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Small wetlands are essential for preserving global biodiversity, yet they are frequently neglected in conservation strategies due to vague definitions and a lack of research attention. In this study, we conducted thirty-six surveys via the point count method in the Xiaohongxiang Wetland, Anning City, Yunnan Province, China, from November 2023 to June 2024. We aimed to evaluate the impact of various habitats surrounding Xiaohongxiang Wetland (wetlands, villages, farmlands, cherry plantations and pine forests) on the taxonomic, functional and phylogenetic diversity of avian species and investigate the significance of these habitats for ecological conservation and restoration efforts. A total of 62 species were recorded. Small wetlands are vital for supporting common waterbirds, but may not safeguard rare species effectively. While cherry plantations and pine forests enhance avian diversity near wetlands, their low functional diversity could limit the ecological niches available to birds. This indicates that monoculture plantations might restrict the habitat variety needed for a diverse bird community. Our study found no clear phylogenetic clustering or overdispersion amongst bird species across habitats, suggesting that community assembly is shaped by competitive exclusion, habitat filtering and neutral processes. Despite a limited sample size, our results highlight a gap between taxonomic and functional diversity, indicating that multidimensional biodiversity metrics are essential for thoroughly evaluating wetland restoration and habitat impacts on bird diversity.

Abstract The rise of the convergence of hypervirulence and carbapenem resistance in Klebsiella pneumoniae has been increasingly reported in recent years, however, there are few outbreak cases for these producing NDM carbapenemase. In this study, ST65-KL2 and ST11-KL64 hypervirulent and carbapenem-resistant K. pneumoniae (hvCRKP) were identified from two different outbreak cases: (1) clonal spreading of ST65-KL2 in five patients within transplantation wards spanning three months; and (2) clonal transmission of ST11-KL64 in ten patients across 10 months. The representative strains of ST65-KL2 and ST11-KL64 hvCRKP, K22877 and K56649, produced carbapenemase NDM-5 and dual carbapenemases KPC-2 and NDM-13, respectively, and both exhibited high-level carbapenem resistance. Moreover, virulent analysis showed that K22877 and K56649 were hypervirulent and the former possessed stronger virulence. Evolutionary pathways suggested ST65-KL2 and ST11-KL64 hvCRKP could be classified as CR-hvKP (hvKP acquiring carbapenem resistance) and hv-CRKP (CRKP acquiring hypervirulence), respectively. Unexpectedly, ST65-KL2 CR-hvKP showed resistance to ciprofloxacin mediated by plasmid acquisition as its spread, and ST11-KL64 hv-CRKP developed into enhanced virulence and macrophage resistance. Furthermore, compared to the ST65-KL2 CR-hvKP, the ST11-KL64 hv-CRKP tends to cause occult and persistent infection. Global genome analysis revealed ST11-KL64 hv-CRKP and ST65-KL2 CR-hvKP mainly carried bla KPC-2 and had significant differences in Ompk35/36, ybt, resistance and virulence. Effective surveillance should be implemented and novel therapeutic strategies are urgently needed to deal with refractory infections.

Abstract SARS-CoV-2’s rapid global transmission depends on spike RBD’s strong affinity to hACE2. In the context of binding hot spots well defined, the work investigated how interfacial subregions of SARS-CoV-2 spike RBD to hACE2 affect intermolecular affinity and their potential distinct roles involved in association and dissociation kinetics due to their local structural characteristics. Three spatially consecutive subregions of SARS-CoV-2 RBD were structurally partitioned across RBD’s receptor binding motif (RBM). Their impacts on binding affinity and kinetics were differentiated through a comprehensive SPR measurement of hACE2 binding by chimeric swap mutants of respective subdomains from SARS-CoV-2 VOCs & phylogenetically close sarbecoviruses, and further compared with those of included single mutations across RBM and around the RBD core. The data supports that the intermediate interfacial subregion of RBD involving key residue at 417 is the rate-limiting effector of association kinetics and the subregion encompassing residues at 501/498/449 is the key binding energy contributor dictating dissociation kinetics, both of which relate to SARS-CoV-2’s adaptive mutational evolution and host tropism closely. The kinetic data and structural analysis of local mutations’ impact on spike RBD’s binding and thermal stability provide a new perspective in evaluating SARS-CoV-2 evolution and other sarbecoviruses’ evolvable binding to hACE2. The inherent binding mode offers direct clues of valid epitope in designing new antibodies that the coronavirus can’t elude.

Abstract Aerobic glycolysis is a hallmark of cancer and is regulated by growth factors, protein kinases and transcription factors. However, it remains poorly understood how these components interact to regulate aerobic glycolysis coordinately. Here, we show that sine oculis homeobox 1 (SIX1) phosphorylation integrates growth factors (e.g. TGFβ, EGF) to control aerobic glycolysis and determines its tumor-promoting activity. SIX1 is phosphorylated at serine 225 (S225) by growth factors-activated protein kinases ERK1/2 and its phosphorylation is responsible for glycolysis stimulated by some growth factors. SIX1 is dephosphorylated by the atypical protein phosphatase eyes absent 4 (EYA4). Phosphorylation blocks non-canonical ubiquitination and degradation of SIX1 through the E3 ubiquitin ligase FZR1. Unexpectedly, the non-canonical phosphorylation mimic SIX1 (S225K), but not the canonical phosphorylation mimic SIX1 (S225D/E), phenocopies the effects of SIX1 phosphorylation on glycolysis and cancer cell growth and metastasis in vitro and in mice. Compared to normal liver tissues, SIX1 phosphorylation at S225 (pS225) is upregulated in human liver cancer tissues. ERK1/2 expression is positively correlated with pS225 and EYA4 expression is negatively associated with pS225 in liver cancer specimens. Moreover, low expression of pS225 had longer disease-free survival and overall survival in patients with liver cancer. Thus, we identify a common mechanism underlying growth factors-mediated glycolysis, and provide a previously unidentified mode for non-classical phosphorylation mimics of a protein. Targeting growth factors/SIX1 signaling pathway may be beneficial to cancer treatment.

The switch/sucrose non‐fermenting (SWI/SNF) complex family includes important chromatin‐remodeling factors that are frequently mutated in lung adenocarcinoma (LUAD). However, the role of one family member, SMARCA4, in LUAD prognosis and immunotherapy sensitivity remains unclear. In the present study, 6745 LUAD samples from the cBioPortal database were used to analyze the relationships between SMARCA4 mutations and patient prognoses and clinical characteristics. Additionally, we examined the correlation between SMARCA4 mutations and prognosis in patients treated with immunotherapy using two immune‐related datasets. SMARCA4 mutations and low expression were associated with shorter survival, and mutations were associated with a high tumor mutational burden and high microsatellite instability. SMARCA4 mutations were accompanied by KRAS, KEAP1, TP53 and STK11 mutations. No significant difference was observed in the immunotherapy response between patients with and without SMARCA4 mutations. When KRAS or STK11 mutations were present, immunotherapy effectiveness was poorer; however, when both SMARCA4 and TP53 mutations were present, immunotherapy was more effective. Furthermore, low SMARCA4 expression predicted a higher immunophenoscore, and SMARCA4 expression was correlated with certain immune microenvironment features. Taken together, our results suggest that SMARCA4 mutations and low expression might be associated with poor LUAD prognosis. Additionally, immunotherapy efficacy in patients with SMARCA4 mutations depended on the co‐mutant genes. Thus, SMARCA4 could be an important factor to be considered for LUAD diagnosis and treatment.

