Development of a long noncoding RNA-based machine learning model to predict COVID-19 in-hospital mortality.

Tools for predicting COVID-19 outcomes enable personalized healthcare, potentially easing the disease burden. This collaborative study by 15 institutions across Europe aimed to develop a machine learning model for predicting the risk of in-hospital mortality post-SARS-CoV-2 infection. Blood samples and clinical data from 1286 COVID-19 patients collected from 2020 to 2023 across four cohorts in Europe and Canada were analyzed, with 2906 long non-coding RNAs profiled using targeted sequencing. From a discovery cohort combining three European cohorts and 804 patients, age and the long non-coding RNA LEF1-AS1 were identified as predictive features, yielding an AUC of 0.83 (95% CI 0.82-0.84) and a balanced accuracy of 0.78 (95% CI 0.77-0.79) with a feedforward neural network classifier. Validation in an independent Canadian cohort of 482 patients showed consistent performance. Cox regression analysis indicated that higher levels of LEF1-AS1 correlated with reduced mortality risk (age-adjusted hazard ratio 0.54, 95% CI 0.40-0.74). Quantitative PCR validated LEF1-AS1's adaptability to be measured in hospital settings. Here, we demonstrate a promising predictive model for enhancing COVID-19 patient management.

HCG18, LEF1AS1 and lncCEACAM21 as biomarkers of disease severity in the peripheral blood mononuclear cells of COVID-19 patients.

BACKGROUND: Even after 3 years from SARS-CoV-2 identification, COVID-19 is still a persistent and dangerous global infectious disease. Significant improvements in our understanding of the disease pathophysiology have now been achieved. Nonetheless, reliable and accurate biomarkers for the early stratification of COVID-19 severity are still lacking. Long noncoding RNAs (LncRNAs) are ncRNAs longer than 200 nucleotides, regulating the transcription and translation of protein-coding genes and they can be found in the peripheral blood, thus holding a promising biomarker potential. Specifically, peripheral blood mononuclear cells (PBMCs) have emerged as a source of indirect biomarkers mirroring the conditions of tissues: they include monocytes, B and T lymphocytes, and natural killer T cells (NKT), being highly informative for immune-related events. METHODS: We profiled by RNA-Sequencing a panel of 2906 lncRNAs to investigate their modulation in PBMCs of a pilot group of COVID-19 patients, followed by qPCR validation in 111 hospitalized COVID-19 patients. RESULTS: The levels of four lncRNAs were found to be decreased in association with COVID-19 mortality and disease severity: HLA Complex Group 18-242 and -244 (HCG18-242 and HCG18-244), Lymphoid Enhancer Binding Factor 1-antisense 1 (LEF1-AS1) and lncCEACAM21 (i.e. ENST00000601116.5, a lncRNA in the CEACAM21 locus). Interestingly, these deregulations were confirmed in an independent patient group of hospitalized patients and by the re-analysis of publicly available single-cell transcriptome datasets. The identified lncRNAs were expressed in all of the PBMC cell types and inversely correlated with the neutrophil/lymphocyte ratio (NLR), an inflammatory marker. In vitro, the expression of LEF1-AS1 and lncCEACAM21 was decreased upon THP-1 monocytes exposure to a relevant stimulus, hypoxia. CONCLUSION: The identified COVID-19-lncRNAs are proposed as potential innovative biomarkers of COVID-19 severity and mortality.

GATA3 as a Blood-Based RNA Biomarker for Idiopathic Parkinson's Disease.

Finding novel biomarkers for Parkinson's disease (PD) is crucial for early disease diagnosis, severity assessment and identifying novel disease-modifying drug targets. Our study aimed at investigating the GATA3 mRNA levels in whole blood samples of idiopathic PD (iPD) patients with different disease severities as a biomarker for iPD. The present study is a cross-sectional, case-control study, with samples obtained from the Luxembourg Parkinson's cohort (LuxPARK). iPD (N = 319) patients, along with age-matched controls without PD (non-PD; N = 319) were included in this study. Blood GATA3 mRNA expression was measured using quantitative reverse transcription PCR (RT-qPCR) assays. The capacity of GATA3 expression levels to establish the diagnosis of iPD (primary end-point) and assess disease severity (secondary end-point) was determined. The blood levels of GATA3 were significantly lower in iPD patients, compared to non-PD controls (p ≤ 0.001). Logistic regression models showed a significant association of GATA3 expression with iPD diagnosis after adjustment for the confounders (p = 0.005). Moreover, the addition of GATA3 expression to a baseline clinical model improved its iPD diagnosis capacity (p = 0.005). There was a significant association of GATA3 expression levels with the overall disease severity (p = 0.002), non-motor experiences of daily living (nm-EDL; p = 0.003) and sleep disturbances (p = 0.01). Our results suggest that GATA3 expression measured in blood may serve as a novel biomarker and may help in the diagnosis of iPD and assessment of disease severity.

The circadian clock remains intact, but with dampened hormonal output in heart failure.

BACKGROUND: Circadian (24-h) rhythms are important regulators in physiology and disease, but systemic disease may disrupt circadian rhythmicity. Heart failure (HF) is a systemic disease affecting hormonal regulation. We investigate whether HF affects the rhythmic expression of melatonin and cortisol, main endocrine products of the central clock, and cardiac-specific troponin in patients. We corroborate the functionality of the peripheral clock directly in the organs of translational models, inaccessible in human participants. METHODS: We included 46 HF patients (71.7% male, median age of 60 years, NYHA class II (32.6%) or III (67.4%), ischemic cardiomyopathy (43.5%), comorbidities: diabetes 21.7%, atrial fibrillation 30.4%), and 24 matched controls. Blood was collected at seven time-points during a 24-h period (totalling 320 HF and 167 control samples) for melatonin, cortisol, and cardiac troponin T (cTnT) measurements after which circadian rhythms were assessed through cosinor analyses, both on the individual and the group level. Next, we analysed peripheral circadian clock functionality using cosinor analysis in male animal HF models: nocturnal mice and diurnal zebrafish, based on expression of core clock genes in heart, kidneys, and liver, every 4 h during a 24-h period in a light/darkness synchronised environment. FINDINGS: Melatonin and cortisol concentrations followed a physiological 24-h pattern in both patients and controls. For melatonin, acrophase occurred during the night for both groups, with significantly decreased amplitude (median 5.2 vs 8.8, P = 0.0001) and circadian variation ([maximum]/[minimum]) in heart failure patients. For cortisol, mesor showed a significant increase for HF patients (mean 331.9 vs 275.1, P = 0.017) with a difference of 56.8 (95% CI 10.3-103.3) again resulting in a relatively lower variation: median 3.9 vs 6.3 (P = 0.0058). A nocturnal blood pressure dip was absent in 77.8% of HF patients. Clock gene expression profiles (Bmal, Clock, Per, Cry) were similar and with expected phase relations in animal HF models and controls, demonstrating preserved peripheral clock functionality in HF. Furthermore, oscillations in diurnal zebrafish were expectedly in opposite phases to those of nocturnal mice. Concordantly, cTnT concentrations in HF patients revealed significant circadian oscillations. INTERPRETATION: Central clock output is dampened in HF patients while the molecular peripheral clock, as confirmed in animal models, remains intact. This emphasises the importance of taking timing into account in research and therapy for HF, setting the stage for another dimension of diagnostic, prognostic and therapeutic approaches. FUNDING: Hartstichting.

Regulation of N6-Methyladenosine after Myocardial Infarction.

Development of heart failure (HF) after myocardial infarction (MI) is responsible for premature death. Complex cellular and molecular mechanisms are involved in this process. A number of studies have linked the epitranscriptomic RNA modification N6-methyladenosine (m6A) with HF, but it remains unknown how m6A affects the risk of developing HF after MI. We addressed the regulation of m6A and its demethylase fat mass and obesity-associated (FTO) after MI and their association with HF. Using liquid chromatography coupled to mass spectrometry, we observed an increase of m6A content in the infarcted area of rat hearts subjected to coronary ligation and a decrease in blood. FTO expression measured by quantitative PCR was downregulated in the infarcted hearts. In whole blood samples collected at the time of reperfusion in MI patients, m6A content was lower in patients who developed HF as attested by a 4-month ejection fraction (EF) of ≤40% as compared to patients who did not develop HF (EF > 50%). M6A content was higher in females. These results show that m6A measured in blood is associated with HF development after MI and motivate further investigation of the potential role of m6A as a novel epitranscriptomics biomarker and therapeutic target of HF.

N6-Methyladenine in Eukaryotic DNA: Tissue Distribution, Early Embryo Development, and Neuronal Toxicity.

DNA methylation is one of the most important epigenetic modifications and is closely related with several biological processes such as regulation of gene transcription and the development of non-malignant diseases. The prevailing dogma states that DNA methylation in eukaryotes occurs essentially through 5-methylcytosine (5mC) but recently adenine methylation was also found to be present in eukaryotes. In mouse embryonic stem cells, 6-methyladenine (6mA) was associated with the repression and silencing of genes, particularly in the X-chromosome, known to play an important role in cell fate determination. Here, we have demonstrated that 6mA is a ubiquitous eukaryotic epigenetic modification that is put in place during epigenetically sensitive periods such as embryogenesis and fetal development. In somatic cells there are clear tissue specificity in 6mA levels, with the highest 6mA levels being observed in the brain. In zebrafish, during the first 120 h of embryo development, from a single pluripotent cell to an almost fully formed individual, 6mA levels steadily increase. An identical pattern was observed over embryonic days 7-21 in the mouse. Furthermore, exposure to a neurotoxic environmental pollutant during the same early life period may led to a decrease in the levels of this modification in female rats. The identification of the periods during which 6mA epigenetic marks are put in place increases our understanding of this mammalian epigenetic modification, and raises the possibility that it may be associated with developmental processes.

The Long Noncoding RNA Landscape of Cardiac Regeneration in Zebrafish.

BACKGROUND: Novel therapeutic targets of heart failure (HF) are needed. Long noncoding RNAs (lncRNAs) are engaged during cardiac regeneration. Unlike in humans, zebrafish naturally undergo cardiac regeneration after HF. We aimed to describe the landscape of lncRNAs during regeneration in a zebrafish model of HF and to investigate their human homologs. METHODS: HF was established in adult zebrafish through thrice-weekly incubations with an anemia-inducing drug, phenylhydrazine hydrochloride (PHZ). After 5 weeks, PHZ treatment ceased and the fish were followed through a regeneration period of 14 days. Total RNA was extracted from the hearts of adult zebrafish after establishment of HF and at 2, 5, and 9 days after treatment cessation (9 hearts per condition at each time point). Gene regulation patterns were characterized with the use of bioinformatics and validated with the use of quantitative polymerase chain reaction. RESULTS: We obtained 14,340 lncRNAs from the reannotated Affymetrix zebrafish microarray. Of these, 187 lncRNAs were found to be differentially expressed (false discovery rate < 0.05 and fold change ≥ 2) at at least 1 time point. 85% of differentially expressed lncRNAs overlapped or were close to (distance < 10 kb) protein-coding genes which were mostly related to muscle development in Gene Ontology analyses. Fifty-seven lncRNAs had human homologs, according to orientation relative to their conserved protein-coding neighbours. CONCLUSIONS: LncRNAs are differentially expressed during regeneration after HF in adult zebrafish and could be potential future therapeutic targets. The extent to which lncRNAs contribute to cardiac regeneration is a worthy avenue for future research.

Non-Coding RNAs in the Brain-Heart Axis: The Case of Parkinson's Disease.

Parkinson's disease (PD) is a complex and heterogeneous disorder involving multiple genetic and environmental influences. Although a wide range of PD risk factors and clinical markers for the symptomatic motor stage of the disease have been identified, there are still no reliable biomarkers available for the early pre-motor phase of PD and for predicting disease progression. High-throughput RNA-based biomarker profiling and modeling may provide a means to exploit the joint information content from a multitude of markers to derive diagnostic and prognostic signatures. In the field of PD biomarker research, currently, no clinically validated RNA-based biomarker models are available, but previous studies reported several significantly disease-associated changes in RNA abundances and activities in multiple human tissues and body fluids. Here, we review the current knowledge of the regulation and function of non-coding RNAs in PD, focusing on microRNAs, long non-coding RNAs, and circular RNAs. Since there is growing evidence for functional interactions between the heart and the brain, we discuss the benefits of studying the role of non-coding RNAs in organ interactions when deciphering the complex regulatory networks involved in PD progression. We finally review important concepts of harmonization and curation of high throughput datasets, and we discuss the potential of systems biomedicine to derive and evaluate RNA biomarker signatures from high-throughput expression data.

Restoration of cardiac function after anaemia-induced heart failure in zebrafish.

AIMS: New therapeutic approaches are needed to fight against the growing epidemic of heart failure. Unlike mammals, zebrafish possess the incredible ability to regenerate cardiac tissue after acute trauma such as apical resection. Yet, the ability of zebrafish to recover after a chronic stress leading to heart failure has not been reported. The aim of this study was to test whether zebrafish can recover a normal cardiac function after anaemia-induced heart failure. METHODS AND RESULTS: Eight- to ten-month-old zebrafish were treated with phenylhydrazine hydrochloride, an anaemia inducer, to generate heart failure. Treatment was stopped after 5 weeks and fish were followed-up for 3 weeks. Assessment of ventricular function by ultrasound at the end of the treatment revealed an increase in ventricle diameter (+47%) and a decrease in heart rate (-36%) and fractional shortening (-30%). A decrease in swim capacity was also observed (-31%). Tissue staining showed a thickening of the ventricular wall (5-fold), cell apoptosis and proliferation but no fibrosis. Expression of foetal genes, angiogenic factor and inflammation markers was increased, and ß-adrenergic receptor-1 was decreased. Three weeks after phenylhydrazine hydrochloride withdrawal, all parameters returned to baseline and the fish recovered a normal cardiac function, tissue morphology and gene expression. CONCLUSIONS: Zebrafish are able to completely recover from anaemia-induced heart failure. This model represents a unique opportunity to investigate the mechanisms of cardiac repair and may lead to the discovery of novel therapeutic targets of heart failure.

Hypoxia inhibits lymphatic thoracic duct formation in zebrafish.

Hypoxia promotes blood vessel growth through up-regulation of pro-angiogenic pathways but its role on the lymphatic system remains unclear. The homeobox transcription factor Prox1 is a master control gene for generating lymphatic endothelial cells (LECs) and is up-regulated by hypoxia-inducible factors in mammals. While vascular endothelial growth factor A (VEGFA) is critical for angiogenesis, VEGFC and its receptor VEGF receptor-3 (VEGFR-3) are essential for the initial sprouting and directed migration as well as for the subsequent survival of LECs. The aim of this study was to determine the effects of hypoxia on the development of the lymphatic system in zebrafish. Zebrafish embryos were obtained from Tg(SAGFF27C; UAS:GFP) animals carrying a lymphatic reporter gene coupled to green fluorescent protein (GFP). Exposure of 1-day old zebrafish embryos to hypoxic conditions (5% O2) for 24 h inhibited thoracic duct formation (-27%, p < 0.0001). Hypoxia inhibited the expression of pro-lymphangiogenic factors prox1a, vegfc and vegfr-3. This inhibition was relieved after re-oxygenation. On the other hand, hypoxia increased the expression of vegfa, a pro-angiogenic factor. In conclusion, hypoxia has opposite effects on vascular development in zebrafish, inhibiting the development of the lymphatic vascular system while promoting the development of the blood vascular system.

Use of Coronary Ultrasound Imaging to Evaluate Ventricular Function in Adult Zebrafish.

So far, imaging of the adult zebrafish heart and assessment of heart failure in adult zebrafish have been very limited. Here, we describe a new method for in vivo imaging of the hypertrabeculated heart of the adult zebrafish using miniaturized cardiac ultrasound catheters obtained from the cardiac catheterization laboratory. This method allows the observation of the ventricle of zebrafish and the assessment of ventricular diameters during diastole and systole, as well as heart rate and fractional shortening. Significant changes in these parameters were detected through the use of an adult zebrafish heart failure model induced by chronic anemia. This imaging technique opens the door to detailed in vivo analysis of the adult heart failure phenotype in zebrafish.