Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 948
Filter
Add more filters

Publication year range
1.
Nature ; 609(7929): 1012-1020, 2022 09.
Article in English | MEDLINE | ID: mdl-36131015

ABSTRACT

Medulloblastoma, a malignant childhood cerebellar tumour, segregates molecularly into biologically distinct subgroups, suggesting that a personalized approach to therapy would be beneficial1. Mouse modelling and cross-species genomics have provided increasing evidence of discrete, subgroup-specific developmental origins2. However, the anatomical and cellular complexity of developing human tissues3-particularly within the rhombic lip germinal zone, which produces all glutamatergic neuronal lineages before internalization into the cerebellar nodulus-makes it difficult to validate previous inferences that were derived from studies in mice. Here we use multi-omics to resolve the origins of medulloblastoma subgroups in the developing human cerebellum. Molecular signatures encoded within a human rhombic-lip-derived lineage trajectory aligned with photoreceptor and unipolar brush cell expression profiles that are maintained in group 3 and group 4 medulloblastoma, suggesting a convergent basis. A systematic diagnostic-imaging review of a prospective institutional cohort localized the putative anatomical origins of group 3 and group 4 tumours to the nodulus. Our results connect the molecular and phenotypic features of clinically challenging medulloblastoma subgroups to their unified beginnings in the rhombic lip in the early stages of human development.


Subject(s)
Cell Lineage , Cerebellar Neoplasms , Medulloblastoma , Metencephalon , Animals , Cerebellar Neoplasms/classification , Cerebellar Neoplasms/embryology , Cerebellar Neoplasms/pathology , Cerebellum/embryology , Humans , Medulloblastoma/classification , Medulloblastoma/embryology , Medulloblastoma/pathology , Metencephalon/embryology , Mice , Neurons/pathology , Prospective Studies
2.
Proc Natl Acad Sci U S A ; 121(11): e2312136121, 2024 Mar 12.
Article in English | MEDLINE | ID: mdl-38446848

ABSTRACT

Anxiety is a remarkably common condition among patients with pharyngitis, but the relationship between these disorders has received little research attention, and the underlying neural mechanisms remain unknown. Here, we show that the densely innervated pharynx transmits signals induced by pharyngeal inflammation to glossopharyngeal and vagal sensory neurons of the nodose/jugular/petrosal (NJP) superganglia in mice. Specifically, the NJP superganglia project to norepinephrinergic neurons in the nucleus of the solitary tract (NTSNE). These NTSNE neurons project to the ventral bed nucleus of the stria terminalis (vBNST) that induces anxiety-like behaviors in a murine model of pharyngeal inflammation. Inhibiting this pharynx→NJP→NTSNE→vBNST circuit can alleviate anxiety-like behaviors associated with pharyngeal inflammation. This study thus defines a pharynx-to-brain axis that mechanistically links pharyngeal inflammation and emotional response.


Subject(s)
Pharyngitis , Pharynx , Humans , Animals , Mice , Anxiety , Brain , Sensory Receptor Cells , Inflammation
3.
Am J Hum Genet ; 110(11): 1853-1862, 2023 11 02.
Article in English | MEDLINE | ID: mdl-37875120

ABSTRACT

The heritability explained by local ancestry markers in an admixed population (hγ2) provides crucial insight into the genetic architecture of a complex disease or trait. Estimation of hγ2 can be susceptible to biases due to population structure in ancestral populations. Here, we present heritability estimation from admixture mapping summary statistics (HAMSTA), an approach that uses summary statistics from admixture mapping to infer heritability explained by local ancestry while adjusting for biases due to ancestral stratification. Through extensive simulations, we demonstrate that HAMSTA hγ2 estimates are approximately unbiased and are robust to ancestral stratification compared to existing approaches. In the presence of ancestral stratification, we show a HAMSTA-derived sampling scheme provides a calibrated family-wise error rate (FWER) of ∼5% for admixture mapping, unlike existing FWER estimation approaches. We apply HAMSTA to 20 quantitative phenotypes of up to 15,988 self-reported African American individuals in the Population Architecture using Genomics and Epidemiology (PAGE) study. We observe hˆγ2 in the 20 phenotypes range from 0.0025 to 0.033 (mean hˆγ2 = 0.012 ± 9.2 × 10-4), which translates to hˆ2 ranging from 0.062 to 0.85 (mean hˆ2 = 0.30 ± 0.023). Across these phenotypes we find little evidence of inflation due to ancestral population stratification in current admixture mapping studies (mean inflation factor of 0.99 ± 0.001). Overall, HAMSTA provides a fast and powerful approach to estimate genome-wide heritability and evaluate biases in test statistics of admixture mapping studies.


Subject(s)
Black or African American , Genetics, Population , Humans , Chromosome Mapping , Phenotype , Polymorphism, Single Nucleotide/genetics
4.
Am J Hum Genet ; 110(11): 1950-1958, 2023 11 02.
Article in English | MEDLINE | ID: mdl-37883979

ABSTRACT

As large-scale genomic screening becomes increasingly prevalent, understanding the influence of actionable results on healthcare utilization is key to estimating the potential long-term clinical impact. The eMERGE network sequenced individuals for actionable genes in multiple genetic conditions and returned results to individuals, providers, and the electronic health record. Differences in recommended health services (laboratory, imaging, and procedural testing) delivered within 12 months of return were compared among individuals with pathogenic or likely pathogenic (P/LP) findings to matched individuals with negative findings before and after return of results. Of 16,218 adults, 477 unselected individuals were found to have a monogenic risk for arrhythmia (n = 95), breast cancer (n = 96), cardiomyopathy (n = 95), colorectal cancer (n = 105), or familial hypercholesterolemia (n = 86). Individuals with P/LP results more frequently received services after return (43.8%) compared to before return (25.6%) of results and compared to individuals with negative findings (24.9%; p < 0.0001). The annual cost of qualifying healthcare services increased from an average of $162 before return to $343 after return of results among the P/LP group (p < 0.0001); differences in the negative group were non-significant. The mean difference-in-differences was $149 (p < 0.0001), which describes the increased cost within the P/LP group corrected for cost changes in the negative group. When stratified by individual conditions, significant cost differences were observed for arrhythmia, breast cancer, and cardiomyopathy. In conclusion, less than half of individuals received billed health services after monogenic return, which modestly increased healthcare costs for payors in the year following return.


Subject(s)
Breast Neoplasms , Cardiomyopathies , Adult , Humans , Female , Prospective Studies , Patient Acceptance of Health Care , Arrhythmias, Cardiac , Breast Neoplasms/genetics , Cardiomyopathies/genetics
5.
Am J Hum Genet ; 109(4): 669-679, 2022 04 07.
Article in English | MEDLINE | ID: mdl-35263625

ABSTRACT

One mechanism by which genetic factors influence complex traits and diseases is altering gene expression. Direct measurement of gene expression in relevant tissues is rarely tenable; however, genetically regulated gene expression (GReX) can be estimated using prediction models derived from large multi-omic datasets. These approaches have led to the discovery of many gene-trait associations, but whether models derived from predominantly European ancestry (EA) reference panels can map novel associations in ancestrally diverse populations remains unclear. We applied PrediXcan to impute GReX in 51,520 ancestrally diverse Population Architecture using Genomics and Epidemiology (PAGE) participants (35% African American, 45% Hispanic/Latino, 10% Asian, and 7% Hawaiian) across 25 key cardiometabolic traits and relevant tissues to identify 102 novel associations. We then compared associations in PAGE to those in a random subset of 50,000 White British participants from UK Biobank (UKBB50k) for height and body mass index (BMI). We identified 517 associations across 47 tissues in PAGE but not UKBB50k, demonstrating the importance of diverse samples in identifying trait-associated GReX. We observed that variants used in PrediXcan models were either more or less differentiated across continental-level populations than matched-control variants depending on the specific population reflecting sampling bias. Additionally, variants from identified genes specific to either PAGE or UKBB50k analyses were more ancestrally differentiated than those in genes detected in both analyses, underlining the value of population-specific discoveries. This suggests that while EA-derived transcriptome imputation models can identify new associations in non-EA populations, models derived from closely matched reference panels may yield further insights. Our findings call for more diversity in reference datasets of tissue-specific gene expression.


Subject(s)
Cardiovascular Diseases , Genome-Wide Association Study , Genetic Predisposition to Disease , Humans , Life Style , Polymorphism, Single Nucleotide , Transcriptome
6.
Am J Hum Genet ; 109(12): 2185-2195, 2022 12 01.
Article in English | MEDLINE | ID: mdl-36356581

ABSTRACT

By combining data from 160,500 individuals with breast cancer and 226,196 controls of Asian and European ancestry, we conducted genome- and transcriptome-wide association studies of breast cancer. We identified 222 genetic risk loci and 137 genes that were associated with breast cancer risk at a p < 5.0 × 10-8 and a Bonferroni-corrected p < 4.6 × 10-6, respectively. Of them, 32 loci and 15 genes showed a significantly different association between ER-positive and ER-negative breast cancer after Bonferroni correction. Significant ancestral differences in risk variant allele frequencies and their association strengths with breast cancer risk were identified. Of the significant associations identified in this study, 17 loci and 14 genes are located 1Mb away from any of the previously reported breast cancer risk variants. Pathways analyses including 221 putative risk genes identified multiple signaling pathways that may play a significant role in the development of breast cancer. Our study provides a comprehensive understanding of and new biological insights into the genetics of this common malignancy.


Subject(s)
Breast Neoplasms , Genome-Wide Association Study , Female , Humans , Genetic Predisposition to Disease , Polymorphism, Single Nucleotide/genetics , Transcriptome/genetics , Breast Neoplasms/genetics , Case-Control Studies
7.
J Virol ; 98(4): e0006424, 2024 Apr 16.
Article in English | MEDLINE | ID: mdl-38488360

ABSTRACT

As one of the most important causative agents of severe gastroenteritis in children, piglets, and other young animals, species A rotaviruses have adversely impacted both human health and the global swine industry. Vaccines against rotaviruses (RVs) are insufficiently effective, and no specific treatment is available. To understand the relationships between porcine RV (PoRV) infection and enterocytes in terms of the cellular lipid metabolism, we performed an untargeted liquid chromatography mass spectrometry (LC-MS) lipidomics analysis of PoRV-infected IPEC-J2 cells. Herein, a total of 451 lipids (263 upregulated lipids and 188 downregulated lipids), spanning sphingolipid, glycerolipid, and glycerophospholipids, were significantly altered compared with the mock-infected group. Interestingly, almost all the ceramides among these lipids were upregulated during PoRV infection. LC-MS analysis was used to validated the lipidomics data and demonstrated that PoRV replication increased the levels of long-chain ceramides (C16-ceramide, C18-ceramide, and C24-ceramide) in cells. Furthermore, we found that these long-chain ceramides markedly inhibited PoRV infection and that their antiviral actions were exerted in the replication stage of PoRV infection. Moreover, downregulation of endogenous ceramides with the ceramide metabolic inhibitors enhanced PoRV propagation. Increasing the levels of ceramides by the addition of C6-ceramide strikingly suppressed the replication of diverse RV strains. We further found that the treatment with an apoptotic inhibitor could reverse the antiviral activity of ceramide against PoRV replication, demonstrating that ceramide restricted RV infection by inducing apoptosis. Altogether, this study revealed that ceramides played an antiviral role against RV infection, providing potential approaches for the development of antiviral therapies.IMPORTANCERotaviruses (RVs) are among the most important zoonosis viruses, which mainly infected enterocytes of the intestinal epithelium causing diarrhea in children and the young of many mammalian and avian species. Lipids play an essential role in viral infection. A comprehensive understanding of the interaction between RV and lipid metabolism in the enterocytes will be helpful to control RV infection. Here, we mapped changes in enterocyte lipids following porcine RV (PoRV) infection using an untargeted lipidomics approach. We found that PoRV infection altered the metabolism of various lipid species, especially ceramides (derivatives of the sphingosine). We further demonstrated that PoRV infection increased the accumulation of ceramides and that ceramides exerted antiviral effects on RV replication by inducing apoptosis. Our findings fill a gap in understanding the alterations of lipid metabolism in RV-infected enterocytes and highlight the antiviral effects of ceramides on RV infection, suggesting potential approaches to control RV infection.


Subject(s)
Ceramides , Rotavirus Infections , Rotavirus , Animals , Ceramides/metabolism , Lipid Metabolism , Lipidomics , Rotavirus/physiology , Swine , Enterocytes/metabolism , Enterocytes/virology , Rotavirus Infections/metabolism , Cell Line
8.
J Virol ; 98(5): e0021224, 2024 May 14.
Article in English | MEDLINE | ID: mdl-38591886

ABSTRACT

Porcine rotaviruses (PoRVs) cause severe economic losses in the swine industry. P[7] and P[23] are the predominant genotypes circulating on farms, but no vaccine is yet available. Here, we developed a bivalent subunit PoRV vaccine using truncated versions (VP4*) of the VP4 proteins from P[7] and P[23]. The vaccination of mice with the bivalent subunit vaccine elicited more robust neutralizing antibodies (NAbs) and cellular immune responses than its components, even at high doses. The bivalent subunit vaccine and inactivated bivalent vaccine prepared from strains PoRVs G9P[7] and G9P[23] were used to examine their protective efficacy in sows and suckling piglets after passive immunization. The immunized sows showed significantly elevated NAbs in the serum and colostrum, and the suckling piglets acquired high levels of sIgA antibodies from the colostrum. Challenging subunit-vaccinated or inactivated-vaccinated piglets with homologous virulent strains did not induce diarrhea, except in one or two piglets, which had mild diarrhea. Immunization with the bivalent subunit vaccine and inactivated vaccine also alleviated the microscopic lesions in the intestinal tissues caused by the challenge with the corresponding homologous virulent strain. However, all the piglets in the challenged group displayed mild to watery diarrhea and high levels of viral shedding, whereas the feces and intestines of the piglets in the bivalent subunit vaccine and inactivated vaccine groups had lower viral loads. In summary, our data show for the first time that a bivalent subunit vaccine combining VP4*P[7] and VP4*P[23] effectively protects piglets against the diarrhea caused by homologous virulent strains.IMPORTANCEPoRVs are the main causes of diarrhea in piglets worldwide. The multisegmented genome of PoRVs allows the reassortment of VP4 and VP7 genes from different RV species and strains. The P[7] and P[23] are the predominant genotypes circulating in pig farms, but no vaccine is available at present in China. Subunit vaccines, as nonreplicating vaccines, are an option to cope with variable genotypes. Here, we have developed a bivalent subunit candidate vaccine based on a truncated VP4 protein, which induced robust humoral and cellular immune responses and protected piglets against challenge with homologous PoRV. It also appears to be safe. These data show that the truncated VP4-protein-based subunit vaccine is a promising candidate for the prevention of PoRV diarrhea.


Subject(s)
Rotavirus Vaccines , Vaccines, Subunit , Animals , Female , Mice , Antibodies, Neutralizing/blood , Antibodies, Neutralizing/immunology , Antibodies, Viral/blood , Antibodies, Viral/immunology , Capsid Proteins/immunology , Capsid Proteins/genetics , Diarrhea/prevention & control , Diarrhea/virology , Diarrhea/veterinary , Diarrhea/immunology , Genotype , Immunity, Cellular , Mice, Inbred BALB C , Rotavirus/immunology , Rotavirus Infections/prevention & control , Rotavirus Infections/veterinary , Rotavirus Infections/immunology , Rotavirus Infections/virology , Rotavirus Vaccines/immunology , Rotavirus Vaccines/administration & dosage , Swine , Swine Diseases/prevention & control , Swine Diseases/virology , Swine Diseases/immunology , Vaccination , Vaccines, Subunit/immunology , Vaccines, Subunit/administration & dosage , Vaccines, Synthetic/immunology , Vaccines, Synthetic/administration & dosage
9.
Nature ; 570(7762): 514-518, 2019 06.
Article in English | MEDLINE | ID: mdl-31217584

ABSTRACT

Genome-wide association studies (GWAS) have laid the foundation for investigations into the biology of complex traits, drug development and clinical guidelines. However, the majority of discovery efforts are based on data from populations of European ancestry1-3. In light of the differential genetic architecture that is known to exist between populations, bias in representation can exacerbate existing disease and healthcare disparities. Critical variants may be missed if they have a low frequency or are completely absent in European populations, especially as the field shifts its attention towards rare variants, which are more likely to be population-specific4-10. Additionally, effect sizes and their derived risk prediction scores derived in one population may not accurately extrapolate to other populations11,12. Here we demonstrate the value of diverse, multi-ethnic participants in large-scale genomic studies. The Population Architecture using Genomics and Epidemiology (PAGE) study conducted a GWAS of 26 clinical and behavioural phenotypes in 49,839 non-European individuals. Using strategies tailored for analysis of multi-ethnic and admixed populations, we describe a framework for analysing diverse populations, identify 27 novel loci and 38 secondary signals at known loci, as well as replicate 1,444 GWAS catalogue associations across these traits. Our data show evidence of effect-size heterogeneity across ancestries for published GWAS associations, substantial benefits for fine-mapping using diverse cohorts and insights into clinical implications. In the United States-where minority populations have a disproportionately higher burden of chronic conditions13-the lack of representation of diverse populations in genetic research will result in inequitable access to precision medicine for those with the highest burden of disease. We strongly advocate for continued, large genome-wide efforts in diverse populations to maximize genetic discovery and reduce health disparities.


Subject(s)
Asian People/genetics , Black People/genetics , Genome-Wide Association Study/methods , Hispanic or Latino/genetics , Minority Groups , Multifactorial Inheritance/genetics , Women's Health , Body Height/genetics , Cohort Studies , Female , Genetics, Medical/methods , Health Equity/trends , Health Status Disparities , Humans , Male , United States
10.
PLoS Genet ; 18(6): e1009814, 2022 06.
Article in English | MEDLINE | ID: mdl-35771864

ABSTRACT

A common strategy for the functional interpretation of genome-wide association study (GWAS) findings has been the integrative analysis of GWAS and expression data. Using this strategy, many association methods (e.g., PrediXcan and FUSION) have been successful in identifying trait-associated genes via mediating effects on RNA expression. However, these approaches often ignore the effects of splicing, which can carry as much disease risk as expression. Compared to expression data, one challenge to detect associations using splicing data is the large multiple testing burden due to multidimensional splicing events within genes. Here, we introduce a multidimensional splicing gene (MSG) approach, which consists of two stages: 1) we use sparse canonical correlation analysis (sCCA) to construct latent canonical vectors (CVs) by identifying sparse linear combinations of genetic variants and splicing events that are maximally correlated with each other; and 2) we test for the association between the genetically regulated splicing CVs and the trait of interest using GWAS summary statistics. Simulations show that MSG has proper type I error control and substantial power gains over existing multidimensional expression analysis methods (i.e., S-MultiXcan, UTMOST, and sCCA+ACAT) under diverse scenarios. When applied to the Genotype-Tissue Expression Project data and GWAS summary statistics of 14 complex human traits, MSG identified on average 83%, 115%, and 223% more significant genes than sCCA+ACAT, S-MultiXcan, and UTMOST, respectively. We highlight MSG's applications to Alzheimer's disease, low-density lipoprotein cholesterol, and schizophrenia, and found that the majority of MSG-identified genes would have been missed from expression-based analyses. Our results demonstrate that aggregating splicing data through MSG can improve power in identifying gene-trait associations and help better understand the genetic risk of complex traits.


Subject(s)
Genome-Wide Association Study , Quantitative Trait Loci , Humans , Genome-Wide Association Study/methods , Phenotype , Polymorphism, Single Nucleotide , Quantitative Trait Loci/genetics
11.
Nano Lett ; 2024 May 15.
Article in English | MEDLINE | ID: mdl-38747518

ABSTRACT

Splash, one of the most visually apparent droplet dynamics, can manifest on any surface above a certain impact velocity, regardless of surface wettability. Previous studies demonstrate that elevating the substrate temperature can suppress droplet splash, which is unfavorable for many practical applications, such as spray cooling and combustion. Here, we report that the suppression effect of substrate temperature on splash is nullified by utilizing surfaces with nanostructures. By manipulating air evacuation time through surface nanostructures, we have identified a pathway for precise control over the splash threshold and the ability to tailor the dependence of the splash onset on surface temperature. We further propose a theoretical criterion to determine different splash regimes by considering the competition between air evacuation and the development of flow instabilities. Our findings underscore the crucial role of nanostructures in splash dynamics, offering valuable insights for the control of splash in various industrial scenarios.

12.
Gut ; 73(6): 985-999, 2024 05 10.
Article in English | MEDLINE | ID: mdl-38123979

ABSTRACT

OBJECTIVE: The gain of function (GOF) CTNNB1 mutations (CTNNB1 GOF ) in hepatocellular carcinoma (HCC) cause significant immune escape and resistance to anti-PD-1. Here, we aimed to investigate the mechanism of CTNNB1 GOF HCC-mediated immune escape and raise a new therapeutic strategy to enhance anti-PD-1 efficacy in HCC. DESIGN: RNA sequencing was performed to identify the key downstream genes of CTNNB1 GOF associated with immune escape. An in vitro coculture system, murine subcutaneous or orthotopic models, spontaneously tumourigenic models in conditional gene-knock-out mice and flow cytometry were used to explore the biological function of matrix metallopeptidase 9 (MMP9) in tumour progression and immune escape. Single-cell RNA sequencing and proteomics were used to gain insight into the underlying mechanisms of MMP9. RESULTS: MMP9 was significantly upregulated in CTNNB1 GOF HCC. MMP9 suppressed infiltration and cytotoxicity of CD8+ T cells, which was critical for CTNNB1 GOF to drive the suppressive tumour immune microenvironment (TIME) and anti-PD-1 resistance. Mechanistically, CTNNB1 GOF downregulated sirtuin 2 (SIRT2), resulting in promotion of ß-catenin/lysine demethylase 4D (KDM4D) complex formation that fostered the transcriptional activation of MMP9. The secretion of MMP9 from HCC mediated slingshot protein phosphatase 1 (SSH1) shedding from CD8+ T cells, leading to the inhibition of C-X-C motif chemokine receptor 3 (CXCR3)-mediated intracellular of G protein-coupled receptors signalling. Additionally, MMP9 blockade remodelled the TIME and potentiated the sensitivity of anti-PD-1 therapy in HCC. CONCLUSIONS: CTNNB1 GOF induces a suppressive TIME by activating secretion of MMP9. Targeting MMP9 reshapes TIME and potentiates anti-PD-1 efficacy in CTNNB1 GOF HCC.


Subject(s)
CD8-Positive T-Lymphocytes , Carcinoma, Hepatocellular , Liver Neoplasms , Matrix Metalloproteinase 9 , beta Catenin , beta Catenin/metabolism , beta Catenin/genetics , Carcinoma, Hepatocellular/genetics , Carcinoma, Hepatocellular/immunology , Carcinoma, Hepatocellular/drug therapy , Carcinoma, Hepatocellular/pathology , Animals , Liver Neoplasms/genetics , Liver Neoplasms/immunology , Liver Neoplasms/drug therapy , Liver Neoplasms/pathology , Mice , Matrix Metalloproteinase 9/metabolism , Matrix Metalloproteinase 9/genetics , CD8-Positive T-Lymphocytes/immunology , Humans , Mutation , Programmed Cell Death 1 Receptor/metabolism , Programmed Cell Death 1 Receptor/antagonists & inhibitors , Immune Checkpoint Inhibitors/pharmacology , Immune Checkpoint Inhibitors/therapeutic use , Tumor Escape/genetics , Tumor Escape/drug effects , Tumor Microenvironment/immunology , Cell Line, Tumor
13.
Mol Cancer ; 23(1): 57, 2024 03 19.
Article in English | MEDLINE | ID: mdl-38504268

ABSTRACT

Urine-based testing is promising for noninvasive diagnosis of urothelial carcinoma (UC) but has suboptimal sensitivity for early-stage tumors. Herein, we developed a multitarget urine tumor DNA test, UI-Seek, for UC detection and evaluated its clinical feasibility. The prediction model was developed in a retrospective cohort (n = 382), integrating assays for FGFR3 and TERT mutations and aberrant ONECUT2 and VIM methylation to generate a UC-score. The test performance was validated in a double-blinded, multicenter, prospective trial (n = 947; ChiCTR2300076543) and demonstrated a sensitivity of 91.37% and a specificity of 95.09%. The sensitivity reached 75.81% for low-grade Ta tumors and exceeded 93% in high-grade Ta and higher stages (T1 to T4). Simultaneous identification of both bladder and upper urinary tract tumors was enabled with sensitivities exceeding 90%. No significant confounding effects were observed regarding benign urological diseases or non-UC malignancies. The test showed improved sensitivities over urine cytology, the NMP22 test, and UroVysion FISH alongside comparable specificities. The single-target accuracy was greater than 98% as confirmed by Sanger sequencing. Post-surgery UC-score decreased in 97.7% of subjects. Overall, UI-Seek demonstrated robust performance and considerable potential for the early detection of UC.


Subject(s)
Carcinoma, Transitional Cell , Urinary Bladder Neoplasms , Humans , Urinary Bladder Neoplasms/diagnosis , Urinary Bladder Neoplasms/genetics , Urinary Bladder Neoplasms/pathology , Carcinoma, Transitional Cell/diagnosis , Carcinoma, Transitional Cell/genetics , Carcinoma, Transitional Cell/urine , Retrospective Studies , Prospective Studies , Sensitivity and Specificity , Treatment Outcome , DNA , Biomarkers, Tumor/genetics , Transcription Factors , Homeodomain Proteins
14.
Cancer Causes Control ; 35(6): 897-906, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38332239

ABSTRACT

PURPOSE: We aimed to characterize genetic correlations and causal associations between circulating C-reactive protein (CRP) levels and the risk of lung cancer (LC). METHODS: Leveraging summary statistics from genome-wide association studies of circulating CRP levels among 575,531 individuals of European ancestry, and LC risk among 29,266 cases and 56,450 controls, we investigated genetic associations of circulating CRP levels with the risk of overall lung cancer and its histological subtypes, by using linkage disequilibrium score (LDSC) regression and Mendelian randomization (MR) analyses. RESULTS: Significant positive genetic correlations between circulating CRP levels and the risk of LC and its histological subtypes were identified from LDSC regression, with correlation coefficients ranging from 0.12 to 0.26, and all false discovery adjusted p < 0.05. Univariable MR demonstrated a nominal association between CRP levels and an increased risk of lung squamous cell carcinoma (SCC) (inverse variance-weighted OR = 1.15, 95% CI 1.01-1.30). However, this association disappeared when multivariable MR included cigarettes per day and/or body mass index. By using our recently developed constrained maximum likelihood-based MR method, we identified significant associations of CRP levels with the risk of overall LC (OR 1.06, 95% CI 1.03-1.09), SCC (OR 1.06, 95% CI 1.02-1.09), and small cell lung cancer (SCLC, OR 1.09, 95% CI 1.03-1.15). Moreover, most univariable and multivariable MR analyses also revealed consistent CRP-SCLC associations. CONCLUSION: There may be a genetic and causal association between circulating CRP levels and the risk of SCLC, which is in line with previous population-based observational studies.


Subject(s)
C-Reactive Protein , Genome-Wide Association Study , Lung Neoplasms , Mendelian Randomization Analysis , Humans , Lung Neoplasms/genetics , Lung Neoplasms/blood , Lung Neoplasms/epidemiology , C-Reactive Protein/analysis , C-Reactive Protein/metabolism , C-Reactive Protein/genetics , Risk Factors , Case-Control Studies , Genetic Predisposition to Disease , Polymorphism, Single Nucleotide , Linkage Disequilibrium , Male , Female
15.
Microb Pathog ; 190: 106612, 2024 May.
Article in English | MEDLINE | ID: mdl-38467166

ABSTRACT

Rotavirus group A (RVA) is a main pathogen causing diarrheal diseases in humans and animals. Various genotypes are prevalent in the Chinese pig herd. The genetic diversity of RVA lead to distinctly characteristics. In the present study, a porcine RVA strain, named AHFY2022, was successfully isolated from the small intestine tissue of piglets with severe diarrhea. The AHFY2022 strain was identified by cytopathic effects (CPE) observation, indirect immunofluorescence assay (IFA), electron microscopy (EM), high-throughput sequencing, and pathogenesis to piglets. The genomic investigation using NGS data revealed that AHFY2022 exhibited the genotypes G9-P[23]-I5-R1-C1-M1-A8-N1-T1-E1-H1, using the online platform the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) (https://www.bv-brc.org/). Moreover, experimental inoculation in 5-day-old and 27-day-old piglets demonstrated that AHFY2022 caused severe diarrhea, fecal shedding, small intestinal villi damage, and colonization in all challenged piglets. Taken together, our results detailed the virological features of the porcine rotavirus G9P[23] from China, including the whole-genome sequences, genotypes, growth kinetics in MA104 cells and the pathogenicity in suckling piglets.


Subject(s)
Diarrhea , Genome, Viral , Genotype , Phylogeny , Rotavirus Infections , Rotavirus , Swine Diseases , Animals , Rotavirus/genetics , Rotavirus/isolation & purification , Rotavirus/classification , Rotavirus/pathogenicity , Swine , Rotavirus Infections/virology , Rotavirus Infections/veterinary , China , Swine Diseases/virology , Diarrhea/virology , Diarrhea/veterinary , Intestine, Small/virology , Intestine, Small/pathology , Feces/virology , High-Throughput Nucleotide Sequencing
16.
Opt Lett ; 49(5): 1333-1336, 2024 Mar 01.
Article in English | MEDLINE | ID: mdl-38427006

ABSTRACT

This Letter proposes a novel, to the best of our knowledge, matrix digitization method for a photonic analog-to-digital converter with phase-shifted optical quantization (PSOQ-ADC). This method overcomes the issues of excessive bit width of the output code and the generation of invalid codes encountered by the traditional direct digitization method. A PSOQ-ADC was fabricated on a lithium niobate on insulator (LNOI) platform, and an experimental platform was built. The results show that RF signals at 1/2/5 GHz, which were sampled by a 50GS/s optical pulse train, were digitized successfully with the matrix digitization method, producing 5-bit codes without invalid codes. In comparison, the direct digitization method yields 10-bit codes, and as the optical signal-to-noise ratio (OSNR) decreases, the ratio of invalid codes increases in the direct digitization method; even with Hamming distance correction, its effective number of bits (ENOB) remains smaller than that of the matrix digitization.

17.
Phys Rev Lett ; 133(5): 053802, 2024 Aug 02.
Article in English | MEDLINE | ID: mdl-39159106

ABSTRACT

Non-Abelian holonomy, a noncommutative process that measures the parallel transport of non-Abelian gauge fields, has so far been realized in degenerate Hermitian systems with degenerate eigenstates or nondegenerate non-Hermitian systems with exceptional points. Here, we introduce non-Abelian holonomy into degenerate non-Hermitian systems possessing degenerate exceptional points and degenerate energy topologies. The interplay between energy degeneracy and energy topology around exceptional points leads to a non-Abelian holonomy with multiple energy levels and multiple degenerate levels simultaneously, going beyond that in degenerate Hermitian systems with a single energy level, or in nondegenerate non-Hermitian systems with a single degenerate level. We exploit an on-chip photonic platform to experimentally demonstrate the holonomy induced non-Abelian phenomenon, including the switching of eigenstates associated with different degenerate exceptional points and sequence-dependent holonomic outcomes. Our work shifts the paradigm of non-Abelian holonomy and adds new degrees of freedom for non-Abelian applications.

18.
Chemistry ; 30(41): e202401208, 2024 Jul 19.
Article in English | MEDLINE | ID: mdl-38953321

ABSTRACT

Anion exchange membrane fuel cell (AEMFC) is an emerging and promising technology that can help realize a carbon-neutral, sustainable economy. Also, compared to the proton exchange membrane counterpart, AEMFC can achieve comparable cell outputs with lower costs due to the applicability of non-platinum group metal electrocatalysts for the reaction on the electrodes' surfaces. However, the wide application of the AEMFCs has been impeded by the unsatisfactory stability and performance of the hydroxide-conductive membranes in the past. Recently researchers have made breakthroughs using polyarylene (PA)-based AEMs. This article summarizes the recent advances of a class of AEMs with aromatic backbone without ether bonds, mainly synthesized by Friedel-Crafts polycondensation. Such PA-based AEMs showed high chemical/mechanical stabilities and ionic conductivity, and even the fuel cell with those AEMs showed impressive peak power density of up to 2.58 W cm-2. In this concept article, we classify major strategies for making PA-based AEMs to show the recent trends, highlight synthesis, characterization, and properties, and provide a brief outlook.

19.
Biometrics ; 80(1)2024 Jan 29.
Article in English | MEDLINE | ID: mdl-38364804

ABSTRACT

Researchers interested in understanding the relationship between a readily available longitudinal binary outcome and a novel biomarker exposure can be confronted with ascertainment costs that limit sample size. In such settings, two-phase studies can be cost-effective solutions that allow researchers to target informative individuals for exposure ascertainment and increase estimation precision for time-varying and/or time-fixed exposure coefficients. In this paper, we introduce a novel class of residual-dependent sampling (RDS) designs that select informative individuals using data available on the longitudinal outcome and inexpensive covariates. Together with the RDS designs, we propose a semiparametric analysis approach that efficiently uses all data to estimate the parameters. We describe a numerically stable and computationally efficient EM algorithm to maximize the semiparametric likelihood. We examine the finite sample operating characteristics of the proposed approaches through extensive simulation studies, and compare the efficiency of our designs and analysis approach with existing ones. We illustrate the usefulness of the proposed RDS designs and analysis method in practice by studying the association between a genetic marker and poor lung function among patients enrolled in the Lung Health Study (Connett et al, 1993).


Subject(s)
Models, Statistical , Humans , Computer Simulation , Sample Size , Probability , Data Interpretation, Statistical , Sampling Studies , Longitudinal Studies
20.
Diabetes Obes Metab ; 26(7): 2869-2880, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38685601

ABSTRACT

AIM: To investigate the associations of individual and combined healthy lifestyle factors (HLS) with the risk of stroke in individuals with diabetes in China. METHODS: This prospective analysis included 41 314 individuals with diabetes [15 191 from the Comprehensive Research on the Prevention and Control of the Diabetes (CRPCD) project and 26 123 from the China Kadoorie Biobank (CKB) study]. Associations of lifestyle factors, including cigarette smoking, alcohol consumption, physical activity, diet, body shape and sleep duration, with the risk of stroke, intracerebral haemorrhage (ICH) and ischaemic stroke (IS) were assessed using Cox proportional hazard models. RESULTS: During median follow-up periods of 8.02 and 9.05 years, 2499 and 4578 cases of stroke, 2147 and 4024 of IS, and 160 and 728 of ICH were documented in individuals with diabetes in the CRPCD and CKB cohorts, respectively. In the CRPCD cohort, patients with ≥5 HLS had a 14% lower risk of stroke (hazard ratio (HR): 0.86, 95% confidence interval (CI): 0.75-0.98) than those with ≤2 HLS. In the CKB cohort, the adjusted HR (95% CI) for patients with ≥5 HLS were 0.74 (0.66-0.83) for stroke, 0.74 (0.66-0.83) for IS, and 0.57 (0.42-0.78) for ICH compared with those with ≤2 HLS. The pooled adjusted HR (95% CI) comparing patients with ≥5 HLS versus ≤2 HLS was 0.79 (0.69-0.92) for stroke, 0.80 (0.68-0.93) for IS, and 0.60 (0.46-0.78) for ICH. CONCLUSIONS: Maintaining a healthy lifestyle was associated with a lower risk of stroke, IS and ICH among individuals with diabetes.


Subject(s)
Life Style , Stroke , Humans , China/epidemiology , Female , Male , Middle Aged , Prospective Studies , Stroke/epidemiology , Stroke/prevention & control , Stroke/etiology , Aged , Risk Factors , Healthy Lifestyle , Diabetes Mellitus/epidemiology , Exercise , Adult , Alcohol Drinking/adverse effects , Alcohol Drinking/epidemiology , Proportional Hazards Models , Cerebral Hemorrhage/epidemiology , Cohort Studies
SELECTION OF CITATIONS
SEARCH DETAIL