Hypoxia plays a major role in the etiology and pathogenesis of most of the leading causes of morbidity and mortality, whether cardiovascular diseases, cancer, respiratory diseases or stroke. Despite ...active research on hypoxia-signaling pathways, the understanding of regulatory mechanisms, especially in specific tissues, still remain elusive. With the accessibility of thousands of potentially diverse genomic datasets, computational methods are utilized to generate new hypotheses. Here we utilized Boolean implication relationship, a powerful method to probe symmetrically and asymmetrically related genes, to identify novel hypoxia related genes. We used a well-known hypoxia-responsive gene, VEGFA, with very large human expression datasets (n = 25,955) to identify novel hypoxia-responsive candidate gene/s. Further, we utilized in-vitro analysis using human endothelial cells exposed to 1% O2 environment for 2, 8, 24 and 48 hours to validate top candidate genes. Out of the top candidate genes (n = 19), 84% genes were previously reported as hypoxia related, validating our results. However, we identified FAM114A1 as a novel candidate gene significantly upregulated in the endothelial cells at 8, 24 and 48 hours of 1% O2 environment. Additional evidence, particularly the localization of intronic miRNA and numerous HREs further support and strengthen our finding. Current results on FAM114A1 provide an example demonstrating the utility of powerful computational methods, like Boolean implications, in playing a major role in hypothesis building and discovery.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Structural and transcriptional changes during early brain maturation follow fixed developmental programs defined by genetics. However, whether this is true for functional network activity remains ...unknown, primarily due to experimental inaccessibility of the initial stages of the living human brain. Here, we developed human cortical organoids that dynamically change cellular populations during maturation and exhibited consistent increases in electrical activity over the span of several months. The spontaneous network formation displayed periodic and regular oscillatory events that were dependent on glutamatergic and GABAergic signaling. The oscillatory activity transitioned to more spatiotemporally irregular patterns, and synchronous network events resembled features similar to those observed in preterm human electroencephalography. These results show that the development of structured network activity in a human neocortex model may follow stable genetic programming. Our approach provides opportunities for investigating and manipulating the role of network activity in the developing human cortex.
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•Long-term, single-cell transcriptomics reveals cortical organoid developmental dynamics•Cortical organoids exhibit phase-amplitude coupling during network-synchronous events•Differential role of glutamate and GABA in initiating and maintaining oscillations•Network-level events are similar to the human preterm neonatal EEG features
Oscillatory activity is a candidate mechanism for how neural populations are temporally organized. Cortical organoids exhibit periodic and highly regular nested oscillatory network events that are dependent on glutamatergic and GABAergic signaling. The emerging development of network activity transitions to more spatiotemporally complex activity, capturing features of preterm infant electroencephalography.
Acute respiratory failure is a life-threatening clinical outcome in critically ill pediatric patients. In severe cases, patients can require mechanical ventilation (MV) for survival. Early ...recognition of these patients can potentially help clinicians alter the clinical course and lead to improved outcomes.
To build a data-driven model for early prediction of the need for mechanical ventilation in pediatric intensive care unit (PICU) patients.
The study consists of a single-center retrospective observational study on a cohort of 13,651 PICU patients admitted between 1/01/2010 and 5/15/2018 with a prevalence of 8.06% for MV due to respiratory failure. XGBoost (extreme gradient boosting) and a convolutional neural network (CNN) using medication history were used to develop a prediction model that could yield a time-varying "risk-score"-a continuous probability of whether a patient will receive MV-and an ideal global threshold was calculated from the receiver operating characteristics (ROC) curve. The early prediction point (EPP) was the first time the risk-score surpassed the optimal threshold, and the interval between the EPP and the start of the MV was the early warning period (EWT). Spectral clustering identified patient groups based on risk-score trajectories after EPP.
A clinical and medication history-based model achieved a 0.89 area under the ROC curve (AUROC), 0.6 sensitivity, 0.95 specificity, 0.55 positive predictive value (PPV), and 0.95 negative predictive value (NPV). Early warning time (EWT) median inter-quartile range of this model was 9.94.2-69.2 hours. Clustering risk-score trajectories within a six-hour window after the early prediction point (EPP) established three patient groups, with the highest risk group's PPV being 0.92.
