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1.
Bioengineering (Basel) ; 11(5)2024 May 09.
Article in English | MEDLINE | ID: mdl-38790341

ABSTRACT

Effective oral care is important for maintaining a high quality of life. Therefore, plaque control can prevent the development and recurrence of periodontitis. Brushing with a toothbrush and toothpaste is a common way to remove plaque; however, excessive brushing or brushing with abrasive toothpaste can cause wear and tear on the dental crown. Hence, we aimed to quantitatively compare the plaque-removal efficiency and tooth wear of toothbrushes using the bioelectric effect (BE) with those of electric-mechanical toothbrushes. To generate the BE signal, an electronic circuit was developed and embedded in a toothbrush. Further, typodonts were coated with cultured artificial plaques and placed in a brushing simulator. A toothpaste slurry was applied, and the typodonts were eluted with tap water after brushing. The plaques of the typodonts were captured, and the images were quantified. For the tooth wear experiment, polymethyl methacrylate disk resin blocks were brushed twice a day, and the thickness of the samples was measured. Subsequently, statistical differences between the experimental toothbrushes and typical toothbrushes were analyzed. The BE toothbrush had a higher plaque-removal efficiency and could minimize tooth wear. This study suggests that the application of BE may be a new solution for oral care.

2.
Nat Genet ; 55(7): 1138-1148, 2023 07.
Article in English | MEDLINE | ID: mdl-37308787

ABSTRACT

Human genetic studies of smoking behavior have been thus far largely limited to common variants. Studying rare coding variants has the potential to identify drug targets. We performed an exome-wide association study of smoking phenotypes in up to 749,459 individuals and discovered a protective association in CHRNB2, encoding the ß2 subunit of the α4ß2 nicotine acetylcholine receptor. Rare predicted loss-of-function and likely deleterious missense variants in CHRNB2 in aggregate were associated with a 35% decreased odds for smoking heavily (odds ratio (OR) = 0.65, confidence interval (CI) = 0.56-0.76, P = 1.9 × 10-8). An independent common variant association in the protective direction ( rs2072659 ; OR = 0.96; CI = 0.94-0.98; P = 5.3 × 10-6) was also evident, suggesting an allelic series. Our findings in humans align with decades-old experimental observations in mice that ß2 loss abolishes nicotine-mediated neuronal responses and attenuates nicotine self-administration. Our genetic discovery will inspire future drug designs targeting CHRNB2 in the brain for the treatment of nicotine addiction.


Subject(s)
Nicotine , Tobacco Use Disorder , Humans , Animals , Mice , Smoking/genetics , Tobacco Use Disorder/genetics , Phenotype , Odds Ratio
3.
Int J Mol Sci ; 24(3)2023 Feb 02.
Article in English | MEDLINE | ID: mdl-36769186

ABSTRACT

H2 permeation in peroxide-crosslinked EPDM blended with carbon black (CB) and silica fillers was studied at pressures ranging from 1.2 MPa to 90 MPa via the volumetric analysis technique. H2 uptake in the CB-filled EPDM revealed dual-sorption behaviors via Henry's law and the Langmuir model, which were attributed to H2 absorption by the polymer chains and H2 adsorption at the filler interfaces, respectively. Additionally, single-sorption mechanisms were observed for neat EPDM and silica-blended EPDM according to Henry's law, indicating H2 absorption by the polymer chain. The linear decreases in the diffusivity with filler content for the silica-blended EPDMs were attributed to increases in the diffusion paths caused by the filler. Exponential decreases in the diffusivity with increasing filler content and in the permeation with the physical/mechanical properties for CB-filled EPDMs were caused by decreases in the fractional free volume due to increased densities for the EPDM composites. Moreover, good filler-dependent correlations between permeability and density, hardness, and tensile strength were demonstrated for EPDMs used as sealing materials for O-rings. From the resulting equation, we predicted the permeation value without further measurements. Thus, we can select EPDM candidates satisfying the permeation guidelines used in hydrogen infrastructure for the future hydrogen economy.


Subject(s)
Polymers , Soot , Polymers/chemistry , Silicon Dioxide , Hydrogen , Ethylenes
5.
Nature ; 612(7939): 301-309, 2022 12.
Article in English | MEDLINE | ID: mdl-36450978

ABSTRACT

Clonal haematopoiesis involves the expansion of certain blood cell lineages and has been associated with ageing and adverse health outcomes1-5. Here we use exome sequence data on 628,388 individuals to identify 40,208 carriers of clonal haematopoiesis of indeterminate potential (CHIP). Using genome-wide and exome-wide association analyses, we identify 24 loci (21 of which are novel) where germline genetic variation influences predisposition to CHIP, including missense variants in the lymphocytic antigen coding gene LY75, which are associated with reduced incidence of CHIP. We also identify novel rare variant associations with clonal haematopoiesis and telomere length. Analysis of 5,041 health traits from the UK Biobank (UKB) found relationships between CHIP and severe COVID-19 outcomes, cardiovascular disease, haematologic traits, malignancy, smoking, obesity, infection and all-cause mortality. Longitudinal and Mendelian randomization analyses revealed that CHIP is associated with solid cancers, including non-melanoma skin cancer and lung cancer, and that CHIP linked to DNMT3A is associated with the subsequent development of myeloid but not lymphoid leukaemias. Additionally, contrary to previous findings from the initial 50,000 UKB exomes6, our results in the full sample do not support a role for IL-6 inhibition in reducing the risk of cardiovascular disease among CHIP carriers. Our findings demonstrate that CHIP represents a complex set of heterogeneous phenotypes with shared and unique germline genetic causes and varied clinical implications.


Subject(s)
COVID-19 , Cardiovascular Diseases , Humans , Clonal Hematopoiesis/genetics , Cardiovascular Diseases/epidemiology , Cardiovascular Diseases/genetics
6.
N Engl J Med ; 387(4): 332-344, 2022 07 28.
Article in English | MEDLINE | ID: mdl-35939579

ABSTRACT

BACKGROUND: Exome sequencing in hundreds of thousands of persons may enable the identification of rare protein-coding genetic variants associated with protection from human diseases like liver cirrhosis, providing a strategy for the discovery of new therapeutic targets. METHODS: We performed a multistage exome sequencing and genetic association analysis to identify genes in which rare protein-coding variants were associated with liver phenotypes. We conducted in vitro experiments to further characterize associations. RESULTS: The multistage analysis involved 542,904 persons with available data on liver aminotransferase levels, 24,944 patients with various types of liver disease, and 490,636 controls without liver disease. We found that rare coding variants in APOB, ABCB4, SLC30A10, and TM6SF2 were associated with increased aminotransferase levels and an increased risk of liver disease. We also found that variants in CIDEB, which encodes a structural protein found in hepatic lipid droplets, had a protective effect. The burden of rare predicted loss-of-function variants plus missense variants in CIDEB (combined carrier frequency, 0.7%) was associated with decreased alanine aminotransferase levels (beta per allele, -1.24 U per liter; 95% confidence interval [CI], -1.66 to -0.83; P = 4.8×10-9) and with 33% lower odds of liver disease of any cause (odds ratio per allele, 0.67; 95% CI, 0.57 to 0.79; P = 9.9×10-7). Rare coding variants in CIDEB were associated with a decreased risk of liver disease across different underlying causes and different degrees of severity, including cirrhosis of any cause (odds ratio per allele, 0.50; 95% CI, 0.36 to 0.70). Among 3599 patients who had undergone bariatric surgery, rare coding variants in CIDEB were associated with a decreased nonalcoholic fatty liver disease activity score (beta per allele in score units, -0.98; 95% CI, -1.54 to -0.41 [scores range from 0 to 8, with higher scores indicating more severe disease]). In human hepatoma cell lines challenged with oleate, CIDEB small interfering RNA knockdown prevented the buildup of large lipid droplets. CONCLUSIONS: Rare germline mutations in CIDEB conferred substantial protection from liver disease. (Funded by Regeneron Pharmaceuticals.).


Subject(s)
Apoptosis Regulatory Proteins , Germ-Line Mutation , Liver Diseases , Apoptosis Regulatory Proteins/genetics , Apoptosis Regulatory Proteins/metabolism , Genetic Predisposition to Disease/genetics , Genetic Predisposition to Disease/prevention & control , Humans , Liver/metabolism , Liver Diseases/genetics , Liver Diseases/metabolism , Liver Diseases/prevention & control , Transaminases/genetics , Exome Sequencing
7.
Nat Genet ; 54(4): 382-392, 2022 04.
Article in English | MEDLINE | ID: mdl-35241825

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters human host cells via angiotensin-converting enzyme 2 (ACE2) and causes coronavirus disease 2019 (COVID-19). Here, through a genome-wide association study, we identify a variant (rs190509934, minor allele frequency 0.2-2%) that downregulates ACE2 expression by 37% (P = 2.7 × 10-8) and reduces the risk of SARS-CoV-2 infection by 40% (odds ratio = 0.60, P = 4.5 × 10-13), providing human genetic evidence that ACE2 expression levels influence COVID-19 risk. We also replicate the associations of six previously reported risk variants, of which four were further associated with worse outcomes in individuals infected with the virus (in/near LZTFL1, MHC, DPP9 and IFNAR2). Lastly, we show that common variants define a risk score that is strongly associated with severe disease among cases and modestly improves the prediction of disease severity relative to demographic and clinical factors alone.


Subject(s)
COVID-19 , Angiotensin-Converting Enzyme 2/genetics , COVID-19/genetics , Genome-Wide Association Study , Humans , Risk Factors , SARS-CoV-2/genetics
8.
Diabetologia ; 65(2): 387-401, 2022 02.
Article in English | MEDLINE | ID: mdl-34932134

ABSTRACT

AIMS/HYPOTHESIS: We aimed to characterise and quantify the expression of HLA class II (HLA-II) in human pancreatic tissue sections and to analyse its induction in human islets. METHODS: We immunostained human pancreatic tissue sections from non-diabetic (n = 5), autoantibody positive (Aab+; n = 5), and type 1 diabetic (n = 5) donors, obtained from the Network of Pancreatic Organ Donors (nPOD), with HLA-II, CD68 and insulin. Each tissue section was acquired with a widefield slide scanner and then analysed with QuPath software. In total, we analysed 7415 islets that contained 338,480 cells. Widefield microscopy was further complemented by high resolution imaging of 301 randomly selected islets, acquired using a Zeiss laser scanning confocal (LSM880) to confirm our findings. Selected beta cells were acquired in enhanced resolution using LSM880 with an Airyscan detector. Further, we cultured healthy isolated human islets and reaggregated human islet microtissues with varying concentrations of proinflammatory cytokines (IFN-γ, TNF-α and IL-1ß). After proinflammatory cytokine culture, islet function was measured by glucose-stimulated insulin secretion, and HLA-I and HLA-II expression was subsequently evaluated with immunostaining or RNA sequencing. RESULTS: Insulin-containing islets (ICIs) of donors with type 1 diabetes had a higher percentage of HLA-II positive area (24.31%) compared with type 1 diabetic insulin-deficient islets (IDIs, 0.67%), non-diabetic (3.80%), and Aab+ (2.31%) donors. In ICIs of type 1 diabetic donors, 45.89% of the total insulin signal co-localised with HLA-II, and 27.65% of the islet beta cells expressed both HLA-II and insulin, while in non-diabetic and Aab+ donors 0.96% and 0.59% of the islet beta cells, respectively, expressed both markers. In the beta cells of donors with type 1 diabetes, HLA-II was mostly present in the cell cytoplasm, co-localising with insulin. In the experiments with human isolated islets and reaggregated human islets, we observed changes in insulin secretion upon stimulation with proinflammatory cytokines, as well as higher expression of HLA-II and HLA-I when compared with controls cultured with media, and an upregulation of HLA-I and HLA-II RNA transcripts. CONCLUSIONS/INTERPRETATION: After a long-standing controversy, we provide definitive evidence that HLA-II can be expressed by pancreatic beta cells from patients with type 1 diabetes. Furthermore, this upregulation can be induced in vitro in healthy isolated human islets or reaggregated human islets by treatment with proinflammatory cytokines. Our findings support a role for HLA-II in type 1 diabetes pathogenesis since HLA-II expressing beta cells can potentially become a direct target of autoreactive CD4+ lymphocytes.


