SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape.

The 501Y.V2 variants of SARS-CoV-2 containing multiple mutations in spike are now dominant in South Africa and are rapidly spreading to other countries. Here, experiments with 18 pseudotyped viruses showed that the 501Y.V2 variants do not confer increased infectivity in multiple cell types except for murine ACE2-overexpressing cells, where a substantial increase in infectivity was observed. Notably, the susceptibility of the 501Y.V2 variants to 12 of 17 neutralizing monoclonal antibodies was substantially diminished, and the neutralization ability of the sera from convalescent patients and immunized mice was also reduced for these variants. The neutralization resistance was mainly caused by E484K and N501Y mutations in the receptor-binding domain of spike. The enhanced infectivity in murine ACE2-overexpressing cells suggests the possibility of spillover of the 501Y.V2 variants to mice. Moreover, the neutralization resistance we detected for the 501Y.V2 variants suggests the potential for compromised efficacy of monoclonal antibodies and vaccines.

The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity.

The spike protein of SARS-CoV-2 has been undergoing mutations and is highly glycosylated. It is critically important to investigate the biological significance of these mutations. Here, we investigated 80 variants and 26 glycosylation site modifications for the infectivity and reactivity to a panel of neutralizing antibodies and sera from convalescent patients. D614G, along with several variants containing both D614G and another amino acid change, were significantly more infectious. Most variants with amino acid change at receptor binding domain were less infectious, but variants including A475V, L452R, V483A, and F490L became resistant to some neutralizing antibodies. Moreover, the majority of glycosylation deletions were less infectious, whereas deletion of both N331 and N343 glycosylation drastically reduced infectivity, revealing the importance of glycosylation for viral infectivity. Interestingly, N234Q was markedly resistant to neutralizing antibodies, whereas N165Q became more sensitive. These findings could be of value in the development of vaccine and therapeutic antibodies.

UHRF2 commissions the completion of DNA demethylation through allosteric activation by 5hmC and K33-linked ubiquitination of XRCC1.

The transition of oxidized 5-methylcytosine (5mC) intermediates into the base excision repair (BER) pipeline to complete DNA demethylation remains enigmatic. We report here that UHRF2, the only paralog of UHRF1 in mammals that fails to rescue Uhrf1-/- phenotype, is physically and functionally associated with BER complex. We show that UHRF2 is allosterically activated by 5-hydroxymethylcytosine (5hmC) and acts as a ubiquitin E3 ligase to catalyze K33-linked polyubiquitination of XRCC1. This nonproteolytic action stimulates XRCC1's interaction with the ubiquitin binding domain-bearing RAD23B, leading to the incorporation of TDG into BER complex. Integrative epigenomic analysis in mouse embryonic stem cells reveals that Uhrf2-fostered TDG-RAD23B-BER complex is functionally linked to the completion of DNA demethylation at active promoters and that Uhrf2 ablation impedes DNA demethylation on latent enhancers that undergo poised-to-active transition during neuronal commitment. Together, these observations highlight an essentiality of 5hmC-switched UHRF2 E3 ligase activity in commissioning the accomplishment of active DNA demethylation.

Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants.

Omicron (B.1.1.529), the most heavily mutated SARS-CoV-2 variant so far, is highly resistant to neutralizing antibodies, raising concerns about the effectiveness of antibody therapies and vaccines1,2. Here we examined whether sera from individuals who received two or three doses of inactivated SARS-CoV-2 vaccine could neutralize authentic Omicron. The seroconversion rates of neutralizing antibodies were 3.3% (2 out of 60) and 95% (57 out of 60) for individuals who had received 2 and 3 doses of vaccine, respectively. For recipients of three vaccine doses, the geometric mean neutralization antibody titre for Omicron was 16.5-fold lower than for the ancestral virus (254). We isolated 323 human monoclonal antibodies derived from memory B cells in triple vaccinees, half of which recognized the receptor-binding domain, and showed that a subset (24 out of 163) potently neutralized all SARS-CoV-2 variants of concern, including Omicron. Therapeutic treatments with representative broadly neutralizing monoclonal antibodies were highly protective against infection of mice with SARS-CoV-2 Beta (B.1.351) and Omicron. Atomic structures of the Omicron spike protein in complex with three classes of antibodies that were active against all five variants of concern defined the binding and neutralizing determinants and revealed a key antibody escape site, G446S, that confers greater resistance to a class of antibodies that bind on the right shoulder of the receptor-binding domain by altering local conformation at the binding interface. Our results rationalize the use of three-dose immunization regimens and suggest that the fundamental epitopes revealed by these broadly ultrapotent antibodies are rational targets for a universal sarbecovirus vaccine.

SNP rs4971059 predisposes to breast carcinogenesis and chemoresistance via TRIM46-mediated HDAC1 degradation.

Identification of the driving force behind malignant transformation holds the promise to combat the relapse and therapeutic resistance of cancer. We report here that the single nucleotide polymorphism (SNP) rs4971059, one of 65 new breast cancer risk loci identified in a recent genome-wide association study (GWAS), functions as an active enhancer of TRIM46 expression. Recreating the G-to-A polymorphic switch caused by the SNP via CRISPR/Cas9-mediated homologous recombination leads to an overt upregulation of TRIM46. We find that TRIM46 is a ubiquitin ligase that targets histone deacetylase HDAC1 for ubiquitination and degradation and that the TRIM46-HDAC1 axis regulates a panel of genes, including ones critically involved in DNA replication and repair. Consequently, TRIM46 promotes breast cancer cell proliferation and chemoresistance in vitro and accelerates tumor growth in vivo. Moreover, TRIM46 is frequently overexpressed in breast carcinomas, and its expression is correlated with lower HDAC1 expression, higher histological grades, and worse prognosis of the patients. Together, our study links SNP rs4971059 to replication and to breast carcinogenesis and chemoresistance and support the pursuit of TRIM46 as a potential target for breast cancer intervention.

BRD4-directed super-enhancer organization of transcription repression programs links to chemotherapeutic efficacy in breast cancer.

BRD4 is well known for its role in super-enhancer organization and transcription activation of several prominent oncogenes including c-MYC and BCL2 As such, BRD4 inhibitors are being pursued as promising therapeutics for cancer treatment. However, drug resistance also occurs for BRD4-targeted therapies. Here, we report that BRD4 unexpectedly interacts with the LSD1/NuRD complex and colocalizes with this repressive complex on super-enhancers. Integrative genomic and epigenomic analyses indicate that the BRD4/LSD1/NuRD complex restricts the hyperactivation of a cluster of genes that are functionally linked to drug resistance. Intriguingly, treatment of breast cancer cells with a small-molecule inhibitor of BRD4, JQ1, results in no immediate activation of the drug-resistant genes, but long-time treatment or destabilization of LSD1 by PELI1 decommissions the BRD4/LSD1/NuRD complex, leading to resistance to JQ1 as well as to a broad spectrum of therapeutic compounds. Consistently, PELI1 is up-regulated in breast carcinomas, its level is negatively correlated with that of LSD1, and the expression level of the BRD4/LSD1/NuRD complex-restricted genes is strongly correlated with a worse overall survival of breast cancer patients. Together, our study uncovers a functional duality of BRD4 in super-enhancer organization of transcription activation and repression linking to oncogenesis and chemoresistance, respectively, supporting the pursuit of a combined targeting of BRD4 and PELI1 in effective treatment of breast cancer.

Rational prediction of immunogenicity clustering through cross-reactivity analysis of thirteen SARS-CoV-2 variants.

SARS-CoV-2 breakthrough infections in vaccinated individuals underscore the threat posed by continuous mutating variants, such as Omicron, to vaccine-induced immunity. This necessitates the search for broad-spectrum immunogens capable of countering infections from such variants. This study evaluates the immunogenicity relationship among SARS-CoV-2 variants, from D614G to XBB, through Guinea pig vaccination, covering D614G, Alpha, Beta, Gamma, Delta, BA.1, BA.2, BA.2.75, BA.2.75.2, BA.5, BF.7, BQ.1.1, and XBB, employing three immunization strategies: three-dose monovalent immunogens, three-dose bivalent immunogens, and a two-dose vaccination with D614G followed by a booster immunization with a variant strain immunogen. Three distinct immunogenicity clusters were identified: D614G, Alpha, Beta, Gamma, and Delta as cluster 1, BA.1, BA.2, and BA.2.75 as cluster 2, BA.2.75.2, BA.5, BF.7, BQ.1.1, and XBB as cluster 3. Broad-spectrum protection could be achieved through a combined immunization strategy using bivalent immunogens or D614G and XBB, or two initial D614G vaccinations followed by two XBB boosters. A comparison of neutralizing antibody levels induced by XBB boosting and equivalent dosing of D614G and XBB revealed that the XBB booster produced higher antibody levels. The study suggests that vaccine antigen selection should focus on the antigenic alterations among variants, eliminating the need for updating vaccine components for each variant.

Tellurium(IV) Halide Achieving Effective Nonlinear-Optical Activity: The Role of Chiral Ligands and Lattice Distortion.

Chiral organic-inorganic hybrid metal halides are a promising class of nonlinear-optical materials with unique optical properties and flexible crystal structures. However, the structures and properties of chiral hybrid tellurium halides, especially second harmonic generation (SHG), have not been reported. Here, by introducing chiral organic molecule (R/S)-methylbenzylammonium (R/S-MBA), we synthesized a pair of novel zero-dimensional (0D) chiral tellurium-based hybrid halides with noncentrosymmetric space group C2, (R/S-MBA)2TeCl6 (R/S-Cl). Single-crystal X-ray diffraction analysis and solid-state circular dichroism (CD) spectra confirm that R/S-Cl shows obvious enantiomer enrichment. Moreover, the resulting chiral products present an efficient SHG response. Interestingly, through manipulation of halogen atoms, two pairs of achiral tellurium halides, (R/S-MBA)2TeBr6 (R/S-Br) and (R/S-MBA)2TeI6 (R/S-I), were obtained, both of which crystallize in the centrosymmetric space group R3̅. It is noteworthy that R/S-I has a narrow band gap of 1.55 eV, which is smaller than that of most 0D metal halides and comparable to that of three-dimensional lead halide, showing its potential as a highly efficient light absorber.

Highly Selective Protic-Solvent-Mediated Organic-Inorganic Hybrid Cuprous Bromides Achieving Structural Transformation.

The potential application of stimuli-responsive hybrid copper halides in information storage and switch devices has generated significant interest. However, their transformation mechanism needs to be further studied deeply. Herein, two zero-dimensional (0D) organic-inorganic hybrids, namely, (TBA)CuBr2 (1) with linear [CuBr2]- units and (TBA)2Cu4Br6 (2) with [Cu4Br6]2- clusters (TBA+ = (C4H9)4N+), are synthesized using simple solvent evaporation approaches. Interestingly, upon exposure to distinct protic solvents, such as methanol, ethanol, ethylene glycol, or hot water, 1 undergoes a transformation into 2 with varying degrees of transition, accompanied by a change in luminescence color from cyan to orange (or mixed color) under high-energy emission (e.g., 254 nm) excitation. Hot water can trigger 1 to completely transform into 2 because of its large contact angle difference in the solvents. Furthermore, 2 can be converted back to 1 through a simple solid-state mechanochemical reaction. Additionally, the structure of 2 remains unchanged even after immersion in 80 °C H2O for 168 h due to the dense organic framework. This study provides valuable insights for exploring reversible structural transformation materials in the 0D metal halide system.

SCFJFK is functionally linked to obesity and metabolic syndrome.