This study uses a unique method to extract and apply medication history information, such as time-varying variables, to identify patients who may need mechanical ventilation for respiratory failure and provide an early warning period to avert it.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Over the past two decades, Opioid Use Disorder (OUD) among pregnant women has become a major global public health concern. OUD has been characterized as a problematic pattern of opioid use despite ...adverse physical, psychological, behavioral, and or social consequences. Due to the relapsing-remitting nature of this disorder, pregnant mothers are chronically exposed to exogenous opioids, resulting in adverse neurological and neuropsychiatric outcomes. Collateral fetal exposure to opioids also precipitates severe neurodevelopmental and neurocognitive sequelae. At present, much of what is known regarding the neurobiological consequences of OUD and prenatal opioid exposure (POE) has been derived from preclinical studies in animal models and postnatal or postmortem investigations in humans. However, species-specific differences in brain development, variations in subject age/health/background, and disparities in sample collection or storage have complicated the interpretation of findings produced by these explorations. The ethical or logistical inaccessibility of human fetal brain tissue has also limited direct examinations of prenatal drug effects. To circumvent these confounding factors, recent groups have begun employing induced pluripotent stem cell (iPSC)-derived brain organoid technology, which provides access to key aspects of cellular and molecular brain development, structure, and function
. In this review, we endeavor to encapsulate the advancements in brain organoid culture that have enabled scientists to model and dissect the neural underpinnings and effects of OUD and POE. We hope not only to emphasize the utility of brain organoids for investigating these conditions, but also to highlight opportunities for further technical and conceptual progress. Although the application of brain organoids to this critical field of research is still in its nascent stages, understanding the neurobiology of OUD and POE via this modality will provide critical insights for improving maternal and fetal outcomes.
About 1.2 to 33% of high-altitude populations suffer from Monge’s disease or chronic mountain sickness (CMS). Number of factors such as age, sex, and population of origin (older, male, Andean) ...contribute to the percentage reported from a variety of samples. It is estimated that there are around 83 million people who live at altitudes > 2500 m worldwide and are at risk for CMS. In this review, we focus on a human “experiment in nature” in various high-altitude locations in the world—namely, Andean, Tibetan, and Ethiopian populations that have lived under chronic hypoxia conditions for thousands of years. We discuss the adaptive as well as mal-adaptive changes at the genomic and physiological levels. Although different genes seem to be involved in adaptation in the three populations, we can observe convergence at genetic and signaling, as well as physiological levels. What is important is that we and others have shown that lessons learned from the genes mined at high altitude can be helpful in better understanding and treating diseases that occur at sea level. We discuss two such examples: EDNRB and SENP1 and their role in cardiac tolerance and in the polycythemic response, respectively.
Cerebral cavernous malformations (CCMs) are common neurovascular lesions caused by loss-of-function mutations in 1 of 3 genes, including KRIT1 (CCM1), CCM2, and PDCD10 (CCM3), and generally regarded ...as an endothelial cell-autonomous disease. Here we reported that proliferative astrocytes played a critical role in CCM pathogenesis by serving as a major source of VEGF during CCM lesion formation. An increase in astrocyte VEGF synthesis is driven by endothelial nitric oxide (NO) generated as a consequence of KLF2- and KLF4-dependent elevation of eNOS in CCM endothelium. The increased brain endothelial production of NO stabilized HIF-1α in astrocytes, resulting in increased VEGF production and expression of a "hypoxic" program under normoxic conditions. We showed that the upregulation of cyclooxygenase-2 (COX-2), a direct HIF-1α target gene and a known component of the hypoxic program, contributed to the development of CCM lesions because the administration of a COX-2 inhibitor significantly prevented the progression of CCM lesions. Thus, non-cell-autonomous crosstalk between CCM endothelium and astrocytes propels vascular lesion development, and components of the hypoxic program represent potential therapeutic targets for CCMs.
Monge's disease (chronic mountain sickness (CMS)) is a maladaptive condition caused by chronic (years) exposure to high-altitude hypoxia. One of the defining features of CMS is excessive ...erythrocytosis with extremely high hematocrit levels. In the Andean population, CMS prevalence is vastly different between males and females, being rare in females. Furthermore, there is a sharp increase in CMS incidence in females after menopause. In this study, we assessed the role of sex hormones (testosterone, progesterone, and estrogen) in CMS and non-CMS cells using a well-characterized in vitro erythroid platform. While we found that there was a mild (nonsignificant) increase in RBC production with testosterone, we observed that estrogen, in physiologic concentrations, reduced sharply CD235a
cells (glycophorin A; a marker of RBC), from 56% in the untreated CMS cells to 10% in the treated CMS cells, in a stage-specific and dose-responsive manner. At the molecular level, we determined that estrogen has a direct effect on GATA1, remarkably decreasing the messenger RNA (mRNA) and protein levels of GATA1 (p < 0.01) and its target genes (Alas2, BclxL, and Epor, p < 0.001). These changes result in a significant increase in apoptosis of erythroid cells. We also demonstrate that estrogen regulates erythropoiesis in CMS patients through estrogen beta signaling and that its inhibition can diminish the effects of estrogen by significantly increasing HIF1, VEGF, and GATA1 mRNA levels. Taken altogether, our results indicate that estrogen has a major impact on the regulation of erythropoiesis, particularly under chronic hypoxic conditions, and has the potential to treat blood diseases, such as high altitude severe erythrocytosis.
Hypoxia is a common pathological element in many human diseases. Understanding the mechanisms that underlie hypoxia tolerance or susceptibility is essential for developing novel strategies for ...treatment or prevention. Through experimental evolution, we obtained a Drosophila melanogaster population that can live perpetually in severe, normally lethal, hypoxic environments. We generated a Panel of Low Oxygen Tolerant (PLOT) isofemale lines (total 79 lines) from this hypoxia tolerant population to study or identify the specific genetic mechanisms that are responsible for the hypoxia tolerant trait. These isofemale lines showed significantly higher hypoxia tolerance as compared to their wildtype parental isofemale lines and the wildtype DGRP (Drosophila melanogaster Genetic Reference Panel) isofemale lines. For example, 95% of the PLOT lines showed hypoxia tolerance with eclosion rate >50% at 5% O2 level. In contrast, none of the parental lines and only 15% of the DGRP lines had similar eclosion rates under the same hypoxic condition. Furthermore, under the lethal condition with 4% O2, our PLOT lines exhibited a wide range of eclosion rate from 1% to 80% with a clear pattern of Gaussian‐Distribution, demonstrating that these PLOT flies may provide us a unique opportunity to study the molecular basis of stress‐directed evolution, such as the role of genetic variations in the protein coding regions and functional DNA elements in hypoxia adaptation. These PLOT lines can also be used to study phenotypic plasticity as well as genetic‐epigenetic interactions in hypoxic, or other stressful, environments.
Obstructive sleep apnea (OSA) is a common disorder characterized by intermittent hypoxia and hypercapnia (IHC) during sleep. OSA has been shown to be a risk factor for atherosclerosis, but the ...relation of IHC to the induction or progression of atherosclerosis is not well understood. To dissect the mechanisms involved, we compared atherosclerotic lesion formation in two mouse models, i.e., apolipoprotein E (ApoE) and low density lipoprotein receptor (Ldlr)-deficient mice, with or without IHC exposure. Ten-week-old ApoE
or Ldlr
mice were fed a high-fat diet for 4 or 8 weeks while being exposed to IHC for 10 hours/day or room air (RA) for 24 hours/day. En face lesions of the aorta, aortic arch, and pulmonary artery (PA) were examined. Moreover, 3,3-dimethyl-1-butanol (DMB), an inhibitor of microbial trimethylamine (TMA) production, was used to determine the contribution of TMA-oxide (TMAO) to IHC-induced atherosclerosis. Eight weeks of IHC exposure expedited the formation of atherosclerosis in both the PA and aortic arch of ApoE
mice, but only in the PA of Ldlr
mice (ApoE
PA 8 wk, IHC 35.4 ± 1.9% versus RA 8.0 ± 2.8%, P < 0.01). The atherosclerotic lesions evolved faster and to a more severe extent in ApoE
mice as compared with Ldlr
mice (PA IHC 8 wk, ApoE
35.4 ± 1.9% versus Ldlr
8.2 ± 1.5%, P < 0.01). DMB significantly attenuated but did not totally eliminate IHC-induced PA atherosclerosis. Our findings suggest that IHC, a hallmark of OSA, accelerates the progression of atherosclerosis in the aorta and especially in the PA. This process is partly inhibited by DMB, demonstrating that microbial metabolites may serve as therapeutic targets for OSA-induced atherosclerosis.
The hypoxic response is an ancient stress response triggered by low ambient oxygen (O
2
)
1
. It is controlled by hypoxia inducible transcription factor-1 (HIF-1), whose α subunit is rapidly degraded ...under normoxic conditions but stabilized when O
2
-dependent prolyl hydroxylases (PHDs) that target its O
2
-dependent degradation domain (ODD) are inhibited
2
–
4
. Thus the amount of HIF-1α, which controls many genes involved in energy metabolism and angiogenesis is regulated post-translationally. Another ancient stress response is the innate immune response, regulated by several transcription factors, among which NF-κB plays a central role
5
,
6
. NF-κB activation is controlled by IκB kinases (IKK), mainly IKKβ, which are required for phosphorylation-induced degradation of IκB inhibitors in response to infection and inflammation
6
. Recently, IKKβ was found to be activated in hypoxic cell cultures when PHDs that suppress its activation are inhibited
7
. However, defining the relationship between NF-κB and HIF-1α has proven elusive. Using
in vitro
systems, it was reported that HIF-1α activates NF-κB
8
, that NF-κB controls HIF-1α transcription
9
and that activation of HIF-1α may be concurrent to inhibition of NF-κB
10
. We used mice lacking IKKβ in different cell types to demonstrate that NF-κB is a critical transcriptional activator of HIF-1α in macrophages responding to bacterial infection and in liver and brain of hypoxic animals. IKKβ deficiency results in defective induction of various HIF-1α target genes including vascular endothelial growth factor (VEGF) and elevated astrogliosis in hypoxic mice. Hence, IKKβ provides an important physiological link between the hypoxic response and innate immunity/inflammation, two ancient stress response systems.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK