a selected group of COVID-19 patients under 65 years who required intubation or resulting in death (n = 44). To this end, different etiopathogenic mechanisms were explored using gene prioritization-based analysis in which genes involved in immune response, immunodeficiencies or blood coagulation were studied. We detected 44 different variants of interest, in 29 different patients (66%). Some of these variants were previously described as pathogenic and were located in genes mainly involved in immune response. A network analysis, including the 42 genes with candidate variants, showed three main components, consisting of 25 highly interconnected genes related to immune response and two additional networks composed by genes enriched in carbohydrate metabolism and in DNA metabolism and repair processes. In conclusion, we have detected candidate variants that may potentially influence COVID-19 outcome in our cohort of patients. Further studies are needed to confirm the ultimate role of the genetic variants described in the present study on COVID-19 severity.

SARS-CoV-2 Point Mutation and Deletion Spectra and Their Association with Different Disease Outcomes.

Mutant spectra of RNA viruses are important to understand viral pathogenesis and response to selective pressures. There is a need to characterize the complexity of mutant spectra in coronaviruses sampled from infected patients. In particular, the possible relationship between SARS-CoV-2 mutant spectrum complexity and disease associations has not been established. In the present study, we report an ultradeep sequencing (UDS) analysis of the mutant spectrum of amplicons from the nsp12 (polymerase)- and spike (S)-coding regions of 30 nasopharyngeal isolates (diagnostic samples) of SARS-CoV-2 of the first COVID-19 pandemic wave (Madrid, Spain, April 2020) classified according to the severity of ensuing COVID-19. Low-frequency mutations and deletions, counted relative to the consensus sequence of the corresponding isolate, were overwhelmingly abundant. We show that the average number of different point mutations, mutations per haplotype, and several diversity indices was significantly higher in SARS-CoV-2 isolated from patients who developed mild disease than in those associated with moderate or severe disease (exitus). No such bias was observed with RNA deletions. Location of amino acid substitutions in the three-dimensional structures of nsp12 (polymerase) and S suggest significant structural or functional effects. Thus, patients who develop mild symptoms may be a richer source of genetic variants of SARS-CoV-2 than patients with moderate or severe COVID-19. IMPORTANCE The study shows that mutant spectra of SARS-CoV-2 from diagnostic samples differ in point mutation abundance and complexity and that significantly larger values were observed in virus from patients who developed mild COVID-19 symptoms. Mutant spectrum complexity is not a uniform trait among isolates. The nature and location of low-frequency amino acid substitutions present in mutant spectra anticipate great potential for phenotypic diversification of SARS-CoV-2.

Estrategia comunitaria municipal «yonomebenzo». Actividades y resultados en el período 2017-2020 / Municipal community strategy

Objetivo: Describir las actividades, el proceso y los resultados de la estrategia comunitaria Yonomebenzo desde 2017 a 2020. Metodología:Monitorización del proceso mediante evaluaciones periódicas para comprobar su impacto y desarrollar las actividades pendientes. Adaptación a la pandemia del coronavirus.Trabajar sobre la factibilidad del proceso a medio y largo plazo mediante el desarrollo de distintas estrategias. Intervención: Escuela del sueño: servicio centrado en personas ancianas ofreciendo alternativas saludables para facilitar el descanso nocturno.Oficina municipal del sueño: espacio abierto a población general sobre hábitos correctos de sueño.Mapeo de activos en salud (localizasalud): desarrollado en coordinación con Comisión de Salud Comunitaria municipal, enmarcado en la estrategia de Promoción de Salud y Prevención del Ministerio de Sanidad.Estrategia municipal de farmacias comunitarias: red voluntaria de 18 farmacias comunitarias. Factibilidad del proceso:A medio plazo: a través de los recursos económicos de ayudas del Ministerio de Sanidad y presupuestos municipales participativos.A largo plazo: municipalización de distintas actividades para financiarlas mediante presupuestos ordinarios. Intervenciones pendientes: Adaptación de actividades al contexto de la pandemia. Evaluación: Monitorización del consumo de benzodiacepinas (BZD) en dosis diaria definida/1.000 habitantes/año (DHD) y su adecuación. Aplicabilidad de la estrategia:Implicarla en contexto comunitario de atención centrada en el paciente, con profesionales de distintos ámbitos, asociaciones municipales y ciudadanía para mejorar el uso de BZD y desmedicalizar procesos cotidianos.Incorporar esta actividad comunitaria como programa municipal.Empoderar la población para controlar su propia salud. (AU)

