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1.
Front Med (Lausanne) ; 11: 1400585, 2024.
Article in English | MEDLINE | ID: mdl-38887672

ABSTRACT

Clinical trials (CTs) are essential for medical advancements but face significant challenges, particularly in professional training and role clarity. Principal investigators, clinical research coordinators (CRCs), nurses, clinical trial pharmacists, and monitors are key players. Each faces unique challenges, such as maintaining protocol compliance, managing investigational products, and ensuring data integrity. Clinical trials' complexity and evolving nature demand specialized and ongoing training for these professionals. Addressing these challenges requires clear role delineation, continuous professional development, and supportive workplace environments to improve retention and trial outcomes. Enhanced training programs and a collaborative approach are essential for the successful conduct of clinical trials and the advancement of medical research.

2.
Nat Commun ; 15(1): 5148, 2024 Jun 18.
Article in English | MEDLINE | ID: mdl-38890274

ABSTRACT

Telomere length is an important biomarker of organismal aging and cellular replicative potential, but existing measurement methods are limited in resolution and accuracy. Here, we deploy digital telomere measurement (DTM) by nanopore sequencing to understand how distributions of human telomere length change with age and disease. We measure telomere attrition and de novo elongation with up to 30 bp resolution in genetically defined populations of human cells, in blood cells from healthy donors and in blood cells from patients with genetic defects in telomere maintenance. We find that human aging is accompanied by a progressive loss of long telomeres and an accumulation of shorter telomeres. In patients with defects in telomere maintenance, the accumulation of short telomeres is more pronounced and correlates with phenotypic severity. We apply machine learning to train a binary classification model that distinguishes healthy individuals from those with telomere biology disorders. This sequencing and bioinformatic pipeline will advance our understanding of telomere maintenance mechanisms and the use of telomere length as a clinical biomarker of aging and disease.


Subject(s)
Machine Learning , Telomere Homeostasis , Telomere , Humans , Telomere/genetics , Telomere/metabolism , Telomere Homeostasis/genetics , Adult , Healthy Aging/genetics , Middle Aged , Male , Aged , Female , Telomere Shortening/genetics , Aging/genetics , Nanopore Sequencing/methods , Young Adult
3.
medRxiv ; 2024 Jan 23.
Article in English | MEDLINE | ID: mdl-38343838

ABSTRACT

We aimed to identify circRNAs associated with Parkinson's disease (PD) by leveraging 1,848 participants and 1,789 circRNA from two of the largest publicly available studies with longitudinal clinical and blood transcriptomic data. To comprehensively understand changes in circRNAs we performed a cross-sectional study utilizing the last visit of each participant, and a longitudinal (mix model) analysis that included 1,166 participants with at least two time points. We identified 192 circRNAs differentially expressed in PD participants compared to healthy controls, with effects that were consistent in the mixed models, mutation carriers, and diverse ancestry. Finally, we included the 149 circRNA in a model with a ROC AUC of 0.825, showing that have the potential to aid the diagnosis of PD. Overall, we demonstrated that circRNAs play an important role in PD and can be leveraged as biomarkers.

4.
Nutrients ; 16(2)2024 Jan 19.
Article in English | MEDLINE | ID: mdl-38276544

ABSTRACT

Vitamin D deficiency is highly prevalent, and recent evidence suggests a possible association between vitamin D deficiency and various health conditions. The aim of this study was to assess monthly calcifediol treatments for vitamin D deficiency (or biweekly, if the deficiency was severe) in a young adult population with no associated comorbidities. This multicentre phase I trial started with a four month open-label treatment phase (TP) that included 101 participants (65% women with mean age 29.8 years). Eighty-two percent of the subjects (79/96) achieved 25(OH)D levels within the target range (20-60 ng/mL) by the end of the TP, and they were subsequently randomised and subjected to a double-blind, placebo-controlled, five month follow-up phase (FP). At the end of the FP, 89% of participants maintained vitamin D levels of >20 ng/mL with calcifediol, versus 49% with placebo (p < 0.001). Subjects receiving monthly calcifediol during both phases (n = 32) maintained 25(OH)D levels >20 ng/mL, whereas those on the placebo during the FP (n = 38) exhibited deficiency levels of 25(OH)D by the end of the study. No clinically relevant changes in bone metabolism parameters or toxic 25(OH)D levels were observed, and no serious adverse events were reported throughout the study. Calcifediol is a safe and effective treatment for vitamin D deficiency in the young adult population, but long-term use may be required to sustain optimal 25(OH)D levels.


