Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma.

The immune microenvironment of hepatocellular carcinoma (HCC) is poorly characterized. Combining two single-cell RNA sequencing technologies, we produced transcriptomes of CD45+ immune cells for HCC patients from five immune-relevant sites: tumor, adjacent liver, hepatic lymph node (LN), blood, and ascites. A cluster of LAMP3+ dendritic cells (DCs) appeared to be the mature form of conventional DCs and possessed the potential to migrate from tumors to LNs. LAMP3+ DCs also expressed diverse immune-relevant ligands and exhibited potential to regulate multiple subtypes of lymphocytes. Of the macrophages in tumors that exhibited distinct transcriptional states, tumor-associated macrophages (TAMs) were associated with poor prognosis, and we established the inflammatory role of SLC40A1 and GPNMB in these cells. Further, myeloid and lymphoid cells in ascites were predominantly linked to tumor and blood origins, respectively. The dynamic properties of diverse CD45+ cell types revealed by this study add new dimensions to the immune landscape of HCC.

Disruption of an antimycobacterial circuit between dendritic and helper T cells in human SPPL2a deficiency.

Human inborn errors of IFN-γ immunity underlie mycobacterial diseases. We describe patients with Mycobacterium bovis (BCG) disease who are homozygous for loss-of-function mutations of SPPL2A. This gene encodes a transmembrane protease that degrades the N-terminal fragment (NTF) of CD74 (HLA invariant chain) in antigen-presenting cells. The CD74 NTF therefore accumulates in the HLA class II+ myeloid and lymphoid cells of SPPL2a-deficient patients. This toxic fragment selectively depletes IL-12- and IL-23-producing CD1c+ conventional dendritic cells (cDC2s) and their circulating progenitors. Moreover, SPPL2a-deficient memory TH1* cells selectively fail to produce IFN-γ when stimulated with mycobacterial antigens in vitro. Finally, Sppl2a-/- mice lack cDC2s, have CD4+ T cells that produce small amounts of IFN-γ after BCG infection, and are highly susceptible to infection with BCG or Mycobacterium tuberculosis. These findings suggest that inherited SPPL2a deficiency in humans underlies mycobacterial disease by decreasing the numbers of cDC2s and impairing IFN-γ production by mycobacterium-specific memory TH1* cells.

Lineage specification of human dendritic cells is marked by IRF8 expression in hematopoietic stem cells and multipotent progenitors.

The origin and specification of human dendritic cells (DCs) have not been investigated at the clonal level. Through the use of clonal assays, combined with statistical computation, to quantify the yield of granulocytes, monocytes, lymphocytes and three subsets of DCs from single human CD34+ progenitor cells, we found that specification to the DC lineage occurred in parallel with specification of hematopoietic stem cells (HSCs) to the myeloid and lymphoid lineages. This started as a lineage bias defined by specific transcriptional programs that correlated with the combinatorial 'dose' of the transcription factors IRF8 and PU.1, which was transmitted to most progeny cells and was reinforced by upregulation of IRF8 expression driven by the hematopoietic cytokine FLT3L during cell division. We propose a model in which specification to the DC lineage is driven by parallel and inheritable transcriptional programs in HSCs and is reinforced over cell division by recursive interactions between transcriptional programs and extrinsic signals.

Induction of mouse totipotent stem cells by a defined chemical cocktail.

In mice, only the zygotes and blastomeres from 2-cell embryos are authentic totipotent stem cells (TotiSCs) capable of producing all the differentiated cells in both embryonic and extraembryonic tissues and forming an entire organism1. However, it remains unknown whether and how totipotent stem cells can be established in vitro in the absence of germline cells. Here we demonstrate the induction and long-term maintenance of TotiSCs from mouse pluripotent stem cells using a combination of three small molecules: the retinoic acid analogue TTNPB, 1-azakenpaullone and the kinase blocker WS6. The resulting chemically induced totipotent stem cells (ciTotiSCs), resembled mouse totipotent 2-cell embryo cells at the transcriptome, epigenome and metabolome levels. In addition, ciTotiSCs exhibited bidirectional developmental potentials and were able to produce both embryonic and extraembryonic cells in vitro and in teratoma. Furthermore, following injection into 8-cell embryos, ciTotiSCs contributed to both embryonic and extraembryonic lineages with high efficiency. Our chemical approach to totipotent stem cell induction and maintenance provides a defined in vitro system for manipulating and developing understanding of the totipotent state and the development of multicellular organisms from non-germline cells.

A small-molecule inhibitor of TopBP1 exerts anti-MYC activity and synergy with PARP inhibitors.

We have previously identified TopBP1 (topoisomerase IIß-binding protein 1) as a promising target for cancer therapy, given its role in the convergence of Rb, PI(3)K/Akt, and p53 pathways. Based on this, we conducted a large-scale molecular docking screening to identify a small-molecule inhibitor that specifically targets the BRCT7/8 domains of TopBP1, which we have named 5D4. Our studies show that 5D4 inhibits TopBP1 interactions with E2F1, mutant p53, and Cancerous Inhibitor of Protein Phosphatase 2A. This leads to the activation of E2F1-mediated apoptosis and the inhibition of mutant p53 gain of function. In addition, 5D4 disrupts the interaction of TopBP1 with MIZ1, which in turn allows MIZ1 to bind to its target gene promoters and repress MYC activity. Moreover, 5D4 inhibits the association of the TopBP1-PLK1 complex and prevents the formation of Rad51 foci. When combined with inhibitors of PARP1/2 or PARP14, 5D4 synergizes to effectively block cancer cell proliferation. Our animal studies have demonstrated the antitumor activity of 5D4 in breast and ovarian cancer xenograft models. Moreover, the effectiveness of 5D4 is further enhanced when combined with a PARP1/2 inhibitor talazoparib. Taken together, our findings strongly support the potential use of TopBP1-BRCT7/8 inhibitors as a targeted cancer therapy.

SR45a plays a key role in enhancing cotton resistance to Verticillium dahliae by alternative splicing of immunity genes.

Alternative splicing (AS) of pre-mRNAs increases the diversity of transcriptome and proteome and plays fundamental roles in plant development and stress responses. However, the prevalent changes in AS events and the regulating mechanisms of plants in response to pathogens remain largely unknown. Here, we show that AS changes are an important mechanism conferring cotton immunity to Verticillium dahliae (Vd). GauSR45a, encoding a serine/arginine-rich RNA binding protein, was upregulated expression and underwent AS in response to Vd infection in Gossypium australe, a wild diploid cotton species highly resistant to Vd. Silencing GauSR45a substantially reduced the splicing ratio of Vd-induced immune-associated genes, including GauBAK1 (BRI1-associated kinase 1) and GauCERK1 (chitin elicitor receptor kinase 1). GauSR45a binds to the GAAGA motif that is commonly found in the pre-mRNA of genes essential for PTI, ETI, and defense. The binding between GauSR45a and the GAAGA motif in the pre-mRNA of BAK1 was enhanced by two splicing factors of GauU2AF35B and GauU1-70 K, thereby facilitating exon splicing; silencing either AtU2AF35B or AtU1-70 K decreased the resistance to Vd in transgenic GauSR45a Arabidopsis. Overexpressing the short splicing variant of BAK1GauBAK1.1 resulted in enhanced Verticillium wilt resistance rather than the long one GauBAK1.2. Vd-induced far more AS events were in G. barbadense (resistant tetraploid cotton) than those in G. hirsutum (susceptible tetraploid cotton) during Vd infection, indicating resistance divergence in immune responses at a genome-wide scale. We provided evidence showing a fundamental mechanism by which GauSR45a enhances cotton resistance to Vd through global regulation of AS of immunity genes.

Generating synthetic population for simulating the spatiotemporal dynamics of epidemics.

Agent-based models have gained traction in exploring the intricate processes governing the spread of infectious diseases, particularly due to their proficiency in capturing nonlinear interaction dynamics. The fidelity of agent-based models in replicating real-world epidemic scenarios hinges on the accurate portrayal of both population-wide and individual-level interactions. In situations where comprehensive population data are lacking, synthetic populations serve as a vital input to agent-based models, approximating real-world demographic structures. While some current population synthesizers consider the structural relationships among agents from the same household, there remains room for refinement in this domain, which could potentially introduce biases in subsequent disease transmission simulations. In response, this study unveils a novel methodology for generating synthetic populations tailored for infectious disease transmission simulations. By integrating insights from microsample-derived household structures, we employ a heuristic combinatorial optimizer to recalibrate these structures, subsequently yielding synthetic populations that faithfully represent agent structural relationships. Implementing this technique, we successfully generated a spatially-explicit synthetic population encompassing over 17 million agents for Shenzhen, China. The findings affirm the method's efficacy in delineating the inherent statistical structural relationship patterns, aligning well with demographic benchmarks at both city and subzone tiers. Moreover, when assessed against a stochastic agent-based Susceptible-Exposed-Infectious-Recovered model, our results pinpointed that variations in population synthesizers can notably alter epidemic projections, influencing both the peak incidence rate and its onset.

Membrane insertion mechanism of the caveola coat protein Cavin1.

Caveolae are small plasma membrane invaginations, important for control of membrane tension, signaling cascades, and lipid sorting. The caveola coat protein Cavin1 is essential for shaping such high curvature membrane structures. Yet, a mechanistic understanding of how Cavin1 assembles at the membrane interface is lacking. Here, we used model membranes combined with biophysical dissection and computational modeling to show that Cavin1 inserts into membranes. We establish that initial phosphatidylinositol (4, 5) bisphosphate [PI(4,5)P2]-dependent membrane adsorption of the trimeric helical region 1 (HR1) of Cavin1 mediates the subsequent partial separation and membrane insertion of the individual helices. Insertion kinetics of HR1 is further enhanced by the presence of flanking negatively charged disordered regions, which was found important for the coassembly of Cavin1 with Caveolin1 in living cells. We propose that this intricate mechanism potentiates membrane curvature generation and facilitates dynamic rounds of assembly and disassembly of Cavin1 at the membrane.

High Breakthrough Pressure in Hydrogels Enabled Ultrastable Treatment of Hypersaline Wastewaters.

Surface effects of low-surface-tension contaminants accumulating at the evaporation surface easily induce wetting in membrane distillation, especially in hypersaline scenarios. Herein, we propose a novel strategy to eliminate the surface effect and redistribute contaminants at the evaporation interface simply by incorporating a layer of hydrogel. The as-fabricated composite membrane exhibits remarkable stability, even when exposed to solution with salt concentration of 5 M and surfactant concentration of 8 mM. Breakthrough pressure of the membrane reaches 20 bar in the presence of surfactants, surpassing commercial hydrophobic membranes by one to two magnitudes. Density functional theory and molecular dynamics simulations reveal the important role of the hydrogel-surfactant interaction in suppressing the surface effect. As a proof of concept, we demonstrate the membrane in stably processing synthetic wastewater containing 144 mg L-1 surfactants, 1 g L-1 mineral oils, and 192 g L-1 NaCl, showing its potential in addressing challenges of hypersaline water treatment.

Protein structuromics: A new method for protein structure-function crosstalk in glioma.

Glioma is a type of tumor that starts in the glial cells of the brain or spine. Since the 1800s, when the disease was first named, its survival rates have always been unsatisfactory. Despite great advances in molecular biology and traditional treatment methods, many questions regarding cancer occurrence and the underlying mechanism remain to be answered. In this study, we assessed the protein structural features of 20 oncogenes and 20 anti-oncogenes via protein structure and dynamic analysis methods and 3D structural and systematic analyses of the structure-function relationships of proteins. All of these results directly indicate that unfavorable group proteins show more complex structures than favorable group proteins. As the tumor cell microenvironment changes, the balance of oncogene-related and anti-oncogene-related proteins is disrupted, and most of the structures of the two groups of proteins will be disrupted. However, more unfavorable group proteins will maintain and refold to achieve their correct shape faster and perform their functions more quickly than favorable group proteins, and the former thus support cancer development. We hope that these analyses will help promote mechanistic research and the development of new treatments for glioma.

OTSUCNV: an adaptive segmentation and OTSU-based anomaly classification method for CNV detection using NGS data.

