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1.
Cell ; 177(2): 428-445.e18, 2019 04 04.
Article in English | MEDLINE | ID: mdl-30951670

ABSTRACT

The heterogeneity of small extracellular vesicles and presence of non-vesicular extracellular matter have led to debate about contents and functional properties of exosomes. Here, we employ high-resolution density gradient fractionation and direct immunoaffinity capture to precisely characterize the RNA, DNA, and protein constituents of exosomes and other non-vesicle material. Extracellular RNA, RNA-binding proteins, and other cellular proteins are differentially expressed in exosomes and non-vesicle compartments. Argonaute 1-4, glycolytic enzymes, and cytoskeletal proteins were not detected in exosomes. We identify annexin A1 as a specific marker for microvesicles that are shed directly from the plasma membrane. We further show that small extracellular vesicles are not vehicles of active DNA release. Instead, we propose a new model for active secretion of extracellular DNA through an autophagy- and multivesicular-endosome-dependent but exosome-independent mechanism. This study demonstrates the need for a reassessment of exosome composition and offers a framework for a clearer understanding of extracellular vesicle heterogeneity.


Subject(s)
Exosomes/metabolism , Exosomes/physiology , Annexin A1/metabolism , Argonaute Proteins/metabolism , Cell Line, Tumor , Cell Membrane/metabolism , Cell-Derived Microparticles/metabolism , DNA/metabolism , Exosomes/chemistry , Extracellular Vesicles , Female , Humans , Lysosomes/metabolism , Male , Proteins/metabolism , RNA/metabolism
2.
Cell ; 174(3): 576-589.e18, 2018 07 26.
Article in English | MEDLINE | ID: mdl-30033361

ABSTRACT

Genome-wide association studies (GWAS) have identified rs11672691 at 19q13 associated with aggressive prostate cancer (PCa). Here, we independently confirmed the finding in a cohort of 2,738 PCa patients and discovered the biological mechanism underlying this association. We found an association of the aggressive PCa-associated allele G of rs11672691 with elevated transcript levels of two biologically plausible candidate genes, PCAT19 and CEACAM21, implicated in PCa cell growth and tumor progression. Mechanistically, rs11672691 resides in an enhancer element and alters the binding site of HOXA2, a novel oncogenic transcription factor with prognostic potential in PCa. Remarkably, CRISPR/Cas9-mediated single-nucleotide editing showed the direct effect of rs11672691 on PCAT19 and CEACAM21 expression and PCa cellular aggressive phenotype. Clinical data demonstrated synergistic effects of rs11672691 genotype and PCAT19/CEACAM21 gene expression on PCa prognosis. These results provide a plausible mechanism for rs11672691 associated with aggressive PCa and thus lay the ground work for translating this finding to the clinic.


Subject(s)
Prostatic Neoplasms/genetics , RNA, Long Noncoding/genetics , RNA, Untranslated/genetics , Adult , Alleles , Cell Line, Tumor , Chromosomes, Human, Pair 19/genetics , Cohort Studies , Gene Expression Regulation, Neoplastic/genetics , Gene Frequency/genetics , Genetic Predisposition to Disease/genetics , Genome-Wide Association Study , Genotype , Homeodomain Proteins , Humans , Male , Middle Aged , Polymorphism, Single Nucleotide/genetics , Prognosis
3.
Nat Immunol ; 21(12): 1563-1573, 2020 12.
Article in English | MEDLINE | ID: mdl-33106669

ABSTRACT

Chronic cytomegalovirus (CMV) infection leads to long-term maintenance of extraordinarily large CMV-specific T cell populations. The magnitude of this so-called 'memory inflation' is thought to mainly depend on antigenic stimulation during the chronic phase of infection. However, by mapping the long-term development of CD8+ T cell families derived from single naive precursors, we find that fate decisions made during the acute phase of murine CMV infection can alter the level of memory inflation by more than 1,000-fold. Counterintuitively, a T cell family's capacity for memory inflation is not determined by its initial expansion. Instead, those rare T cell families that dominate the chronic phase of infection show an early transcriptomic signature akin to that of established T central memory cells. Accordingly, a T cell family's long-term dominance is best predicted by its early content of T central memory precursors, which later serve as a stem-cell-like source for memory inflation.


Subject(s)
Clonal Evolution/immunology , Host-Pathogen Interactions/immunology , Immunologic Memory , T-Lymphocyte Subsets/immunology , T-Lymphocyte Subsets/metabolism , Virus Diseases/etiology , Virus Diseases/metabolism , Acute Disease , Animals , Biomarkers , Chronic Disease , Cytomegalovirus/immunology , Cytomegalovirus Infections/immunology , Cytomegalovirus Infections/virology , Gene Expression Profiling , Humans , Immunophenotyping , Mice , Muromegalovirus/immunology
4.
Immunity ; 54(10): 2288-2304.e7, 2021 10 12.
Article in English | MEDLINE | ID: mdl-34437840

ABSTRACT

Upon viral infection, natural killer (NK) cells expressing certain germline-encoded receptors are selected, expanded, and maintained in an adaptive-like manner. Currently, these are thought to differentiate along a common pathway. However, by fate mapping of single NK cells upon murine cytomegalovirus (MCMV) infection, we identified two distinct NK cell lineages that contributed to adaptive-like responses. One was equivalent to conventional NK (cNK) cells while the other was transcriptionally similar to type 1 innate lymphoid cells (ILC1s). ILC1-like NK cells showed splenic residency and strong cytokine production but also recognized and killed MCMV-infected cells, guided by activating receptor Ly49H. Moreover, they induced clustering of conventional type 1 dendritic cells and facilitated antigen-specific T cell priming early during MCMV infection, which depended on Ly49H and the NK cell-intrinsic expression of transcription factor Batf3. Thereby, ILC1-like NK cells bridge innate and adaptive viral recognition and unite critical features of cNK cells and ILC1s.


Subject(s)
Adaptive Immunity/immunology , Cell Lineage/immunology , Herpesviridae Infections/immunology , Immunity, Innate/immunology , Killer Cells, Natural/immunology , Animals , Female , Male , Mice , Mice, Inbred BALB C , Mice, Inbred C57BL , Muromegalovirus
5.
Immunity ; 52(6): 1075-1087.e8, 2020 06 16.
Article in English | MEDLINE | ID: mdl-32445619

ABSTRACT

Enhancing immune cell functions in tumors remains a major challenge in cancer immunotherapy. Hypoxia is a common feature of solid tumors, and cells adapt by upregulating the transcription factor HIF-1α. Here, we defined the transcriptional landscape of mouse tumor-infiltrating natural killer (NK) cells by using single-cell RNA sequencing. Conditional deletion of Hif1a in NK cells resulted in reduced tumor growth, elevated expression of activation markers, effector molecules, and an enriched NF-κB pathway in tumor-infiltrating NK cells. Interleukin-18 (IL-18) from myeloid cells was required for NF-κB activation and the enhanced anti-tumor activity of Hif1a-/- NK cells. Extended culture with an HIF-1α inhibitor increased human NK cell responses. Low HIF1A expression was associated with high expression of IFNG in human tumor-infiltrating NK cells, and an enriched NK-IL18-IFNG signature in solid tumors correlated with increased overall patient survival. Thus, inhibition of HIF-1α unleashes NK cell anti-tumor activity and could be exploited for cancer therapy.


Subject(s)
Cytotoxicity, Immunologic , Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , Killer Cells, Natural/immunology , Killer Cells, Natural/metabolism , Lymphocyte Activation/immunology , Lymphocytes, Tumor-Infiltrating/immunology , Lymphocytes, Tumor-Infiltrating/metabolism , Animals , Biomarkers , Computational Biology , Cytokines/metabolism , High-Throughput Nucleotide Sequencing , Humans , Hypoxia-Inducible Factor 1, alpha Subunit/genetics , Lymphocyte Activation/genetics , Mice , Mice, Knockout , Myeloid Cells/immunology , Myeloid Cells/metabolism , Neoplasms/immunology , Neoplasms/metabolism , Neoplasms/mortality , Prognosis , Single-Cell Analysis , Transcriptome , Tumor Microenvironment/immunology
6.
Nat Immunol ; 16(9): 918-26, 2015 Sep.
Article in English | MEDLINE | ID: mdl-26237551

ABSTRACT

Mucosal immunity protects a host from intestinal inflammation and infection and is profoundly influenced by symbiotic bacteria. Here we report that in mice symbiotic bacteria directed selective cargo sorting in Paneth cells to promote symbiosis through Nod2, a cytosolic bacterial sensor, and the multifunctional protein kinase LRRK2, both encoded by inflammatory bowel disease (IBD)-associated genes. Commensals recruited Nod2 onto lysozyme-containing dense core vesicles (DCVs), which was required for DCV localization of LRRK2 and a small GTPase, Rab2a. Deficiency of Nod2, LRRK2 or Rab2a or depletion of commensals resulted in lysosomal degradation of lysozyme. Thus, commensal bacteria and host factors orchestrate the lysozyme-sorting process to protect the host from enteric infection, implicating Paneth cell dysfunction in IBD pathogenesis.


Subject(s)
Enterocolitis/immunology , Immunity, Mucosal/immunology , Inflammatory Bowel Diseases/immunology , Intestines/immunology , Listeriosis/immunology , Paneth Cells/immunology , Protein Serine-Threonine Kinases/immunology , Symbiosis/immunology , Animals , Enterocolitis/genetics , Immunity, Mucosal/genetics , Inflammatory Bowel Diseases/genetics , Intestines/microbiology , Leucine-Rich Repeat Serine-Threonine Protein Kinase-2 , Listeriosis/genetics , Lysosomes , Mice , Mice, Knockout , Muramidase , Nod2 Signaling Adaptor Protein/genetics , Nod2 Signaling Adaptor Protein/immunology , Protein Serine-Threonine Kinases/genetics , Secretory Vesicles/immunology , Symbiosis/genetics , rab GTP-Binding Proteins/genetics , rab GTP-Binding Proteins/immunology
7.
Proc Natl Acad Sci U S A ; 121(20): e2400610121, 2024 May 14.
Article in English | MEDLINE | ID: mdl-38713623

ABSTRACT

Chromatin replication is intricately intertwined with the recycling of parental histones to the newly duplicated DNA strands for faithful genetic and epigenetic inheritance. The transfer of parental histones occurs through two distinct pathways: leading strand deposition, mediated by the DNA polymerase ε subunits Dpb3/Dpb4, and lagging strand deposition, facilitated by the MCM helicase subunit Mcm2. However, the mechanism of the facilitation of Mcm2 transferring parental histones to the lagging strand while moving along the leading strand remains unclear. Here, we show that the deletion of Pol32, a nonessential subunit of major lagging-strand DNA polymerase δ, results in a predominant transfer of parental histone H3-H4 to the leading strand during replication. Biochemical analyses further demonstrate that Pol32 can bind histone H3-H4 both in vivo and in vitro. The interaction of Pol32 with parental histone H3-H4 is disrupted through the mutation of the histone H3-H4 binding domain within Mcm2. Our findings identify the DNA polymerase δ subunit Pol32 as a critical histone chaperone downstream of Mcm2, mediating the transfer of parental histones to the lagging strand during DNA replication.


Subject(s)
DNA Replication , DNA-Directed DNA Polymerase , Saccharomyces cerevisiae Proteins , DNA Polymerase III/metabolism , DNA Polymerase III/genetics , Histones/metabolism , Minichromosome Maintenance Complex Component 2/metabolism , Minichromosome Maintenance Complex Component 2/genetics , Protein Binding , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/genetics , DNA-Directed DNA Polymerase/metabolism
8.
N Engl J Med ; 388(5): 406-417, 2023 02 02.
Article in English | MEDLINE | ID: mdl-36577095

ABSTRACT

BACKGROUND: Nirmatrelvir-ritonavir has been authorized for emergency use by many countries for the treatment of coronavirus disease 2019 (Covid-19). However, the supply falls short of the global demand, which creates a need for more options. VV116 is an oral antiviral agent with potent activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). METHODS: We conducted a phase 3, noninferiority, observer-blinded, randomized trial during the outbreak caused by the B.1.1.529 (omicron) variant of SARS-CoV-2. Symptomatic adults with mild-to-moderate Covid-19 with a high risk of progression were assigned to receive a 5-day course of either VV116 or nirmatrelvir-ritonavir. The primary end point was the time to sustained clinical recovery through day 28. Sustained clinical recovery was defined as the alleviation of all Covid-19-related target symptoms to a total score of 0 or 1 for the sum of each symptom (on a scale from 0 to 3, with higher scores indicating greater severity; total scores on the 11-item scale range from 0 to 33) for 2 consecutive days. A lower boundary of the two-sided 95% confidence interval for the hazard ratio of more than 0.8 was considered to indicate noninferiority (with a hazard ratio of >1 indicating a shorter time to sustained clinical recovery with VV116 than with nirmatrelvir-ritonavir). RESULTS: A total of 822 participants underwent randomization, and 771 received VV116 (384 participants) or nirmatrelvir-ritonavir (387 participants). The noninferiority of VV116 to nirmatrelvir-ritonavir with respect to the time to sustained clinical recovery was established in the primary analysis (hazard ratio, 1.17; 95% confidence interval [CI], 1.01 to 1.35) and was maintained in the final analysis (median, 4 days with VV116 and 5 days with nirmatrelvir-ritonavir; hazard ratio, 1.17; 95% CI, 1.02 to 1.36). In the final analysis, the time to sustained symptom resolution (score of 0 for each of the 11 Covid-19-related target symptoms for 2 consecutive days) and to a first negative SARS-CoV-2 test did not differ substantially between the two groups. No participants in either group had died or had had progression to severe Covid-19 by day 28. The incidence of adverse events was lower in the VV116 group than in the nirmatrelvir-ritonavir group (67.4% vs. 77.3%). CONCLUSIONS: Among adults with mild-to-moderate Covid-19 who were at risk for progression, VV116 was noninferior to nirmatrelvir-ritonavir with respect to the time to sustained clinical recovery, with fewer safety concerns. (Funded by Vigonvita Life Sciences and others; ClinicalTrials.gov number, NCT05341609; Chinese Clinical Trial Registry number, ChiCTR2200057856.).


Subject(s)
Antiviral Agents , COVID-19 Drug Treatment , COVID-19 , Adult , Humans , Antiviral Agents/administration & dosage , Antiviral Agents/adverse effects , Antiviral Agents/therapeutic use , COVID-19/virology , COVID-19 Drug Treatment/methods , Ritonavir/administration & dosage , Ritonavir/adverse effects , Ritonavir/therapeutic use , SARS-CoV-2 , Administration, Oral , Single-Blind Method , Disease Progression
9.
Brief Bioinform ; 25(2)2024 Jan 22.
Article in English | MEDLINE | ID: mdl-38517695

ABSTRACT

Given the universality of autopolyploid species in nature, it is crucial to develop genomic selection methods that consider different allele dosages for autopolyploid breeding. However, no method has been developed to deal with autopolyploid data regardless of the ploidy level. In this study, we developed a modified genomic best linear unbiased prediction (GBLUP) model (polyGBLUP) through constructing additive and dominant genomic relationship matrices based on different allele dosages. polyGBLUP could carry out genomic prediction for autopolyploid species regardless of the ploidy level. Through comprehensive simulations and analysis of real data of autotetraploid blueberry and guinea grass and autohexaploid sweet potato, the results showed that polyGBLUP achieved higher prediction accuracy than GBLUP and its superiority was more obvious when the ploidy level of autopolyploids is high. Furthermore, when the dominant effect was added to polyGBLUP (polyGDBLUP), the greater the dominance degree, the more obvious the advantages of polyGDBLUP over the diploid models in terms of prediction accuracy, bias, mean squared error and mean absolute error. For real data, the superiority of polyGBLUP over GBLUP appeared in blueberry and sweet potato populations and a part of the traits in guinea grass population due to the high correlation coefficients between diploid and polyploidy genomic relationship matrices. In addition, polyGDBLUP did not produce higher prediction accuracy than polyGBLUP for most traits of real data as dominant genetic variance was not captured for these traits. Our study will be a significant promising method for genomic prediction of autopolyploid species.


Subject(s)
Genome , Genomics , Humans , Genomics/methods , Phenotype , Ploidies , Polyploidy , Models, Genetic , Genotype , Polymorphism, Single Nucleotide
10.
Brief Bioinform ; 25(4)2024 May 23.
Article in English | MEDLINE | ID: mdl-38856170

ABSTRACT

In the application of genomic prediction, a situation often faced is that there are multiple populations in which genomic prediction (GP) need to be conducted. A common way to handle the multi-population GP is simply to combine the multiple populations into a single population. However, since these populations may be subject to different environments, there may exist genotype-environment interactions which may affect the accuracy of genomic prediction. In this study, we demonstrated that multi-trait genomic best linear unbiased prediction (MTGBLUP) can be used for multi-population genomic prediction, whereby the performances of a trait in different populations are regarded as different traits, and thus multi-population prediction is regarded as multi-trait prediction by employing the between-population genetic correlation. Using real datasets, we proved that MTGBLUP outperformed the conventional multi-population model that simply combines different populations together. We further proposed that MTGBLUP can be improved by partitioning the global between-population genetic correlation into local genetic correlations (LGC). We suggested two LGC models, LGC-model-1 and LGC-model-2, which partition the genome into regions with and without significant LGC (LGC-model-1) or regions with and without strong LGC (LGC-model-2). In analysis of real datasets, we demonstrated that the LGC models could increase universally the prediction accuracy and the relative improvement over MTGBLUP reached up to 163.86% (25.64% on average).


Subject(s)
Genomics , Models, Genetic , Genomics/methods , Genetics, Population/methods , Quantitative Trait Loci , Humans , Algorithms , Genotype
11.
EMBO Rep ; 25(3): 1589-1622, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38297188

ABSTRACT

Embryonic genome activation (EGA) occurs during preimplantation development and is characterized by the initiation of de novo transcription from the embryonic genome. Despite its importance, the regulation of EGA and the transcription factors involved in this process are poorly understood. Paired-like homeobox (PRDL) family proteins are implicated as potential transcriptional regulators of EGA, yet the PRDL-mediated gene regulatory networks remain uncharacterized. To investigate the function of PRDL proteins, we are identifying the molecular interactions and the functions of a subset family of the Eutherian Totipotent Cell Homeobox (ETCHbox) proteins, seven PRDL family proteins and six other transcription factors (TFs), all suggested to participate in transcriptional regulation during preimplantation. Using mass spectrometry-based interactomics methods, AP-MS and proximity-dependent biotin labeling, and chromatin immunoprecipitation sequencing we derive the comprehensive regulatory networks of these preimplantation TFs. By these interactomics tools we identify more than a thousand high-confidence interactions for the 21 studied bait proteins with more than 300 interacting proteins. We also establish that TPRX2, currently assigned as pseudogene, is a transcriptional activator.


Subject(s)
Homeodomain Proteins , Transcription Factors , Humans , Transcription Factors/metabolism , Homeodomain Proteins/genetics , Genes, Homeobox , Genome
12.
Nature ; 583(7816): 437-440, 2020 07.
Article in English | MEDLINE | ID: mdl-32434211

ABSTRACT

In December 2019, coronavirus disease 2019 (COVID-19), which is caused by the new coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified in Wuhan (Hubei province, China)1; it soon spread across the world. In this ongoing pandemic, public health concerns and the urgent need for effective therapeutic measures require a deep understanding of the epidemiology, transmissibility and pathogenesis of COVID-19. Here we analysed clinical, molecular and immunological data from 326 patients with confirmed SARS-CoV-2 infection in Shanghai. The genomic sequences of SARS-CoV-2, assembled from 112 high-quality samples together with sequences in the Global Initiative on Sharing All Influenza Data (GISAID) dataset, showed a stable evolution and suggested that there were two major lineages with differential exposure history during the early phase of the outbreak in Wuhan. Nevertheless, they exhibited similar virulence and clinical outcomes. Lymphocytopenia, especially reduced CD4+ and CD8+ T cell counts upon hospital admission, was predictive of disease progression. High levels of interleukin (IL)-6 and IL-8 during treatment were observed in patients with severe or critical disease and correlated with decreased lymphocyte count. The determinants of disease severity seemed to stem mostly from host factors such as age and lymphocytopenia (and its associated cytokine storm), whereas viral genetic variation did not significantly affect outcomes.


Subject(s)
Betacoronavirus/genetics , Betacoronavirus/pathogenicity , Coronavirus Infections/immunology , Coronavirus Infections/virology , Host-Pathogen Interactions/immunology , Lymphopenia/virology , Pneumonia, Viral/immunology , Pneumonia, Viral/virology , Respiratory Distress Syndrome/virology , Adolescent , Adult , Aged , Aged, 80 and over , Aging , Animals , Asymptomatic Infections/epidemiology , Betacoronavirus/classification , Betacoronavirus/isolation & purification , COVID-19 , China/epidemiology , Cohort Studies , Coronavirus Infections/complications , Coronavirus Infections/epidemiology , Critical Illness/epidemiology , Disease Progression , Evolution, Molecular , Female , Genetic Variation , Genome, Viral/genetics , Hospitalization/statistics & numerical data , Humans , Inflammation Mediators/immunology , Interleukin-6/blood , Interleukin-6/immunology , Interleukin-8/blood , Interleukin-8/immunology , Lymphocyte Count , Lymphopenia/complications , Male , Middle Aged , Pandemics , Phylogeny , Pneumonia, Viral/complications , Pneumonia, Viral/epidemiology , Respiratory Distress Syndrome/complications , SARS-CoV-2 , T-Lymphocytes/cytology , T-Lymphocytes/immunology , Time Factors , Treatment Outcome , Virulence/genetics , Virus Shedding , Young Adult , Zoonoses/transmission , Zoonoses/virology
13.
Nucleic Acids Res ; 52(13): 7665-7686, 2024 Jul 22.
Article in English | MEDLINE | ID: mdl-38850159

ABSTRACT

Genomic instability is one of the hallmarks of cancer. While loss of histone demethylase KDM6A increases the risk of tumorigenesis, its specific role in maintaining genomic stability remains poorly understood. Here, we propose a mechanism in which KDM6A maintains genomic stability independently on its demethylase activity. This occurs through its interaction with SND1, resulting in the establishment of a protective chromatin state that prevents replication fork collapse by recruiting of RPA and Ku70 to nascent DNA strand. Notably, KDM6A-SND1 interaction is up-regulated by KDM6A SUMOylation, while KDM6AK90A mutation almost abolish the interaction. Loss of KDM6A or SND1 leads to increased enrichment of H3K9ac and H4K8ac but attenuates the enrichment of Ku70 and H3K4me3 at nascent DNA strand. This subsequently results in enhanced cellular sensitivity to genotoxins and genomic instability. Consistent with these findings, knockdown of KDM6A and SND1 in esophageal squamous cell carcinoma (ESCC) cells increases genotoxin sensitivity. Intriguingly, KDM6A H101D & P110S, N1156T and D1216N mutations identified in ESCC patients promote genotoxin resistance via increased SND1 association. Our finding provides novel insights into the pivotal role of KDM6A-SND1 in genomic stability and chemoresistance, implying that targeting KDM6A and/or its interaction with SND1 may be a promising strategy to overcome the chemoresistance.


Subject(s)
Drug Resistance, Neoplasm , Genomic Instability , Histone Demethylases , Humans , Genomic Instability/genetics , Drug Resistance, Neoplasm/genetics , Histone Demethylases/metabolism , Histone Demethylases/genetics , Cell Line, Tumor , Mutation , Histones/metabolism , Esophageal Neoplasms/genetics , Esophageal Neoplasms/metabolism , Nuclear Proteins/metabolism , Nuclear Proteins/genetics , Sumoylation , Endonucleases/metabolism , Endonucleases/genetics , DNA Replication , Chromatin/metabolism , Chromatin/genetics , Ku Autoantigen/metabolism , Ku Autoantigen/genetics
14.
Hepatology ; 2024 Jul 08.
Article in English | MEDLINE | ID: mdl-38976867

ABSTRACT

BACKGROUND AIMS: Studies have shown that blocking the PD-1/PD-L1 pathway may lead to a potential cure for HBV infections. ASC22 (Envafolimab) is a humanized, single-domain PD-L1 antibody administered subcutaneously. This study aimed to evaluate the efficacy and safety of ASC22 in virally suppressed chronic hepatitis B (CHB) patients on nucleos(t)ide analogs (NAs). APPROACH AND RESULTS: This randomized, single-blind, phase IIb trial enrolled CHB patients in two cohorts for a 24-week treatment with ASC22 or placebo (PBO) once every 2 weeks and 24-week follow-up. In total, 60, 59, and 30 patients were treated with 1.0, 2.5 mg/kg ASC22 and PBO, respectively. The mean HBsAg changes from baseline at week 24 and 24 week follow-up periods were -0.309 (p<0.001) and -0.272 (p<0.023) log10 IU/mL in the 1.0 mg/kg ASC22 group, -0.231 (p=0.007) and -0.205 (p=0.12) log10 IU/mL in the 2.5 mg/kg ASC22 group, and-0.003 and -0.063 log10 IU/mL in the PBO group, respectively (ITT population). Three out of ten patients with baseline HBsAg levels ≤100 IU/mL in the 1.0 mg/kg group obtained on-treatment HBsAg loss. Most AEs were mild (97.9%). There were no study drug-related serious AEs in the 1.0 mg/kg ASC22 group. CONCLUSIONS: Subcutaneous administration of 1.0 mg/kg ASC22 Q2W for 24 weeks was shown to be safe and well tolerated in virally suppressed CHB patients on NAs and can induce HBsAg decline, especially in patients with HBsAg ≤100 IU/mL.

15.
Nucleic Acids Res ; 51(13): 6770-6783, 2023 07 21.
Article in English | MEDLINE | ID: mdl-37309889

ABSTRACT

Ataxia-telangiectasia mutated (ATM) drives the DNA damage response via modulation of multiple signal transduction and DNA repair pathways. Previously, ATM activity was implicated in promoting the non-homologous end joining (NHEJ) pathway to repair a subset of DNA double-stranded breaks (DSBs), but how ATM performs this function is still unclear. In this study, we identified that ATM phosphorylates the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a core NHEJ factor, at its extreme C-terminus at threonine 4102 (T4102) in response to DSBs. Ablating phosphorylation at T4102 attenuates DNA-PKcs kinase activity and this destabilizes the interaction between DNA-PKcs and the Ku-DNA complex, resulting in decreased assembly and stabilization of the NHEJ machinery at DSBs. Phosphorylation at T4102 promotes NHEJ, radioresistance, and increases genomic stability following DSB induction. Collectively, these findings establish a key role for ATM in NHEJ-dependent repair of DSBs through positive regulation of DNA-PKcs.


Subject(s)
Ataxia Telangiectasia , DNA-Activated Protein Kinase , Humans , DNA-Activated Protein Kinase/genetics , DNA Repair , Threonine/genetics , Ataxia Telangiectasia Mutated Proteins/metabolism , DNA End-Joining Repair , DNA/genetics
16.
Semin Cancer Biol ; 91: 1-15, 2023 06.
Article in English | MEDLINE | ID: mdl-36801447

ABSTRACT

Personalized treatment strategies for cancer frequently rely on the detection of genetic alterations which are determined by molecular biology assays. Historically, these processes typically required single-gene sequencing, next-generation sequencing, or visual inspection of histopathology slides by experienced pathologists in a clinical context. In the past decade, advances in artificial intelligence (AI) technologies have demonstrated remarkable potential in assisting physicians with accurate diagnosis of oncology image-recognition tasks. Meanwhile, AI techniques make it possible to integrate multimodal data such as radiology, histology, and genomics, providing critical guidance for the stratification of patients in the context of precision therapy. Given that the mutation detection is unaffordable and time-consuming for a considerable number of patients, predicting gene mutations based on routine clinical radiological scans or whole-slide images of tissue with AI-based methods has become a hot issue in actual clinical practice. In this review, we synthesized the general framework of multimodal integration (MMI) for molecular intelligent diagnostics beyond standard techniques. Then we summarized the emerging applications of AI in the prediction of mutational and molecular profiles of common cancers (lung, brain, breast, and other tumor types) pertaining to radiology and histology imaging. Furthermore, we concluded that there truly exist multiple challenges of AI techniques in the way of its real-world application in the medical field, including data curation, feature fusion, model interpretability, and practice regulations. Despite these challenges, we still prospect the clinical implementation of AI as a highly potential decision-support tool to aid oncologists in future cancer treatment management.


Subject(s)
Artificial Intelligence , Neoplasms , Humans , Neoplasms/diagnosis , Neoplasms/genetics , Neoplasms/therapy , Precision Medicine/methods , Medical Oncology/methods , Diagnostic Imaging/methods
17.
Carcinogenesis ; 45(5): 351-357, 2024 May 19.
Article in English | MEDLINE | ID: mdl-38310539

ABSTRACT

Immune checkpoint inhibitors (ICIs) have become prominent therapies for gastrointestinal cancer (GC). However, it is urgent to screen patients who can benefit from ICIs. Protein patched homolog 1 (PTCH1) is a frequently altered gene in GC. We attempt to explore the association between PTCH1 mutation and immunotherapy efficacy. The Memorial Sloan Kettering Cancer Center (MSKCC) cohort (n = 236) with GC (esophageal, gastric and colorectal cancers) patients receiving ICIs was used for discovery and the Peking University Cancer Hospital (PUCH) GC cohort (n = 92) was used for validation. Overall survival (OS) and tumor mutational burden (TMB) of the PTCH1 mutant-type (PTCH1-MUT) and PTCH1 wild-type (PTCH1-WT) groups were compared. Furthermore, GC data were collected from The Cancer Genome Atlas to assess the potential mechanisms. In the MSKCC cohort, PTCH1-MUT group showed significantly better OS (P = 0.017) and higher TMB. Multivariate analysis showed that PTCH1 mutation was associated with better OS. In the PUCH cohort, PTCH1-MUT group showed significantly longer OS (P = 0.036) and progression-free survival, and higher durable clinical benefit and TMB. Immune cell infiltration analysis revealed that PTCH1-MUT group had significantly higher distributions of CD8 T cells, CD4 T cells, NK cells, mast cells and M1 cells. The PTCH1-MUT group showed significantly higher expression of most immune-related genes. Gene set enrichment analysis showed that the PTCH1-MUT group had enriched INF-γ response, INF-α response, glycolysis and reactive oxygen species pathway gene sets. PTCH1 mutation may represent a potential biomarker for predicting ICIs response in GC. Nevertheless, prospective cohort studies should be performed to further validate our results.