Abstract Macrophages are crucial in the heart’s development, function, and injury. As part of the innate immune system, they act as the first line of defense during cardiac injury and repair. After events such as myocardial infarction or myocarditis, numerous macrophages are recruited to the affected areas of the heart to clear dead cells and facilitate tissue repair. This review summarizes the roles of resident and recruited macrophages in developing cardiovascular diseases. We also describe how macrophage phenotypes dynamically change within the cardiovascular disease microenvironment, exhibiting distinct pro-inflammatory and anti-inflammatory functions. Recent studies reveal the values of targeting macrophages in cardiovascular diseases treatment and the novel bioengineering technologies facilitate engineered macrophages as a promising therapeutic strategy. Engineered macrophages have strong natural tropism and infiltration for cardiovascular diseases aiming to reduce inflammatory response, inhibit excessive fibrosis, restore heart function and promote heart regeneration. We also discuss recent studies highlighting therapeutic strategies and new approaches targeting engineered macrophages, which can aid in heart injury recovery.

Abstract Antimicrobial peptides (AMPs) have caught the attention of researchers over the last couple of years due to their unique membrane lytic mechanism for combating antibiotic resistance, which differs from the molecular targets of traditional antibiotics. Although natural AMPs exhibit potential antimicrobial activity against a wide range of microorganisms, some drawbacks, such as toxicity, low antibacterial activity, and high production costs limit their clinical application. To enhance the antimicrobial activity of a series of HSP peptides derived from the natural peptide HSP-1, this study optimized them using a variety of strategies, including net charge, hydrophobic moment, hydrophobicity, and helicity. Optimizing the antimicrobial action of HSP peptides depended mostly on net charge, hydrophobic moment, and hydrophobicity rather than helicity. HSP-M4 may be designed to combat microbial infections because the antimicrobial activity and cytotoxicity assays showed that they exhibited low cytotoxicity and prominent antimicrobial activity, respectively.

Abstract Insulin-like growth factor-binding protein 5 (IGFBP5) has been shown to be useful for the diagnosis and treatment of multiple tumors and cerebrovascular diseases. However, it is unknown whether IGFBP5 is involved in myocardial repair following myocardial infarction (MI). Here we show high expression of IGFBP5 in multiple models of ischemic and hypoxic injury. IGFBP5 affected the proliferation of neonatal rat cardiomyocytes (NRCMs) and the cardiomyocyte apoptosis induced by oxygen-glucose deprivation (OGD). Subsequently, heart-specific IGFBP5 knockdown inhibited myocardial apoptosis and increased cardiomyocyte proliferation in mice with MI. During the chronic remodeling stage, heart-specific regulation of IGFBP5 ameliorated pathological cardiac remodeling and dysfunction. Mechanistically, IGFBP5 regulated cardiomyocyte survival through the insulin-like growth factor 1 (IGF1) receptor (IGF1R)/protein kinase B (PKB/AKT) pathway. In summary, our results provide mechanistic insights into the effect of IGFBP5 on cardiomyocyte during cardiac repair. IGFBP5 may represent a therapeutic target for myocardial ischemic injury.

Despite advances in treatment, prostate cancer remains a leading cause of cancer-related deaths among men, highlighting the urgent need for innovative therapeutic strategies. MicroRNAs (miRNAs) have emerged as key regulatory molecules in cancer biology. In this research, we investigated the tumor-suppressive role of miR-5100 in PCa and its underlying molecular mechanism. By using RT-qPCR, we observed lower miR-5100 expression in PCa cell lines than in benign prostate cells. Functional assays demonstrated that miR-5100 overexpression significantly suppressed PCa cell proliferation, migration, and invasion. By using RNA-sequencing, we identified 446 down-regulated and 806 upregulated candidate miR-5100 target genes overrepresenting cell cycle terms. Mechanistically, E2F7 was confirmed as a direct target of miR-5100 using the reporter gene assay and RIP assay. By conducting flow cytometry analysis, cell cycle progression was blocked at the S phase. E2F7 overexpression partially mitigated the suppressive impact of miR-5100 in PCa cells. In conclusion, miR-5100 is a tumor suppressor in PCa by blocking cell cycle and targeting E2F7.

Abstract Influenza A virus (IAV) has developed multiple tactics to hinder the innate immune response including the epigenetic regulation during IAV infection, but the novel epigenetic factors and their mechanism in innate immunity remain well studied. Here, through a non-biased high-throughput sgRNA screening of 1041 known epigenetic modifiers in a cellular model of IAV-induced interferon-beta (IFN-β) production, we identified nei endonuclease VIII-like 1 (NEIL1) as a critical regulator of IFN-β in response to viral infection. Further studies showed that NEIL1 promoted the replication of the influenza virus by regulating the methylation of cytonuclear IFN-β promoter (mainly CpG-345), inhibiting the expression of IFN-β and IFN-stimulating genes. The structural domains of NEIL1, especially the catalytic domain, were critical for the suppression of IFN-β production, but the enzymatic activity of NEIL1 was dispensable. Furthermore, our results revealed that NEIL1 relied on interactions with the N- and C-terminus of the nucleoprotein (NP) of IAV, and NEIL1 expression facilitated the entry of the NP into the nucleus, which further enhanced the stability of the viral ribonucleoprotein (vRNP) complex and thus contributed to IAV replication and transcription. These findings reveal an enzyme-independent mechanism of host NEIL1 that negatively regulates IFN-β expression, thereby facilitating IAV propagation. Our study provides new insights into the roles of NEIL1, both in directly promoting virus replication and in evading innate immunity in IAV infection.

Abstract Intervertebral disc degeneration (IVDD), a disease associated with ageing, is characterised by a notable increase in senescent nucleus pulposus cells (NPCs) as IVDD progresses. However, the specific mechanisms that regulate the senescence of NPCs remain unknown. In this study, we observed impaired autophagy in IVDD-NPCs, which contributed to the upregulation of NPCs senescence and the senescence-associated secretory phenotype (SASP). The dysregulated SASP disrupted NPCs viability and initiated extracellular matrix degradation. Conversely, the restoration of autophagy reversed the senescence phenotype by inhibiting GATA binding protein 4 (GATA4). Moreover, we made the novel observation that a cross-talk between histone H3 lysine 4 trimethylation (H3K4me3) modification and N6-methyladenosine(m6A)-methylated modification regulates autophagy in IVDD-NPCs. Mechanistically, lysine methyltransferase 2A (KMT2A) promoted the expression of methyltransferase-like 3 (METTL3) through H3K4me3 modification, whereas METTL3-mediated m6A modification reduced the expression of autophagy-associated 4a (ATG4a) by attenuating its RNA stability, leading to autophagy damage in NPCs. Silencing KMT2A and METTL3 enhanced autophagic flux and suppressed SASP expression in IVDD-NPCs. Therefore, targeting the H3K4me3-regulated METTL3/ATG4a/GATA4 axis may represent a promising new therapeutic strategy for IVDD.

Abstract Background Ancient Chang’an in the Tang Dynasty (618–907 AD) was one of the world’s largest and most populated cities and acted as the eastern end of the world-famous Silk Road. However, little is known about the genetics of Chang’an people and whether the Western Regions-related gene flows have been prevalent in this cosmopolitan city. Results Here, we present seven genomes from Xingfulindai (XFLD) sites dating to the Tang Dynasty in Chang’an. We observed that four of seven XFLD individuals (XFLD_1) were genetically homogenous with the Late Neolithic Wadian, Pingliangtai, and Haojiatai populations from the middle reaches of the Yellow River Basin (YR_LN), with no genetic influence from the Western Eurasian or other non-Yellow River-related lineages. The remaining three XFLD individuals were a mixture of YR_LN-related ancestry and ~ 3–15% Western Eurasian-related ancestry. Mixtures of XFLD_1 and Western Eurasian-related ancestry drove the main gradient of genetic variation in northern and central Shaanxi Province today. Conclusions Our study underlined the widespread distribution of the YR_LN-related ancestry alongside the Silk Road within the territory of China during the historical era and provided direct evidence of trans-Eurasian communication in Chang’an from a genetic perspective.