Subject(s)
Calcifediol , Vitamin D Deficiency , Adult , Female , Humans , Male , Young Adult , Calcifediol/adverse effects , Calcifediol/therapeutic use , Double-Blind Method , Vitamin D , Vitamin D Deficiency/drug therapy
5.
bioRxiv ; 2023 Dec 01.
Article in English | MEDLINE | ID: mdl-38077053

ABSTRACT

Telomere length is an important biomarker of organismal aging and cellular replicative potential, but existing measurement methods are limited in resolution and accuracy. Here, we deploy digital telomere measurement by nanopore sequencing to understand how distributions of human telomere length change with age and disease. We measure telomere attrition and de novo elongation with unprecedented resolution in genetically defined populations of human cells, in blood cells from healthy donors and in blood cells from patients with genetic defects in telomere maintenance. We find that human aging is accompanied by a progressive loss of long telomeres and an accumulation of shorter telomeres. In patients with defects in telomere maintenance, the accumulation of short telomeres is more pronounced and correlates with phenotypic severity. We apply machine learning to train a binary classification model that distinguishes healthy individuals from those with telomere biology disorders. This sequencing and bioinformatic pipeline will advance our understanding of telomere maintenance mechanisms and the use of telomere length as a clinical biomarker of aging and disease.

6.
Article in English | MEDLINE | ID: mdl-38131730

ABSTRACT

To understand whether patient safety and human factors are considered in healthcare technology procurement, we analyzed the case of infusion pumps as their use critically affects patient safety. We reviewed infusion pump procurements in the Spanish Public Sector Procurement Database. Sixty-three batches in 29 tenders for supplying 12.224 volumetric and syringe infusion pumps and consumables for an overall budget of EUR 30.4 M were identified and reviewed. Concepts related to "ease of use" were identified in the selection requirements of 35 (55.6%) batches, as part of the criteria for the selection of pumps in 23 (36.5%) batches, related to "intuitiveness" in the selection requirements of 35 (55.6%) batches, and in the criteria in 10 (15.9%) batches. No method to evaluate the ease of use, intuitiveness, or usability was mentioned. A review of the procurement teams responsible for the evaluation of the tenders showed no reported human factors or patient safety expertise. We conclude that infusion pump procurement considers usability as a relevant criterion for selection. However, no human factor experts nor specific methods for evaluation of the technology in this field are usually defined. Potential room for refining the selection of healthcare technology to improve patient safety is detected.


Subject(s)
Infusion Pumps , Patient Safety , Humans , Databases, Factual , Health Facilities , Spain
7.
Plants (Basel) ; 12(11)2023 Jun 03.
Article in English | MEDLINE | ID: mdl-37299192

ABSTRACT

The Afromontane and Afroalpine areas constitute some of the main biodiversity hotspots of Africa. They are particularly rich in plant endemics, but the biogeographic origins and evolutionary processes leading to this outstanding diversity are poorly understood. We performed phylogenomic and biogeographic analyses of one of the most species-rich plant genera in these mountains, Helichrysum (Compositae-Gnaphalieae). Most previous studies have focused on Afroalpine elements of Eurasian origin, and the southern African origin of Helichrysum provides an interesting counterexample. We obtained a comprehensive nuclear dataset from 304 species (≈50% of the genus) using target-enrichment with the Compositae1061 probe set. Summary-coalescent and concatenation approaches combined with paralog recovery yielded congruent, well-resolved phylogenies. Ancestral range estimations revealed that Helichrysum originated in arid southern Africa, whereas the southern African grasslands were the source of most lineages that dispersed within and outside Africa. Colonization of the tropical Afromontane and Afroalpine areas occurred repeatedly throughout the Miocene-Pliocene. This timing coincides with mountain uplift and the onset of glacial cycles, which together may have facilitated both speciation and intermountain gene flow, contributing to the evolution of the Afroalpine flora.

8.
Cancers (Basel) ; 15(4)2023 Feb 08.
Article in English | MEDLINE | ID: mdl-36831412

ABSTRACT

Breast cancer is the leading cause of cancer-related deaths among women worldwide. HER2-positive breast cancer, which represents 15-20% of all cases, is characterized by the overexpression of the HER2 receptor. Despite the variety of treatments available for HER2-positive breast cancer, both targeted and untargeted, many patients do not respond to therapy and relapse and eventually metastasize, with a poor prognosis. Immunotherapeutic approaches aim to enhance the antitumor immune response to prevent tumor relapse and metastasis. Several immunotherapies have been approved for solid tumors, but their utility for HER2-positive breast cancer has yet to be confirmed. In this review, we examine the different immunotherapeutic strategies being tested in HER2-positive breast cancer, from long-studied cancer vaccines to immune checkpoint blockade, which targets immune checkpoints in both T cells and tumor cells, as well as the promising adoptive cell therapy in various forms. We discuss how some of these new approaches may contribute to the prevention of tumor progression and be used after standard-of-care therapies for resistant HER2-positive breast tumors, highlighting the benefits and drawbacks of each. We conclude that immunotherapy holds great promise for the treatment of HER2-positive tumors, with the potential to completely eradicate tumor cells and prevent the progression of the disease.

9.
Cardiovasc Drugs Ther ; 37(5): 905-916, 2023 10.
Article in English | MEDLINE | ID: mdl-35467312

ABSTRACT

PURPOSE: To assess the cost-effectiveness of evolocumab, a PCSK9 (proprotein convertase subtilisin/kexin type 9) inhibitor, compared with ezetimibe, both added to background statin therapy in patients with recent acute coronary syndrome (ACS) events (in the past 12 months) and low-density lipoprotein cholesterol (LDL-C) levels ≥ 100 mg/dL in China. METHODS: A health economic evaluation was performed from a Chinese healthcare perspective, using a Markov model over a lifetime horizon based on a baseline cardiovascular (CV) event rate from claims database data and efficacy from the FOURIER trial. The health benefit was reflected in the decrease of LDL-C level, which led to a decrease of cardiovascular events. The costs of cardiovascular events and the utility value of each health state were derived from the published literature. Sensitivity analyses were conducted to evaluate the effects of uncertainty in parameters and the robustness of the model. The cost-effectiveness of evolocumab was also explored in patients with recent myocardial infarction (MI), at very high risk (VHR) of atherosclerotic cardiovascular disease (ASCVD), and homozygous familiar hypercholesterolemia (HoFH). RESULTS: In patients with recent ACS, evolocumab was associated with incremental quality-adjusted life-years (QALYs) of 1.33 and incremental costs of 115,782 yuan versus ezetimibe, both with background statin therapy, resulting in an incremental cost-effectiveness ratio (ICER) of 87,050 yuan per QALY gained. The probability of evolocumab + statins being cost-effective at a threshold of 217,341 yuan (three times per capita GDP, 2020), compared with ezetimibe + statins, was 100% in patients with recent ACS, recent MI, VHR ASCVD, and HoFH. CONCLUSION: Compared with ezetimibe + statins, the combination of evolocumab + statins was found to be cost-effective at a threshold of 217,341 yuan (three times per capita GDP, 2020) in patients with recent ACS events in China.


Subject(s)
Acute Coronary Syndrome , Anticholesteremic Agents , Atherosclerosis , Cardiovascular Diseases , Homozygous Familial Hypercholesterolemia , Hydroxymethylglutaryl-CoA Reductase Inhibitors , Humans , Acute Coronary Syndrome/diagnosis , Acute Coronary Syndrome/drug therapy , Anticholesteremic Agents/adverse effects , Cholesterol, LDL , Cost-Benefit Analysis , Cost-Effectiveness Analysis , Ezetimibe/therapeutic use , Hydroxymethylglutaryl-CoA Reductase Inhibitors/adverse effects , Proprotein Convertase 9
10.
Nucleic Acids Res ; 51(D1): D753-D759, 2023 01 06.
Article in English | MEDLINE | ID: mdl-36477304

ABSTRACT

The MGnify platform (https://www.ebi.ac.uk/metagenomics) facilitates the assembly, analysis and archiving of microbiome-derived nucleic acid sequences. The platform provides access to taxonomic assignments and functional annotations for nearly half a million analyses covering metabarcoding, metatranscriptomic, and metagenomic datasets, which are derived from a wide range of different environments. Over the past 3 years, MGnify has not only grown in terms of the number of datasets contained but also increased the breadth of analyses provided, such as the analysis of long-read sequences. The MGnify protein database now exceeds 2.4 billion non-redundant sequences predicted from metagenomic assemblies. This collection is now organised into a relational database making it possible to understand the genomic context of the protein through navigation back to the source assembly and sample metadata, marking a major improvement. To extend beyond the functional annotations already provided in MGnify, we have applied deep learning-based annotation methods. The technology underlying MGnify's Application Programming Interface (API) and website has been upgraded, and we have enabled the ability to perform downstream analysis of the MGnify data through the introduction of a coupled Jupyter Lab environment.


Subject(s)
Microbiota , Sequence Analysis , Genomics/methods , Metagenome , Metagenomics/methods , Microbiota/genetics , Software , Sequence Analysis/methods
11.
Eur Respir J ; 61(4)2023 04.
Article in English | MEDLINE | ID: mdl-36265882

ABSTRACT

BACKGROUND: Abnormal macrophage function caused by dysfunctional cystic fibrosis transmembrane conductance regulator (CFTR) is a critical contributor to chronic airway infections and inflammation in people with cystic fibrosis (PWCF). Elexacaftor/tezacaftor/ivacaftor (ETI) is a new CFTR modulator therapy for PWCF. Host-pathogen and clinical responses to CFTR modulators are poorly described. We sought to determine how ETI impacts macrophage CFTR function, resulting effector functions and relationships to clinical outcome changes. METHODS: Clinical information and/or biospecimens were obtained at ETI initiation and 3, 6, 9 and 12 months post-ETI in 56 PWCF and compared with non-CF controls. Peripheral blood monocyte-derived macrophages (MDMs) were isolated and functional assays performed. RESULTS: ETI treatment was associated with increased CF MDM CFTR expression, function and localisation to the plasma membrane. CF MDM phagocytosis, intracellular killing of CF pathogens and efferocytosis of apoptotic neutrophils were partially restored by ETI, but inflammatory cytokine production remained unchanged. Clinical outcomes including increased forced expiratory volume in 1 s (+10%) and body mass index (+1.0 kg·m-2) showed fluctuations over time and were highly individualised. Significant correlations between post-ETI MDM CFTR function and sweat chloride levels were observed. However, MDM CFTR function correlated with clinical outcomes better than sweat chloride. CONCLUSION: ETI is associated with unique changes in innate immune function and clinical outcomes.


