Epigenetic balance ensures mechanistic control of MLL amplification and rearrangement.

MLL/KMT2A amplifications and translocations are prevalent in infant, adult, and therapy-induced leukemia. However, the molecular contributor(s) to these alterations are unclear. Here, we demonstrate that histone H3 lysine 9 mono- and di-methylation (H3K9me1/2) balance at the MLL/KMT2A locus regulates these amplifications and rearrangements. This balance is controlled by the crosstalk between lysine demethylase KDM3B and methyltransferase G9a/EHMT2. KDM3B depletion increases H3K9me1/2 levels and reduces CTCF occupancy at the MLL/KMT2A locus, in turn promoting amplification and rearrangements. Depleting CTCF is also sufficient to generate these focal alterations. Furthermore, the chemotherapy doxorubicin (Dox), which associates with therapy-induced leukemia and promotes MLL/KMT2A amplifications and rearrangements, suppresses KDM3B and CTCF protein levels. KDM3B and CTCF overexpression rescues Dox-induced MLL/KMT2A alterations. G9a inhibition in human cells or mice also suppresses MLL/KMT2A events accompanying Dox treatment. Therefore, MLL/KMT2A amplifications and rearrangements are controlled by epigenetic regulators that are tractable drug targets, which has clinical implications.

A MicroRNA Linking Human Positive Selection and Metabolic Disorders.

Positive selection in Europeans at the 2q21.3 locus harboring the lactase gene has been attributed to selection for the ability of adults to digest milk to survive famine in ancient times. However, the 2q21.3 locus is also associated with obesity and type 2 diabetes in humans, raising the possibility that additional genetic elements in the locus may have contributed to evolutionary adaptation to famine by promoting energy storage, but which now confer susceptibility to metabolic diseases. We show here that the miR-128-1 microRNA, located at the center of the positively selected locus, represents a crucial metabolic regulator in mammals. Antisense targeting and genetic ablation of miR-128-1 in mouse metabolic disease models result in increased energy expenditure and amelioration of high-fat-diet-induced obesity and markedly improved glucose tolerance. A thrifty phenotype connected to miR-128-1-dependent energy storage may link ancient adaptation to famine and modern metabolic maladaptation associated with nutritional overabundance.

Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling.

Cell fate transitions involve rapid gene expression changes and global chromatin remodeling, yet the underlying regulatory pathways remain incompletely understood. Here, we identified the RNA-processing factor Nudt21 as a novel regulator of cell fate change using transcription-factor-induced reprogramming as a screening assay. Suppression of Nudt21 enhanced the generation of induced pluripotent stem cells, facilitated transdifferentiation into trophoblast stem cells, and impaired differentiation of myeloid precursors and embryonic stem cells, suggesting a broader role for Nudt21 in cell fate change. We show that Nudt21 directs differential polyadenylation of over 1,500 transcripts in cells acquiring pluripotency, although only a fraction changed protein levels. Remarkably, these proteins were strongly enriched for chromatin regulators, and their suppression neutralized the effect of Nudt21 during reprogramming. Collectively, our data uncover Nudt21 as a novel post-transcriptional regulator of cell fate and establish a direct, previously unappreciated link between alternative polyadenylation and chromatin signaling.

Dissecting dual roles of MyoD during lineage conversion to mature myocytes and myogenic stem cells.

The generation of myotubes from fibroblasts upon forced MyoD expression is a classic example of transcription factor-induced reprogramming. We recently discovered that additional modulation of signaling pathways with small molecules facilitates reprogramming to more primitive induced myogenic progenitor cells (iMPCs). Here, we dissected the transcriptional and epigenetic dynamics of mouse fibroblasts undergoing reprogramming to either myotubes or iMPCs using a MyoD-inducible transgenic model. Induction of MyoD in fibroblasts combined with small molecules generated Pax7+ iMPCs with high similarity to primary muscle stem cells. Analysis of intermediate stages of iMPC induction revealed that extinction of the fibroblast program preceded induction of the stem cell program. Moreover, key stem cell genes gained chromatin accessibility prior to their transcriptional activation, and these regions exhibited a marked loss of DNA methylation dependent on the Tet enzymes. In contrast, myotube generation was associated with few methylation changes, incomplete and unstable reprogramming, and an insensitivity to Tet depletion. Finally, we showed that MyoD's ability to bind to unique bHLH targets was crucial for generating iMPCs but dispensable for generating myotubes. Collectively, our analyses elucidate the role of MyoD in myogenic reprogramming and derive general principles by which transcription factors and signaling pathways cooperate to rewire cell identity.

The Histone Deacetylase SIRT6 Restrains Transcription Elongation via Promoter-Proximal Pausing.

Transcriptional regulation in eukaryotes occurs at promoter-proximal regions wherein transcriptionally engaged RNA polymerase II (Pol II) pauses before proceeding toward productive elongation. The role of chromatin in pausing remains poorly understood. Here, we demonstrate that the histone deacetylase SIRT6 binds to Pol II and prevents the release of the negative elongation factor (NELF), thus stabilizing Pol II promoter-proximal pausing. Genetic depletion of SIRT6 or its chromatin deficiency upon glucose deprivation causes intragenic enrichment of acetylated histone H3 at lysines 9 (H3K9ac) and 56 (H3K56ac), activation of cyclin-dependent kinase 9 (CDK9)-that phosphorylates NELF and the carboxyl terminal domain of Pol II-and enrichment of the positive transcription elongation factors MYC, BRD4, PAF1, and the super elongation factors AFF4 and ELL2. These events lead to increased expression of genes involved in metabolism, protein synthesis, and embryonic development. Our results identified SIRT6 as a Pol II promoter-proximal pausing-dedicated histone deacetylase.

The surveillance of pre-mRNA splicing is an early step in C. elegans RNAi of endogenous genes.

RNAi pathways detect and silence foreign nucleic acids such as viruses as well as endogenous genes in many species. The phylogenetic profile across eukaryotes of proteins that mediate key steps in RNAi is correlated with the profiles of multiple mRNA splicing proteins and with intron number, suggesting that RNAi may surveil mRNA splicing to detect the divergent or absent introns of viruses. Here we examine the role of mRNA splicing in Caenorhabditis elegans RNAi. We found that viable null mutations in U1 and U2 small nuclear ribonucleic protein (snRNP)-specific splicing factor genes cause defects in RNAi. The U1A ortholog rnp-2 is required for normal ERGO-1 Argonaute class 26G siRNA biogenesis, trans-splicing of the eri-6/7 transcript, and targeting of poorly conserved gene transcripts by WAGO Argonaute class 22G siRNAs. We found that gene transcripts engaged by the siRNA-generating machinery are poorly conserved, possess few introns, and often have introns that are divergent from introns with strong consensus splicing sites found in highly conserved genes. We present biochemical evidence that RNAi targeted transcripts are tightly bound to spliceosomes. These findings suggest multiple layers of regulation by the spliceosome at early steps of small RNA-mediated gene silencing.

Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation.

Master regulatory genes require stable silencing by the polycomb group (PcG) to prevent misexpression during differentiation and development. Some PcG proteins covalently modify histones, which contributes to heritable repression. The role for other effects on chromatin structure is less understood. We characterized the organization of PcG target genes in ESCs and neural progenitors using 5C and super-resolution microscopy. The genomic loci of repressed PcG targets formed discrete, small (20-140 Kb) domains of tight interaction that corresponded to locations bound by canonical polycomb repressive complex 1 (PRC1). These domains changed during differentiation as PRC1 binding changed. Their formation depended upon the Polyhomeotic component of canonical PRC1 and occurred independently of PRC1-catalyzed ubiquitylation. PRC1 domains differ from topologically associating domains in size and boundary characteristics. These domains have the potential to play a key role in transmitting epigenetic silencing of PcG targets by linking PRC1 to formation of a repressive higher-order structure.

MYC-Targeting Inhibitors Generated from a Stereodiversified Bicyclic Peptide Library.

Here, we present the second generation of our bicyclic peptide library (NTB), featuring a stereodiversified structure and a simplified construction strategy. We utilized a tandem ring-opening metathesis and ring-closing metathesis reaction (ROM-RCM) to cyclize the linear peptide library in a single step, representing the first reported instance of this reaction being applied to the preparation of macrocyclic peptides. Moreover, the resulting bicyclic peptide can be easily linearized for MS/MS sequencing with a one-step deallylation process. We employed this library to screen against the E363-R378 epitope of MYC and identified several MYC-targeting bicyclic peptides. Subsequent in vitro cell studies demonstrated that one candidate, NT-B2R, effectively suppressed MYC transcription activities and cell proliferation.

A Reversible MnO2 Deposition-Enabled Multicolor Electrochromic Device with Efficient Tunability of Ultraviolet-Visible Light.

Electrochromic technology offers exciting opportunities for smart applications such as energy-saving and interactive systems. However, achieving dual-band regulation together with the multicolor function is still an unmet challenge for electrochromic devices. Herein, an ingenious electrochromic strategy based on reversible manganese oxide (MnO2) electrodeposition, different from traditional ion intercalation/deintercalation-type electrochromic materials is proposed. Such a deposition/dissolution-based MnO2 brings an intriguing electrochromic feature of dual-band regulation for the ultraviolet (UV) and visible lights with high optical modulation (93.2% and 93.6% at 400 and 550 nm, respectively) and remarkable optical memory. Moreover, a demonstrative smart window assembled by MnO2 and Cu electrodes delivers the electrochromic properties of effective dual-band regulation accompanied by multicolor changes (transparent, yellow, and brown). The robust redox deposition/dissolution process endows the MnO2-based electrochromic device with excellent rate capability and an areal capacity of 570 mAh m-2 at 0.1 mA cm-2. It is believed that the metal oxide-based reversible electrodeposition strategy would be an attractive and promising electrochromic technology and provide a train of thought for the development of multifunctional electrochromic devices and applications.

DEPCOD: a tool to detect and visualize co-evolution of protein domains.

Proteins with similar phylogenetic patterns of conservation or loss across evolutionary taxa are strong candidates to work in the same cellular pathways or engage in physical or functional interactions. Our previously published tools implemented our method of normalized phylogenetic sequence profiling to detect functional associations between non-homologous proteins. However, many proteins consist of multiple protein domains subjected to different selective pressures, so using protein domain as the unit of analysis improves the detection of similar phylogenetic patterns. Here we analyze sequence conservation patterns across the whole tree of life for every protein domain from a set of widely studied organisms. The resulting new interactive webserver, DEPCOD (DEtection of Phylogenetically COrrelated Domains), performs searches with either a selected pre-defined protein domain or a user-supplied sequence as a query to detect other domains from the same organism that have similar conservation patterns. Top similarities on two evolutionary scales (the whole tree of life or eukaryotic genomes) are displayed along with known protein interactions and shared complexes, pathway enrichment among the hits, and detailed visualization of sources of detected similarities. DEPCOD reveals functional relationships between often non-homologous domains that could not be detected using whole-protein sequences. The web server is accessible at http://genetics.mgh.harvard.edu/DEPCOD.

Medical waste incineration fly ash-based magnesium potassium phosphate cement: Calcium-reinforced chlorine solidification/stabilization mechanism and optimized carbon reduction process strategy.

The traditional solidification/stabilization (S/S) technology, Ordinary Portland Cement (OPC), has been widely criticized due to its poor resistance to chloride and significant carbon emissions. Herein, a S/S strategy based on magnesium potassium phosphate cement (MKPC) was developed for the medical waste incineration fly ash (MFA) disposal, which harmonized the chlorine stabilization rate and potential carbon emissions. The in-situ XRD results indicated that the Cl- was efficiently immobilized in the MKPC system with coexisting Ca2+ by the formation of stable Ca5(PO4)3Cl through direct precipitation or intermediate transformation (the Cl- immobilization rate was up to 77.29%). Additionally, the MFA-based MKPC also demonstrated a compressive strength of up to 39.6 MPa, along with an immobilization rate exceeding 90% for heavy metals. Notably, despite the deterioration of the aforementioned S/S performances with increasing MFA incorporation, the potential carbon emissions associated with the entire S/S process were significantly reduced. According to the Life Cycle Assessment, the potential carbon emissions decreased to 8.35 × 102 kg CO2-eq when the MFA reached the blending equilibrium point (17.68 wt.%), while the Cl- immobilization rate still remained above 65%, achieving an acceptable equilibrium. This work proposes a low-carbon preparation strategy for MKPC that realizes chlorine stabilization, which is instructive for the design of S/S materials.

Apolipoprotein A-1 protected hepatic ischaemia-reperfusion injury through suppressing macrophage pyroptosis via TLR4-NF-κB pathway.

BACKGROUND AND AIMS: Apolipoprotein A-1 (ApoA-1), the major apolipoprotein of high-density lipoprotein, plays anti-atherogenic role in cardiovascular diseases and exerts anti-inflammation effect in various inflammatory and infectious diseases. However, the role and mechanism of ApoA-1 in hepatic ischaemia-reperfusion (I/R) injury is unknown. METHODS: In this study, we measured ApoA-1 expression in human liver grafts after transplantation. Mice partial hepatic I/R injury model was made in ApoA-1 knockout mice, ApoA-1 mimetic peptide D-4F treatment mice and corresponding control mice to examine the effect of ApoA-1 on liver damage, inflammation response and cell death. Primary hepatocytes and macrophages were isolated for in vitro study. RESULTS: The results showed that ApoA-1 expression was down-regulated in human liver grafts after transplantation and mice livers subjected to hepatic I/R injury. ApoA-1 deficiency aggravated liver damage and inflammation response induced by hepatic I/R injury. Interestingly, we found that ApoA-1 deficiency increased pyroptosis instead of apoptosis during acute phase of hepatic I/R injury, which mainly occurred in macrophages rather than hepatocytes. The inhibition of pyroptosis compensated for the adverse impact of ApoA-1 deficiency. Furthermore, the up-regulated pyroptosis process was testified to be mediated by ApoA-1 through TLR4-NF-κB pathway and TLR4 inhibition significantly improved hepatic I/R injury. In addition, we confirmed that D-4F ameliorated hepatic I/R injury. CONCLUSIONS: Our study has identified the protective role of ApoA-1 in hepatic I/R injury through inhibiting pyroptosis in macrophages via TLR4-NF-κB pathway. The effect of ApoA-1 may provide a novel therapeutic approach for hepatic I/R injury.

METTL3 boosts mitochondrial fission and induces cardiac fibrosis by enhancing LncRNA GAS5 methylation.

Dysregulated mitochondrial metabolism occurs in several pathological processes characterized by cell proliferation and migration. Nonetheless, the role of mitochondrial fission is not well appreciated in cardiac fibrosis, which is accompanied by enhanced fibroblast proliferation and migration. We investigated the causes and consequences of mitochondrial fission in cardiac fibrosis using cultured cells, animal models, and clinical samples. Increased METTL3 expression caused excessive mitochondrial fission, resulting in the proliferation and migration of cardiac fibroblasts that lead to cardiac fibrosis. Knockdown of METTL3 suppressed mitochondrial fission, inhibiting fibroblast proliferation and migration for ameliorating cardiac fibrosis. Elevated METTL3 and N6-methyladenosine (m6A) levels were associated with low expression of long non-coding RNA GAS5. Mechanistically, METTL3-mediated m6A methylation of GAS5 induced its degradation, dependent of YTHDF2. GAS5 could interact with mitochondrial fission marker Drp1 directly; overexpression of GAS5 suppressed Drp1-mediated mitochondrial fission, inhibiting cardiac fibroblast proliferation and migration. Knockdown of GAS5 produced the opposite effect. Clinically, increased METTL3 and YTHDF2 levels corresponded with decreased GAS5 expression, increased m6A mRNA content and mitochondrial fission, and increased cardiac fibrosis in human heart tissue with atrial fibrillation. We describe a novel mechanism wherein METTL3 boosts mitochondrial fission, cardiac fibroblast proliferation, and fibroblast migration: METTL3 catalyzes m6A methylation of GAS5 methylation in a YTHDF2-dependent manner. Our findings provide insight into the development of preventative measures for cardiac fibrosis.

Nickel-Catalyzed Reductive Dicarbofunctionalizations of Alkenes for the Synthesis of Difluorocarbonyl Oxindoles and Isoquinoline-1,3-diones.

A novel and efficient strategy for the construction of difluorocarbonyl-oxindole and difluorocarbonyl-isoquinoline-1,3-dione derivatives involving nickel-catalyzed intramolecular Heck-type cyclizations followed by intermolecular cross-couplings has been developed. This approach features high functional group tolerance, broad substrate scope, and operational simplicity under mild conditions, thus providing a new method for the rapid difluorocarbonyl-functionalization of alkenes to construct the structurally diversified five- and six-membered heterocycles.

Desert Abiotic Carbon Sequestration Weakening by Precipitation.

Desert carbon sequestration plays an active role in promoting carbon neutralization. However, the current understanding of the effect of hydrothermal interactions and soil properties on desert carbon sequestration after precipitation remains unclear. Based on the experiment in the hinterland of the Taklimakan Desert, we found that the heavy precipitation will accelerate the weakening of abiotic carbon sequestration in deserts under the background of global warming and intensified water cycle. The high soil moisture can significantly stimulate sand to release CO2 at an incredible speed by rapidly increasing microbial activity and organic matter diffusion. At this time, the CO2 flux in the shifting sand was synergistically affected by soil temperature and soil moisture. As far as soil properties are concerned, with less organic carbon substrate and stronger soil alkalinity, the carbon sequestration of shifting sand is gradually highlighted and strengthened at low temperature. On the contrary, the carbon sequestration of shifting sand is gradually weakened. Our study provides a new way to assess the contribution of desert to the global carbon cycle and improve the accuracy and scope of application.

Effect of IP-10/CXCR3 signaling pathway on rats with diabetic retinopathy.

This study aimed to investigate the effect of the interferon-inducible protein-10 (IP-10)/C-X-C motif chemokine receptor 3 (CXCR3) signaling pathway on rats with diabetic retinopathy. A total of 21 Sprague-Dawley rats were selected as the objects and divided into control (n=7), model (n=7) and inhibitor (n=7) groups. The rats in control group did not receive any treatment. The diabetic retinopathy model was established using streptozotocin and vascular endothelial growth factor in model group, while the rats in inhibitor group were treated with AMG 487, an inhibitor of the IP-10/CXCR3 signaling pathway, based on the treatment in model group. The changes in gene expression patterns in rats with diabetic retinopathy were screened by sequencing. After the differential genes were determined, the pathways mainly related to the complication were obtained via enrichment analysis. The expression of the IP-10/CXCR3 signaling pathway, the apoptotic cells and the expression of inflammatory molecules (IL-6, IL-12, TNF-α and IL-1ß) in each group of rats were detected. It was shown in volcano plot that there were some differentially expressed genes (fold change >1.2, P<0.01) in retinal tissues of rats in control and model groups. Meanwhile, the heatmap displayed that there were great differences in the gene expression patterns between control and model groups, and the gene expressions of IP-10 and CXCR3 in model group were higher than those in control group (P<0.05). The differential genes in control and model groupwere enriched in such processes as the cAMP metabolic regulatory pathway, chemotaxis of immunocytes, proliferation of endothelial cells, response of cytokine receptors, apoptosis, mTOR signaling pathway and TGF-ß-related signaling pathway. The mRNA expressions of IP-10 and CXCR3 in model group were higher than those in control group (P<0.05), while they were notably lower in inhibitor group than those in model group (P<0.05). Besides, the protein levels of IP-10 and CXCR3 were identical to the mRNA levels. The apoptotic cells were increased markedly in model group compared with those in control group (P<0.05) and inhibitor group (P<0.05). Model group exhibited higher expression levels of IL-6, TNF-α and IL-1ß in retinal tissues than control group (P<0.05), while inhibitor group had distinctly lower expression levels of IL-6, TNF-α and IL-1ß in retinal tissues than model group (P<0.05). The IP-10/CXCR3 signaling pathway can affect rats with diabetic retinopathy.

Noise effective masking level for bone conduction of wide-spectrum short-duration signals in normal hearing adults.