Abstract The intricate tumor microenvironment presents formidable obstacles to the efficacy of adoptive T cell therapy in the management of solid tumors by limiting the infiltration and inducing exhaustion of the transferred T cells. Here, we developed a bacterial-based adjuvant approach that augments the efficacy of adoptive T-cell therapy for solid tumor treatment. Our study reveals that intratumor injection of E. coli MG1655 normalizes tumor vasculatures and reprograms tumor-associated macrophages into M1 phenotype that produce abundant CCL5, together facilitating tumor infiltration of adoptively transferred T cells. The depletion of tumor-associated macrophages or CCL5 neutralization in vivo leads to the significantly decreased solid tumor infiltration of adoptive T cells in the presence of bacteriotherapy. This combinatorial therapy, consisting of E. coli adjuvant and adoptive T-cell therapy, effectively eradicates early-stage melanoma and inhibits the progression of pancreatic tumors. Notably, this dual strategy also strengthened the distal tumor control capabilities of adoptive T-cell therapy through the induction of in situ tumor vaccination. This dual therapeutic approach involving bacterial therapy targeting the interior of solid tumors and adoptive T-cell therapy attacking the tumor periphery exhibits potent therapeutic efficacy in achieving the eradication of advanced-stage tumors, including melanoma and hepatocellular carcinoma, by converging attacks from both inside and outside the tumor tissues.

Abstract Background Identification of drug–target interactions is an indispensable part of drug discovery. While conventional shallow machine learning and recent deep learning methods based on chemogenomic properties of drugs and target proteins have pushed this prediction performance improvement to a new level, these methods are still difficult to adapt to novel structures. Alternatively, large-scale biological and pharmacological data provide new ways to accelerate drug–target interaction prediction. Methods Here, we propose DrugMAN, a deep learning model for predicting drug–target interaction by integrating multiplex heterogeneous functional networks with a mutual attention network (MAN). DrugMAN uses a graph attention network-based integration algorithm to learn network-specific low-dimensional features for drugs and target proteins by integrating four drug networks and seven gene/protein networks collected by a certain screening conditions, respectively. DrugMAN then captures interaction information between drug and target representations by a mutual attention network to improve drug–target prediction. Results DrugMAN achieved the best performance compared with cheminformation-based methods SVM, RF, DeepPurpose and network-based deep learing methods DTINet and NeoDT in four different scenarios, especially in real-world scenarios. Compared with SVM, RF, deepurpose, DTINet, and NeoDT, DrugMAN showed the smallest decrease in AUROC, AUPRC, and F1-Score from warm-start to Both-cold scenarios. This result is attributed to DrugMAN’s learning from heterogeneous data and indicates that DrugMAN has a good generalization ability. Taking together, DrugMAN spotlights heterogeneous information to mine drug–target interactions and can be a powerful tool for drug discovery and drug repurposing.

Spinal cord injury triggers leukocyte mobilization from the peripheral circulation to the injury site, exacerbating spinal cord damage. Simultaneously, bone marrow hematopoietic stem cells (HSCs) and splenic leukocytes rapidly mobilize to replenish the depleted peripheral blood leukocyte pool. However, current treatments for spinal cord injuries overlook interventions targeting peripheral immune organs and tissues, highlighting the need to develop novel drugs capable of effectively regulating peripheral immunity and treating spinal cord injuries. In this study, we designed, synthesized, and characterized novel Ejiao carbon dots (EJCDs) that inhibit myeloid cell proliferation and peripheral migration by promoting HSC self-renewal, and distinct differentiation into erythroid progenitors in vitro and in vivo. Additionally, EJCDs attenuate the immune response in the spleen, leukocytes’ reservoir, following spinal cord injury by diminishing the local infiltration of monocytes and macrophages while promoting motor function recovery. These effects are mediated through the downregulation of CCAAT enhancer binding protein-β expression in the spleen and the upregulation of FZD4 protein expression in Lin− Sca-1+ c-kit+ cells (LSKs) within the bone marrow. Our findings demonstrate that EJCDs effectively reduce myeloid cell infiltration post-spinal cord injury and promote neurological recovery, making them promising therapeutic candidates for treating spinal cord injuries.

Ectopia lentis (EL), characterised by impaired zonular fibers originating from non-pigmented ciliary epithelial cells (NPCEC), presents formidable surgical complexities and potential risks of visual impairment. Cataract surgery is the only treatment method for EL, but it leads to the loss of accommodative power of the lens post-operatively. Furthermore, the challenge of repairing zonular ligaments in situ remains a significant global issue. Ocular tissue and aqueous humour samples from patients with EL were subjected to RNA sequencing and Olink high-throughput proteomic analysis, revealing the downregulation of pathogenic genes (FBN1, MFAP2) and upregulation of secretory proteins (IL-12, MMP-1). The high expression of FBN1 and MFAP2 in NPCECs suggests their potential as candidates for zonular fiber construction; however, the limited availability of donor sources restricts the feasibility of NPCEC transplantation therapy. The reprogramming and directional differentiation of induced pluripotent stem cells (iPSC) to NPCEC was successfully achieved using the developed biomimetic scaffolds that mimic the microstructures of natural radial zonular fibers. Excitingly, the single injection of induced NPCEC-like cells significantly contributed to restoring and enhancing mechanical properties in zonular fiber structures in a rabbit model with EL. This proposed in situ iPSC-based regeneration technique might serve as an innovative therapeutic strategy for clinical EL patients, reduce the cataract surgery rate, and retain the adjustment capacity of inherent lentis.

Interbody fusion devices are critical in spinal surgery to restore spinal stability, reduce pain and improve function. Polyetheretherketone (PEEK) has become a commonly used alternative material for fusion cages owing to its excellent mechanical properties and biocompatibility, but its biological inertness limits bone regeneration and may lead to poor fusion. In this study, a novel strategy for preparing bioactive biomineralized PEEK cages was developed using a unique combination of osteoinductive CaP bioceramic fillings in the cage window, acid sulfonation and simulated body fluid incubation. In vitro experiments showed that biomineralized PEEK cages and CaP bioceramics regulate immunity and promote angiogenesis and bone integration via activation of hypoxia-inducible factor 1-alpha and cyclic guanosine monophosphate/protein kinase G signaling pathways. In vivo goat spinal fusion experiments demonstrated that PEEK cages filled with CaP bioceramics resulted in good bone growth and spinal fusion. Therefore, the high mechanical strength and good biocompatibility of biomineralized PEEK cages, together with the excellent bioactivity and degradation properties of CaP bioceramics, provide an ideal microenvironment for bone fusion. The development of this composite material not only addresses some of the limitations of existing fusion devices but also will facilitate the development of spinal fusion technology.

The primary function of terminators is to terminate transcription in gene expression. Although some studies have suggested that terminators also contribute positively to upstream gene expression, the extent and underlying mechanism of this effect remain largely unexplored. Here, the correlation between terminating strength and upstream mRNA stability was investigated by constructing a terminator mutation library through randomizing 5 nucleotides, assisted by FlowSeq technology, terminator variants were categorized based on the downstream fluorescence intensity, followed by high-throughput sequencing. To examine the impact of terminators on mRNA stability, the abundance of downstream gene transcripts for each terminator variant was quantified through cDNA sequencing. The results revealed that the transcript abundance controlled by strong terminators was, on average 2.2 times greater than those controlled by weak terminators on average. Moreover, several distinct features could be ascribed to high relative abundance of upstream gene transcript, including a high GC content at the base region of hairpin, and a high AT content in downstream of the U-tract. Additionally, these terminators showed a free energy between −28 and −22 kcal/mol, and a stem length of 14 nt. Finally, these features ascribed the upstream beneficial terminator were validated across various expression systems. By incorporating the optimal terminator downstream of RSF, GSH and HIS in three different strains, the fermentation productions-NMN SAM and VD13 exhibited a remarkable enhancement of 30 %–70 %. The findings presented here uncovered the terminator characteristics contributed to the upstream mRNA stability, providing guiding principles for gene circuit design.