Copy-number variations (CNVs), which refer to deletions and duplications of chromosomal segments, represent a significant source of variation among individuals, contributing to human evolution and being implicated in various diseases ranging from mental illness and developmental disorders to cancer. Despite the development of several methods for detecting copy number variations based on next-generation sequencing (NGS) data, achieving robust detection performance for CNVs with arbitrary coverage and amplitude remains challenging due to the inherent complexity of sequencing samples. In this paper, we propose an alternative method called OTSUCNV for CNV detection on whole genome sequencing (WGS) data. This method utilizes a newly designed adaptive sequence segmentation algorithm and an OTSU-based CNV prediction algorithm, which does not rely on any distribution assumptions or involve complex outlier factor calculations. As a result, the effective detection of CNVs is achieved with lower computational complexity. The experimental results indicate that the proposed method demonstrates outstanding performance, and hence it may be used as an effective tool for CNV detection.

4f/5d Hybridization Induced Single-Electron Delocalization in an Azide-Bridged Dicerium Complex.

Dilanthanide complexes with one-electron delocalization are important targets for understanding the specific 4f/5d-bonding feature in lanthanide chemistry. Here, we report an isolable azide-bridged dicerium complex 3 [{(TrapenTMS)Ce}2(µ-N3)]• [Trapen = tris (2-aminobenzyl)amine; TMS = SiMe3], which is synthesized by the reaction of tripodal ligand-supported (TrapenTMS)CeIVCl complex 2 with NaN3. The structure and bonding nature of 3 are fully characterized by X-ray crystal diffraction analysis, electron paramagnetic resonance (EPR), magnetic measurement, cyclic voltammetry, X-ray absorption spectroscopy, and quantum-theoretical studies. Complex 3 presents a trans-bent central Ce-N3-Ce unit with a single electron of two mixed-valent Ce atoms. The unique low-temperature (2 K) anisotropic EPR signals [g = 1.135, 2.003, and 3.034] of 3 indicate that its spin density is distributed on the central Ce-N3-Ce unit with marked electron delocalization. Quantum chemical analyses show strong 4f/5d orbital mixing in the singly occupied molecular orbital of 3, which allows for the unpaired electron to extend throughout the cerium-azide-cerium unit via a multicentered one-electron (Ce-N3-Ce) interaction. This work extends the family of mixed-valent dilanthanide complexes and provides a paradigm for understanding the bonding motif of ligand-bridged dilanthanide complexes.

Characterization and the first complete genome sequence of a novel strain of Bergeyella porcorum isolated from pigs in China.

BACKGROUND: Bergeyella porcorum is a newly identified bacterium that has an ambiguous relationship with pneumonia in pigs. However, few studies have adequately characterized this species. RESULTS: In this study, we analyzed the morphological, physiological, and genomic characteristics of the newly identified B. porcorum sp. nov. strain QD2021 isolated from pigs. The complete genome sequence of the B. porcorum QD2021 strain consists of a single circular chromosome (2,271,736 bp, 38.51% G + C content), which encodes 2,578 genes. One plasmid with a size of 70,040 bp was detected. A total of 121 scattered repeat sequences, 319 tandem repeat sequences, 4 genomic islands, 5 prophages, 3 CRISPR sequences, and 51 ncRNAs were predicted. The coding genes of the B. porcorum genome were successfully annotated across eight databases (NR, GO, KEGG, COG, TCDB, Pfam, Swiss-Prot and CAZy) and four pathogenicity-related databases (PHI, CARD, VFDB and ARDB). In addition, a comparative genome analysis was performed to explore the evolutionary relationships of B. porcorum QD2021. CONCLUSIONS: To our knowledge, this is the first study to provide fundamental phenotypic and whole-genome sequences for B. porcorum. Our results extensively expand the current knowledge and could serve as a valuable genomic resource for future research on B. porcorum.

Vortex electromagnetic wave imaging with orbital angular momentum and waveform degrees of freedom.