Objective: Report the activities, process and results obtained from the Yonomebenzo community strategy from 2017 to 2020. Methodology: Follow up has been performed by means of periodic evaluations to verify the impact and develop new and pending activities.Adapting to the coronavirus pandemic.Medium and long-term feasibility has been improved by means of different strategies. Intervention. In addition to the activities performed up until 2016, new activities include:Sleeping school: focused on elderly people, offering healthy tips to improve night rest.Municipal Sleep Support Office: available for the entire population, emphasizes correct sleep hygiene.Health assets mapping (localizasalud): in collaboration with the municipal Community Health Commission, a Health Promotion and Prevention strategy carried out by the Ministry.Community-Pharmacies Municipal Strategy: implying 18 voluntary community pharmacies. Feasibility of the process:Medium term: by means of financial grants from the Ministry and participatory municipal budgets.Long term: municipalization of different activities to finance them by means of ordinary budgets. Interventions pending. Adaptation of activities against the backdrop of the pandemic. Evaluation. Monitoring of benzodiazepine (BZD) consumption as daily defined dose/1000 inhabitants/year (DDD) and its suitability. Application of the strategy:Implicate this into a community context for patient-focused care, with professionals from different areas, municipal associations and citizens to improve the use of BZD and stop treating ordinary processes as medical issues.Incorporate this community activity as a municipal programme.Empower the population to monitors its own health. (AU)

An Approach to Growth Delimitation of Straight Line Segment Classifiers Based on a Minimum Bounding Box.

Several supervised machine learning algorithms focused on binary classification for solving daily problems can be found in the literature. The straight-line segment classifier stands out for its low complexity and competitiveness, compared to well-knownconventional classifiers. This binary classifier is based on distances between points and two labeled sets of straight-line segments. Its training phase consists of finding the placement of labeled straight-line segment extremities (and consequently, their lengths) which gives the minimum mean square error. However, during the training phase, the straight-line segment lengths can grow significantly, giving a negative impact on the classification rate. Therefore, this paper proposes an approach for adjusting the placements of labeled straight-line segment extremities to build reliable classifiers in a constrained search space (tuned by a scale factor parameter) in order to restrict their lengths. Ten artificial and eight datasets from the UCI Machine Learning Repository were used to prove that our approach shows promising results, compared to other classifiers. We conclude that this classifier can be used in industry for decision-making problems, due to the straightforward interpretation and classification rates.

High SARS-CoV-2 viral load is associated with a worse clinical outcome of COVID-19 disease.

COVID-19 severity and progression are determined by several host and virological factors that may influence the final outcome of SARS-CoV-2-infected patients. The objective of this work was to determine a possible association between viral load, obtained from nasopharyngeal swabs, and the severity of the infection in a cohort of 448 SARS-CoV-2-infected patients from a hospital in Madrid during the first outbreak of the pandemic in Spain. To perform this, we clinically classified patients as mild, moderate and severe COVID-19 according to a number of clinical parameters such as hospitalization requirement, need of oxygen therapy, admission to intensive care units and/or death. Also, Ct values were determined using SARS-CoV-2-specific oligonucleotides directed to ORF1ab. Here we report a statistically significant association between viral load and disease severity, a high viral load being associated with worse clinical prognosis, independently of several previously identified risk factors such as age, sex, hypertension, cardiovascular disease, diabetes, obesity and lung disease (asthma and chronic obstructive pulmonary disease). The data presented here reinforce viral load as a potential biomarker for predicting disease severity in SARS-CoV-2-infected patients. It is also an important parameter in viral evolution since it relates to the numbers and types of variant genomes present in a viral population, a potential determinant of disease progression.

RPE65-related retinal dystrophy: Mutational and phenotypic spectrum in 45 affected patients.

INTRODUCTION: Biallelic pathogenic RPE65 variants are related to a spectrum of clinically overlapping inherited retinal dystrophies (IRD). Most affected individuals progress to severe disease, with 50% of patients becoming legally blind by 20 years of age. Deeper knowledge of the mutational spectrum and the phenotype-genotype correlation in RPE65-related IRD is needed. PATIENTS AND METHODS: Forty-five affected subjects from 27 unrelated families with a clinical diagnosis of RPE65-related IRD were included. Clinical evaluation consisted of self-reported ophthalmological history and objective ophthalmological examination. Patients' genotype was classified according to variant class (truncating or missense) or to variant location at different protein domains. The main phenotypic outcome measure was age at onset (AAO) of symptomatic disease and a Kaplan-Meier analysis of disease symptom event-free survival was performed. RESULTS: Twenty-nine different RPE65 variants were identified in our cohort, 7 of them novel. Patients carrying two missense alleles showed a later disease onset than those with 1 or 2 truncating variants (log-rank test p <0.05). While 60% of patients carrying a missense/missense genotype presented symptoms before or during the first year of life, almost all patients with at least 1 truncating allele (91%) had an AAO ≤1 year (p <0.05). CONCLUSION: Our findings suggest an association between the type of RPE65 variant carried and AAO. These findings provide useful data on RPE65-associated IRD phenotypes and may help improve clinical and therapeutic management of these patients.