Both β-catenin and STAT3 drive colorectal cancer (CRC) growth, progression, and immune evasion, and their co-overexpression is strongly associated with a poor prognosis. However, current small molecule inhibitors have limited efficacy due to the reciprocal feedback activation between STAT3 and β-catenin. Inspired by the PROteolysis TArgeting Chimera (PROTAC), a promising pharmacological modality for the selective degradation of proteins, we developed a strategy of nanoengineered peptide PROTACs (NP-PROTACs) to degrade both β-catenin and STAT3 effectively. The NP-PROTACs were engineered by coupling the peptide PROTACs with DSPE-PEG via disulfide bonds and self-assembled into nanoparticles. Notably, the dual degradation of β-catenin and STAT3 mediated by NP-PROTACs led to a synergistic antitumor effect compared to single-target treatment. Moreover, NP-PROTACs treatment enhanced CD103+ dendritic cell infiltration and T-cell cytotoxicity, alleviating the immunosuppressive microenvironment induced by β-catenin/STAT3 in CRC. These results highlight the potential of NP-PROTACs in facilitating the simultaneous degradation of two pathogenic proteins, thereby providing a novel avenue for cancer therapy.

The development of photothermal agents with high photothermal conversion efficiency (PCE) and long absorption wavelengths is crucial for safe and effective anti-cancer treatment. However, achieving these advantages often requires precise molecular design and complex synthetic procedures. In this study, we present a simple, precise, and effective method for fabricating photothermal agents with high PCE using long wavelength excitation. This approach involves linking two electron-donating components, diphenylamine (DPA), and an electron-withdrawing squaraine (SQ), via a π-bridge thiophene (T). The resulting D-π-A-π-D structure leads to a red-shifted absorption band. Within the DTS structure, DPA functions as a molecular rotor, T serves as a coplanar backbone, and SQ promotes J aggregation. When DTS nanoparticles (NPs) are fabricated using an amphiphilic nano-carrier, the maximum absorption wavelength shifts from 701 to 803 nm. This shift is accompanied by reduced fluorescence and an exceptionally high PCE of 86.0 %. Both in vitro and in vivo assessments confirm that DTS NPs exhibit strong potential for photothermal antitumor therapy. Overall, this strategy offers a valuable framework for designing photothermal agents with clinical applications in mind, offering a simpler and more efficient approach to achieving high PCE and long absorption wavelengths.

The osteoporotic bone defect caused by excessive activity of osteoclasts has posed a challenge for public healthcare. However, most existing bioinert bone cement fails to effectively regulate the pathological bone microenvironment and reconstruct bone homeostasis in the presence of osteoclast overactivity and osteoblast suppression. Herein, inspired by natural bone tissue, an in-situ modulation system for osteoporotic bone regeneration is developed by fabricating an injectable double-crosslinked PEGylated poly(glycerol sebacate) (PEGS)/calcium phosphate cement (CPC) loaded with sodium alendronate (ALN) (PEGS/CPC@ALN) adhesive bone cement. By incorporating ALN, the organic-inorganic interconnection within PEGS/CPC@ALN results in a 100 % increase in compression modulus and energy dissipation efficiency. Additionally, PEGS/CPC@ALN effectively adheres to the bone by bonding with amine and calcium ions present on the bone surface. Moreover, this in-situ regulation system comprehensively mitigates excessive bone resorption through the buffering effect of CPC to improve the acidic microenvironment of osteoporotic bone and the release of ALN to inhibit hyperactive osteoclasts, and facilitates stem cell proliferation and differentiation into osteoblasts through calcium ion release. Overall, the PEGS/CPC@ALN effectively regulates the pathological microenvironment of osteoporosis while promoting bone regeneration through synergistic effects of drugs and materials, thereby improving bone homeostasis and enabling minimally invasive treatment for osteoporotic defects.

The Pholcus yichengicus species group currently contains 47 species. It is mainly distributed in central and southern China, as well as northern Thailand.Pholcus changli Yao, sp. nov. is described as a new species of the P. yichengicus species group collected from northern China (Hebei Province).

Abstract Osteoarthritis (OA) poses a significant challenge in orthopedics. Inflammatory pathways are regarded as central mechanisms in the onset and progression of OA. Growing evidence suggests that senescence acts as a mediator in inflammation-induced OA. Given the lack of effective treatments for OA, there is an urgent need for a clearer understanding of its pathogenesis. In this review, we systematically summarize the cross-talk between cellular senescence and inflammation in OA. We begin by focusing on the mechanisms and hallmarks of cellular senescence, summarizing evidence that supports the relationship between cellular senescence and inflammation. We then discuss the mechanisms of interaction between cellular senescence and inflammation, including senescence-associated secretory phenotypes (SASP) and the effects of pro- and anti-inflammatory interventions on cellular senescence. Additionally, we focus on various types of cellular senescence in OA, including senescence in cartilage, subchondral bone, synovium, infrapatellar fat pad, stem cells, and immune cells, elucidating their mechanisms and impacts on OA. Finally, we highlight the potential of therapies targeting senescent cells in OA as a strategy for promoting cartilage regeneration.

Abstract Osteoporosis (OP) is a common and fracture-prone skeletal disease characterized by deteriorated trabecular microstructure and pathologically involving various forms of regulated bone cell death. However, the exact role, cellular nature and regulatory mechanisms of ferroptosis in OP are not fully understood. Here, we reported that OP femurs from ovariectomized (Ovx) mice exhibited pronounced iron deposition, ferroptosis, and transcriptional suppression of a key anti-ferroptotic factor GPX4 (glutathione peroxidase 4). GPX4 suppression was accompanied by hypermethylation of the Gpx4 promoter and an increase in DNA methyltransferases DNMT1/3a/3b and was transcriptionally promoted by repressive KLF5 and the transcriptional corepressors NCoR and SnoN. Conversely, DNMT inhibition with SGI-1027 reversed promoter hypermethylation, GPX4 suppression and ferroptotic osteoporosis. In cultured primary bone cells, ferric ammonium citrate (FAC) mimicking iron loading similarly induced GPX4 suppression and ferroptosis in osteoblasts but not in osteoclasts, which were rescued by siRNA-mediated individual knockdown of DNMT 1/3a/3b. Intriguingly, SGI-1027 alleviated the ferroptotic changes caused by FAC, but not by a GPX4 inactivator RSL3. More importantly, we generated a strain of osteoblast-specific Gpx4 haplo-deficient mice Gpx4 Ob+/− that developed spontaneous and more severe ferroptotic OP alterations after Ovx operation, and showed that GPX4 inactivation by RSL3 or semi-knockout in osteoblasts largely abolished the anti-ferroptotic and osteoprotective effects of SGI-1027. Taken together, our data suggest that GPX4 epigenetic suppression caused by DNMT aberration and the resulting osteoblastic ferroptosis contribute significantly to OP pathogenesis, and that the strategies preserving GPX4 by DNMT intervention are potentially effective to treat OP and related bone disorders.

Abstract Topologically associating domains (TADs) are essential units of genome architecture, influencing transcriptional regulation and diseases. Despite numerous methods proposed for TAD identification, it remains challenging due to complex background and nested TAD structures. We introduce HTAD, a human-in-the-loop TAD caller that combines machine learning with human supervision to achieve high accuracy. HTAD begins with feature extraction for potential TAD border pairs, followed by an interactive labeling process through active learning. Performance assessments using public curation and synthetic datasets demonstrate HTAD’s superiority over other state-of-the-art methods and reveal highly hierarchical TAD structures, offering a human-in-the-loop solution for detecting complex genomic patterns.

Abstract Background CRISPR/Cas13 system, recognized for its compact size and specificity in targeting RNA, is currently employed for RNA degradation. However, the potential of various CRISPR/Cas13 subtypes, particularly concerning the knockdown of endogenous transcripts, remains to be comprehensively characterized in plants. Results Here we present a full spectrum of editing profiles for seven Cas13 orthologs from five distinct subtypes: VI-A (LwaCas13a), VI-B (PbuCas13b), VI-D (RfxCas13d), VI-X (Cas13x.1 and Cas13x.2), and VI-Y (Cas13y.1 and Cas13y.2). A systematic evaluation of the knockdown effects on two endogenous transcripts (GhCLA and GhPGF in cotton) as well as an RNA virus (TMV in tobacco) reveals that RfxCas13d, Cas13x.1, and Cas13x.2 exhibit enhanced stability with editing efficiencies ranging from 58 to 80%, closely followed by Cas13y.1 and Cas13y.2. Notably, both Cas13x.1 and Cas13y.1 can simultaneously degrade two endogenous transcripts through a tRNA-crRNA cassette approach, achieving editing efficiencies of up to 50%. Furthermore, different Cas13 orthologs enable varying degrees of endogenous transcript knockdown with minimal off-target effects, generating germplasms that exhibit a diverse spectrum of mutant phenotypes. Transgenic tobacco plants show significant reductions in damage, along with mild oxidative stress and minimal accumulation of viral particles after TMV infection. Conclusions In conclusion, our study presents an efficient and reliable platform for transcriptome editing that holds promise for plant functional research and future crop improvement.

Abstract Juvenile hormone (JH) represses insect metamorphosis and stimulates reproduction. JH titers are generally low in juveniles, drop to a nadir during metamorphosis, increase after eclosion and peak in vitellogenic phase. We found that Jhamt, a rate-limiting enzyme in JH biosynthesis, mirrors JH titer patterns in the migratory locust. Knocking down Jhamt reduced JH titers, led to precocious nymphal ecdysis, metamorphosis and impaired vitellogenesis. Jhamt is negatively regulated by miR-276 and positively by miR-182013-5p. miR-276 is abundant in late nymphal but low in adults, while miR-182013-5p shows the opposite pattern. In nymphs, miR-276 binds more to Jhamt, while in adults, miR-182013-5p dominates. Functionally, miR-276 reduced Jhamt and JH levels, shortening nymphal development and inhibiting Vg expression. Conversely, miR-182013-5p increased Jhamt and JH levels, prolonging nymphal development and enhancing Vg expression. Our findings identify miR-276 and miR-182013-5p as dual regulators in JH biosynthesis, acting as “brake” and “accelerator,” respectively. This study provides new insights into JH titer fluctuations and miRNA regulation in insect metamorphosis and reproduction.

Abstract Microscopy is an indispensable tool for collecting biomedical information in pathological diagnosis, but manual annotation, measurement and interpretation are labor-intensive and costly. Here, we propose a task-driven framework powered by large models that excel in visual analysis and real-time control, paving the way for the next generation of microscopes. We achieve proof-of-concept success on clinical tasks, specifically in adaptive analysis of H&E-stained liver tissue slides. This work demonstrates the advanced capabilities for future digital pathology, setting a new standard for intelligent, efficient, and real-time analysis in clinical applications.

Abstract Hematologic malignancies cause significant morbidity/mortality in both children and young adults (CYAs) as well as older adults (OAs). Yet their biological underpinnings remain inadequately understood. Here, we analyzed clinical and genomic disparities between CYAs and OAs in various hematologic malignancies. We found substantial differences in clinical features such as patient sex, ethnicity, metastasis rates, and tumor subtypes. Genomically, most CYA hematologic malignancies indicated lower mutational burden. Subsequently, we identified differentially mutated genes (DMGs) with varying mutation rates between CYAs and OAs, noting fewer mutations in CYAs for most genes such as TP53, TET2, and DNMT3A. In contrast, several DMGs (i.e., NRAS, KRAS, SMARCA4, ID3, PTPN11, WT1, and KIT) were overrepresented in CYAs. We further investigated human protein interacting partners of these identified DMGs that were highly mutated in CYAs/OAs, respectively, and found significant differences in network topological and functional roles. Notably, CYA malignancies demonstrated extensive copy number alterations (CNAs) and more driver gene fusions. In particular, four CNA differential genes (i.e., ARID1B, MYB, TP53, and ESR1) were overrepresented as amplifications and deletions in CYAs and OAs, respectively. Ultimately, we demonstrated a landscape comparative view of clinically actionable genetic events in CYAs and OAs, providing clues for age-related personalized treatment.

Abstract To gain deeper insights into pathogenesis of herpes zoster, the peripheral blood mononuclear cells (PBMCs) from male patients mostly were subjected to single-cell RNA-seq (scRNA-seq) and ATAC-seq analysis. Here we show a detailed immune cell profile in the onset of and recovery from herpes zoster, revealing proportion alterations of the subpopulations, which were validated by flow cytometric analysis and comparison of blood routine data. The integrative analysis of the transcriptomes and epigenomes provided a comprehensive description and validation of the key changes in peripheral blood. This study may provide deep insight into the immune profile during herpes zoster progression and holds potential clinical significance.

Abstract Background Inflammatory bowel disease (IBD), a persistent gastrointestinal disease, is featured with impaired gut immunity. Previous studies have demonstrated that tuft cells can regulate the intestinal type 2 immune response by activating downstream ILC2 and Th2 cells and repair gut barrier upon invasion of parasitic helminths, bacteria, protozoans, and enteritis through different chemo-sensing receptors, such as bitter taste receptors. Berberine is a widely used in the treatment of diarrhea in clinic, however the mechanism underlying this effect is not clear. In this study, we aim to explore the relationship between berberine and tuft cells in dextran sulfate sodium (DSS) -induced colitis. Results Our data showed that berberine significantly ameliorated DSS-induced colitis and regulating type 2 innate immune lymphocytes (ILC2) and Th2 immune cells via tuft cells in the gut. Furthermore, the effect of berberine on colitis was partially abolished by U73122, a bitter taste receptor inhibitor, suggesting that bitter taste signalling pathway played an important role in the effect of berberine on relieving colitis. Conclusions Berberine ameliorates dextran sulfate sodium -induced colitis through tuft cells and bitter taste signalling. Our study reveals the unique pharmacological mechanisms of berberine in the context of colitis, laying the foundation for further clinical applications of this compound.

Abstract Neutrophils, the most abundant type of granulocyte, are widely recognized as one of the pivotal contributors to the acute inflammatory response. Initially, neutrophils were considered the mobile infantry of the innate immune system, tasked with the immediate response to invading pathogens. However, recent studies have demonstrated that neutrophils are versatile cells, capable of regulating various biological processes and impacting both human health and disease. Cytokines and other active mediators regulate the functional activity of neutrophils by activating multiple receptors on these cells, thereby initiating downstream signal transduction pathways. Dysfunctions in neutrophils and disruptions in neutrophil homeostasis have been implicated in the pathogenesis of numerous diseases, including cancer and inflammatory disorders, often due to aberrant intracellular signaling. This review provides a comprehensive synthesis of neutrophil biological functions, integrating recent advancements in this field. Moreover, it examines the biological roles of receptors on neutrophils and downstream signaling pathways involved in the regulation of neutrophil activity. The pathophysiology of neutrophils in numerous human diseases and emerging therapeutic approaches targeting them are also elaborated. This review also addresses the current limitations within the field of neutrophil research, highlighting critical gaps in knowledge that warrant further investigation. In summary, this review seeks to establish a comprehensive and multidimensional model of neutrophil regulation, providing new perspectives for potential clinical applications and further research.

Abstract Retinitis pigmentosa (RP) is characterized by progressive photoreceptor cells death accelerated by the proliferation and activation of microglia pathologically. No consensus exists on the treatment. Minocycline is recognized as a microglia inhibitor with great anti-inflammatory and neuro-protective functions. However, efficacy of minocycline in RP patients is lacking. We conducted a prospective, open-label, and single-arm trial, in which daily oral minocycline of 100 mg was administered for 12 months in RP patients with light-adapted 30 Hz flicker electroretinography (ERG) amplitude >0 µV in at least one eye (NCT04068207). The primary outcome was the proportion of participants with improvement in the ERG amplitude at month 12. The secondary outcomes included improvements of the following items: other ERGs amplitudes, visual field, best-corrected visual acuity, contrast sensitivity, color vision, and NEI-VFQ-25. 35 of 288 patients met inclusive criteria were enrolled (median [IQR] age, 36 [31–45] years; 17 female [48.6%]). 32 participants completed all examinations, while 3 participants completed the 12-month online visit via conducting NEI-VFQ-25. The primary outcome showed improvement was 34.3% (12 of 35 [95% CI 19.1–52.2]). Similarly, all secondary outcomes showed improvements. Adverse events were reported in 22 participants (62.9%) and were all resolved without extra medication during the study period. No severe adverse events were recorded. Our findings identified daily oral minocycline of 100 mg for 12 months was beneficial in improving the visual function of RP patients with good safety. This study indicates minocycline may be a promising therapy for RP, but a randomized controlled trial is still needed of further exploration.

The activity of Hippo signaling is commonly dysregulated in various human malignancies, including hepatocellular carcinoma (HCC). YAP, the key effector of Hippo pathway, is regulated through several posttranslational modifications. However, the mechanism by which YAP is regulated by arginine methylation remains unknown. In this study, immunoprecipitation and mass spectrometry were used to identify the arginine methylation site of YAP in HCC cells. The transcriptional activity of YAP and TEAD were further characterized by real‐time qPCR and immunofluorescence assay, and a subcutaneous and orthotopic tumor mouse model was used to assess the effect of PRMT1‐knockdown on HCC tumor growth. The result of mass spectrometry analysis identified that YAP was methylated at arginine 124. Moreover, we found that arginine methyltransferase PRMT1 interacted with YAP to mediate its arginine methylation, thus inhibited YAP phosphorylation and promoted YAP activity in the nucleus. PRMT1 was up‐regulated in HCC tissues and positively associated with the expressions of YAP target genes. Silencing PRMT1 in HCC cells inhibited cell proliferation and tumor growth, while PRMT1‐overexpression promoted HCC growth through YAP methylation. Our study reveals that PRMT1‐mediated arginine methylation at R124 is mutually exclusive with YAP S127 phosphorylation, thereby facilitating YAP activity in the nucleus and promoting tumorigenesis in HCC.

Radiotherapy is a cornerstone in the treatment of various tumors, yet radioresistance often leads to treatment failure and tumor recurrence. Several factors contribute to this resistance, including hypoxia, DNA repair mechanisms, and cancer stem cells. This review explores the diverse elements that drive tumor radiotherapy resistance. Historically, resistance has been attributed to cellular repair and tumor repopulation, but recent research has expanded this understanding. The tumor microenvironment – characterized by hypoxia, immune evasion, and stromal interactions – further complicates treatment. Additionally, molecular mechanisms such as aberrant signaling pathways, epigenetic modifications, and non-B-DNA structures play significant roles in mediating resistance. This review synthesizes current knowledge, highlighting the interplay of these factors and their clinical implications. Understanding these mechanisms is crucial for developing strategies to overcome resistance and improve therapeutic outcomes in cancer patients.

Abstract Developmental plasticity is critical for plants to adapt to constantly changing environments. Plant root hairs display dramatic plasticity under different environments and therefore play crucial roles in defense against environmental stressors. Here, we report the isolation of an Arabidopsis mutant, salinity over-sensitive mutant 1–1 (som1-1), also exhibiting root hair developmental defects. Map-based cloning and allelic analyses confirmed that som1-1 is a new mutant allele of SPIRRIG (SPI), which encodes a Beige and Chediak Higashi (BEACH) domain-containing protein. SPI has been reported to facilitate actin dependent root hair development by temporally and spatially regulating the expression of BRICK1 (BRK1), a subunit of the SCAR/WAVE actin nucleating promoting complex. Our living cell imaging examinations revealed that salt stress induces an altered actin organization in root hair that mimics those in the spi mutant, implying SPI may respond to salt stress induced root hair plasticity by modulating actin cytoskeleton organization. Furthermore, we found BRK1 is also involved in root hair developmental change under salt stress, and overexpression of BRK1 resulted in root hairs over-sensitive to salt stress as those in spi mutant. Moreover, based on biochemical analyses, we found BRK1 is unstable and SPI mediates BRK1 stability. Functional loss of SPI results in the accumulation of steady-state of BRK1.

Abstract Background RNA methylation, an important reversible post-transcriptional modification in eukaryotes, has emerged as a prevalent epigenetic alteration. However, the role of the m6A reader YTH domain family 2 (YTHDF2) has not been reported in anaplastic thyroid cancer (ATC) and its biological mechanism is unclear. Methods The relationship between YTHDF2 expression and ATC was determined using data sets and tissue samples. A range of analytical techniques were employed to investigate the regulatory mechanism of YTHDF2 in ATC, including bioinformatics analysis, m6A dot-blot analysis, methylated RNA immunoprecipitation sequencing (MeRIP-seq), RNA immunoprecipitation (RIP) assays, RNA sequencing, RNA stability assays and dual luciferase reporter gene assays. In vitro and in vivo assays were also conducted to determine the contribution of YTHDF2 to ATC development. Results YTHDF2 expression was significantly increased in ATC. The comprehensive in vitro and in vivo experiments demonstrated that YTHDF2 knockdown significantly attenuated ATC proliferation, invasion, migration, and apoptosis promotion, whereas YTHDF2 overexpression yielded the opposite trend. Mechanistically, RNA-seq, MeRIP-seq and RIP-seq analysis, and molecular biology experiments demonstrated that YTHDF2 accelerated the degradation of DNA damage-inducible transcript 4 or regulated in DNA damage and development 1 (DDIT4, or REDD1) mRNA in an m6A-dependent manner, which in turn activated the AKT/mTOR signaling pathway and induced activation of epithelial-mesenchymal transition (EMT), thereby promoting ATC tumor progression. Conclusions This study is the first to demonstrate that elevated YTHDF2 expression levels suppress DDIT4 expression in an m6A-dependent manner and activate the AKT/mTOR signaling pathway, thereby promoting ATC progression. YTHDF2 plays a pivotal role in ATC progression, and it may serve as a promising therapeutic target in the future.

Abstract Osteoporosis, a metabolic disorder, remains challenging to treat due to limited understanding of its underlying mechanism. The annual cycle of “cyclic physiological osteoporosis (CPO)” and its full reversal in male deer represents a unique natural model for studying this condition. Deer antlers, weighing up to 25 kg/pair, derive over 60% of their mineral contents from deer skeleton during mineralization. Based on the literature, we propose to divide CPO and its reversal into two phases: Phase I (approximately 115 days): from hard antler casting to the end of antler linear growth, marked by simultaneous robust antler ossification and CPO development; and Phase II (up to 165 days): from end of Phase I to the onset of antler skin shedding, characterized by complete antler mineralization and CPO reversal. This review analyzes the paradoxical occurrence of robust antler ossification and skeleton CPO within the same endocrine microenvironment during phase I; total antler mineralization and full reversal of deer skeleton CPO in phase II. Furthermore, we will discuss potential insights for osteoporosis treatment using deer materials from the period of Phase II. Our goal is to identify novel substances and therapies that could be applied in clinical setting to effectively treat osteoporosis.