The vortex electromagnetic wave has shown great prospects of radar applications, due to the orbital angular momentum (OAM) degree of freedom. However, the radiation energy convergence of the OAM beam remains a hard problem to be solved for radar target imaging in realistic scenario. In this paper, an OAM beam generation method is developed exploiting the OAM and waveform degrees of freedom simultaneously, which can collimate the beams with different OAM modes. Furthermore, the echo demodulation and the imaging methods are proposed to reconstruct the target profiles in the range and azimuth domain. Simulation and experimental results both validate that the OAM-based radar imaging can achieve azimuthal super-resolution beyond the diffraction limit of the array aperture. This work can advance the system design of vortex electromagnetic wave radar and its real-world applications.

PSCK9 inhibitors reduced early recurrent stroke in patients with symptomatic intracranial atherosclerotic stenosis.

BACKGROUND: Symptomatic intracranial atherosclerotic stenosis (ICAS) is prone to cause early recurrent stroke (ERS). Proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibitors lower low-density lipoprotein cholesterol (LDL-C) levels and prevent cardiovascular events. This multicentre, hospital-based prospective cohort study was designed to investigate whether PCSK9 inhibitors would prevent ERS in patients with symptomatic ICAS. METHODS: From 1 October 2020 to 30 September 2022, consecutive patients with acute ischaemic stroke attributed to ICAS admitted within 1 week after onset were enrolled and followed up for 1 month. Patients were divided into two groups, the PCSK9 inhibitors group receiving PCSK9 inhibitors add-on therapy, and the control group receiving statins and/or ezetimibe. The primary outcome was ERS. Cox proportional hazard models and Kaplan-Meier survival curve were used to estimate the association between PCSK9 inhibitors and ERS. RESULTS: At the end of follow-up, the LDL-C levels were further lowered by PCSK9 inhibitors add-on therapy (n=232, from 3.06±1.16 mmol/L to 2.12±1.19 mmol/L) than statins and/or ezetimibe treatment (n=429, from 2.91±1.05 mmol/L to 2.64±0.86 mmol/L, p<0.001). The Kaplan-Meier survival curves showed that PCSK9 inhibitors add-on therapy significantly reduced ERS (5.59%, 24/429, vs 2.16%, 5/232; log-rank test, p=0.044). The multivariate Cox regression analysis revealed that, after adjusting for confounders with a p value less than 0.05 in univariate analysis or of particular importance, the HR was 0.335 (95% CI 0.114 to 0.986, p=0.047), compared with the control group. CONCLUSIONS: In our study, PCSK9 inhibitors add-on therapy further reduced LDL-C levels and ERS in patients with symptomatic ICAS.

Engineering industrial yeast for improved tolerance and robustness.

As an important cell factory, industrial yeast has been widely used for the production of compounds ranging from bulk chemicals to complex natural products. However, various adverse conditions including toxic products, extreme pH, and hyperosmosis etc., severely restrict microbial growth and metabolic performance, limiting the fermentation efficiency and diminishing its competitiveness. Therefore, enhancing the tolerance and robustness of yeasts is critical to ensure reliable and sustainable production of metabolites in complex industrial production processes. In this review, we provide a comprehensive review of various strategies for improving the tolerance of yeast cells, including random mutagenesis, system metabolic engineering, and material-mediated immobilization cell technology. It is expected that this review will provide a new perspective to realize the response and intelligent regulation of yeast cells to environmental stresses.

Pd-Adsorbed SiN3 Monolayer as a Promising Gas Scavenger for SF6 Partial Discharge Decomposition Components: Insights from the First-Principles Study.

Gas-insulated switchgear (GIS) equipment must be protected by detecting and eliminating the toxic SF6 partial discharge decomposition components. This study employs first-principles calculations to thoroughly investigate the interaction between a Pd-adsorbed SiN3 monolayer (Pd-SiN3) and four typical SF6 decomposition gases (H2S, SO2, SOF2, and SO2F2). The study also investigates the associated geometric, electrical, and optical characteristics along with the sensing sensitivity and desorption efficiency. The ab initio molecular dynamics (AIMD) simulations demonstrated the favorable stability of the Pd-SiN3 monolayer. Furthermore, the Pd-SiN3 monolayer exhibited strong chemisorption behavior toward H2S, SO2, SOF2, and SO2F2 gases because of the higher adsorption energies of -2.717, -2.917, -2.457, and -2.025 eV, respectively. Furthermore, significant changes occur in the electronic and optical characteristics of the Pd-SiN3 monolayer following the adsorption of these gases, resulting in remarkable sensitivity of the Pd-SiN3 monolayer in relation to electrical conductivity and optical absorption. Meanwhile, all of these gas adsorption systems exhibited extremely long recovery times. The aforementioned theoretical findings suggest that the Pd-SiN3 monolayer has the potential to be an effective gas scavenger for the storage or removal of the SF6 decomposition components. Additionally, it might function as a reliable one-time sensor for detecting these gases. The results potentially provide valuable theoretical guidance for maintaining the normal operation of the SF6 insulation devices.