Subject(s)
Biomarkers, Tumor , Gastrointestinal Neoplasms , Immune Checkpoint Inhibitors , Mutation , Patched-1 Receptor , Humans , Patched-1 Receptor/genetics , Immune Checkpoint Inhibitors/therapeutic use , Biomarkers, Tumor/genetics , Female , Gastrointestinal Neoplasms/genetics , Gastrointestinal Neoplasms/drug therapy , Gastrointestinal Neoplasms/pathology , Male , Middle Aged , Aged , Prognosis , Adult
18.
Hum Genet ; 2024 Jun 08.
Article in English | MEDLINE | ID: mdl-38850429

ABSTRACT

Hypospadias refers to the abnormal position of the male urethral orifice, which not only leads to urination disorder but also causes sexual dysfunction in adulthood. However, the complex and diverse pathogenic factors of hypospadias are still unclear. To study the pathogenesis and prognosis of hypospadias, we counted the serological indexes of children with hypospadias, and found that sSBP, TC and LDL increased in children with mild, moderate and severe hypospadias. Subsequently, we used quantitative proteomics to find differential proteins in mild, moderate and severe hypospadias. After bioinformatics analysis and biochemical experiments on the screened DEPs, we found that the expression of proteins related to immune inflammation, coagulation, blood pressure and inflammation, and blood lipid were differential expressed in the prepuce tissue of children with hypospadias. We further confirmed that the proteins FGB, FGG, SERPINA1, and AGT involved in the angiotensin system, cholesterol metabolism, and coagulation were significantly up-regulated by biochemical experiments. In particular, the AGT protein of the angiotensin system involved in blood pressure regulation, we have shown that it increases with the severity of hypospadias. This study suggests that children with hypospadias are more likely to suffer from hyperlipidemia and cardiovascular disease (CVD). Our findings provide a theoretical basis for early monitoring of blood lipids and blood pressure to prevent CVD in children with hypospadias.

19.
Small ; : e2401429, 2024 May 29.
Article in English | MEDLINE | ID: mdl-38808805

ABSTRACT

Plastics serve as an essential foundation in contemporary society. Nevertheless, meeting the rigorous performance demands in advanced applications and addressing their end-of-life disposal are two critical challenges that persist. Here, an innovative and facile method is introduced for the design and scalable production of polycarbonate, a key engineering plastic, simultaneously achieving high performance and closed-loop chemical recyclability. The bisphenol framework of polycarbonate is strategically adjusted from the low-bond-dissociation-energy bisphenol A to high-bond-dissociation-energy 4,4'-dihydroxydiphenyl, in combination with the incorporation of polysiloxane segments. As expected, the enhanced bond dissociation energy endows the polycarbonate with an extremely high glow-wire flammability index surpassing 1025 °C, a 0.8 mm UL-94 V-0 rating, a high LOI value of 39.2%, and more than 50% reduction of heat and smoke release. Furthermore, the π-π stacking interactions within biphenyl structures resulted in a significant enhancement of mechanical strength by as more as 37.7%, and also played a positive role in achieving a lower dielectric constant. Significantly, the copolymer exhibited outstanding closed-loop chemical recyclability, allowing for facile depolymerization into bisphenol monomers and the repolymerized copolymer retains its high heat and fire resistance. This work provides a novel insight in the design of high-performance and closed-loop chemical recyclable polymeric materials.

20.
Small ; 20(24): e2306389, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38168513

ABSTRACT

In view of the increased levels of reactive oxygen species (ROS) that disturb the osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs), the repair of diabetic bone defects remains a great challenge. Herein, a factor-free hydrogel is reported with ROS scavenging and responsive degradation properties for enhanced diabetic bone healing. These hydrogels contain ROS-cleavable thioketal (TK) linkers and ultraviolet (UV)-responsive norbornene (NB) groups conjugated with 8-arm PEG macromers, which are formed via UV crosslinking-mediated gelation. Upon reacting with high levels of ROS in the bone defect microenvironment, ROS-cleavable TK linkers are destroyed, allowing the responsive degradation of hydrogels, which promotes the migration of BMSCs. Moreover, ROS levels are reduced through hydrogel-mediated ROS scavenging to reverse BMSC differentiation from adipogenic to osteogenic phenotype. As such, a favorable microenvironment is created after simultaneous ROS scavenging and hydrogel degradation, leading to the effective repair of bone defects in diabetic mouse models, even without the addition of growth factors. Thus, this study presents a responsive hydrogel platform that regulates ROS scavenging and stromal degradation in bone engineering.


Subject(s)
Cell Differentiation , Hydrogels , Mesenchymal Stem Cells , Osteogenesis , Reactive Oxygen Species , Animals , Reactive Oxygen Species/metabolism , Hydrogels/chemistry , Mesenchymal Stem Cells/metabolism , Mesenchymal Stem Cells/drug effects , Osteogenesis/drug effects , Mice , Cell Differentiation/drug effects , Diabetes Mellitus, Experimental , Free Radical Scavengers/pharmacology , Free Radical Scavengers/chemistry , Wound Healing/drug effects , Bone and Bones , Male
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