Abstract Human stem cells are undifferentiated cells with the capacity for self-renewal and differentiation into distinct cell lineages, playing important role in the development and maintenance of diverse tissues and organs. The microenvironment of stem cell provides crucial factors and components that exert significant influence over the determination of cell fate. Among these factors, cytokines from the transforming growth factor β (TGFβ) superfamily, including TGFβ, bone morphogenic protein (BMP), Activin and Nodal, have been identified as important regulators governing stem cell maintenance and differentiation. In this review, we present a comprehensive overview of the pivotal roles played by TGFβ superfamily signaling in governing human embryonic stem cells, somatic stem cells, induced pluripotent stem cells, and cancer stem cells. Furthermore, we summarize the latest research and advancements of TGFβ family in various cancer stem cells and stem cell-based therapy, discussing their potential clinical applications in cancer therapy and regeneration medicine.

Abstract Prenatal dexamethasone exposure (PDE) has long-term consequences in bone development, though the underlying mechanisms remain unclear. Our results show that PDE offspring exhibit reduced bone mass, fewer osteoblasts and diminished osteoprogenitors proliferation. Further analyses show that PDE increases MKP-1 expression, while decreasing H3 lysine 9 dimethylation (H3K9me2) and H3 lysine 27 trimethylation (H3K27me3) at the Mkp-1 gene locus. Mechanistically, dexamethasone suppresses osteoprogenitors proliferation by upregulating MKP-1 expression, notably through the inhibition of H3K9me2 and H3K27me3 modifications, which promote demethylation and transcriptional activation of the Mkp-1 gene. Importantly, restoring histone methylation balance with PFI-90 or GSK-J4 treatment blocks the inhibitory effects of PDE on MAPK signaling in osteoprogenitors, and mitigates the detrimental impact of PDE on osteoprogenitor proliferation and bone development in the offspring. This study provides new insights into the epigenetic mechanism by which PDE disrupts long-term programming of fetal osteoprogenitor proliferation, ultimately impairing long bone growth in offspring.

Abstract As the main cause of visual function deficits in children and adolescents worldwide, amblyopia causes serious impairment of monocular visual acuity and stereopsis. The recovery of visual functions from amblyopia beyond the critical period is slow and incomplete due to the limited plasticity of the mature cortex; notably, visual stimulation training seems to be an effective therapeutic strategy in clinical practice. However, the precise neural basis and cellular mechanisms that underlie amblyopia and visual stimulation treatment remain to be elucidated. Using monocular deprivation in juvenile mice to model amblyopia, we employed two-photon calcium imaging and chemogenetic techniques to investigate the visual responses of individual excitatory neurons and parvalbumin (PV+) interneurons in the primary visual cortex (V1) of amblyopic mice. We demonstrate that amblyopic mice exhibit an excitation/inhibition (E/I) imbalance. Moreover, visual stimulation decreases the response of PV+ interneurons, reactivates the ocular dominance plasticity of excitatory neurons, and promotes vision recovery in adult amblyopic mice. Our results reveal a dynamic E/I balance between excitatory neurons and PV+ interneurons that may underlie the neural mechanisms of amblyopia during cortical development and visual stimulation-mediated functional recovery from adult amblyopia, providing evidence for therapeutic applications that rely on reactivating adult cortical plasticity.

Abstract Ceramides are lipids that play vital roles in complex lipid synthesis, membrane function, and cell signaling. Disrupted ceramide homeostasis is implicated in cell-death and several neurologic diseases. Ceramides are often analyzed in tissue, but this approach fails to resolve cell-type differences in ceramide homeostasis that are likely essential to understanding cell and non-cell autonomous contributions to neurodegeneration. We show that human iPSC-derived neurons and glia differ in their rate of ceramide synthesis, ceramide isoform composition, and responses to altered ceramide levels. RNA-sequencing of cells treated to increase or decrease ceramides revealed connections to inflammation, ER stress, and apoptosis. Moreover, introducing labeled sphinganine showed that glia readily synthesize ceramide de novo and that neurons are relatively more sensitive to ceramide toxicity. Our findings provide a framework for understanding neurologic diseases with sphingolipid alternations and insights into designing therapeutics that target ceramide for treating them.

Abstract Soils support a highly diverse community of plant pathogens, which are highly responsive to global change. Climate and livestock grazing are the main global changes in grasslands, yet, how long-term grazing alone, and in interaction with climate, influence the distribution of soil-borne plant pathogens remain virtually unknown. Here, we present the first long-term regional-scale experimental investigation on the impacts of livestock grazing on soil-borne fungal plant pathogens and their association with plant community across 10 experimental sites spanning a climate gradient in the steppe in Northern China. Our results showed that long-term grazing effects on the diversity and proportion of soil-borne fungal plant pathogens are strongly controlled by temperature, with grazing increasing pathogen richness and proportions largely in cooler grasslands. We further show that long-term grazing supported stronger connections between soil-borne fungal pathogens and plant communities. Our work demonstrates that climate controls the effects of grazing on plant pathogens, which is critical to understand and manage grasslands in a changing world.

Abstract The emergence of drug-resistant Staphylococcus aureus (S. aureus) has resulted in infections in humans and animals that may lead to a crisis in the absence of highly effective drugs. Consequently, the development of alternative or complementary antimicrobial agents is urgently needed. Here, a series of peptides derived from AP138 were designed with high expression, antimicrobial activity, and antibiofilm properties via bioinformatics. Among them, the best derived peptide, A24 (S9A), demonstrated the greatest stability and bactericidal efficiency against multidrug-resistant S. aureus in a physiological environment, with a high hydrophobicity of 35%. This peptide exhibited superior performance compared to the preclinical or clinical antimicrobial peptides (AMPs). A24 displayed increased biocompatibility in vitro and in vivo, exhibiting a low hemolysis rate (less than 3%), minimal cytotoxicity (survival rate exceeding 85%), and no histotoxicity. A24 had the capacity to destroy cell walls, increase cell membrane permeability, and induce increases in intracellular ATP and ROS levels, which resulted in the rapid death of S. aureus. A24 inhibited the formation of early biofilms and eliminated both mature biofilms (40–50%) and persisters (99.9%). Therapeutic doses of A24 were shown to exhibit favorable safety profiles and bactericidal efficacy in vivo and could reduce bacterial loads of multidrug-resistant S. aureus by 4–5 log10 CFU/0.1g levels in mouse peritonitis and endometritis models. Furthermore, A24 increased the survival rate to 100% and exhibited anti-inflammatory properties in a mouse model. The aforementioned data illustrate the potential of A24 as a pharmaceutical agent for the treatment of bacterial infections, including peritonitis and endometritis, in animal husbandry with multidrug-resistant S. aureus infections.

