CD301b^(+) macrophage: the new booster for activating bone regeneration in periodontitis treatment

Periodontal bone regeneration is a major challenge in the treatment of periodontitis.Currently the main obstacle is the difficulty of restoring the regenerative vitality of periodontal osteoblast lineages suppressed by inflammation,via conventional treatment.CD301b^(+)macrophages were recently identified as a subpopulation that is characteristic of a regenerative environment,but their role in periodontal bone repair has not been reported.

Research progress on immunotherapy targeting the tumor immune microenvironment for cholangiocarcinoma

Cholangiocarcinoma(CCA)is the second most common hepatobiliary cancer,and its incidence has increased significantly in recent years.CCA has poor prognosis owing to the limited diagnosis and treatment options.The tumor immune microenvironment(TIME),which comprises immune cells,cytokines,and chemokines,plays a significant role in cancer progression,the evasion of immune surveillance,and therapeutic responses.Immunotherapeutic strategies targeting the TIME offer the potential for the recognition and eradication of CCA.This review discusses the cellular and molecular components of the TIME in CCA and immunotherapeutic strategies targeting it.

α-Synuclein pathology from the body to the brain:so many seeds so close to the central soil

α-Synuclein is a protein that mainly exists in the presynaptic terminals.Abnormal folding and accumulation of α-synuclein are found in several neurodegenerative diseases,including Parkinson’s disease.Aggregated and highly phospho rylated a-synuclein constitutes the main component of Lewy bodies in the brain,the pathological hallmark of Parkinson s disease.For decades,much attention has been focused on the accumulation of α-synuclein in the brain parenchyma rather than considering Parkinson s disease as a systemic disease.Recent evidence demonstrates that,at least in some patients,the initial α-synuclein pathology originates in the peripheral organs and spreads to the brain.Injection of α-synuclein preformed fibrils into the gastrointestinal tra ct trigge rs the gutto-brain propagation of α-synuclein pathology.However,whether α-synuclein pathology can occur spontaneously in peripheral organs independent of exogenous α-synuclein preformed fibrils or pathological α-synuclein leakage from the central nervous system remains under investigation.In this review,we aimed to summarize the role of peripheral α-synuclein pathology in the pathogenesis of Parkinson’s disease.We also discuss the pathways by which α-synuclein pathology spreads from the body to the brain.

Chromatin conformation of human oral epithelium can identify orofacial cleft missing functional variants

Genome-wide association studies(GWASs) are the most widely used method to identify genetic risk loci associated with orofacial clefts(OFC). However, despite the increasing size of cohort, GWASs are still insufficient to detect all the heritability,suggesting there are more associations under the current stringent statistical threshold. In this study, we obtained an integrated epigenomic dataset based on the chromatin conformation of a human oral epithelial cell line(HIOEC) using RNA-seq, ATAC-seq,H3K27ac Ch IP-seq, and DLO Hi-C. Presumably, this epigenomic dataset could reveal the missing functional variants located in the oral epithelial cell active enhancers/promoters along with their risk target genes, despite relatively less-stringent statistical association with OFC. Taken a non-syndromic cleft palate only(NSCPO) GWAS data of the Chinese Han population as an example, 3664 SNPs that cannot reach the strict significance threshold were subjected to this functional identification pipeline.In total, 254 potential risk SNPs residing in active cis-regulatory elements interacting with 1 718 promoters of oral epitheliumexpressed genes were screened. Gapped k-mer machine learning based on enhancers interacting with epithelium-expressed genes along with in vivo and in vitro reporter assays were employed as functional validation. Among all the potential SNPs, we chose and confirmed that the risk alleles of rs560789 and rs174570 reduced the epithelial-specific enhancer activity by preventing the binding of transcription factors related to epithelial development. In summary, we established chromatin conformation datasets of human oral epithelial cells and provided a framework for testing and understanding how regulatory variants impart risk for clefts.

Circulating nucleic acids as liquid biopsies for disease prediction,screening and diagnosis

Liquid biopsy used molecular information in body liquid to perform early diagnosis,screening,monitoring,prognosis,and treatment of various diseases.Circulating free nucleic acids(cfNA)are important diagnostic biomarkers,providing a window to accurately and immediately observe the body's vital activity status.With the development of gene sequencing technology and bioinformatics technology,genetic,epigenetic,and fragtomics alterations that can be detected in cfDNA,as well as the expression level of miRNA and cf-mRNA can be quantified,this can reflect its tissue origin,gene regulation,genome evolution,and disease pathogenesis.This review focuses on the clinical utility of cfNA in different body liquids(blood,urine,bile),and discusses the diagnostic efficacy and accuracy of cfNA as diagnostic biomarkers in a variety of diseases.Blood is widely used to diagnose various tissue lesions for liquid biopsies as a body fluid circulating throughout the body,reflecting the state of the entire body.Bile and urine,as local circulating body fluids,can better reflect the changing state of tissues around the biliary tract and tissues around the bladder,respectively.In addition,normalized sample preservation,cfNA extraction,and detection procedures will help the practical application of cfNA in the clinic.

Asymmetric Two-Component Alkenyl Catellani Reaction for the Construction of C—N Axial Chirality

Herein,we report an asymmetric two-component alkenyl Catellani reaction for the construction of C—N axial chirality through a palladium/chiral norbornene cooperative catalysis and an axial-to-axial chirality transfer process.Various partially aromatic iodinated 2-pyridones,quinolones,coumarin and uracil substrates react with 2,6-disubstituted aryl bromides with a tethered amide group,to afford a wide variety of polycyclic C—N atropisomers(38 examples,up to 97%e.e.).The obtained C—N axial chirality originates from the preformed transient C—C axial chirality with high fidelity.The synthetic utility of this chemistry is demonstrated by facile prepa-ration of complex quinoline and pyridine based C—N atropisomers through a N-deprotection and aromatization sequence.In addi-tion,a remote axial-to-central diastereoinduction process dictated by C—N axial chirality is observed with excellent diastereocontrol.

Disulfiram ameliorates STING/MITA-dependent inflammation and autoimmunity by targeting RNF115

STING(also known as MITA)is an adaptor protein that mediates cytoplasmic DNA-triggered signaling,and aberrant activation of STING/MITA by cytosolic self-DNA or gain-of-function mutations causes severe inflammation.Here,we show that STING-mediated inflammation and autoimmunity are promoted by RNF115 and alleviated by the RNF115 inhibitor disulfiram(DSF).Knockout of RNF115 or treatment with DSF significantly inhibit systemic inflammation and autoimmune lethality and restore immune cell development in Trex1^(–/–)mice and STING^(N153S/WT) bone marrow chimeric mice.In addition,knockdown or pharmacological inhibition of RNF115 substantially downregulate the expression of IFN-α,IFN-γand proinflammatory cytokines in PBMCs from patients with systemic lupus erythematosus(SLE)who exhibit high concentrations of dsDNA in peripheral blood.Mechanistically,knockout or inhibition of RNF115 impair the oligomerization and Golgi localization of STING in various types of cells transfected with cGAMP and in organs and cells from Trex1^(–/–)mice.Interestingly,knockout of RNF115 inhibits the activation and Golgi localization of STINGN153S as well as the expression of proinflammatory cytokines in myeloid cells but not in endothelial cells or fibroblasts.Taken together,these findings highlight the RNF115-mediated cell type-specific regulation of STING and STINGN153S and provide potential targeted intervention strategies for STING-related autoimmune diseases.

Prioritization of risk genes in colorectal cancer by integrative analysis of multi-omics data and gene networks

Genome-wide association studies(GWASs)have identified over 140 colorectal cancer(CRC)-associated loci;however,target genes at the majority of loci and underlying molecular mechanisms are poorly understood.Here,we utilized a Bayesian approach,integrative risk gene selector(iRIGS),to prioritize risk genes at CRC GWAS loci by integrating multi-omics data.As a result,a total of 105 high-confidence risk genes(HRGs)were identified,which exhibited strong gene dependencies for CRC and enrichment in the biological processes implicated in CRC.Among the 105 HRGs,CEBPB,located at the 20q13.13 locus,acted as a transcription factor playing critical roles in cancer.Our subsequent assays indicated the tumor promoter function of CEBPB that facilitated CRC cell proliferation by regulating multiple oncogenic pathways such as MAPK,PI3K-Akt,and Ras signaling.Next,by integrating a fine-mapping analysis and three independent case-control studies in Chinese populations consisting of 8,039 cases and 12,775 controls,we elucidated that rs1810503,a putative functional variant regulating CEBPB,was associated with CRC risk(OR=0.90,95%CI=0.86–0.93,P=1.07×10^(−7)).The association between rs1810503 and CRC risk was further validated in three additional multi-ancestry populations consisting of 24,254 cases and 58,741 controls.Mechanistically,the rs1810503 A to T allele change weakened the enhancer activity in an allele-specific manner to decrease CEBPB expression via longrange promoter-enhancer interactions,mediated by the transcription factor,REST,and thus decreased CRC risk.In summary,our study provides a genetic resource and a generalizable strategy for CRC etiology investigation,and highlights the biological implications of CEBPB in CRC tumorigenesis,shedding new light on the etiology of CRC.

HUNK inhibits cargo uptake and lysosomal traffic in the caveolar pathway via the AGAP3/ARF6

Endocytosis is a crucial cellular process that takes up cargos by enclosing them in membrane-bound vesicles,and transports cargos to different parts of the cell,such as the lysosomes[1].Endocytosis is classified into several mechanistically and morphologically pathways,including clathrin-mediated endocytosis(CME)and caveolae-mediated endocytosis(CavME)[1,2].

Lysosomal cholesterol accumulation is commonly found in most peroxisomal disorders and reversed by 2-hydroxypropyl-β-cyclodextrin

Peroxisomal disorders(PDs)are a heterogenous group of diseases caused by defects in peroxisome biogenesis or functions.Xlinked adrenoleukodystrophy is the most prevalent form of PDs and results from mutations in the ABCD1 gene,which encodes a transporter mediating the uptake of very long-chain fatty acids(VLCFAs).The curative approaches for PDs are very limited.Here,we investigated whether cholesterol accumulation in the lysosomes is a biochemical feature shared by a broad spectrum of PDs.We individually knocked down fifteen PD-associated genes in cultured cells and found ten induced cholesterol accumulation in the lysosome.2-Hydroxypropyl-β-cyclodextrin(HPCD)effectively alleviated the cholesterol accumulation phenotype in PD-mimicking cells through reducing intracellular cholesterol content as well as promoting cholesterol redistribution to other cellular membranes.In ABCD1 knockdown cells,HPCD treatment lowered reactive oxygen species and VLCFA to normal levels.In Abcd1 knockout mice,HPCD injections reduced cholesterol and VLCFA sequestration in the brain and adrenal cortex.The plasma levels of adrenocortical hormones were increased and the behavioral abnormalities were greatly ameliorated upon HPCD administration.Together,our results suggest that defective cholesterol transport underlies most,if not all,PDs,and that HPCD can serve as a novel and effective strategy for the treatment of PDs.

Quick assembly of 1-alkylidenyl-tetrahydroisoquinolines via a Catellani reaction/NBS-mediated cyclization sequence and synthetic applications

We herein disclose a modular synthesis of 1-bromomethylene-THIQs involving a Catellani reaction of aryl iodides,aziridines,and terminal alkynes followed by an N-bromosuccinimide(NBS)-mediated cyclization.This approach features mild reaction conditions,wide substrate scope,good step-economy and good scalability.Based on this new method,we have accomplished the concise total synthesis of(±)-cularine,formal synthesis of 8-oxopseudopalmatine as well as the first total synthesis of dactyllactone A,demonstrating the wide synthetic potential of this method.

Bisulfite-free mapping of DNA cytosine modifications:challenges and perspectives

The mapping of DNA cytosine modifications is crucial for understanding the dynamic landscape of epigenetic regulation.While bisulfite sequencing has been the gold standard for decades,it suffers from limitations such as DNA degradation and low library quality due to harsh chemical treatment.In recent years,bisulfite-free methods have emerged as promising alternatives for detecting and quantifying DNA cytosine modifications.These methods employ enzymatic and chemical strategies to investigate cytosine modifications without the need for bisulfite treatment.This review provides an overview of the historical context of bisulfite-based methods and presents the current landscape of bisulfite-free methods.The advantages and limitations of each approach are discussed,along with insights into their applications.Furthermore,the review explores the existing challenges in the field and presents future perspectives and potential directions for advancing bisulfite-free mapping methods.The continued progress in bisulfite-free techniques holds great promise for unraveling the intricate nature of DNA cytosine modifications and their functional implications in diverse biological processes and diseases.

Mitochondrial DNA-triggered innate immune response:mechanisms and diseases

Various cellular stress conditions trigger mitochondrial DNA(mtDNA)release from mitochondria into the cytosol.The released mtDNA is sensed by the cGAS-MITA/STING pathway,resulting in the induced expression of type I interferon and other effector genes.These processes contribute to the innate immune response to viral infection and other stress factors.The deregulation of these processes causes autoimmune diseases,inflammatory metabolic disorders and cancer.Therefore,the cGAS-MITA/STING pathway is a potential target for intervention in infectious,inflammatory and autoimmune diseases as well as cancer.In this review,we focus on the mechanisms underlying the mtDNA-triggered activation of the cGAS-MITA/STING pathway,the effects of the pathway under various physiological and pathological conditions,and advances in the development of drugs that target cGAS and MITA/STING.

A self-monitoring microneedle patch for light-controlled synergistic treatment of melanoma

Melanoma is the most aggressive and malignant form of skin cancer.Current melanoma treatment methods generally suffer from frequent drug administration as well as difficulty in direct monitoring of drug release.Here,a self-monitoring microneedle(MN)-based drug delivery system,which integrates a dissolving MN patch with aggregation-induced emission(AIE)-active PATC microparticles,is designed to achieve light-controlled pulsatile chemo-photothermal synergistic therapy of melanoma.The PATC polymeric particles,termed D/I@PATC,encapsulate both of chemotherapeutic drug doxorubicin(DOX)and the photothermal agent indocyanine green(ICG).Upon light illumination,PATC gradually dissociates into smaller particles,causing the release of encapsulated DOX and subsequent fluorescence intensity change of PATC particles,thereby not only enabling direct observation of the drug release process under light stimuli,but also facilitating verification of drug release by fluorescence recovery after light trigger.Moreover,encapsulation of ICG in PATC particles displays significant improvement of its photothermal stability both in vitro and in vivo.In a tumor-bearing mouse,the application of one D/I@PATC MN patch combining with two cycles of light irradiation showed excellent controllable chemo-photothermal efficacy and exhibited~97%melanoma inhibition rate without inducing any evident systemic toxicity,suggesting a great potential for skin cancer treatment in clinics.

Engineered geranyl diphosphate methyltransferase produces 2-methyl-dimethylallyl diphosphate as a noncanonical C_(6) unit for terpenoid biosynthesis

Terpenoids constitute the largest class of natural products with complex structures,essential functions,and versatile applications.Creation of new building blocks beyond the conventional five-carbon(C_(5))units,dimethylallyl diphosphate(DMAPP)and isopentenyl diphosphate,expands significantly the chemical space of terpenoids.Structure-guided engineering of an S-adenosylmethionine-dependent geranyl diphosphate(GPP)C2-methyltransferase from Streptomyces coelicolor yielded variants converting DMAPP to a new C_(6) unit,2-methyl-DMAPP.Mutation of the Gly residue at the position 202 resulted in a smaller substrate-binding pocket to fit DMAPP instead of its native substrate GPP.Replacement of Phe residue at the position 222 with a Tyr residue contributed to DMAPP binding via hydrogen bond.Furthermore,using Escherichia coli as the chassis,we demonstrated that 2-methyl-DMAPP was accepted as a start unit to generate noncanonical trans-and cis-prenyl diphosphates(C_(5n+1))and terpenoids.This work provides insights into substrate recognition of prenyl diphosphate methyltransferases,and strategies to diversify terpenoids by expanding the building block portfolio.

The application of CRISPR-Cas in disease diagnosis and treatment

Clustered regularly interspaced short palindromic repeat(CRISPR)has been gaining much attention in the modern medical field and has been widely used for the diagnosis and treatment of diseases in recent years.In this review,we will introduce the application of CRISPR in disease diagnosis and treatment,including its use in detecting pathogens,gene mutations,and genetic diseases,as well as its application in gene therapy for single-gene diseases,cancer,viral infectious diseases,and cardiovascular diseases.Additionally,we will discuss the potential future directions and challenges of CRISPR in the diagnosis and treatment of diseases,and provide a thorough overview of the ways in which CRISPR is used for diagnosing and treating diseases.

Combined targeting of CCL7 and Flt3L to promote the expansion and infiltration of cDC1s in tumors enhances T-cell activation and anti-PD-1 therapy effectiveness in NSCLC

mmune checkpoint inhibitors(ICIs),represented by anti-PD-1/PD-L1 antibodies,have been widely applied in various cancers,and the efficacy of ICIs is closely associated with the tumor immune microenvironment(TIME)[1,2].We previously demonstrated that the alveolar macrophage-derived chemokine CCL7 recruited conventional type 1 dendritic cells(cDC1s)to remodel the TIME,thereby promoting the expansion of T cells to inhibit non-small cell lung cancer(NSCLC)progression in KrasLSL-G12D/+Tp53fl/fl(KP)and KrasLSL-G12D/+Lkb1fl/fl(KL)mouse models[3].Here,we showed that the fusion protein PD-1Ab7,in which CCL7 was fused with the single-chain variable fragment region(scFv)of an anti-PD-1 antibody(PD-1Ab),exhibited antitumor activity superior to that of PD-1Ab in a manner dependent on cDC1s.In addition,Fms-like tyrosine kinase 3 ligand(Flt3L)synergized with PD-1Ab7 to inhibit NSCLC progression in both the KP and the KL mouse models.Mechanistically,Flt3L promoted the generation and proliferation of cDC1s,whereas PD-1Ab7 increased the infiltration and migration of cDC1s in the TIME to potentiate the activation and proliferation of T cells.These findings not only highlight the essential roles of the PD-1Ab-based chemokine fusion strategy in targeting cDC1s and T cells to potentiate the efficacy of ICIs for cancer prevention but also provide therapeutic lead molecules for antitumor therapy.

SEL1L preserves CD8^(+) T-cell survival and homeostasis by fine-tuning PERK signaling and the IL-15 receptor-mediated mTORC1 axis

SEL1L-mediated endoplasmic reticulum-associated degradation(ERAD)plays critical roles in controlling protein homeostasis by degrading misfolded or terminal unfolded proteins.However,it remains unclear how SEL1L regulates peripheral T-cell survival and homeostasis.Herein,we found that SEL1L deficiency led to a greatly reduced frequency and number of mature T cells,which was further validated by adoptive transfer experiments or bone marrow chimera experiments,accompanied by the induction of multiple forms of cell death.Furthermore,SEL1L deficiency selectively disrupted naïve CD8+T-cell homeostasis,as indicated by the severe loss of the naïve T-cell subset but an increase in the memory T-cell subset.We also found that SEL1L deficiency fueled mTORC1/c-MYC activation and induced a metabolic shift,which was largely attributable to enhanced expression of the IL-15 receptorαandβchains.Mechanistically,single-cell transcriptomic profiling and biochemical analyses further revealed that Sel1l−/−CD8+T cells harbored excessive ER stress,particularly aberrant activation of the PERK-ATF4-CHOP-Bim pathway,which was alleviated by supplementing IL-7 or IL-15.Importantly,PERK inhibition greatly resolved the survival defects of Sel1l−/−CD8+T cells.In addition,IRE1αdeficiency decreased mTORC1 signaling in Sel1l−/−naïve CD8+T cells by downregulating the IL-15 receptorαchain.Altogether,these observations suggest that the ERAD adaptor molecule SEL1L acts as an important checkpoint for preserving the survival and homeostasis of peripheral T cells by regulating the PERK signaling cascade and IL-15 receptor-mediated mTORC1 axis.

A genetic variant in the immune-related gene ERAP1 affects colorectal cancer prognosis

Background:Findings on the association of genetic factors and colorectal cancer(CRC)survival are limited and inconsistent,and revealing the mechanism underlying their prognostic roles is of great importance.This study aimed to explore the relationship between functional genetic variations and the prognosis of CRC and further reveal the possible mechanism.Methods:We first systematically performed expression quantitative trait locus(eQTL)analysis using The Cancer Genome Atlas(TCGA)dataset.Then,the Kaplan-Meier analysis was used to filter out the survival-related eQTL target genes of CRC patients in two public datasets(TCGA and GSE39582 dataset from the Gene Expression Omnibus database).The seven most potentially functional eQTL single nucleotide polymorphisms(SNPs)associated with six survival-related eQTL target genes were genotyped in 907 Chinese CRC patients with clinical prognosis data.The regulatory mechanism of the survival-related SNP was further confirmed by functional experiments.Results:The rs71630754 regulating the expression of endoplasmic reticulum aminopeptidase 1(ERAP1)was significantly associated with the prognosis of CRC(additive model,hazard ratio[HR]:1.43,95%confidence interval[CI]:1.08-1.88,P=0.012).The results of dual-luciferase reporter assay and electrophoretic mobility shift assay showed that the A allele of the rs71630754 could increase the binding of transcription factor 3(TCF3)and subsequently reduce the expression of ERAP1.The results of bioinformatic analysis showed that lower expression of ERAP1 could affect the tumor immune microenvironment and was significantly associated with severe survival outcomes.Conclusion:The rs71630754 could influence the prognosis of CRC patients by regulating the expression of the immune-related gene ERAP1.Trial Registration:No.NCT00454519(https://clinicaltrials.gov/)

Translation landscape of SARS-CoV-2 noncanonical subgenomic RNAs

The ongoing COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)with a positive-stranded RNA genome. Current proteomic studies of SARS-CoV-2 mainly focus on the proteins encoded by its genomic RNA(gRNA) or canonical subgenomic RNAs(sgRNAs). Here, we systematically investigated the translation landscape of SARS-CoV-2, especially its noncanonical sgRNAs. We first constructed a strict pipeline, named vipep, for identifying reliable peptides derived from RNA viruses using RNA-seq and mass spectrometry data. We applied vipep to analyze 24 sets of mass spectrometry data related to SARS-CoV-2infection. In addition to known canonical proteins, we identified many noncanonical sgRNA-derived peptides,which stably increase after viral infection. Furthermore, we explored the potential functions of those proteins encoded by noncanonical sgRNAs and found that they can bind to viral RNAs and may have immunogenic activity. The generalized vipep pipeline is applicable to any RNA viruses and these results have expanded the SARSCoV-2 translation map, providing new insights for understanding the functions of SARS-CoV-2 sgRNAs.