Subject(s)
Cystic Fibrosis , Humans , Cystic Fibrosis/drug therapy , Cystic Fibrosis Transmembrane Conductance Regulator/genetics , Cystic Fibrosis Transmembrane Conductance Regulator/metabolism , Chlorides/metabolism , Chloride Channel Agonists/therapeutic use , Mutation , Macrophages/metabolism
12.
Hypertension ; 80(1): 84-96, 2023 01.
Article in English | MEDLINE | ID: mdl-36337053

ABSTRACT

BACKGROUND: Resolution of inflammation is orchestrated by specialized proresolving lipid mediators (SPMs), and this would be impaired in some cardiovascular diseases. Among SPMs, resolvins (Rv) have beneficial effects in cardiovascular pathologies, but little is known about their effect on cardiovascular damage in hypertension. METHODS: Aorta, small mesenteric arteries, heart, and peritoneal macrophages were taken from C57BL/6J mice, infused or not with angiotensin II (AngII; 1.44 mg/kg/day, 14 days) in presence or absence of resolvin D2 (RvD2) (100 ng/mice, every second day) starting 1 day before or 7 days after AngII infusion. RESULTS: Enzymes and receptors involved in SPMs biosynthesis and signaling were increased in aorta or heart from AngII-infused mice. We also observed a differential regulation of SPMs in heart from these mice. Preventive treatment with RvD2 partially avoided AngII-induced hypertension and protected the heart and large and small vessels against functional and structural alterations induced by AngII. RvD2 increased the availability of vasoprotective factors, modified SPMs profile, decreased cardiovascular fibrosis, and increased the infiltration of pro-resolving macrophages. When administered in hypertensive animals with established cardiovascular damage, RvD2 partially improved cardiovascular function and structure, decreased fibrosis, reduced the infiltration of neutrophils, and shifted macrophage phenotype toward a pro-resolving phenotype. CONCLUSIONS: There is a disbalance between proinflammatory and resolution mediators in hypertension. RvD2 protects cardiovascular function and structure when administered before and after the development of hypertension by modulating vascular factors, fibrosis and inflammation. Activating resolution mechanisms by treatment with RvD2 may represent a novel therapeutic strategy for the treatment of hypertensive cardiovascular disease.


Subject(s)
Angiotensin II , Hypertension , Mice , Animals , Mice, Inbred C57BL , Hypertension/chemically induced , Hypertension/drug therapy , Fibrosis
13.
Heliyon ; 8(11): e11364, 2022 Nov.
Article in English | MEDLINE | ID: mdl-36387471

ABSTRACT

The aim of this study is to design and validate an instrument that allows the evaluation of educational experiences and formative assessment in the metaverse from a holistic perspective. Hence, a research design based on the development of a scale has been used. Three hundred and sixty-two Spanish secondary school students participated in the study, selected through purposive sampling. The instrument created has been subjected to an analysis of content validity, validity by expert judgment, construct validity, and reliability. For data analysis, the SPSS and AMOS programs have been used. An exploratory factor analysis and a confirmatory factor analysis have been performed to determine the construct validity. In addition, the Cronbach's alpha has been calculated to verify the internal consistency of the tool. The results reveal several findings that position the resulting questionnaire as a valid and reliable instrument to evaluate educational experiences and practices in the metaverse. In short, this study has led to the development of a comprehensive evaluation tool at the service of educators or any institution interested in implementing its educational praxis within the metaverse, a field of research that has yet to be explored.

14.
Cancer Res ; 82(24): 4670-4679, 2022 12 16.
Article in English | MEDLINE | ID: mdl-36222720

ABSTRACT

Antibody-drug conjugates (ADC) are antineoplastic agents recently introduced into the antitumor arsenal. T-DM1, a trastuzumab-based ADC that relies on lysosomal processing to release the payload, is approved for HER2-positive breast cancer. Next-generation ADCs targeting HER2, such as [vic-]trastuzumab duocarmazine (SYD985), bear linkers cleavable by lysosomal proteases and membrane-permeable drugs, mediating a bystander effect by which neighboring antigen-negative cells are eliminated. Many antitumor therapies, like DNA-damaging agents or CDK4/6 inhibitors, can induce senescence, a cellular state characterized by stable cell-cycle arrest. Another hallmark of cellular senescence is the enlargement of the lysosomal compartment. Given the relevance of the lysosome to the mechanism of action of ADCs, we hypothesized that therapies that induce senescence would potentiate the efficacy of HER2-targeting ADCs. Treatment with the DNA-damaging agent doxorubicin and CDK4/6 inhibitor induced lysosomal enlargement and senescence in several breast cancer cell lines. While senescence-inducing drugs did not increase the cytotoxic effect of ADCs on target cells, the bystander effect was enhanced when HER2-negative cells were cocultured with HER2-low cells. Knockdown experiments demonstrated the importance of cathepsin B in the enhanced bystander effect, suggesting that cathepsin B mediates linker cleavage. In breast cancer patient-derived xenografts, a combination treatment of CDK4/6 inhibitor and SYD985 showed improved antitumor effects over either treatment alone. These data support the strategy of combining next-generation ADCs targeting HER2 with senescence-inducing therapies for tumors with heterogenous and low HER2 expression. SIGNIFICANCE: Combining ADCs against HER2-positive breast cancers with therapies that induce cellular senescence may improve their therapeutic efficacy by facilitating a bystander effect against antigen-negative tumor cells.


Subject(s)
Antineoplastic Agents , Breast Neoplasms , Immunoconjugates , Female , Humans , Antineoplastic Agents/pharmacology , Antineoplastic Agents/therapeutic use , Breast Neoplasms/drug therapy , Cathepsin B/metabolism , Cell Line, Tumor , Immunoconjugates/pharmacology , Immunoconjugates/therapeutic use , Receptor, ErbB-2/metabolism , Trastuzumab/pharmacology , Trastuzumab/therapeutic use , Xenograft Model Antitumor Assays , Animals
15.
Bol Med Hosp Infant Mex ; 79(4): 215-221, 2022.
Article in English | MEDLINE | ID: mdl-36100204

ABSTRACT

Cystic fibrosis is an autosomal recessive inherited disease caused by mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR). CFTR is a protein that transports ions across the membrane of lung epithelial cells. Loss of its function leads to the production of thick sticky mucus, where various bacterial pathogens can establish and adapt, contributing to the gradual loss of lung function. In this review, evidence of the molecular mechanisms used by Pseudomonas aeruginosa and Burkholderia cenocepacia to survive and persist in the pulmonary environment will be provided. Additionally, new therapeutic strategies based on CFTR function modulators will be described.


La fibrosis quística es una enfermedad hereditaria autosómica recesiva que se origina por mutaciones en el gen regulador de conductancia transmembranal de la fibrosis quística (CFTR, cystic fibrosis transmembrane conductance regulator). El CFTR es una proteína que transporta iones a través de la membrana de las células epiteliales pulmonares. La pérdida de su función conlleva la producción de un moco pegajoso y espeso, donde se pueden establecer y adaptar diversos patógenos bacterianos que contribuyen a la pérdida gradual de la función pulmonar. En este artículo de revisión se dará evidencia de los mecanismos moleculares que utilizan Pseudomonas aeruginosa y Burkholderia cenocepacia para sobrevivir y persistir en el ambiente pulmonar. Adicionalmente, se describirán las nuevas estrategias de terapia a base de moduladores de la función del CFTR.


Subject(s)
Cystic Fibrosis Transmembrane Conductance Regulator , Cystic Fibrosis , Cystic Fibrosis Transmembrane Conductance Regulator/genetics , Cystic Fibrosis Transmembrane Conductance Regulator/metabolism , Cystic Fibrosis Transmembrane Conductance Regulator/therapeutic use , Epithelial Cells/metabolism , Epithelial Cells/microbiology , Fibrosis , Humans , Pseudomonas aeruginosa
16.
Cerebrovasc Dis Extra ; 12(3): 103-108, 2022.
Article in English | MEDLINE | ID: mdl-36007497

ABSTRACT

INTRODUCTION: Prealbumin is a marker of malnutrition and inflammation. It has been associated with poor prognosis in cardiovascular disease, but less is known in stroke patients. Our objective was to evaluate the association of prealbumin levels at admission with prognosis in patients with stroke treated with mechanical thrombectomy. METHODS: Retrospective study of a prospective database of consecutive patients treated with mechanical thrombectomy. Clinical, radiological, and blood parameters including serum prealbumin, and prognostic variables such as respiratory infection, in-hospital mortality, and the modified Rankin scale at 3 months were collected. RESULTS: We included 319 patients between 2018 and 2019. Prealbumin levels were significantly lower in patients older than 80 years, women, patients with a prestroke Rankin score >2, a glomerular filtrate rate <60 mL/min, and in those with atrial fibrillation. Regarding prognostic variables, prealbumin levels were not associated with respiratory infection. Low prealbumin levels were associated with poor functional prognosis (Rankin score >2), in-hospital mortality, and 3-month mortality. In multivariate analysis, prealbumin was an independent risk factor associated with mortality at 3 months, OR 0.92 [0.86-0.98], p = 0.019. CONCLUSION: Lower prealbumin levels at admission behaved as an independent predictor of long-term mortality in patients treated with mechanical thrombectomy. These results should be replicated in other cohorts.


Subject(s)
Brain Ischemia , Stroke , Female , Humans , Prealbumin/analysis , Prognosis , Retrospective Studies , Stroke/diagnosis , Stroke/therapy , Thrombectomy/adverse effects , Thrombectomy/methods , Treatment Outcome , Aged, 80 and over
17.
Gigascience ; 112022 08 11.
Article in English | MEDLINE | ID: mdl-35950838

ABSTRACT

Metagenomics is a culture-independent method for studying the microbes inhabiting a particular environment. Comparing the composition of samples (functionally/taxonomically), either from a longitudinal study or cross-sectional studies, can provide clues into how the microbiota has adapted to the environment. However, a recurring challenge, especially when comparing results between independent studies, is that key metadata about the sample and molecular methods used to extract and sequence the genetic material are often missing from sequence records, making it difficult to account for confounding factors. Nevertheless, these missing metadata may be found in the narrative of publications describing the research. Here, we describe a machine learning framework that automatically extracts essential metadata for a wide range of metagenomics studies from the literature contained in Europe PMC. This framework has enabled the extraction of metadata from 114,099 publications in Europe PMC, including 19,900 publications describing metagenomics studies in European Nucleotide Archive (ENA) and MGnify. Using this framework, a new metagenomics annotations pipeline was developed and integrated into Europe PMC to regularly enrich up-to-date ENA and MGnify metagenomics studies with metadata extracted from research articles. These metadata are now available for researchers to explore and retrieve in the MGnify and Europe PMC websites, as well as Europe PMC annotations API.


Subject(s)
Metadata , Metagenomics , Access to Information , Cross-Sectional Studies , Longitudinal Studies , Machine Learning , Metagenomics/methods
18.
J Immunol ; 209(6): 1212-1223, 2022 09 15.
Article in English | MEDLINE | ID: mdl-35995507

ABSTRACT

Chronic lymphocytic leukemia (CLL) is the most common adult leukemia, but, despite advances in treatment, many patients still experience relapse. CLL cells depend on interactions with supportive cells, and nurse-like cells (NLCs) are the major such cell type. However, little is known about how NLCs develop. Here, we performed DNA methylation analysis of CLL patient-derived NLCs using the 850K Illumina array, comparing CD14+ cells at day 1 (monocytes) versus day 14 (NLCs). We found a strong loss of methylation in AP-1 transcription factor binding sites, which may be driven by MAPK signaling. Testing of individual MAPK pathways (MEK, p38, and JNK) revealed a strong dependence on MEK/ERK for NLC development, because treatment of patient samples with the MEK inhibitor trametinib dramatically reduced NLC development in vitro. Using the adoptive transfer Eµ-TCL1 mouse model of CLL, we found that MEK inhibition slowed CLL progression, leading to lower WBC counts and to significantly longer survival time. There were also lower numbers of mouse macrophages, particularly within the M2-like population. In summary, NLC development depends on MEK signaling, and inhibition of MEK leads to increased survival time in vivo. Hence, targeting the MEK/ERK pathway may be an effective treatment strategy for CLL.


Subject(s)
Leukemia, Lymphocytic, Chronic, B-Cell , Animals , Cell Differentiation , Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy , Leukemia, Lymphocytic, Chronic, B-Cell/genetics , Mice , Mitogen-Activated Protein Kinase Kinases/metabolism , Monocytes/metabolism , Transcription Factor AP-1/metabolism
19.
Bol. méd. Hosp. Infant. Méx ; 79(4): 215-221, Jul.-Aug. 2022. tab, graf
Article in Spanish | LILACS-Express | LILACS | ID: biblio-1403642

ABSTRACT

Resumen La fibrosis quística es una enfermedad hereditaria autosómica recesiva que se origina por mutaciones en el gen regulador de conductancia transmembranal de la fibrosis quística (CFTR, cystic fibrosis transmembrane conductance regulator). El CFTR es una proteína que transporta iones a través de la membrana de las células epiteliales pulmonares. La pérdida de su función conlleva la producción de un moco pegajoso y espeso, donde se pueden establecer y adaptar diversos patógenos bacterianos que contribuyen a la pérdida gradual de la función pulmonar. En este artículo de revisión se dará evidencia de los mecanismos moleculares que utilizan Pseudomonas aeruginosa y Burkholderia cenocepacia para sobrevivir y persistir en el ambiente pulmonar. Adicionalmente, se describirán las nuevas estrategias de terapia a base de moduladores de la función del CFTR.


Abstract Cystic fibrosis is an autosomal recessive inherited disease caused by mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR). CFTR is a protein that transports ions across the membrane of lung epithelial cells. Loss of its function leads to the production of thick sticky mucus, where various bacterial pathogens can establish and adapt, contributing to the gradual loss of lung function. In this review, evidence of the molecular mechanisms used by Pseudomonas aeruginosa and Burkholderia cenocepacia to survive and persist in the pulmonary environment will be provided. Additionally, new therapeutic strategies based on CFTR function modulators will be described.

20.
Proc Natl Acad Sci U S A ; 119(21): e2202012119, 2022 05 24.
Article in English | MEDLINE | ID: mdl-35588457

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS­CoV-2) is a worldwide health concern, and new treatment strategies are needed. Targeting inflammatory innate immunity pathways holds therapeutic promise, but effective molecular targets remain elusive. Here, we show that human caspase-4 (CASP4) and its mouse homolog, caspase-11 (CASP11), are up-regulated in SARS­CoV-2 infections and that CASP4 expression correlates with severity of SARS­CoV-2 infection in humans. SARS­CoV-2­infected Casp11−/− mice were protected from severe weight loss and lung pathology, including blood vessel damage, compared to wild-type (WT) mice and mice lacking the caspase downstream effector gasdermin-D (Gsdmd−/−). Notably, viral titers were similar regardless of CASP11 knockout. Global transcriptomics of SARS­CoV-2­infected WT, Casp11−/−, and Gsdmd−/− lungs identified restrained expression of inflammatory molecules and altered neutrophil gene signatures in Casp11−/− mice. We confirmed that protein levels of inflammatory mediators interleukin (IL)-1ß, IL-6, and CXCL1, as well as neutrophil functions, were reduced in Casp11−/− lungs. Additionally, Casp11−/− lungs accumulated less von Willebrand factor, a marker for endothelial damage, but expressed more Kruppel-Like Factor 2, a transcription factor that maintains vascular integrity. Overall, our results demonstrate that CASP4/11 promotes detrimental SARS­CoV-2­induced inflammation and coagulopathy, largely independently of GSDMD, identifying CASP4/11 as a promising drug target for treatment and prevention of severe COVID-19.


Subject(s)
COVID-19 , Caspases, Initiator/metabolism , SARS-CoV-2 , Thromboinflammation , Animals , COVID-19/enzymology , COVID-19/pathology , Caspases, Initiator/genetics , Disease Progression , Humans , Lung/pathology , Mice , Mice, Knockout , Severity of Illness Index , Thromboinflammation/enzymology , Thromboinflammation/genetics
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