Subject(s)
Diabetes Mellitus, Type 1/metabolism , Histocompatibility Antigens Class II/metabolism , Insulin-Secreting Cells/metabolism , Adolescent , Adult , Autoantibodies/blood , Cells, Cultured , Child , Female , Glucose/pharmacology , Humans , Insulin/metabolism , Insulin Secretion , Insulin-Secreting Cells/drug effects , Male , Tissue Donors , Up-Regulation , Young Adult
9.
Nature ; 599(7886): 628-634, 2021 11.
Article in English | MEDLINE | ID: mdl-34662886

ABSTRACT

A major goal in human genetics is to use natural variation to understand the phenotypic consequences of altering each protein-coding gene in the genome. Here we used exome sequencing1 to explore protein-altering variants and their consequences in 454,787 participants in the UK Biobank study2. We identified 12 million coding variants, including around 1 million loss-of-function and around 1.8 million deleterious missense variants. When these were tested for association with 3,994 health-related traits, we found 564 genes with trait associations at P ≤ 2.18 × 10-11. Rare variant associations were enriched in loci from genome-wide association studies (GWAS), but most (91%) were independent of common variant signals. We discovered several risk-increasing associations with traits related to liver disease, eye disease and cancer, among others, as well as risk-lowering associations for hypertension (SLC9A3R2), diabetes (MAP3K15, FAM234A) and asthma (SLC27A3). Six genes were associated with brain imaging phenotypes, including two involved in neural development (GBE1, PLD1). Of the signals available and powered for replication in an independent cohort, 81% were confirmed; furthermore, association signals were generally consistent across individuals of European, Asian and African ancestry. We illustrate the ability of exome sequencing to identify gene-trait associations, elucidate gene function and pinpoint effector genes that underlie GWAS signals at scale.


Subject(s)
Biological Specimen Banks , Databases, Genetic , Exome Sequencing , Exome/genetics , Africa/ethnology , Asia/ethnology , Asthma/genetics , Diabetes Mellitus/genetics , Europe/ethnology , Eye Diseases/genetics , Female , Genetic Predisposition to Disease/genetics , Genetic Variation , Genome-Wide Association Study , Humans , Hypertension/genetics , Liver Diseases/genetics , Male , Mutation , Neoplasms/genetics , Quantitative Trait, Heritable , United Kingdom
10.
Science ; 373(6550)2021 07 02.
Article in English | MEDLINE | ID: mdl-34210852

ABSTRACT

Large-scale human exome sequencing can identify rare protein-coding variants with a large impact on complex traits such as body adiposity. We sequenced the exomes of 645,626 individuals from the United Kingdom, the United States, and Mexico and estimated associations of rare coding variants with body mass index (BMI). We identified 16 genes with an exome-wide significant association with BMI, including those encoding five brain-expressed G protein-coupled receptors (CALCR, MC4R, GIPR, GPR151, and GPR75). Protein-truncating variants in GPR75 were observed in ~4/10,000 sequenced individuals and were associated with 1.8 kilograms per square meter lower BMI and 54% lower odds of obesity in the heterozygous state. Knock out of Gpr75 in mice resulted in resistance to weight gain and improved glycemic control in a high-fat diet model. Inhibition of GPR75 may provide a therapeutic strategy for obesity.


Subject(s)
Body Mass Index , Exome/genetics , Obesity/genetics , Receptors, G-Protein-Coupled/genetics , Animals , Genetic Variation , Humans , Mice , Mice, Knockout , Sequence Analysis, DNA , Weight Gain/genetics
11.
Am J Hum Genet ; 108(7): 1350-1355, 2021 07 01.
Article in English | MEDLINE | ID: mdl-34115965

ABSTRACT

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), a respiratory illness that can result in hospitalization or death. We used exome sequence data to investigate associations between rare genetic variants and seven COVID-19 outcomes in 586,157 individuals, including 20,952 with COVID-19. After accounting for multiple testing, we did not identify any clear associations with rare variants either exome wide or when specifically focusing on (1) 13 interferon pathway genes in which rare deleterious variants have been reported in individuals with severe COVID-19, (2) 281 genes located in susceptibility loci identified by the COVID-19 Host Genetics Initiative, or (3) 32 additional genes of immunologic relevance and/or therapeutic potential. Our analyses indicate there are no significant associations with rare protein-coding variants with detectable effect sizes at our current sample sizes. Analyses will be updated as additional data become available, and results are publicly available through the Regeneron Genetics Center COVID-19 Results Browser.


Subject(s)
COVID-19/diagnosis , COVID-19/genetics , Exome Sequencing , Exome/genetics , Genetic Predisposition to Disease , Hospitalization/statistics & numerical data , COVID-19/immunology , COVID-19/therapy , Female , Humans , Interferons/genetics , Male , Prognosis , SARS-CoV-2 , Sample Size
12.
J Biol Chem ; 296: 100732, 2021.
Article in English | MEDLINE | ID: mdl-33933455

ABSTRACT

The nuclear factor E2-related factor 1 (Nrf1) transcription factor performs a critical role in regulating cellular homeostasis as part of the cellular stress response and drives the expression of antioxidants and detoxification enzymes among many other functions. Ubiquitination plays an important role in controlling the abundance and thus nuclear accumulation of Nrf1 proteins, but the regulatory enzymes that act on Nrf1 are not fully defined. Here, we identified ubiquitin specific protease 7 (USP7), a deubiquitinating enzyme, as a novel regulator of Nrf1 activity. We found that USP7 interacts with Nrf1a and TCF11-the two long protein isoforms of Nrf1. Expression of wildtype USP7, but not its catalytically defective mutant, resulted in decreased ubiquitination of TCF11 and Nrf1a, leading to their increased stability and increased transactivation of reporter gene expression by TCF11 and Nrf1a. In contrast, knockdown or pharmacologic inhibition of USP7 dramatically increased ubiquitination of TCF11 and Nrf1a and reduction of their steady state levels. Loss of USP7 function attenuated the induction of Nrf1 protein expression in response to treatment with arsenic and other toxic metals, and inhibition of USP7 activity significantly sensitized cells to arsenic treatment. Collectively, these findings suggest that USP7 may act to modulate abundance of Nrf1 protein to induce gene expression in response to toxic metal exposure.


Subject(s)
Metals/metabolism , NF-E2-Related Factor 1/metabolism , Ubiquitin-Specific Peptidase 7/metabolism , Animals , Cell Line , HCT116 Cells , HEK293 Cells , Humans , Mice , Protein Interaction Maps , Protein Stability
13.
Res Child Adolesc Psychopathol ; 49(4): 443-457, 2021 04.
Article in English | MEDLINE | ID: mdl-33433780

ABSTRACT

Maternal opioid use in pregnancy has increased dramatically. Knowledge about children's longer-term emotional and behavioral development after prenatal opioid exposure is scarce. A regional sample of 89 opioid-exposed and 104 non-exposed comparison children were studied prospectively at ages 2, 4.5, and 9 years using the Strengths and Difficulties Questionnaire (SDQ) completed by primary caregivers. Across all childhood assessments, opioid-exposed children obtained significantly higher total difficulties scores than non-exposed comparison children. Growth curve modeling revealed that, relative to their same age peers, opioid-exposed children's emotional and behavioral difficulties significantly worsened over time. Moreover, fixed effects estimates showed that total difficulties trajectories were poorer for children subject to higher prenatal risk (Est = 1.78, 95% CI = [0.46, 3.09]) who were born to mothers with high levels of social adversity (1.11 [0.51, 1.71]), and were then raised in families characterized by high levels of psychosocial risk (1.94 [0.90, 2.98]) and unstable caregiving (1.91 [0.33, 3.48]). A complex set of pre- and postnatal processes contribute to opioid-exposed children's emotional and behavioral development. Efforts to mitigate the long-term consequences of opioid use in pregnancy need to consider both children's and their caregivers' biopsychosocial risks.


Subject(s)
Opioid-Related Disorders , Prenatal Exposure Delayed Effects , Analgesics, Opioid/adverse effects , Child , Child, Preschool , Emotions , Female , Humans , Mothers , Opioid-Related Disorders/epidemiology , Pregnancy
14.
Preprint in English | medRxiv | ID: ppmedrxiv-20221804

ABSTRACT

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease-19 (COVID-19), a respiratory illness that can result in hospitalization or death. We investigated associations between rare genetic variants and seven COVID-19 outcomes in 543,213 individuals, including 8,248 with COVID-19. After accounting for multiple testing, we did not identify any clear associations with rare variants either exome-wide or when specifically focusing on (i) 14 interferon pathway genes in which rare deleterious variants have been reported in severe COVID-19 patients; (ii) 167 genes located in COVID-19 GWAS risk loci; or (iii) 32 additional genes of immunologic relevance and/or therapeutic potential. Our analyses indicate there are no significant associations with rare protein-coding variants with detectable effect sizes at our current sample sizes. Analyses will be updated as additional data become available, with results publicly browsable at https://rgc-covid19.regeneron.com.

15.
Vaccine ; 38(41): 6388-6401, 2020 09 22.
Article in English | MEDLINE | ID: mdl-32829979

ABSTRACT

INTRODUCTION: Asian-Americans have been documented to have low human papillomavirus (HPV) vaccine initiation and completion. No research has attempted to examine underlying mechanisms of HPV vaccine uptake disparities among Asian-Americans. Using the P3 (practice, provider, and patient) model, this study aimed to identify practice-, provider-, and patient-level determinants of Asian-Americans' HPV vaccine intention and uptake. METHODS: We conducted a systematic review of published literature regarding practice-, provider- and patient-level determinants of vaccine intention (e.g., intention, willingness, or acceptability) and uptake (e.g., initiation or completion). Eligible studies were those presenting empirical/original data, focusing on Asian populations in the U.S., including outcomes related to HPV vaccine intention and uptake, and analyzing data on factors associated with these outcomes separately for Asian groups. RESULTS: Twenty-six studies (19 quantitative and 7 qualitative studies) were included in the review. Most commonly studied subgroups were Koreans (n = 9), Chinese (n = 6), and Cambodians (n = 5). Studies showed varied prevalence across subgroups (intention: 23.4%-72%; initiation: 14%-67%; completion: 9%-63%). Only 3 studies included measurements of practice-level determinants (language services, insurance policy). Twelve studies measured provider-level determinants (most commonly documented: HPV vaccine recommendation). All studies measured patient-level determinants (most commonly documented: HPV and HPV vaccine knowledge, perceived safety, perceived susceptibility, and perceived relationship between HPV vaccine and sexual activity). CONCLUSIONS: Existing research on determinants of HPV vaccine intention and uptake among Asian-Americans currently lacks measurements of practice-level constructs and perspectives of clinic staff and providers, which are needed to guide system-level interventions and provider training. Data regarding patient-level determinants suggest that interventions for Asian-American populations can focus on providing educational information in culturally-appropriate manners, leveraging familial influences, and attending to access-related or cultural beliefs about HPV vaccine. Interventions should take into account varied vaccine intention and uptake prevalence in different Asian subgroups.


Subject(s)
Papillomavirus Infections , Papillomavirus Vaccines , Ambulatory Care Facilities , Health Knowledge, Attitudes, Practice , Humans , Intention , Papillomavirus Infections/prevention & control , Patient Acceptance of Health Care , Vaccination
16.
Am J Respir Crit Care Med ; 202(7): 962-972, 2020 10 01.
Article in English | MEDLINE | ID: mdl-32459537

ABSTRACT

Rationale: Puerto Ricans have the highest childhood asthma prevalence in the United States (23.6%); however, the etiology is uncertain.Objectives: In this study, we sought to uncover the genetic architecture of lung function in Puerto Rican youth with and without asthma who were recruited from the island (n = 836).Methods: We used admixture-mapping and whole-genome sequencing data to discover genomic regions associated with lung function. Functional roles of the prioritized candidate SNPs were examined with chromatin immunoprecipitation sequencing, RNA sequencing, and expression quantitative trait loci data.Measurements and Main Results: We discovered a genomic region at 1q32 that was significantly associated with a 0.12-L decrease in the lung volume of exhaled air (95% confidence interval, -0.17 to -0.07; P = 6.62 × 10-8) with each allele of African ancestry. Within this region, two SNPs were expression quantitative trait loci of TMEM9 in nasal airway epithelial cells and MROH3P in esophagus mucosa. The minor alleles of these SNPs were associated with significantly decreased lung function and decreased TMEM9 gene expression. Another admixture-mapping peak was observed on chromosome 5q35.1, indicating that each Native American ancestry allele was associated with a 0.15-L increase in lung function (95% confidence interval, 0.08-0.21; P = 5.03 × 10-6). The region-based association tests identified four suggestive windows that harbored candidate rare variants associated with lung function.Conclusions: We identified common and rare genetic variants that may play a critical role in lung function among Puerto Rican youth. We independently validated an inflammatory pathway that could potentially be used to develop more targeted treatments and interventions for patients with asthma.


Subject(s)
Asthma/genetics , Black People/genetics , Chromosomes, Human, Pair 1/genetics , Chromosomes, Human, Pair 5/genetics , Forced Expiratory Volume/genetics , Indians, North American/genetics , Lung/physiopathology , Adolescent , Asthma/physiopathology , Bronchi/cytology , Case-Control Studies , Cell Line , Child , Chromatin Immunoprecipitation , Chromosome Mapping , Esophageal Mucosa/metabolism , Female , Gene Expression , Humans , Linkage Disequilibrium , Lung/physiology , Male , Membrane Proteins/genetics , Membrane Proteins/metabolism , Myocytes, Smooth Muscle , Nasal Mucosa/metabolism , Polymorphism, Single Nucleotide , Puerto Rico , Quantitative Trait Loci , Sequence Analysis, RNA , White People/genetics , Whole Genome Sequencing , Young Adult
17.
Nucleic Acids Res ; 48(1): 130-140, 2020 01 10.
Article in English | MEDLINE | ID: mdl-31713617

ABSTRACT

Charcot-Marie-Tooth 1A (CMT1A) is the most common inherited neuropathy without a known therapy, which is caused by a 1.4 Mb duplication on human chromosome 17, which includes the gene encoding the peripheral myelin protein of 22 kDa (PMP22). Overexpressed PMP22 protein from its gene duplication is thought to cause demyelination and subsequently axonal degeneration in the peripheral nervous system (PNS). Here, we targeted TATA-box of human PMP22 promoter to normalize overexpressed PMP22 level in C22 mice, a mouse model of CMT1A harboring multiple copies of human PMP22. Direct local intraneural delivery of CRISPR/Cas9 designed to target TATA-box of PMP22 before the onset of disease, downregulates gene expression of PMP22 and preserves both myelin and axons. Notably, the same approach was effective in partial rescue of demyelination even after the onset of disease. Collectively, our data present a proof-of-concept that CRISPR/Cas9-mediated targeting of TATA-box can be utilized to treat CMT1A.


Subject(s)
Charcot-Marie-Tooth Disease/therapy , Molecular Targeted Therapy/methods , Myelin Proteins/genetics , Myelin Sheath/metabolism , Schwann Cells/metabolism , TATA Box , Animals , Axons , CRISPR-Cas Systems , Charcot-Marie-Tooth Disease/genetics , Charcot-Marie-Tooth Disease/metabolism , Charcot-Marie-Tooth Disease/pathology , Chromosome Duplication , Chromosomes, Human, Pair 17 , Disease Models, Animal , Gene Editing/methods , Humans , Injections , Mice , Myelin Proteins/metabolism , Myelin Sheath/pathology , Primary Cell Culture , Promoter Regions, Genetic , Schwann Cells/pathology , Sciatic Nerve/metabolism , Sciatic Nerve/pathology
18.
J Am Soc Nephrol ; 30(10): 2000-2016, 2019 10.
Article in English | MEDLINE | ID: mdl-31537649

ABSTRACT

BACKGROUND: Although diabetic kidney disease demonstrates both familial clustering and single nucleotide polymorphism heritability, the specific genetic factors influencing risk remain largely unknown. METHODS: To identify genetic variants predisposing to diabetic kidney disease, we performed genome-wide association study (GWAS) analyses. Through collaboration with the Diabetes Nephropathy Collaborative Research Initiative, we assembled a large collection of type 1 diabetes cohorts with harmonized diabetic kidney disease phenotypes. We used a spectrum of ten diabetic kidney disease definitions based on albuminuria and renal function. RESULTS: Our GWAS meta-analysis included association results for up to 19,406 individuals of European descent with type 1 diabetes. We identified 16 genome-wide significant risk loci. The variant with the strongest association (rs55703767) is a common missense mutation in the collagen type IV alpha 3 chain (COL4A3) gene, which encodes a major structural component of the glomerular basement membrane (GBM). Mutations in COL4A3 are implicated in heritable nephropathies, including the progressive inherited nephropathy Alport syndrome. The rs55703767 minor allele (Asp326Tyr) is protective against several definitions of diabetic kidney disease, including albuminuria and ESKD, and demonstrated a significant association with GBM width; protective allele carriers had thinner GBM before any signs of kidney disease, and its effect was dependent on glycemia. Three other loci are in or near genes with known or suggestive involvement in this condition (BMP7) or renal biology (COLEC11 and DDR1). CONCLUSIONS: The 16 diabetic kidney disease-associated loci may provide novel insights into the pathogenesis of this condition and help identify potential biologic targets for prevention and treatment.


Subject(s)
Autoantigens/genetics , Collagen Type IV/genetics , Diabetes Mellitus, Type 1/genetics , Diabetic Nephropathies/genetics , Genome-Wide Association Study , Glomerular Basement Membrane , Mutation , Cohort Studies , Female , Humans , Male
19.
J Paediatr Child Health ; 55(10): 1251-1260, 2019 Oct.
Article in English | MEDLINE | ID: mdl-30756441

ABSTRACT

AIM: Pacific children fare poorly on health and educational outcomes, including literacy. Early interventions are considered critical in reducing educational disparities. A prediction model was constructed to analyse the factors associated with Pacific children's English receptive vocabulary, an important component of English language development. METHODS: A birth cohort study of Pacific children was used to construct a classification tree model and predict the proportions of Pacific children who performed strongly in a standardised test of English receptive vocabulary at 6 years of age (n = 1019). Classification trees were constructed using 10-fold cross-validation (CV) and pruned using the one-standard-error rule. Prediction errors were directly estimated using leave-one-out CV. RESULTS: Analyses of misclassification errors from the pruned model gave false negative and positive rates of 19 and 19% from re-substitution and 54 and 21% from leave-one-out CV estimation, respectively. Of the predictors, maternal acculturation, small birthweight and performance in early developmental screening test at 4 years of age were found to have the highest goodness of split. CONCLUSIONS: The cultural environment to which Pacific children were exposed in early childhood, indicated by the maternal acculturation, was more crucial in distinguishing children with strong English-receptive vocabulary skills than socio-economic or prenatal conditions. This highlights the importance of integrating the cultural environment into designing measures for facilitating Pacific children's language development.


Subject(s)
Acculturation , Health Status Disparities , Native Hawaiian or Other Pacific Islander , Vocabulary , Adult , Child , Decision Trees , Education , Forecasting , Humans , New Zealand , Retrospective Studies , Young Adult
20.
Math Med Biol ; 36(2): 241-267, 2019 06 13.
Article in English | MEDLINE | ID: mdl-29947770

ABSTRACT

Tumorigenesis has been described as a multistep process, where each step is associated with a genetic alteration, in the direction to progressively transform a normal cell and its descendants into a malignant tumour. Into this work, we propose a mathematical model for cancer onset and development, considering three populations: normal, premalignant and cancer cells. The model takes into account three hallmarks of cancer: self-sufficiency on growth signals, insensibility to anti-growth signals and evading apoptosis. By using a nonlinear expression to describe the mutation from premalignant to cancer cells, the model includes genetic instability as an enabling characteristic of tumour progression. Mathematical analysis was performed in detail. Results indicate that apoptosis and tissue repair system are the first barriers against tumour progression. One of these mechanisms must be corrupted for cancer to develop from a single mutant cell. The results also show that the presence of aggressive cancer cells opens way to survival of less adapted premalignant cells. Numerical simulations were performed with parameter values based on experimental data of breast cancer, and the necessary time taken for cancer to reach a detectable size from a single mutant cell was estimated with respect to some parameters. We find that the rates of apoptosis and mutations have a large influence on the pace of tumour progression and on the time it takes to become clinically detectable.


Subject(s)
Carcinogenesis , Genomic Instability , Models, Theoretical , Mutation , Humans
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