Dysregulation of lipid metabolism could lead to the development of metabolic disorders. We report here that the F-box protein JFK promotes excessive lipid accumulation in adipose tissue and contributes to the development of metabolic syndrome. JFK transgenic mice develop spontaneous obesity, accompanied by dyslipidemia, hyperglycemia, and insulin resistance, phenotypes that are further exacerbated under high-fat diets. In contrast, Jfk knockout mice are lean and resistant to diet-induced metabolic malfunctions. Liver-specific reconstitution of JFK expression in Jfk knockout mice leads to hepatic lipid accumulation resembling human hepatic steatosis and nonalcoholic fatty liver disease. We show that JFK interacts with and destabilizes ING5 through assembly of the SCF complex. Integrative transcriptomic and genomic analysis reveals that the SCFJFK -ING5 axis interferes with AMPK activity and fatty acid ß-oxidation, leading to the suppression of hepatic lipid catabolism. Significantly, JFK is upregulated and AMPKα1 is down-regulated in liver tissues from NAFLD patients. These results reveal that SCFJFK is a bona fide E3 ligase for ING5 and link the SCFJFK -ING5 axis to the development of obesity and metabolic syndrome.

Cluster-Centered Excited-State-Induced Bright Low-Energy Emissive Hybrid Copper Iodide Constructing Stable White LEDs.

Herein, we successfully synthesized a stable copper iodide hybrid with a 0D structure, (C20H20P)2Cu2I4, in which [Cu2I4]2- dimers with a short Cu-Cu distance (2.64 Å) are isolated and surrounded by [C20H20P]+ organic cations. Bright broadband yellow emission (576 nm) featuring a wide excitation range from 240 to 450 nm was achieved, along with a large Stokes shift (211 nm), long-lived lifetime (1.99 µs), and zero self-absorption. The results combined with crystal structure, spectroscopy analysis, and theoretical studies reveal that a cluster-centered excited state is responsible for this yellow emission. Importantly, the structure of (C20H20P)2Cu2I4 remains unchanged even after soaking in water for 30 days or heating at 80 °C for 240 h due to the intermolecular interaction. Furthermore, a stable white LED showing a naturally correlated color temperature (CCT) of 6573 K and CIE color coordinate of (0.31, 0.37) was also demonstrated. This work demonstrates efficient light emitters based on lead-free and stable metal halides for lighting, providing an important reference for the development of stable, high-performance metal halide phosphors.

{[In2S7]8-}∞ Chain and Isolated HgS4 Planar Unit Constructed One-Dimensional Pentanary Sulfide K2Ba7HgIn4S16 Exhibiting Nonlinear-Optical Activity.

Hg-based chalcogenides possess diverse structures, large nonlinear-optical (NLO) responses, and suitable birefringences, making them potentially suitable for numerous crucial criteria of practical application as infrared (IR) NLO crystals. Here, a new pentanary Hg-based sulfide K2Ba7HgIn4S16 has been discovered by a high-temperature solid-state method. It crystallizes in the orthorhombic P21212 space group, and its one-dimensional structure is constructed by {[In2S7]8-}∞ chains and isolated [HgS4]6- planar quadrilateral units located bewteeen the chains, representing a novel type of chalcogenide. K2Ba7HgIn4S16 exhibits a moderate NLO effect of 0.5 × AGS at 2.1 µm and a high laser-induced damage threshold of ∼5.8 × AGS, as well as a band gap of 2.98 eV, demonstrating that K2Ba7HgIn4S16 is a potential IR NLO material. This work enriches the structural chemistry of chalcogenides and the family of Hg-based IR NLO chalcogenides.

Dual Monomeric Inorganic Units Constructed Bright Emissive Zero-Dimensional Antimony Chlorides with Solvent-Induced Reversible Structural Transition.

A5M2X11 and A3M2X9 families (A = monovalent organic cation; M = trivalent metal; X = halogen) are receiving increasing attention because of their combination of easy solution processability and superior ferroelectricity properties. However, synthesizing highly efficient A5M2X11 and A3M2X9-type fluorophores with multiple monomeric inorganic units and achieving their structural interconversion remains challenging. Here, we report two novel zero-dimensional (0D) antimony halides, (C10H16N)5Sb2Cl11·C2H3N (1) and (C10H16N)3Sb2Cl9 (2), which not only contain two distinct [SbXn]3-n units but also have excellent orange (590 nm) and yellow-green emission (540 nm) with high PLQY of 17.7% and 31.5%, respectively. Interestingly, a reversible structural conversion could be triggered by acetonitrile steam stimulation, accompanied by luminescence switching properties. This work not only enriches the structure of hybrid Sb-based halides but also provides the possibility of well-known A5M2X11 and A3M2X9 families as structural transformation materials.

High thermoelectric performance of a Sc2Si2Te6 monolayer at medium temperatures: an ab initio study.

Thermoelectric (TE) materials have attracted great attention in solving the problems in the waste heat field, while low figure of merit and poor material stability drastically limit their practical applications. In this work, a two-dimensional (2D) Sc2Si2Te6 monolayer was systematically explored as a promising TE material via ab initio methods. The results reveal that the Sc2Si2Te6 monolayer possesses an indirect band gap with a rhombohedral crystal phase and exhibits excellent dynamic stability. The lower electronic/lattice thermal conductivity and higher electron carrier mobility result in good n-type power factor parameters between 6.24 × 1010 and 1.5 × 1011 W m-1 s-1 K-2 from 300 to 700 K. Such combined merits of low thermal conductivity and high power factor parameters endow the Sc2Si2Te6 monolayer with superior thermoelectric properties with figure of merit (ZT) values of 1.41 and 3.81 at 300 K and 700 K, respectively. This study presented here can shed light on the future design of various 2D materials for thermoelectric applications.

Bimodal regulation of the PRC2 complex by USP7 underlies tumorigenesis.

Although overexpression of EZH2, a catalytic subunit of the polycomb repressive complex 2 (PRC2), is an eminent feature of various cancers, the regulation of its abundance and function remains insufficiently understood. We report here that the PRC2 complex is physically associated with ubiquitin-specific protease USP7 in cancer cells where USP7 acts to deubiquitinate and stabilize EZH2. Interestingly, we found that USP7-catalyzed H2BK120ub1 deubiquitination is a prerequisite for chromatin loading of PRC2 thus H3K27 trimethylation, and this process is not affected by H2AK119 ubiquitination catalyzed by PRC1. Genome-wide analysis of the transcriptional targets of the USP7/PRC2 complex identified a cohort of genes including FOXO1 that are involved in cell growth and proliferation. We demonstrated that the USP7/PRC2 complex drives cancer cell proliferation and tumorigenesis in vitro and in vivo. We showed that the expression of both USP7 and EZH2 elevates during tumor progression, corresponding to a diminished FOXO1 expression, and the level of the expression of USP7 and EZH2 strongly correlates with histological grades and prognosis of tumor patients. These results reveal a dual role for USP7 in the regulation of the abundance and function of EZH2, supporting the pursuit of USP7 as a therapeutic target for cancer intervention.

Pseudotyped Viruses for Phlebovirus.

Rift Valley fever virus (RVFV) is a member of the Phlebovirus genus, one of the 20 genera in the Phenuiviridae family. RVFV causes disease in animals and humans and is transmitted by sandflies or ticks. However, research into RVFV is limited by the requirement for biosafety level 3 (BSL-3) containment. Pseudotyped virus overcomes this limitation as it can be handled in a BSL-2 environment. Pseudotyped RVFV possesses an identical envelope protein structure to that of the authentic virus, simulating the same process of receptor binding and membrane fusion to host cells. Pseudotyped phleboviruses are therefore useful tools to study the infection mechanism of these viruses and for the screening of inhibitory drugs and the development of therapeutic monoclonal antibodies.