Sulfur-Induced Electronic Optimization of N-Doped Carbon with CoP/Co2P Heterostructure by Precursor Design for Rechargeable Zinc-Air Batteries.

Heteroatom doping and heterostructure construction are the key methods to improve the performance of electrocatalysts. However, developing such catalysts remains a challenging task. Herein, we designed two comparable polymers, phytic acid/thiourea polymer (PATP) and phytic acid/urea polymer (PAUP), as precursors, which contain C, N, S/O, and P by microwave heating. To pinpoint how the introduction of sulfur would affect the electronic structure and catalytic activity, these two polymers were physically blended with CoCo-Prussian blue analogue (CoCo-PBA) and further calcination, respectively. The highly dispersed CoP/Co2P-rich interfacial catalysts anchored on the N,S-codoped or N-doped carbon support were successfully prepared (CoP/Co2P@CNS and CoP/Co2P@CN). The prepared CoP/Co2P@CNS catalyst showed good ORR properties (E1/2 = 0.856 V vs RHE) and OER properties (Ej10 = 1.54 V vs RHE), which were superior to the commercial Pt/C and RuO2 catalysts. The reversible oxygen electrode index (ΔE = Ej10 - E1/2) can reach ∼0.684 V. Meanwhile, the rechargeable zinc-air battery assembled with a CoP/Co2P@CNS catalyst as the air cathode also showed excellent performance, with a charge-discharge cycle stability of up to 900 h. DFT calculations further confirm that the introduction of S atoms can affect the electronic structure and enhance the catalytic activity of C and N atoms on carbon support.

Sex-Specific Left Ventricular and Aorta Size Cut-Off Values for Hemodynamically Significant Chronic Aortic Regurgitation　- Implications for Treatment in Asian Populations.

BACKGROUND: There are no sex-specific guidelines for chronic aortic regurgitation (AR). This retrospective study examined sex-specific differences and propose treatment criteria from an Asian AR cohort.Methods and Results: Consecutive 1,305 patients with moderate-severe AR or greater at 3 tertiary centers in Taiwan and Japan (2008-2022) were identified. Study endpoints were aortic valve surgery (AVS), all-cause death (ACD), and cardiovascular death (CVD). The median follow up was 3.9 years (interquartile range 1.3-7.1 years). Compared with men (n=968), women (n=337) were older, had more advanced symptoms, more comorbidities, larger indexed aorta size (iAortamax) and indexed left ventricular (LV) end-systolic dimension (LVESDi; P<0.001 for all). Symptomatic status was poorly correlated with the degree of LV remodeling in women (P≥0.18). Women received fewer AVS (P≤0.001) and men had better overall 10-year survival (P<0.01). Ten-year post-AVS survival (P=0.9) and the progression of LV remodeling were similar between sexes (P≥0.16). Multivariable determinants of ACD and CVD were age, advanced symptoms, iAortamax, LV ejection fraction (LVEF), LVESDi, LV end-systolic volume index (LVESVi), and Taiwanese ethnicity (all P<0.05), but not female sex (P≥0.05). AVS was associated with better survival (P<0.01). Adjusted LVEF, LVESDi, LVESVi, and iAortamaxcut-off values for ACD were 53%, 24.8 mm/m2, 44 mL/m2, and 25.5 mm/m2, respectively, in women and 52%, 23.4 mm/m2, 52 mL/m2, and 23.2 mm/m2, respectively, in men. CONCLUSIONS: Early detection and intervention using sex-specific cut-off values may improve survival in women with AR.