Medicago truncatula Yellow Stripe-Like7 encodes a peptide transporter participating in symbiotic nitrogen fixation.

Yellow Stripe-Like (YSL) proteins are a family of plant transporters that are typically involved in transition metal homeostasis. Three of the four YSL clades (I, II and IV) transport metals complexed with the non-proteinogenic amino acid nicotianamine or its derivatives. No such capability has been shown for any member of clade III, but the link between these YSLs and metal homeostasis could be masked by functional redundancy. We studied the role of the clade III YSL protein MtSYL7 in Medicago truncatula nodules. MtYSL7, which encodes a plasma membrane-bound protein, is mainly expressed in the pericycle and cortex cells of the root nodules. Yeast complementation assays revealed that MtSYL7 can transport short peptides. M. truncatula transposon insertion mutants with decreased expression of MtYSL7 had lower nitrogen fixation rates and showed reduced plant growth whether grown in symbiosis with rhizobia or not. YSL7 mutants accumulated more copper and iron in the nodules, which is likely to result from the increased expression of iron uptake and delivery genes in roots. Taken together, these data suggest that MtYSL7 plays an important role in the transition metal homeostasis of nodules and symbiotic nitrogen fixation.

IL-6-based mortality prediction model for COVID-19: Validation and update in multicenter and second wave cohorts.

BACKGROUND: Coronavirus disease 2019 (COVID-19) is a highly variable condition. Validated tools to assist in the early detection of patients at high risk of mortality can help guide medical decisions. OBJECTIVE: We sought to validate externally, as well as in patients from the second pandemic wave in Europe, our previously developed mortality prediction model for hospitalized COVID-19 patients. METHODS: Three validation cohorts were generated: 2 external with 185 and 730 patients from the first wave and 1 internal with 119 patients from the second wave. The probability of death was calculated for all subjects using our prediction model, which includes peripheral blood oxygen saturation/fraction of inspired oxygen ratio, neutrophil-to-lymphocyte ratio, lactate dehydrogenase, IL-6, and age. Discrimination and calibration were evaluated in the validation cohorts. The prediction model was updated by reestimating individual risk factor effects in the overall cohort (N = 1477). RESULTS: The mortality prediction model showed good performance in the external validation cohorts 1 and 2, and in the second wave validation cohort 3 (area under the receiver-operating characteristic curve, 0.94, 0.86, and 0.86, respectively), with excellent calibration (calibration slope, 0.86, 0.94, and 0.79; intercept, 0.05, 0.03, and 0.10, respectively). The updated model accurately predicted mortality in the overall cohort (area under the receiver-operating characteristic curve, 0.91), which included patients from both the first and second COVID-19 waves. The updated model was also useful to predict fatal outcome in patients without respiratory distress at the time of evaluation. CONCLUSIONS: This is the first COVID-19 mortality prediction model validated in patients from the first and second pandemic waves. The COR+12 online calculator is freely available to facilitate its implementation (https://utrero-rico.shinyapps.io/COR12_Score/).

Genetic landscape of 6089 inherited retinal dystrophies affected cases in Spain and their therapeutic and extended epidemiological implications.

Inherited retinal diseases (IRDs), defined by dysfunction or progressive loss of photoreceptors, are disorders characterized by elevated heterogeneity, both at the clinical and genetic levels. Our main goal was to address the genetic landscape of IRD in the largest cohort of Spanish patients reported to date. A retrospective hospital-based cross-sectional study was carried out on 6089 IRD affected individuals (from 4403 unrelated families), referred for genetic testing from all the Spanish autonomous communities. Clinical, demographic and familiar data were collected from each patient, including family pedigree, age of appearance of visual symptoms, presence of any systemic findings and geographical origin. Genetic studies were performed to the 3951 families with available DNA using different molecular techniques. Overall, 53.2% (2100/3951) of the studied families were genetically characterized, and 1549 different likely causative variants in 142 genes were identified. The most common phenotype encountered is retinitis pigmentosa (RP) (55.6% of families, 2447/4403). The most recurrently mutated genes were PRPH2, ABCA4 and RS1 in autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL) NON-RP cases, respectively; RHO, USH2A and RPGR in AD, AR and XL for non-syndromic RP; and USH2A and MYO7A in syndromic IRD. Pathogenic variants c.3386G > T (p.Arg1129Leu) in ABCA4 and c.2276G > T (p.Cys759Phe) in USH2A were the most frequent variants identified. Our study provides the general landscape for IRD in Spain, reporting the largest cohort ever presented. Our results have important implications for genetic diagnosis, counselling and new therapeutic strategies to both the Spanish population and other related populations.