OBJECTIVE: The objective of this study is to determine the noise effective masking level (EML) and inter-aural attenuation (IA) for click and CE-Chirp signals presented though a Radioear B-81 to elicit the auditory brainstem responses in normally hearing, young adults. DESIGN AND STUDY SAMPLE: A total of 26 conveniently sampled adults (13 male and 13 female, aged 18-25 years; 52 ears), with pure-tone hearing thresholds not >15 dB nHL at octave frequencies from 250 to 8000 Hz, and subjective thresholds for the bone-conducted click and CE-Chirp not >10 dB nHL. RESULTS: At stimulus intensities of 30 and 40 dB nHL, the contralateral EML was 67.86 ± 0.78 and 77.80 ± 0.81 dB SPL (respectively) for the click and 72.11 ± 0.74 and 83.53 ± 0.78 dB SPL (respectively) for the CE-Chirp. At stimulus intensities of 30 and 40 dB nHL, the IA was 3.46 ± 2.34 and 3.38 ± 2.03 dB (respectively) for both the click and the CE-Chirp. CONCLUSION: EML and IA values are reported for click and CE-Chirp signals presented at 30 and 40 dB nHL though a Radioear B-81 to elicit the ABR in normally hearing, young adults.

Hydroxyl-Rich Hydrophilic Endocytosis-Promoting Peptide with No Positive Charge.

Delivering cargo molecules across the plasma membrane is critical for biomedical research, and the need to develop molecularly well-defined tags that enable cargo transportation is ever-increasing. We report here a hydrophilic endocytosis-promoting peptide (EPP6) rich in hydroxyl groups with no positive charge. EPP6 can transport a wide array of small-molecule cargos into a diverse panel of animal cells. Mechanistic studies revealed that it entered the cells through a caveolin- and dynamin-dependent endocytosis pathway, mediated by the surface receptor fibrinogen C domain-containing protein 1. After endocytosis, EPP6 trafficked through early and late endosomes within 30 min. Over time, EPP6 partitioned among cytosol, lysosomes, and some long-lived compartments. It also demonstrated prominent transcytosis abilities in both in vitro and in vivo models. Our study proves that positive charge is not an indispensable feature for hydrophilic cell-penetrating peptides and provides a new category of molecularly well-defined delivery tags for biomedical applications.

Neoadjuvant docetaxel plus carboplatin vs epirubicin plus cyclophosphamide followed by docetaxel in triple-negative, early-stage breast cancer (NeoCART): Results from a multicenter, randomized controlled, open-label phase II trial.

Previous studies have shown that the addition of carboplatin to neoadjuvant chemotherapy improved the pathologic complete response (pCR) rate in patients suffering from triple-negative breast cancer (TNBC) and patients who obtained a pCR could achieve prolonged event-free survival (EFS) and overall survival (OS). However, no studies have assessed the effects of the combination of docetaxel and carboplatin without anthracycline with taxane-based and anthracycline-based regimens. The NeoCART study was designed as a multicenter, randomized controlled, open-label, phase II trial to assess the efficacy and safety of docetaxel combined with carboplatin in untreated stage II-III TNBC. All eligible patients were randomly assigned, at a 1:1 ratio, to an experimental docetaxel plus carboplatin (DCb) for six cycles group (DCb group) or an epirubicin plus cyclophosphamide for four cycles followed by docetaxel for four cycles group (EC-D group). PCR (ypT0/is ypN0) was evaluated as the primary outcome. Between 1 September 2016 and 31 December 2019, 93 patients were randomly assigned and 88 patients were evaluated for the primary endpoint (44 patients in each group). In the primary endpoint analysis, 27 patients in the DCb group (61.4%, 95% CI 47.0-75.8) and 17 patients in the EC-D group achieved a pCR (38.6%, 95% CI 24.3-53.0; odds ratio 2.52, 95% CI 2.4-43.1; Pnoninferiority = .004). Noninferiority was met, and the DCb regimen was confirmed to be superior to the EC-D regimen (P = .044, superiority margin of 5%). At the end of the 37-month median follow-up period, OS and EFS rates were equivalent in both groups.