Integrative genomic and transcriptomic analysis for pinpointing recurrent alterations of plant homeodomain genes and their clinical significance in breast cancer

A wide range of the epigenetic effectors that regulate chromatin modification, gene expression, genomic stability, and DNA repair contain structurally conserved domains called plant homeodomain (PHD) fingers. Alternations of several PHD finger-containing proteins (PHFs) due to genomic amplification, mutations, deletions, and translocations have been linked directly to various types of cancer. However, little is known about the genomic landscape and the clinical significance of PHFs in breast cancer. Hence, we performed a large-scale genomic and transcriptomic analysis of 98 PHF genes in breast cancer using TCGA and METABRIC datasets and correlated the recurrent alterations with clinicopathological features and survival of patients. Different subtypes of breast cancer had different patterns of copy number and expression for each PHF. We identified a subset of PHF genes that was recurrently altered with high prevalence, including PYGO2 (pygopus family PHD finger 2), ZMYND8 (zinc finger, MYND-type containing 8), ASXL1 (additional sex combs like 1) and CHD3 (chromodomain helicase DNA binding protein 3). Copy number increase and overexpression of ZMYND8 were more prevalent in Luminal B subtypes and were significantly associated with shorter survival of breast cancer patients. ZMYND8 was also involved in a positive feedback circuit of the estrogen receptor (ER) pathway, and the expression of ZMYND8 was repressed by the bromodomain and extra terminal (BET) inhibitor in breast cancer. Our findings suggest a promising avenue for future research—to focus on a subset of PHFs to better understand the molecular mechanisms and to identify therapeutic targets in breast cancer

Tet3 regulates synaptic transmission and homeostatic plasticity via DNA oxidation and repair.

Contrary to the long-held belief that DNA methylation of terminally differentiated cells is permanent and essentially immutable, post-mitotic neurons exhibit extensive DNA demethylation. The cellular function of active DNA demethylation in neurons, however, remains largely unknown. Tet family proteins oxidize 5-methylcytosine to initiate active DNA demethylation through the base-excision repair (BER) pathway. We found that synaptic activity bi-directionally regulates neuronal Tet3 expression. Functionally, knockdown of Tet or inhibition of BER in hippocampal neurons elevated excitatory glutamatergic synaptic transmission, whereas overexpressing Tet3 or Tet1 catalytic domain decreased it. Furthermore, dysregulation of Tet3 signaling prevented homeostatic synaptic plasticity. Mechanistically, Tet3 dictated neuronal surface GluR1 levels. RNA-seq analyses further revealed a pivotal role of Tet3 in regulating gene expression in response to global synaptic activity changes. Thus, Tet3 serves as a synaptic activity sensor to epigenetically regulate fundamental properties and meta-plasticity of neurons via active DNA demethylation

Association between Nine Types of TCM Constitution and Five Chronic Diseases: A Correspondence Analysis Based on a Sample of 2,660 Participants

Objective. The purpose of this study was to explore the association of nine types of Traditional Chinese Medicine (TCM) constitution with the five chronic diseases: hypertension, hyperlipidemia, diabetes mellitus, heart disease, and obesity. Methods. Chi-squared test was performed to investigate the distribution characteristics of TCM constitutions in the participants with the five chronic diseases in questionnaire. Correspondence analysis was used to explore the correlation between them. Results. A total of 2,660 participants (1,400 males; 1,260 females) were included in this study. The mean age was 52.54 ± 13.92. Of them, 600 were of gentleness type accounting for 22.56%. Proportions of gentleness type in the chronic diseases (16.00%~23.70%) were less than that in general population (32.14%). The gentleness type and yin-deficiency type were significantly correlated with hypertension and diabetes mellitus, qi-deficiency type was correlated with heart disease, phlegm-dampness type was associated with obesity, and dampness-heat type was correlated with hyperlipidemia. Conclusions. The correlations between TCM constitution types and the five chronic diseases were different. This may have a significant implication for TCM practice, and even the people with gentleness type should not be ignored in health management

White matter hyperintensities burden in the frontal regions is positively correlated to the freezing of gait in Parkinson’s disease

ObjectivePrevious studies have reported that white matter hyperintensities (WMHs) are associated with freezing of gait (FOG), but it is not clear whether their distribution areas have correlations with FOG in Parkinson’s disease (PD) and the potential influencing factors about WMHs.MethodsTwo hundred and forty-six patients with PD who underwent brain MRI were included. Participants were divided into PD with FOG (n = 111) and PD without FOG (n = 135) groups. Scheltens score was used to assess the WMHs burden in the areas of deep white matter hyperintensities (DWMHs), periventricular hyperintensities (PVHs), basal ganglia hyperintensities (BGHs), and infratentorial foci of hyperintensities (ITF). Whole brain WMHs volume was evaluated by automatic segmentation. Binary logistic regression was used to evaluate relationships between WMHs and FOG. The common cerebrovascular risk factors that may affect WMHs were evaluated by mediation analysis.ResultsThere were no statistical differences between PD with and without FOG groups in whole brain WMHs volume, total Scheltens score, BGHs, and ITF. Binary logistic regression showed that the total scores of DWMHs (OR = 1.094; 95% CI, 1.001, 1.195; p = 0.047), sum scores of PVHs and DWMHs (OR = 1.080; 95% CI, 1.003, 1.164; p = 0.042), especially the DWMHs in frontal (OR = 1.263; 95% CI, 1.060, 1.505 p = 0.009), and PVHs in frontal caps (OR = 2.699; 95% CI, 1.337, 5.450; p = 0.006) were associated with FOG. Age, hypertension, and serum alkaline phosphatase (ALP) are positively correlated with scores of DWMHs in frontal and PVHs in frontal caps.ConclusionThese results indicate that WMHs distribution areas especially in the frontal of DWMHs and PVHs play a role in PD patients with FOG

CatNorth: An Improved Gaia DR3 Quasar Candidate Catalog with Pan-STARRS1 and CatWISE

A complete and pure sample of quasars with accurate redshifts is crucial for quasar studies and cosmology. In this paper, we present CatNorth, an improved Gaia DR3 quasar candidate catalog with more than 1.5 million sources in the 3$\pi$ sky built with data from Gaia, Pan-STARRS1, and CatWISE2020. The XGBoost algorithm is used to reclassify the original Gaia DR3 quasar candidates as stars, galaxies, and quasars. To construct training/validation datasets for the classification, we carefully built two different master stellar samples in addition to the spectroscopic galaxy and quasar samples. An ensemble classification model is obtained by averaging two XGBoost classifiers trained with different master stellar samples. Using a probability threshold of $p_{\mathrm{QSO\_mean}}>0.95$ in our ensemble classification model and an additional cut on the logarithmic probability density of zero proper motion, we retrieved 1,545,514 reliable quasar candidates from the parent Gaia DR3 quasar candidate catalog. We provide photometric redshifts for all candidates with an ensemble regression model. For a subset of 89,100 candidates, accurate spectroscopic redshifts are estimated with the Convolutional Neural Network from the Gaia BP/RP spectra. The CatNorth catalog has a high purity of > 90% while maintaining high completeness, which is an ideal sample to understand the quasar population and its statistical properties. The CatNorth catalog is used as the main source of input catalog for the LAMOST phase III quasar survey, which is expected to build a highly complete sample of bright quasars with $i < 19.5$.Comment: 24 pages, 13 figures, submitted to AAS journals. Table 4 (The CatNorth quasar candidate catalog) is available at https://nadc.china-vo.org/res/r101313

Author Correction: WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling.

An amendment to this paper has been published and can be accessed via a link at the top of the paper

Inhibition of CLIC4 Enhances Autophagy and Triggers Mitochondrial and ER Stress-Induced Apoptosis in Human Glioma U251 Cells under Starvation

CLIC4/mtCLIC, a chloride intracellular channel protein, localizes to mitochondria, endoplasmic reticulum (ER), nucleus and cytoplasm, and participates in the apoptotic response to stress. Apoptosis and autophagy, the main types of the programmed cell death, seem interconnected under certain stress conditions. However, the role of CLIC4 in autophagy regulation has yet to be determined. In this study, we demonstrate upregulation and nuclear translocation of the CLIC4 protein following starvation in U251 cells. CLIC4 siRNA transfection enhanced autophagy with increased LC3-II protein and puncta accumulation in U251 cells under starvation conditions. In that condition, the interaction of the 14-3-3 epsilon isoform with CLIC4 was abolished and resulted in Beclin 1 overactivation, which further activated autophagy. Moreover, inhibiting the expression of CLIC4 triggered both mitochondrial apoptosis involved in Bax/Bcl-2 and cytochrome c release under starvation and endoplasmic reticulum stress-induced apoptosis with CHOP and caspase-4 upregulation. These results demonstrate that CLIC4 nuclear translocation is an integral part of the cellular response to starvation. Inhibiting the expression of CLIC4 enhances autophagy and contributes to mitochondrial and ER stress-induced apoptosis under starvation

AI is a viable alternative to high throughput screening: a 318-target study

: High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery