New insights into the basis of neurogenesis defects in Kabuki syndrome

Chromatin modifiers act to coordinate gene expression critical to neuronal differentiation from neural stem/progenitor cells (NSPCs). Loss-of-function variants in genes encoding two such enzymes, lysine-specific methyltransferase 2D (KMT2D) and lysine-specific demethylase 6A (KDM6A/UTX) cause the congenital, multisystem intellectual disability (ID) disorder Kabuki syndrome (KS1 and KS2, respectively). A mouse model of KS1, Kmt2d(+/βgeo), demonstrated visuospatial memory impairments and decreased adult hippocampal neurogenesis in the dentate gyrus (DG). These were reversible upon post-natal treatment by histone deacetylase inhibition (HDACi), but underlying cellular and molecular mechanisms are poorly understood. Here, we moved forward with 3 hypotheses: (1) a dietary alternative may provide a more tolerable therapeutic avenue for chromatin opening in KS, (2) gene expression studies in KMT2D-deficient neuronal cells would yield novel insights into the pathogenesis of KS, and (3) comparison of phenotypes and gene expression abnormalities in KS1 and KS2 could yield a deeper understanding of the molecular mechanisms causing KS-associated ID. We describe the generation and characterization of multiple novel models of KS1 in human and mouse systems. Specifically, I report cell-autonomous defects in proliferation, cell cycle, and survival, accompanied by precocious NSPC maturation in several KMT2D-deficient model systems. Transcriptional suppression in KMT2D-deficient cells produced strong perturbation of hypoxia-responsive metabolism pathways. Functional experiments confirmed abnormalities of cellular hypoxia responses in KMT2D-deficient neural cells, and accelerated NSPC maturation in vivo. These findings support a model in which loss of KMT2D function suppresses expression of oxygen-responsive gene programs that are important to neural progenitor maintenance; this causes precocious neuronal differentiation in a mouse model of KS1. Then characterizing a KS2 mouse model, Kdm6a(tm1d), I found defects of adult hippocampal neurogenesis, cell cycle, and other phenotypes, that suggest shared etiologic mechanisms in KS2 and KS1. This work is the first to identify the specific cellular and molecular defects that occur with loss-of-function of KMT2D and KDM6A in neural model systems. Furthermore, we identify cellular energy metabolism pathways as a critical molecular target in KS-related gene expression alterations, providing novel insights that could inform the treatment of KS

Universal prediction of cell-cycle position using transfer learning.

To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked DownloadBackground: The cell cycle is a highly conserved, continuous process which controls faithful replication and division of cells. Single-cell technologies have enabled increasingly precise measurements of the cell cycle both as a biological process of interest and as a possible confounding factor. Despite its importance and conservation, there is no universally applicable approach to infer position in the cell cycle with high-resolution from single-cell RNA-seq data. Results: Here, we present tricycle, an R/Bioconductor package, to address this challenge by leveraging key features of the biology of the cell cycle, the mathematical properties of principal component analysis of periodic functions, and the use of transfer learning. We estimate a cell-cycle embedding using a fixed reference dataset and project new data into this reference embedding, an approach that overcomes key limitations of learning a dataset-dependent embedding. Tricycle then predicts a cell-specific position in the cell cycle based on the data projection. The accuracy of tricycle compares favorably to gold-standard experimental assays, which generally require specialized measurements in specifically constructed in vitro systems. Using internal controls which are available for any dataset, we show that tricycle predictions generalize to datasets with multiple cell types, across tissues, species, and even sequencing assays. Conclusions: Tricycle generalizes across datasets and is highly scalable and applicable to atlas-level single-cell RNA-seq data. Keywords: Cell cycle; Single-cell RNA-sequencing; Transfer learning.Chan Zuckerberg Initiative DAF Silicon Valley Community Foundation United States Department of Health & Human Services National Institutes of Health (NIH) - USA NIH National Institute of General Medical Sciences (NIGMS) Appeared in source as:National Institute of General Medical Sciences of the National Institutes of Health National Science Foundation (NSF) National Institute of Agin Maryland Stem Cell Research Foundation Kavli Neurodiscovery Institute Johns Hopkins Provost Award Program BRAIN Initiative United States Department of Health & Human Services National Institutes of Health (NIH) - USA NIH National Institute of Neurological Disorders & Stroke (NINDS) Appeared in source as:National Institute of Neurological Disorder

Risk factors associated with adverse fetal outcomes in pregnancies affected by Coronavirus disease 2019 (COVID-19): a secondary analysis of the WAPM study on COVID-19.

Objectives To evaluate the strength of association between maternal and pregnancy characteristics and the risk of adverse perinatal outcomes in pregnancies with laboratory confirmed COVID-19. Methods Secondary analysis of a multinational, cohort study on all consecutive pregnant women with laboratory-confirmed COVID-19 from February 1, 2020 to April 30, 2020 from 73 centers from 22 different countries. A confirmed case of COVID-19 was defined as a positive result on real-time reverse-transcriptase-polymerase-chain-reaction (RT-PCR) assay of nasal and pharyngeal swab specimens. The primary outcome was a composite adverse fetal outcome, defined as the presence of either abortion (pregnancy loss before 22 weeks of gestations), stillbirth (intrauterine fetal death after 22 weeks of gestation), neonatal death (death of a live-born infant within the first 28 days of life), and perinatal death (either stillbirth or neonatal death). Logistic regression analysis was performed to evaluate parameters independently associated with the primary outcome. Logistic regression was reported as odds ratio (OR) with 95% confidence interval (CI). Results Mean gestational age at diagnosis was 30.6+/-9.5 weeks, with 8.0% of women being diagnosed in the first, 22.2% in the second and 69.8% in the third trimester of pregnancy. There were six miscarriage (2.3%), six intrauterine device (IUD) (2.3) and 5 (2.0%) neonatal deaths, with an overall rate of perinatal death of 4.2% (11/265), thus resulting into 17 cases experiencing and 226 not experiencing composite adverse fetal outcome. Neither stillbirths nor neonatal deaths had congenital anomalies found at antenatal or postnatal evaluation. Furthermore, none of the cases experiencing IUD had signs of impending demise at arterial or venous Doppler. Neonatal deaths were all considered as prematurity-related adverse events. Of the 250 live-born neonates, one (0.4%) was found positive at RT-PCR pharyngeal swabs performed after delivery. The mother was tested positive during the third trimester of pregnancy. The newborn was asymptomatic and had negative RT-PCR test after 14 days of life. At logistic regression analysis, gestational age at diagnosis (OR: 0.85, 95% CI 0.8-0.9 per week increase; pPeer reviewe

High-altitude populations need special considerations for COVID-19

Abstract The atmospheric pressure that decreases with altitude affects lung physiology. However, these changes in physiology are not usually considered in ventilator design and testing. We argue that high altitude human populations require special attention to access the international supply of ventilators

Precocious neuronal differentiation and disrupted oxygen responses in Kabuki syndrome.

To access publisher's full text version of this article click on the hyperlink belowChromatin modifiers act to coordinate gene expression changes critical to neuronal differentiation from neural stem/progenitor cells (NSPCs). Lysine-specific methyltransferase 2D (KMT2D) encodes a histone methyltransferase that promotes transcriptional activation and is frequently mutated in cancers and in the majority (>70%) of patients diagnosed with the congenital, multisystem intellectual disability disorder Kabuki syndrome 1 (KS1). Critical roles for KMT2D are established in various non-neural tissues, but the effects of KMT2D loss in brain cell development have not been described. We conducted parallel studies of proliferation, differentiation, transcription, and chromatin profiling in KMT2D-deficient human and mouse models to define KMT2D-regulated functions in neurodevelopmental contexts, including adult-born hippocampal NSPCs in vivo and in vitro. We report cell-autonomous defects in proliferation, cell cycle, and survival, accompanied by early NSPC maturation in several KMT2D-deficient model systems. Transcriptional suppression in KMT2D-deficient cells indicated strong perturbation of hypoxia-responsive metabolism pathways. Functional experiments confirmed abnormalities of cellular hypoxia responses in KMT2D-deficient neural cells and accelerated NSPC maturation in vivo. Together, our findings support a model in which loss of KMT2D function suppresses expression of oxygen-responsive gene programs important to neural progenitor maintenance, resulting in precocious neuronal differentiation in a mouse model of KS1.United States Department of Health & Human Services National Institutes of Health (NIH) - USA Icelandic Research Fund Louma G. Foundation United States Department of Health & Human Services National Institutes of Health (NIH) - USA NIH Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD