Enhanced osteogenic differentiation in zoledronate-treated osteoporotic patients

Bisphosphonates are well known inhibitors of osteoclast activity and thus may be employed to influence osteoblast activity. The present study was designed to evaluate the in vivo effects of zoledronic acid (ZA) on the proliferation and osteoblastic commitment of mesenchymal stem cells (MSC) in osteoporotic patients. We studied 22 postmenopausal osteoporotic patients. Densitometric, biochemical, cellular and molecular data were collected before as well as after 6 and 12 months of ZA treatment. Peripheral blood MSC-like cells were quantified by colony-forming unit fibroblastic assay; their osteogenic differentiation potential was evaluated after 3 and 7 days of induction, respectively. Circulating MSCs showed significantly increased expression levels of osteoblastic marker genes such as Runt-related transcription factor 2 (RUNX2), and Osteonectin (SPARC) during the 12 months of monitoring time. Lumbar bone mineral density (BMD) variation and SPARC gene expression correlated positively. Bone turnover marker levels were significantly lowered after ZA treatment; the effect was more pronounced for C terminal telopeptide (CTX) than for Procollagen Type 1 N-Terminal Propeptide (P1NP) and bone alkaline phosphatase (bALP). Our findings suggest a discrete anabolic activity supported by osteogenic commitment of MSCs, consequent to ZA treatment. We confirm its anabolic effects in vivo on osteogenic precursors

Genetic variation of wild American mink (Neovison vison) in the Province of Santa Cruz. Is the genetic paradox of invasive species met?

Las especies invasoras constituyen una amenaza para la biodiversidad nativa. El éxito de las especies invasoras pese a su baja variabilidad genética se conoce como “paradoja genética”. El visón americano (Neovison vison) fue introducido en varias regiones del planeta como Europa, Asia y América del Sur con fines peleteros. En Argentina fue introducido en la década de 1930 y, como resultado de la liberación de individuos en la na-turaleza, lograron establecerse poblaciones silvestres en la región Patagónica. El objetivo del presente trabajo es estudiar la diversidad genética de una población asilvestrada de la provincia de Santa Cruz y compararla con la de una población en cautiverio. Analizamos un fragmento de 359 pb de la región control de ADN mitocondrial y encontramos índices de variabilidad similares entre la población silvestre y la población cautiva. Al igual que en poblaciones asilvestradas de otras regiones del planeta, no se observa una reducción en la variabilidad genética en la población silvestre de Santa Cruz, probablemente como consecuencia de liberaciones y escapes recurrentes desde diversas fuentes de cautiverio.Alien species represent a threat to native biodiversity. The suc-cess of invasive species despite their reduced genetic diversity is known as “the genetic paradox”. The American mink (Neovison vison) was introduced in several regions of the world, like Europe, Asia and South America. In Argentina, they were introduced in the 1930’s by the fur industry and wild populations were established in Patagonia due to liberations and escapes. In this study, we analyzed the genetic diversity of a wild American mink population of northern Santa Cruz province and compared it with a captive population. We sequenced a 359-bp fragment of the mtDNA control region and found that genetic variability was similar between both groups. Like in other wild invasive populations, genetic variability was not reduced in the population of Santa Cruz, probably as a consequence of frequent releases and escapes from different sources of captive minks.Fil: Malerba, Martina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución. Laboratorio de Ecología y Comportamiento Animal; ArgentinaFil: Fasola, Laura. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Roesler, Carlos Ignacio. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución. Laboratorio de Ecología y Comportamiento Animal; ArgentinaFil: Pereda, Maria Inés. Aves Argentinas; ArgentinaFil: de Miguel, Andrés. Aves Argentinas; ArgentinaFil: Martina, Florencia Lucia. Aves Argentinas; ArgentinaFil: Mahler, Bettina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución. Laboratorio de Ecología y Comportamiento Animal; Argentin

Testing the performance of the imputation of MHC region in large datasets when using different reference panels

The major histocompatibility complex (MHC) contains a group of genes (~260 genes in ~4Mb) involved in several inflammatory disorders and immune response including the HLA-C gene. So far, the IPD-IMGT/HLA database reports more than 4000 different HLA-C alleles. Given the highly polymorphic nature of the gene, GWAS generally don’t study or study only a small subset of polymorphic sites of the region. Imputation procedures may help in gaining additional information on this region. However, the successful imputation of the MHC region would require a reference panel with detailed information. The main goal of this study is to investigate whether imputation procedures using appropriate reference panels may effectively increase the number of polymorphic sites of the MHC region for association with complex traits. We studied the MHC region imputation performances using 3 different reference panels (Michigan and TOPMed imputation servers): TOPMed-r2, 1000 Genomes (Phase3, v5), and the novel four-digit multi-ethnic HLA panel (v1, 2021). Here, 5 datasets with more than 1000 individuals each underwent imputation. We then focused on the imputation results of the MHC region that surround the HLA-C gene (hg19: 31234948-31241032). Imputation reported a different number of markers for the different reference panels: 482 in 1000G, 365 in TOPMed, and 1272 in HLA-panel. Of note, the HLA panels gave a higher number of imputed markers than the others. We then selected the 104 common markers imputed by all the 3 reference panels. Moreover, 162 markers were found only by 1000G panel, 194 by TOPMed, and 998 by the HLA-panel. The first preliminary comparisons showed a high concordance value for the genotype calling by the 3 different reference sets. The efficiency of the imputation was measured by the R-squared (R2) values stratifying the markers into 3 groups according to the minor allele frequency (MAF). The 104 common markers showed high R2 values (>0.96). As expected, in the other marker groups, the R2 mean values were lower for markers with MAF<0.1 (>0.65 in 1000G, 0.15-0.20 in TOPMed, >0.40 in HLA panel). In conclusion, imputation-based procedures with dedicated HLA panels can produce much more high-quality information than other general purpose reference panels for the MHC region

Pocket-sized genomics and transcriptomics analyses: a look at the newborn BioVRPi project

BioVRPi is a newborn project, started in January 2021, that focuses on Raspberry Pi (RPi) employment in bioinformatics, with particular regards on genomics. In the previous years, some research groups have already reported several examples of applications for RPi, including bioinformatic basic training and proteomics. Our project aims to develop and offer a low-cost, stable, and tested bioinformatic environment for students and researchers involved in genomics and transcriptomics fields. Raspberry Pi is a small single-board low-cost computer that was developed by the Raspberry Pi Foundation since 2012. Its original purpose aimed to facilitate computer science basic teaching in developing countries, but the growing worldwide interest has permitted its constant progress and development. Thanks to its features, RPi can suit several disciplines in need for computational supports and reach almost every, if not all, research group in the world. We tested RPi capabilities on real case studies, relatively to Genome-Wide Association Studies (GWAS) for complex traits in Homo sapiens data and in transcriptomic analyses (RNA-seq) on the Strongyloides stercoralis human parasite samples, using two RPi-4 devices equipped with different amount of RAM (8GB for genomics and 2 GB for transcriptome analyses, respectively), and running a 64-bit Operating System. The analyses leveraged on state-of-art bioinformatic toolset, such as Plink and Plink1.9, SAMtools, Bowtie 2, R, and different R packages, all compiled from source code. Moreover, the GWAS was run according to the golden standard protocols and results from the different platforms were compared. The results showed that RPi are effective devices that can efficiently handle whole GWAS and RNA-seq analyses. Benchmarking showed that the computational time taken by RPi was of the same order of magnitude when compared to the ones from a commonly used bioinformatic computer. At last, BioVRPi project shows how to implement new strategies for bioinformatic analyses, in order to provide a having-fun environment to learn and explore new alternatives in bioinformatic data analysis

Biopsychosocial model of resilience in young adults with multiple sclerosis (BPS-ARMS): an observational study protocol exploring psychological reactions early after diagnosis

INTRODUCTION: Multiple sclerosis (MS), the most common neurological disease causing disability in young adults, is widely recognised as a major stress factor. Studies have shown that the first years after the diagnosis are distressing in terms of adjustment to the disease and that MS negatively affects patients' psychological well-being, quality of life (QoL) and social functioning. However, the links between disease-specific variables at diagnosis, resilience and psychological adjustment of patients with MS remain largely unexplored, especially in adolescents and young adults. This observational study aims to fill the gap of knowledge on biopsychosocial characteristics and resilience of young adults with MS to evaluate the relationship among these variables and to develop a biopsychosocial model of resilience. METHODS AND ANALYSIS: Biological and clinical characteristics of young adults newly diagnosed with MS will be investigated by collecting clinical information, performing neurological examinations, MRI and analysing cerebrospinal fluid and blood biomarkers (eg, measures of inflammation), body composition, gut microbiota and movement/perceptual markers. Psychosocial characteristics (eg, psychological distress, coping strategies), QoL, psychological well-being and resilience will be assessed by self-report questionnaires. Comparative statistics (ie, analysis of variance or unpaired samples t-test, correlation and regression analyses) will be applied to evaluate the relationship among biological, psychological and social factors. The results are expected to allow a comprehensive understanding of the determinants of resilience in young patients with MS and to inform resilience interventions, tailored to young patients' specific needs, aiming to reduce the risk of maladaptive reactions to the disease and to improve psychological well-being and QoL. ETHICS AND DISSEMINATION: The study has been approved by the Verona University Hospital Ethics Committee (approval number: 2029CESC). The findings will be disseminated through scientific publications in peer-reviewed journals, conference presentations, social media and specific websites. TRIAL REGISTRATION NUMBER: ClinicalTrials.gov (NCT03825055)

Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes.

We aggregated coding variant data for 81,412 type 2 diabetes cases and 370,832 controls of diverse ancestry, identifying 40 coding variant association signals (P < 2.2 × 10-7); of these, 16 map outside known risk-associated loci. We make two important observations. First, only five of these signals are driven by low-frequency variants: even for these, effect sizes are modest (odds ratio ≤1.29). Second, when we used large-scale genome-wide association data to fine-map the associated variants in their regional context, accounting for the global enrichment of complex trait associations in coding sequence, compelling evidence for coding variant causality was obtained for only 16 signals. At 13 others, the associated coding variants clearly represent 'false leads' with potential to generate erroneous mechanistic inference. Coding variant associations offer a direct route to biological insight for complex diseases and identification of validated therapeutic targets; however, appropriate mechanistic inference requires careful specification of their causal contribution to disease predisposition

Outcomes of COVID-19 patients treated with continuous positive airway pressure outside ICU

Aim We aim at characterizing a large population of Coronavirus 19 (COVID-19) patients with moderate-to-severe hypoxemic acute respiratory failure (ARF) receiving CPAP outside intensive care unit (ICU), and ascertaining whether the duration of CPAP application increased the risk of mortality for patients requiring intubation. Methods In this retrospective, multicentre cohort study, we included COVID-19 adult patients, treated with CPAP outside ICU for hypoxemic ARF from March 1 st to April 15th, 2020. We collected demographic and clinical data, including CPAP therapeutic goal, hospital length of stay (LOS), and 60- day in-hospital mortality. Results The study includes 537 patients with a median age of 69 (IQR, 60-76) years. Males were 391 (73%). According to predefined CPAP therapeutic goal, 397 (74%) patients were included in full treatment subgroup, and 140 (26%) in the do-not intubate (DNI) subgroup. Median CPAP duration was 4 (IQR, 1-8) days, while hospital LOS 16 (IQR, 9-27) days. Sixty-day in-hospital mortality was overall 34% (95%CI, 0.304-0.384), and 21% (95%CI, 0.169-0.249) and 73% (95%CI, 0.648-0.787) for full treatment and DNI subgroups, respectively. In the full treatment subgroup, in-hospital mortality was 42% (95%CI, 0.345-0.488) for 180 (45%) CPAP failures requiring intubation, while 2% (95%CI, 0.008- 0.035) for the remaining 217 (55%) patients who succeeded. Delaying intubation was associated with increased mortality [HR, 1.093 (95%CI, 1.010-1.184)]. Conclusions We described a large population of COVID-19 patients treated with CPAP outside ICU. Intubation delay represents a risk factor for mortality. Further investigation is needed for early identification of CPAP failures

Candidate biomarkers from the integration of methylation and gene expression in discordant autistic sibling pairs

While the genetics of autism spectrum disorders (ASD) has been intensively studied, resulting in the identification of over 100 putative risk genes, the epigenetics of ASD has received less attention, and results have been inconsistent across studies. We aimed to investigate the contribution of DNA methylation (DNAm) to the risk of ASD and identify candidate biomarkers arising from the interaction of epigenetic mechanisms with genotype, gene expression, and cellular proportions. We performed DNAm differential analysis using whole blood samples from 75 discordant sibling pairs of the Italian Autism Network collection and estimated their cellular composition. We studied the correlation between DNAm and gene expression accounting for the potential effects of different genotypes on DNAm. We showed that the proportion of NK cells was significantly reduced in ASD siblings suggesting an imbalance in their immune system. We identified differentially methylated regions (DMRs) involved in neurogenesis and synaptic organization. Among candidate loci for ASD, we detected a DMR mapping to CLEC11A (neighboring SHANK1) where DNAm and gene expression were significantly and negatively correlated, independently from genotype effects. As reported in previous studies, we confirmed the involvement of immune functions in the pathophysiology of ASD. Notwithstanding the complexity of the disorder, suitable biomarkers such as CLEC11A and its neighbor SHANK1 can be discovered using integrative analyses even with peripheral tissues

Trans-ancestry meta-analyses identify rare and common variants associated with blood pressure and hypertension

High blood pressure is a major risk factor for cardiovascular disease and premature death. However, there is limited knowledge on specific causal genes and pathways. To better understand the genetics of blood pressure, we genotyped 242,296 rare, low-frequency and common genetic variants in up to ~192,000 individuals, and used ~155,063 samples for independent replication. We identified 31 novel blood pressure or hypertension associated genetic regions in the general population, including three rare missense variants in RBM47, COL21A1 and RRAS with larger effects (>1.5mmHg/allele) than common variants. Multiple rare, nonsense and missense variant associations were found in A2ML1 and a low-frequency nonsense variant in ENPEP was identified. Our data extend the spectrum of allelic variation underlying blood pressure traits and hypertension, provide new insights into the pathophysiology of hypertension and indicate new targets for clinical intervention

Prescription appropriateness of anti-diabetes drugs in elderly patients hospitalized in a clinical setting: evidence from the REPOSI Register

Diabetes is an increasing global health burden with the highest prevalence (24.0%) observed in elderly people. Older diabetic adults have a greater risk of hospitalization and several geriatric syndromes than older nondiabetic adults. For these conditions, special care is required in prescribing therapies including anti- diabetes drugs. Aim of this study was to evaluate the appropriateness and the adherence to safety recommendations in the prescriptions of glucose-lowering drugs in hospitalized elderly patients with diabetes. Data for this cross-sectional study were obtained from the REgistro POliterapie-Società Italiana Medicina Interna (REPOSI) that collected clinical information on patients aged ≥ 65 years acutely admitted to Italian internal medicine and geriatric non-intensive care units (ICU) from 2010 up to 2019. Prescription appropriateness was assessed according to the 2019 AGS Beers Criteria and anti-diabetes drug data sheets.Among 5349 patients, 1624 (30.3%) had diagnosis of type 2 diabetes. At admission, 37.7% of diabetic patients received treatment with metformin, 37.3% insulin therapy, 16.4% sulfonylureas, and 11.4% glinides. Surprisingly, only 3.1% of diabetic patients were treated with new classes of anti- diabetes drugs. According to prescription criteria, at admission 15.4% of patients treated with metformin and 2.6% with sulfonylureas received inappropriately these treatments. At discharge, the inappropriateness of metformin therapy decreased (10.2%, P < 0.0001). According to Beers criteria, the inappropriate prescriptions of sulfonylureas raised to 29% both at admission and at discharge. This study shows a poor adherence to current guidelines on diabetes management in hospitalized elderly people with a high prevalence of inappropriate use of sulfonylureas according to the Beers criteria