Abstract Background The increasing incidence of childhood obesity annually has led to a surge in physical and mental health risks, making it a significant global public health concern. This study aimed to discover novel biomarkers of childhood simple obesity through integrative multi-omics analysis, uncovering their potential connections and providing fresh research directions for the complex pathogenesis and treatment strategies. Methods Transcriptome, untargeted metabolome, and 16 S rDNA sequencing were conducted on subjects to examine transcripts, metabolites in blood, and gut microflora in stool. Results Transcriptomic analysis identified 599 differentially expressed genes (DEGs), of which 25 were immune-related genes, and participated in immune pathways such as antimicrobial peptides, neutrophil degranulation, and interferons. The optimal random forest model based on these genes exhibited an AUC of 0.844. The metabolomic analysis examined 71 differentially expressed metabolites (DEMs), including 12 immune-related metabolites. Notably, lauric acid showed an extremely strong positive correlation with BMI and showed a good discriminative power for obesity (AUC = 0.82). DEMs were found to be significantly enriched in four metabolic pathways, namely “Aminoacyl-tRNA biosynthesis”, “Valine leucine and isoleucine biosynthesis, and Glycine”, “Serine and threonine metabolism”, and “Biosynthesis of unsaturated fatty acids”. Microbiome analysis revealed 12 differential gut microbiotas (DGMs) at the phylum and genus levels, with p_Firmicutes dominating in the obese group and g_Escherichia-Shigella in the normal group. Subsequently, a Random Forest model was developed based on the DEMs, immune-related DEGs, and metabolites with an AUC value of 0.912. The 14 indicators identified by this model could potentially serve as a set of biomarkers for obesity. The analysis of the inter-omics correlation network found 233 pairs of significant correlations. DEGs BPIFA1, BPI, and SAA1, DEMs Dimethy(tetradecyl)amine, Deoxycholic acid, Pathalic anhydride, and DL-Alanine, and DGMs g_Intestinimonas and g_Turicibacter showed strong connectivity within the network, constituting a large proportion of interactions. Conclusion This study presents the first comprehensive description of the multi-omics characteristics of childhood simple obesity, recognizing promising biomarkers. Immune-related markers offer a new perspective for researching the immunological mechanisms underlying obesity and its associated complications. The revealed interactions among these biomarkers contribute to a deeper understanding the intricate biological regulatory networks associated with obesity.

Abstract Background Cancer-associated fibroblasts (CAFs), a predominant stromal cell type in the tumor microenvironment, significantly affect the progression of oral squamous cell carcinoma (OSCC). Results The specific mechanisms through which CAFs influence the cancer stem cell phenotype in OSCC are not fully understood. This study explored the effects of lactic acid produced by CAFs on the cancer stem cells (CSCs) phenotype of OSCC cells. Our results demonstrated that CAFs exhibit increased glycolysis and lactic acid production. Lactic acid treatment enhances CSCs-related markers expression, sphere formation, and clonogenic ability of OSCC cells. RNA sequencing revealed that lactic acid treatment elevates Discs Large Homolog 5 (DLG5) expression and markedly affects the Hippo pathway. Further investigation revealed that DLG5 mediates the effects of lactic acid on the CSCs phenotype. DLG5 knockdown results in elevated expression of E3 ubiquitin ligase Cullin 3, which can promote the ubiquitination and degradation of MST1, but the expression of phosphorylated MST1 remains unchanged. This leads to enhanced binding of phosphorylated MST1 to YAP1, increasing YAP1 phosphorylation and activating the Hippo pathway. Conclusion Collectively, our findings suggest that lactic acid from CAFs promotes the CSCs phenotype in OSCC through the DLG5/CUL3/MST1 axis. Therefore, targeting lactic acid exchange between CAFs and tumor cells may provide a novel therapeutic approach to suppress the CSCs phenotype in OSCC.

Abstract Advanced pancreatic ductal adenocarcinoma (PDAC) has a dismal prognosis. Immunotherapy alone offers limited efficacy, but it is still unknown whether its combination with chemotherapy could offer synergistic anti-tumor effects. This phase Ib/II study evaluated the safety and efficacy of combining toripalimab with the gemcitabine plus nab-paclitaxel (GnP) regimen as first-line treatment for locally advanced or metastatic PDAC and explored predictive biomarkers (ChiCTR2000032293). The primary endpoints were safety and overall survival (OS). The secondary outcomes were objective response rate (ORR), disease control rate (DCR), and progression-free survival (PFS). Immune-related biomarkers including programmed death-ligand 1 (PD-L1) expression, genetic status, cytokine levels, and spatial features of the tumor immune microenviroment (TIME) were investigated. Neither serious treatment-related adverse events nor grade 4 immune-related adverse events were reported. Among the 72 patients, the median OS was 8.9 months, 12-month OS rate was 31.9%, with median PFS of 5.6 months, ORR of 33.3%, and DCR of 90.3%. Higher PD-L1 expression, without liver metastases were associated with higher ORR, however these factors could not effectively distinguish responders and non-responders. Importantly, dendritic cells - T helper cells - cytotoxic T lymphocytes (DC-Th-CTL) enriched immune niche and their spatial interactions were dominant predictors of response based on TIME analysis using a cyclic multiplex tissue staining assay, with an area under the curve value of 0.8. Overall, GnP plus toripalimab exhibited good safety and differentiated efficacy in selected population, and the spatial interactions of DC-Th-CTL represent promising predictors to efficacy of immunochemotherapy in locally advanced or metastatic PDAC.

Abstract Background Jointly analyzing multiple phenotype/traits may increase power in genetic association studies by aggregating weak genetic effects. The chance that at least one phenotype is missing increases exponentially as the number of phenotype increases especially for a real dataset. It is a common practice to discard individuals with missing phenotype or phenotype with a large proportion of missing values. Such a discarding method may lead to a loss of power or even an insufficient sample size for analysis. To our knowledge, many existing phenotype imputing methods are built on multivariate normal assumptions for analysis. Violation of these assumptions may lead to inflated type I errors or even loss of power in some cases. To overcome these limitations, we propose a novel phenotype imputation method based on a new Gaussian copula model with three different loss functions to address the issue of missing phenotype. Results In a variety of simulations and a real genetic association study for lung function, we show that our method outperforms existing methods and can also increase the power of the association test when compared to other comparable phenotype imputation methods. The proposed method is implemented in an R package available at https://github.com/jane-zizhen-zhao/CopulaPhenoImpute1.0 Conclusions We propose a novel phenotype imputation method with a new Gaussian copula model based on three loss functions. Results of the simulation studies and real data analyses illustrate that the proposed method outperforms comparable methods.

Peiqiang Wu,* Jianlei Zhang,* Li Guo, Bohong Chen, Lingxiao Xiong, Yuefeng Du Department of Urology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, 710061, People’s Republic of China*These authors contributed equally to this workCorrespondence: Yuefeng Du, Department of Urology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, 710061, People’s Republic of China, Email mnwkdyf85323940@xjtu.edu.cnBackground: Prostate cancer (PCa) development largely depends on increased levels of oxidative stress (OS) and a deficient anti-oxidative system. Identifying genes associated with oxidative stress is critical in order to direct PCa therapy and future research.Methods: The TCGA and GTEx databases provided the bulk RNA-seq data, and the GEO database provided the single-cell data GSE141445. Utilizing reactive oxygen species (ROS) markers, single-cell analysis and cluster identification related to oxidative stress were conducted using the R packages “Seurat” and “AUCell”. The differentially expressed genes (DEGs) in normal and PCa samples were identified with the “limma” R package. LASSO regression analysis was used to build a recurrence score (RS) model. The R packages “maftools” and the CIBERSORT method were employed to explore genetic mutation and the infiltrating immune cell, respectively. LAMP5 was chosen for further investigation after random forest analysis was performed.Results: The RS model for PCa was found to be an independent predictor. The tumor immune microenvironment and the frequency of gene mutations differed significantly between the high- and low-risk score groups. Further investigation revealed that downregulation of LAMP5 in PC-3 and DU145 cell lines suppressed cell proliferation and invasion, as demonstrated by the results of in vitro experiments.Conclusion: We successfully created a robust RS model. The result of the study indicates that LAMP5 could contribute to cell proliferation and invasion in PCa.Keywords: prostate cancer, oxidative stress, single-cell analysis, recurrence score model, LAMP5