Pseudotyped Viruses for the Alphavirus Chikungunya Virus.

Members of the genus Alphavirus are mostly mosquito-borne pathogens that cause disease in their vertebrate hosts. Chikungunya virus (CHIKV), which is one member of the genus Alphavirus [1], has been a major health problem in endemic areas since its re-emergence in 2006. CHIKV is transmitted to mammalian hosts by the Aedes mosquito, causing persistent debilitating symptoms in many cases. At present, there is no specific treatment or vaccine. Experiments involving live CHIKV need to be performed in BSL-3 facilities, which limits vaccine and drug research. The emergence of pseudotyped virus technology offered the potential for the development of a safe and effective evaluation method. In this chapter, we review the construction and application of pseudotyped CHIKVs, the findings from which have enhanced our understanding of CHIKV. This will, in turn, enable the exploration of promising therapeutic strategies in animal models, with the ultimate aim of developing effective treatments and vaccines against CHIKV and other related viruses.

Pseudotyped Viruses.

Pseudotyped viruses have been constructed for many viruses. They can mimic the authentic virus and have many advantages compared to authentic viruses. Thus, they have been widely used as a surrogate of authentic virus for viral function analysis, detection of neutralizing antibodies, screening viral entry inhibitors, and others. This chapter reviewed the progress in the field of pseudotyped viruses in general, including the definition and the advantages of pseudotyped viruses, their potential usage, different strategies or vectors used for the construction of pseudotyped viruses, and factors that affect the construction of pseudotyped viruses.

Multi-Stimuli Responsive Luminescence and Domino Phase Transition of Hybrid Copper Halides with Nonlinear Optical Switching Behavior.

Although phase transition materials (PTMs) under external stimuli are of great research interest duo to their rich potential applications, it is still challenging to explore multi-responsive PTMs. Herein, two different phases of organic-inorganic hybrid copper-based halides, α- and ß-Gua3 Cu2 I5 (Gua+ =CN3 H6 + ), were synthesized by solvent evaporation method, which they crystalize in the noncentrosymmetric space group Fdd2 with zero-dimensional structure and centrosymmetric space group C2/c with one-dimensional metal-halogen framework, respectively. Interestingly, it is firstly demonstrated that Gua3 Cu2 I5 simultaneously possesses reversible PL conversion and NLO switching properties in response to thermal stimulus. Strikingly, apart from heat, its structural phase transition can also be triggered by crystalline-phase-recognition (CPR) and mechanical force. These new findings may pave a path for future exploration of PTMs with multiple physical properties.

Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift.

Variants of SARS-CoV-2 continue to emerge, posing great challenges in outbreak prevention and control. It is important to understand in advance the impact of possible variants of concern (VOCs) on infectivity and antigenicity. Here, we constructed one or more of the 15 high-frequency naturally occurring amino acid changes in the receptor-binding domain (RBD) of Alpha, Beta, and Gamma variants. A single mutant of A520S, V367F, and S494P in the above three VOCs enhanced infectivity in ACE2-overexpressing 293T cells of different species, LLC-MK2 and Vero cells. Aggregation of multiple RBD mutations significantly reduces the infectivity of the possible three VOCs. Regarding neutralization, it is noteworthy that E484K, N501Y, K417N, and N439K predispose to monoclonal antibodies (mAbs) protection failure in the 15 high-frequency mutations. Most importantly, almost all possible VOCs (single RBD mutation or aggregation of multiple mutations) showed no more than a fourfold decrease in neutralizing activity with convalescent sera, vaccine sera, and immune sera of guinea pigs with different immunogens, and no significant antigenic drift was formed. In conclusion, our pseudovirus results could reduce the concern that the aggregation of multiple high-frequency mutations in the RBD of the spike protein of the three VOCs would lead to severe antigenic drift, and this would provide value for vaccine development strategies.