Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms

Mammalian DNA methylation patterns are established by two de novo DNA methyltransferases DNMT3A and DNMT3B, which exhibit both redundant and distinctive methylation activities. However, the related molecular basis remains undetermined. Through comprehensive structural, enzymology and cellular characterization of DNMT3A and DNMT3B, we here report a multi-layered substraterecognition mechanism underpinning their divergent genomic methylation activities. A hydrogen bond in the catalytic loop of DNMT3B causes a lower CpG specificity than DNMT3A, while the interplay of target recognition domain and homodimeric interface fine-tunes the distinct target selection between the two enzymes, with Lysine 777 of DNMT3B acting as a unique sensor of the +1 flanking base. The divergent substrate preference between DNMT3A and DNMT3B provides an explanation for site-specific epigenomic alterations seen in ICF syndrome with DNMT3B mutations. Together, this study reveals crucial and distinctive substrate-readout mechanisms of the two DNMT3 enzymes, implicative of their differential roles during development and pathogenesis

Molecular classification of small cell lung cancer subtypes: Characteristics, prognostic factors, and clinical translation

Abstract. Small cell lung cancer (SCLC) is a highly malignant tumor with a very poor prognosis; therefore, more effective treatments are urgently needed for patients afflicted with the disease. In recent years, emerging molecular classifications based on key transcription factors of SCLC have provided more information on the tumor pathophysiology, metastasis, immune microenvironment, and acquired therapeutic resistance and reflected the intertumoral heterogeneity of the various SCLC phenotypes. Additionally, advances in genomics and single-cell sequencing analysis have further revealed the high intratumoral heterogeneity and plasticity of the disease. Herein, we review and summarize these recent lines of evidence and discuss the possible pathogenesis of SCLC

Tropical cyclogenesis bias over the central North Pacific in CMIP6 simulations

Current coupled climate models contain large biases in simulating tropical cyclogenesis, reducing the confidence in tropical cyclone (TC) projection. In this study, we investigated the influence of sea surface temperature (SST) biases on TC genesis in the Coupled Model Intercomparison Project Phase 6 simulations from 1979 to 2014. Positive TC genesis biases were found over the tropical Central North Pacific (CNP) in most of climate models, including the high-resolution models. Compared to coupled models, TC genesis density (TCGD) simulations over CNP in uncoupled models forced by observational SST improved obviously. A warm SST bias over the tropical CNP in the coupled models is the main cause of TC genesis biases. The SST bias-induced diabatic heating leads to an anomalous Gill-type atmospheric circulation response, which contributes to a series of favorable environmental conditions for TC formation over the CNP. Numerical experiments were also performed with HiRAM to demonstrate the influence of SST biases on the TCGD simulation, further confirmed our conclusion. The current results highlight the importance of improving TC simulation in state-of-the-art climate models by reducing SST simulation bias

Structure-guided functional suppression of AML-associated DNMT3A hotspot mutations

DNA methyltransferases DNMT3A- and DNMT3B-mediated DNA methylation critically regulate epigenomic and transcriptomic patterning during development. The hotspot DNMT3A mutations at the site of Arg822 (R882) promote polymerization, leading to aberrant DNA methylation that may contribute to the pathogenesis of acute myeloid leukemia (AML). However, the molecular basis underlying the mutation-induced functional misregulation of DNMT3A remains unclear. Here, we report the crystal structures of the DNMT3A methyltransferase domain, revealing a molecular basis for its oligomerization behavior distinct to DNMT3B, and the enhanced intermolecular contacts caused by the R882H or R882C mutation. Our biochemical, cellular, and genomic DNA methylation analyses demonstrate that introducing the DNMT3B-converting mutations inhibits the R882H-/R882C-triggered DNMT3A polymerization and enhances substrate access, thereby eliminating the dominant-negative effect of the DNMT3A R882 mutations in cells. Together, this study provides mechanistic insights into DNMT3A R882 mutations-triggered aberrant oligomerization and DNA hypomethylation in AML, with important implications in cancer therapy

Atmospheric modes fiddling the simulated ENSO impact on tropical cyclone genesis over the Northwest Pacific

Abstract The El Niño-Southern Oscillation (ENSO) is crucial to the interannual variability of tropical cyclone (TC) genesis over the western North Pacific (WNP). However, most state-of-the-art climate models exhibit a consistent pattern of uncertainty in the simulated TC genesis frequency (TCGF) over the WNP in ENSO phases. Here, we analyze large ensemble simulations of TC-resolved climate models to identify the source of this uncertainty. Results show that large uncertainty appears in the South China Sea and east of the Philippines, primarily arising from two distinct atmospheric modes: the Matsuno-Gill-mode (MG-mode) and the Pacific-Japan-like pattern (PJ-mode). These two modes are closely associated with anomalous diabatic heating linked to tropical precipitation bias in model simulations. By conditionally constraining either of the modes, we can significantly reduce model uncertainty in simulating the dipole structure of the TCGF anomalies, confirming that it is the atmospheric circulation bias in response to tropical precipitation bias that causes uncertainty in the simulated WNP TCGF

Precision Detection Technology: Equipping Precision Oncology with Wings

In recent years, precision medical detection techniques experienced a rapid transformation from low-throughput to high-throughput genomic sequencing, from multicell promiscuous detection to single-cell precision sequencing. The emergence of liquid biopsy technology has compensated for the many limitations of tissue biopsy, leading to a tremendous transformation in precision detection. Precision detection techniques contribute to monitoring disease development more closely, evaluating therapeutic effects more scientifically, and developing new targets and new drugs. In the future, the role of precision detection and the joint detection in epigenetics, rare gene detection, individualized targeted therapy, and multigene targeted drug combination therapy should be extensively explored. This article reviews the changes in precision medical detection technology in the era of precision medicine, as well as the development, clinical application, and future challenges of liquid biopsy

Inhibition of HIV-1 Viral Infection by an Engineered CRISPR Csy4 RNA Endoribonuclease

<div><p>The bacterial defense system CRISPR (clustered regularly interspaced short palindromic repeats) has been explored as a powerful tool to edit genomic elements. In this study, we test the potential of CRISPR Csy4 RNA endoribonuclease for targeting HIV-1. We fused human codon-optimized Csy4 endoribonuclease with VPR, a HIV-1 viral preintegration complex protein. An HIV-1 cell model was modified to allow quantitative detection of active virus production. We found that the <i>trans</i>-expressing VPR-Csy4 almost completely blocked viral infection in two target cell lines (SupT1, Ghost). In the MAGI cell assay, where the HIV-1 LTR β-galactosidase is expressed under the control of the <i>tat</i> gene from an integrated provirus, VPR-Csy4 significantly blocked the activity of the provirus-activated HIV-1 reporter. This proof-of-concept study demonstrates that Csy4 endoribonuclease is a promising tool that could be tailored further to target HIV-1.</p></div

Expression of innate defense genes.

<p>Forty-eight hours after viral infection, Ghost cells were collected for RNA analysis using real-time PCR. All data shown are mean±SEM from three independent experiments by normalization over controls.</p

Epigenetic Targeting of Granulin in Hepatoma Cells by Synthetic CRISPR dCas9 Epi-suppressors

The CRISPR-associated Cas9 system can modulate disease-causing alleles both in vivo and ex vivo, raising the possibility of therapeutic genome editing. In addition to gene targeting, epigenetic modulation by the catalytically inactive dCas9 may also be a potential form of cancer therapy. Granulin (GRN), a potent pluripotent mitogen and growth factor that promotes cancer progression by maintaining self-renewal of hepatic stem cancer cells, is upregulated in hepatoma tissues and is associated with decreased tumor survival in patients with hepatoma. We synthesized a group of dCas9 epi-suppressors to target GRN by tethering the C terminus of dCas9 with three epigenetic suppressor genes: DNMT3a (DNA methyltransferase), EZH2 (histone 3 lysine 27 methyltransferase), and KRAB (the Krüppel-associated box transcriptional repression domain). In conjunction with guide RNAs (gRNAs), the dCas9 epi-suppressors caused significant decreases in GRN mRNA abundance in Hep3B hepatoma cells. These dCas9 epi-suppressors initiated de novo CpG DNA methylation in the GRN promoter, and they produced histone codes that favor gene suppression, including decreased H3K4 methylation, increased H3K9 methylation, and enhanced HP1a binding. Epigenetic knockdown of GRN led to the inhibition of cell proliferation, decreased tumor sphere formation, and reduced cell invasion. These changes were achieved at least partially through the MMP/TIMP pathway. This study thus demonstrates the potential utility of using dCas9 epi-suppressors in the development of epigenetic targeting against tumors