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1.
EBioMedicine ; 103: 105126, 2024 Apr 16.
Article in English | MEDLINE | ID: mdl-38631091

ABSTRACT

BACKGROUND: This study investigates the associations between air pollution and colorectal cancer (CRC) risk and survival from an epigenomic perspective. METHODS: Using a newly developed Air Pollutants Exposure Score (APES), we utilized a prospective cohort study (UK Biobank) to investigate the associations of individual and combined air pollution exposures with CRC incidence and survival, followed by an up-to-date systematic review with meta-analysis to verify the associations. In epigenetic two-sample Mendelian randomization analyses, we examine the associations between genetically predicted DNA methylation related to air pollution and CRC risk. Further genetic colocalization and gene-environment interaction analyses provided different insights to disentangle pathogenic effects of air pollution via epigenetic modification. FINDINGS: During a median 12.97-year follow-up, 5767 incident CRC cases among 428,632 participants free of baseline CRC and 533 deaths in 2401 patients with CRC were documented in the UK Biobank. A higher APES score was associated with an increased CRC risk (HR, 1.03, 95% CI = 1.01-1.06; P = 0.016) and poorer survival (HR, 1.13, 95% CI = 1.03-1.23; P = 0.010), particularly among participants with insufficient physical activity and ever smokers (Pinteraction > 0.05). A subsequent meta-analysis of seven observational studies, including UK Biobank data, corroborated the association between PM2.5 exposure (per 10 µg/m3 increment) and elevated CRC risk (RR,1.42, 95% CI = 1.12-1.79; P = 0.004; I2 = 90.8%). Genetically predicted methylation at PM2.5-related CpG site cg13835894 near TMBIM1/PNKD and cg16235962 near CXCR5, and NO2-related cg16947394 near TMEM110 were associated with an increased CRC risk. Gene-environment interaction analysis confirmed the epigenetic modification of aforementioned CpG sites with CRC risk and survival. INTERPRETATION: Our study suggests the association between air pollution and CRC incidence and survival, underscoring the possible modifying roles of epigenomic factors. Methylation may partly mediate pathogenic effects of air pollution on CRC, with annotation to epigenetic alterations in protein-coding genes TMBIM1/PNKD, CXCR5 and TMEM110. FUNDING: Xue Li is supported by the Natural Science Fund for Distinguished Young Scholars of Zhejiang Province (LR22H260001), the National Nature Science Foundation of China (No. 82204019) and Healthy Zhejiang One Million People Cohort (K-20230085). ET is supported by a Cancer Research UK Career Development Fellowship (C31250/A22804). MGD is supported by the MRC Human Genetics Unit Centre Grant (U127527198).

2.
Nat Commun ; 15(1): 3557, 2024 Apr 26.
Article in English | MEDLINE | ID: mdl-38670944

ABSTRACT

Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV. Our cis-eQTL/mQTL and colocalization analyses using colorectal tissue-specific transcriptome and methylome data separately from 1299 and 321 individuals, along with functional genomic investigation, uncovered 136 putative CRC susceptibility genes, including 56 genes not previously reported. Analyses of single-cell RNA-seq data from colorectal tissues revealed 17 putative CRC susceptibility genes with distinct expression patterns in specific cell types. Analyses of whole exome sequencing data provided additional support for several target genes identified in this study as CRC susceptibility genes. Enrichment analyses of the 136 genes uncover pathways not previously linked to CRC risk. Our study substantially expanded association signals for CRC and provided additional insight into the biological mechanisms underlying CRC development.


Subject(s)
Asian People , Colorectal Neoplasms , Genetic Predisposition to Disease , Genome-Wide Association Study , Polymorphism, Single Nucleotide , Quantitative Trait Loci , White People , Humans , Colorectal Neoplasms/genetics , Asian People/genetics , White People/genetics , Exome Sequencing , Case-Control Studies , Transcriptome , Chromosome Mapping , Male , Female , East Asian People
3.
Br J Cancer ; 130(9): 1585-1591, 2024 May.
Article in English | MEDLINE | ID: mdl-38480934

ABSTRACT

BACKGROUND: To investigate the association between circulating 25-hydroxyvitamin D (25-OHD) and colorectal cancer (CRC) survival outcomes. METHODS: We conducted analyses among the Study of Colorectal Cancer in Scotland (SOCCS) and the UK Biobank (UKBB). Both cancer-specific survival (CSS) and overall survival (OS) outcomes were examined. The 25-OHD levels were categorised into three groups, and multi-variable Cox-proportional hazard models were applied to estimate hazard ratios (HRs). We performed individual-level Mendelian randomisation (MR) through the generated polygenic risk scores (PRS) of 25-OHD and summary-level MR using the inverse-variance weighted (IVW) method. RESULTS: We observed significantly poorer CSS (HR = 0.65,95%CI = 0.55-0.76,P = 1.03 × 10-7) and OS (HR = 0.66,95%CI = 0.58-0.75,P = 8.15 × 10-11) in patients with the lowest compared to those with the highest 25-OHD after adjusting for covariates. These associations remained across patients with varied tumour sites and stages. However, we found no significant association between 25-OHD PRS and either CSS (HR = 0.98,95%CI = 0.80-1.19,P = 0.83) or OS (HR = 1.07,95%CI = 0.91-1.25,P = 0.42). Furthermore, we found no evidence for causal effects by conducting summary-level MR analysis for either CSS (IVW:HR = 1.04,95%CI = 0.85-1.28,P = 0.70) or OS (IVW:HR = 1.10,95%CI = 0.93-1.31,P = 0.25). CONCLUSION: This study supports the observed association between lower circulating 25-OHD and poorer survival outcomes for CRC patients. Whilst the genotype-specific association between better outcomes and higher 25-OHD is intriguing, we found no support for causality using MR approaches.


Subject(s)
Colorectal Neoplasms , Mendelian Randomization Analysis , Vitamin D , Vitamin D/analogs & derivatives , Humans , Colorectal Neoplasms/genetics , Colorectal Neoplasms/mortality , Colorectal Neoplasms/blood , Colorectal Neoplasms/pathology , Vitamin D/blood , Male , Female , Prospective Studies , Middle Aged , Aged , Scotland/epidemiology , Proportional Hazards Models , Adult
4.
Dalton Trans ; 53(8): 3459-3464, 2024 Feb 20.
Article in English | MEDLINE | ID: mdl-38317527

ABSTRACT

The threshold structural transformation of the DUT-4 metal-organic framework (MOF) from an ordered to distorted phase during exposure to ambient conditions has been revealed. The in situ X-ray diffraction analysis, in situ Raman and FTIR spectroscopy, scanning electron microscopy and synchronous thermal analysis have been used for investigation. The reversible effect of exposure time and humidity on such a phase transition has been confirmed. We also demonstrated that the observed phase transition correlated well with changes in the optical and electronic properties of DUT-4, paving the way to a new family of MOF-based phase change materials for optoelectronic applications.

5.
Nat Commun ; 14(1): 6147, 2023 10 02.
Article in English | MEDLINE | ID: mdl-37783704

ABSTRACT

Polygenic risk scores (PRS) have great potential to guide precision colorectal cancer (CRC) prevention by identifying those at higher risk to undertake targeted screening. However, current PRS using European ancestry data have sub-optimal performance in non-European ancestry populations, limiting their utility among these populations. Towards addressing this deficiency, we expand PRS development for CRC by incorporating Asian ancestry data (21,731 cases; 47,444 controls) into European ancestry training datasets (78,473 cases; 107,143 controls). The AUC estimates (95% CI) of PRS are 0.63(0.62-0.64), 0.59(0.57-0.61), 0.62(0.60-0.63), and 0.65(0.63-0.66) in independent datasets including 1681-3651 cases and 8696-115,105 controls of Asian, Black/African American, Latinx/Hispanic, and non-Hispanic White, respectively. They are significantly better than the European-centric PRS in all four major US racial and ethnic groups (p-values < 0.05). Further inclusion of non-European ancestry populations, especially Black/African American and Latinx/Hispanic, is needed to improve the risk prediction and enhance equity in applying PRS in clinical practice.


Subject(s)
Colorectal Neoplasms , Ethnicity , Humans , Ethnicity/genetics , Genome-Wide Association Study , Genetic Predisposition to Disease , Polymorphism, Single Nucleotide , Risk Factors , Multifactorial Inheritance , Colorectal Neoplasms/diagnosis , Colorectal Neoplasms/genetics
6.
ACS Appl Mater Interfaces ; 15(40): 47541-47551, 2023 Oct 11.
Article in English | MEDLINE | ID: mdl-37773641

ABSTRACT

Laser conversion of metal-organic frameworks (MOFs) has recently emerged as a fast and low-energy consumptive approach to create scalable MOF derivatives for catalysis, energy, and optics. However, due to the virtually unlimited MOF structures and tunable laser parameters, the results of their interaction are unpredictable and poorly controlled. Here, we experimentally base a general approach to create nano- to centimeter-scale MOF derivatives with the desired nonlinear optical and catalytic properties. Five three- and two-dimensional MOFs, differing in chemical composition, topology, and thermal resistance, have been selected as precursors. Tuning the laser parameters (i.e., pulse duration from fs to ns and repetition rate from kHz to MHz), we switch between ultrafast nonthermal destruction and thermal decomposition of MOFs. We have established that regardless of the chemical composition and MOF topology, the tuning of the laser parameters allows obtaining a series of structurally different derivatives, and the transition from femtosecond to nanosecond laser regimes ensures the scaling of the derivatives from nano- to centimeter scales. Herein, the thermal resistance of MOFs affects the structure and chemical composition of the resulting derivatives. Finally, we outline the "laser parameters versus MOF structure" space, in which one can create the desired and scalable platforms with nonlinear optical properties from photoluminescence to light control and enhanced catalytic activity.

7.
Small Methods ; 7(11): e2300752, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37702111

ABSTRACT

Two-dimensional metal-organic frameworks (MOFs) occupy a special place among the large family of functional 2D materials. Even at a monolayer level, 2D MOFs exhibit unique sensing, separation, catalytic, electronic, and conductive properties due to the combination of porosity and organo-inorganic nature. However, lab-to-fab transfer for 2D MOF layers faces the challenge of their scalability, limited by weak interactions between the organic and inorganic building blocks. Here, comparing three top-down approaches to fabricate 2D MOF layers (sonication, freeze-thaw, and mechanical exfoliation), The technological criteria have established for creation of the layers of the thickness up to 1 nm with a record aspect ratio up to 2*10^4:1. The freezing-thaw and mechanical exfoliation are the most optimal approaches; wherein the rate and manufacturability of the mechanical exfoliation rivaling the greatest scalability of 2D MOF layers obtained by freezing-thaw (21300:1 vs 1330:1 aspect ratio), leaving the sonication approach behind (with a record 900:1 aspect ratio) have discovered. The high quality 2D MOF layers with a record aspect ratio demonstrate unique optical sensitivity to solvents of a varied polarity, which opens the way to fabricate scalable and freestanding 2D MOF-based atomically thin chemo-optical sensors by industry-oriented approach.

8.
Br J Cancer ; 129(8): 1306-1313, 2023 10.
Article in English | MEDLINE | ID: mdl-37608097

ABSTRACT

BACKGROUND: Tobacco smoking is suggested as a risk factor for colorectal cancer (CRC), but the complex relationship and the potential pathway are not fully understood. METHODS: We performed two-sample Mendelian randomisation (MR) analyses with genetic instruments for smoking behaviours and related DNA methylation in blood and summary-level GWAS data of colorectal cancer to disentangle the relationship. Colocalization analyses and prospective gene-environment interaction analyses were also conducted as replication. RESULTS: Convincing evidence was identified for the pathogenic effect of smoking initiation on CRC risk and suggestive evidence was observed for the protective effect of smoking cessation in the univariable MR analyses. Multivariable MR analysis revealed that these associations were independent of other smoking phenotypes and alcohol drinking. Genetically predicted methylation at CpG site cg17823346 [ZMIZ1] were identified to decrease CRC risk; while genetically predicted methylation at cg02149899 would increase CRC risk. Colocalization and gene-environment interaction analyses added further evidence to the relationship between epigenetic modification at cg17823346 [ZMIZ1] as well as cg02149899 and CRC risk. DISCUSSION: Our study confirms the significant association between tobacco smoking, DNA methylation and CRC risk and yields a novel insight into the pathogenic effect of tobacco smoking on CRC risk.


Subject(s)
Colorectal Neoplasms , Smoking , Humans , Smoking/adverse effects , DNA Methylation , Prospective Studies , Colorectal Neoplasms/genetics , Colorectal Neoplasms/pathology , Tobacco Smoking , Genome-Wide Association Study , Polymorphism, Single Nucleotide
9.
Int J Cancer ; 153(8): 1477-1486, 2023 10 15.
Article in English | MEDLINE | ID: mdl-37449541

ABSTRACT

Aberrant smoking-related DNA methylation has been widely investigated as a carcinogenesis mechanism, but whether the cross-cancer epigenetic pathways exist remains unclear. We conducted two-sample Mendelian randomization (MR) analyses respectively on smoking behaviors (age of smoking initiation, smoking initiation, smoking cessation, and lifetime smoking index [LSI]) and smoking-related DNA methylation to investigate their effect on 15 site-specific cancers, based on a genome-wide association study (GWAS) of 1.2 million European individuals and an epigenome-WAS (EWAS) of 5907 blood samples of Europeans for smoking and 15 GWASs of European ancestry for multiple site-specific cancers. Significantly identified CpG sites were further used for colocalization analysis, and those with cross-cancer effect were validated by overlapping with tissue-specific eQTLs. In the genomic MR, smoking measurements of smoking initiation, smoking cessation and LSI were suggested to be casually associated with risk of seven types of site-specific cancers, among which cancers at lung, cervix and colorectum were provided with strong evidence. In the epigenetic MR, methylation at 75 CpG sites were reported to be significantly associated with increased risks of multiple cancers. Eight out of 75 CpG sites were observed with cross-cancer effect, among which cg06639488 (EFNA1), cg12101586 (CYP1A1) and cg14142171 (HLA-L) were validated by eQTLs at specific cancer sites, and cg07932199 (ATXN2) had strong evidence to be associated with cancers of lung (coefficient, 0.65, 95% confidence interval [CI], 0.31-1.00), colorectum (0.90 [0.61, 1.18]), breast (0.31 [0.20, 0.43]) and endometrium (0.98 [0.68, 1.27]). These findings highlight the potential practices targeting DNA methylation-involved cross-cancer pathways.


Subject(s)
DNA Methylation , Neoplasms , Female , Humans , Smoking/adverse effects , Smoking/genetics , Genome-Wide Association Study , Mendelian Randomization Analysis , Neoplasms/epidemiology , Neoplasms/genetics , CpG Islands/genetics
10.
J Pers Med ; 13(7)2023 Jun 29.
Article in English | MEDLINE | ID: mdl-37511678

ABSTRACT

We aimed to develop and validate prediction models incorporating demographics, clinical features, and a weighted genetic risk score (wGRS) for individual prediction of colorectal cancer (CRC) risk in patients with gastroenterological symptoms. Prediction models were developed with internal validation [CRC Cases: n = 1686/Controls: n = 963]. Candidate predictors included age, sex, BMI, wGRS, family history, and symptoms (changes in bowel habits, rectal bleeding, weight loss, anaemia, abdominal pain). The baseline model included all the non-genetic predictors. Models A (baseline model + wGRS) and B (baseline model) were developed based on LASSO regression to select predictors. Models C (baseline model + wGRS) and D (baseline model) were built using all variables. Models' calibration and discrimination were evaluated through the Hosmer-Lemeshow test (calibration curves were plotted) and C-statistics (corrected based on 1000 bootstrapping). The models' prediction performance was: model A (corrected C-statistic = 0.765); model B (corrected C-statistic = 0.753); model C (corrected C-statistic = 0.764); and model D (corrected C-statistic = 0.752). Models A and C, that integrated wGRS with demographic and clinical predictors, had a statistically significant improved prediction performance. Our findings suggest that future application of genetic predictors holds significant promise, which could enhance CRC risk prediction. Therefore, further investigation through model external validation and clinical impact is merited.

11.
Nutr Metab Cardiovasc Dis ; 33(7): 1316-1322, 2023 Jul.
Article in English | MEDLINE | ID: mdl-37246077

ABSTRACT

AIMS: Previously, no relationship between milk consumption and the risk of type 2 diabetes has been found in prospective cohorts. However, Mendelian randomization allows researchers to almost bypass much residual confounding, providing a more precise effect estimate. This systematic review aims to investigate the risk of type 2 diabetes and levels of HbA1c by assessing all Mendelian Randomization studies investigating this subject matter. DATA SYNTHESIS: PubMed and EMBASE were searched from October 2021 through February 2023. Inclusion and exclusion criteria were formulated to filter out irrelevant studies. Studies were qualitatively assessed with STROBE-MR together with a list of five MR criteria. Six studies were identified, containing several thousand participants. All studies used the SNP rs4988235 as the main exposure and type 2 diabetes and/or HbA1c as the main outcome. Five studies were graded as "good" with STROBE-MR, with one graded as "fair". For the six MR criteria, five studies were graded "good" in four criteria, while two studies were graded "good" in two criteria. Overall, genetically predicted milk consumption did not seem to be associated with an increased risk of type 2 diabetes. CONCLUSIONS: This systematic review found that genetically predicted milk consumption did not seem to increase the risk of type 2 diabetes. Future Mendelian randomization studies concerning this topic should consider conducting two-sample Mendelian Randomization studies, in order to derive a more valid effect estimate.


Subject(s)
Diabetes Mellitus, Type 2 , Milk , Humans , Animals , Milk/adverse effects , Diabetes Mellitus, Type 2/diagnosis , Diabetes Mellitus, Type 2/epidemiology , Diabetes Mellitus, Type 2/genetics , Glycated Hemoglobin , Mendelian Randomization Analysis , Prospective Studies , Polymorphism, Single Nucleotide , Genome-Wide Association Study
12.
Int J Mol Sci ; 24(5)2023 Feb 22.
Article in English | MEDLINE | ID: mdl-36901801

ABSTRACT

Zeolitic imidazolate frameworks (ZIFs) have been extensively examined for their potential in acid-base catalysis. Many studies have demonstrated that ZIFs possess unique structural and physicochemical properties that allow them to demonstrate high activity and yield products with high selectivity. Herein, we highlight the nature of ZIFs in terms of their chemical formulation and the textural, acid-base, and morphological properties that strongly affect their catalytic performance. Our primary focus is the application of spectroscopic methods as instruments for analyzing the nature of active sites because these methods can allow an understanding of unusual catalytic behavior from the perspective of the structure-property-activity relationship. We examine several reactions, such as condensation reactions (the Knoevenagel condensation and Friedländer reactions), the cycloaddition of CO2 to epoxides, the synthesis of propylene glycol methyl ether from propylene oxide and methanol, and the cascade redox condensation of 2-nitroanilines with benzylamines. These examples illustrate the broad range of potentially promising applications of Zn-ZIFs as heterogeneous catalysts.


Subject(s)
Zeolites , Zeolites/chemistry , Imidazoles/chemistry , Catalysis , Structure-Activity Relationship
13.
Genomics ; 115(3): 110616, 2023 05.
Article in English | MEDLINE | ID: mdl-36948276

ABSTRACT

Identifying genetic factors affecting the regulation of the O-6-Methylguanine-DNA Methyltransferase (MGMT) gene and estimating the genetic contribution of the MGMT gene through within-pair correlation in monozygotic twin pairs is of particular importance in various types of cancer such as glioblastoma. We used gene expression data in whole blood from 448 monozygotic twins from the Middle Age Danish Twins (MADT) study to investigate genetic regulation of the MGMT gene by performing a genome-wide association study (GWAS) of the variation in MGMT expression. Additionally, we estimated within-pair dependence measures of the expression values looking for the genetic influence of significant identified genes. We identified 243 single nucleotide polymorphisms (SNPs) significantly (p < 5e-8) associated with expression of MGMT, all located on chromosome 10 near the MGMT gene. Of the 243 SNPs, 7 are novel cis-eQTLs. By further looking into the suggestively significant SNPs (increasing cutoff to p = 1e-6), we identified 11 suggestive trans-eQTLs located on chromosome 17. These variants were in or proximal to a total of seven genes, which may regulate MGMT expression. The within-pair correlation of the expression of MGMT, TRIM37, and SEPT4 provided the upper bound genetic influence of these genes. Overall, identifying cis- or trans-acting genetic variations regulating the MGMT gene can pave the way for a better understanding of the MGMT gene function and ultimately in understanding the patient's sensitivity to therapeutic alkylating agents.


Subject(s)
Glioblastoma , Twins, Monozygotic , Middle Aged , Humans , Genome-Wide Association Study , O(6)-Methylguanine-DNA Methyltransferase/genetics , O(6)-Methylguanine-DNA Methyltransferase/metabolism , Gene Expression , Denmark , Glioblastoma/genetics , Glioblastoma/metabolism , DNA Methylation , Tripartite Motif Proteins/genetics , Tripartite Motif Proteins/metabolism , Ubiquitin-Protein Ligases/genetics , DNA Modification Methylases , Tumor Suppressor Proteins/genetics , DNA Repair Enzymes/genetics , DNA Repair Enzymes/metabolism
14.
medRxiv ; 2023 Jan 19.
Article in English | MEDLINE | ID: mdl-36789420

ABSTRACT

Polygenic risk scores (PRS) have great potential to guide precision colorectal cancer (CRC) prevention by identifying those at higher risk to undertake targeted screening. However, current PRS using European ancestry data have sub-optimal performance in non-European ancestry populations, limiting their utility among these populations. Towards addressing this deficiency, we expanded PRS development for CRC by incorporating Asian ancestry data (21,731 cases; 47,444 controls) into European ancestry training datasets (78,473 cases; 107,143 controls). The AUC estimates (95% CI) of PRS were 0.63(0.62-0.64), 0.59(0.57-0.61), 0.62(0.60-0.63), and 0.65(0.63-0.66) in independent datasets including 1,681-3,651 cases and 8,696-115,105 controls of Asian, Black/African American, Latinx/Hispanic, and non-Hispanic White, respectively. They were significantly better than the European-centric PRS in all four major US racial and ethnic groups (p-values<0.05). Further inclusion of non-European ancestry populations, especially Black/African American and Latinx/Hispanic, is needed to improve the risk prediction and enhance equity in applying PRS in clinical practice.

16.
Nat Genet ; 55(1): 89-99, 2023 01.
Article in English | MEDLINE | ID: mdl-36539618

ABSTRACT

Colorectal cancer (CRC) is a leading cause of mortality worldwide. We conducted a genome-wide association study meta-analysis of 100,204 CRC cases and 154,587 controls of European and east Asian ancestry, identifying 205 independent risk associations, of which 50 were unreported. We performed integrative genomic, transcriptomic and methylomic analyses across large bowel mucosa and other tissues. Transcriptome- and methylome-wide association studies revealed an additional 53 risk associations. We identified 155 high-confidence effector genes functionally linked to CRC risk, many of which had no previously established role in CRC. These have multiple different functions and specifically indicate that variation in normal colorectal homeostasis, proliferation, cell adhesion, migration, immunity and microbial interactions determines CRC risk. Crosstissue analyses indicated that over a third of effector genes most probably act outside the colonic mucosa. Our findings provide insights into colorectal oncogenesis and highlight potential targets across tissues for new CRC treatment and chemoprevention strategies.


Subject(s)
Colorectal Neoplasms , East Asian People , European People , Humans , Colorectal Neoplasms/genetics , East Asian People/genetics , European People/genetics , Genetic Predisposition to Disease , Genome-Wide Association Study , Multiomics , Polymorphism, Single Nucleotide/genetics
17.
Sci Rep ; 12(1): 13609, 2022 08 10.
Article in English | MEDLINE | ID: mdl-35948568

ABSTRACT

Colorectal cancer (CRC) is characterised by heritable risk that is not well understood. Heritable, genetic variation at 11q23.1 is associated with increased colorectal cancer (CRC) risk, demonstrating eQTL effects on 3 cis- and 23 trans-eQTL targets. We sought to determine the relationship between 11q23.1 cis- and trans-eQTL target expression and test for potential cell-specificity. scRNAseq from 32,361 healthy colonic epithelial cells was aggregated and subject to weighted gene co-expression network analysis (WGCNA). One module (blue) included 19 trans-eQTL targets and was correlated with POU2AF2 expression only. Following unsupervised clustering of single cells, the expression of 19 trans-eQTL targets was greatest and most variable in cluster number 11, which transcriptionally resembled tuft cells. 14 trans-eQTL targets were found to demarcate this cluster, 11 of which were corroborated in a second dataset. Intra-cluster WGCNA and module preservation analysis then identified twelve 11q23.1 trans-eQTL targets to comprise a network that was specific to cluster 11. Finally, linear modelling and differential abundance testing showed 11q23.1 trans-eQTL target expression was predictive of cluster 11 abundance. Our findings suggest 11q23.1 trans-eQTL targets comprise a POU2AF2-related network that is likely tuft cell-specific and reduced expression of these genes correlates with reduced tuft cell abundance in silico.


Subject(s)
Colorectal Neoplasms , Quantitative Trait Loci , Cluster Analysis , Colorectal Neoplasms/genetics , Humans
18.
Eur J Epidemiol ; 37(7): 701-712, 2022 Jul.
Article in English | MEDLINE | ID: mdl-35708873

ABSTRACT

Alcohol intake is thought to be a risk factor for breast cancer, but the causal relationship and carcinogenic mechanisms are not clear. We performed an up-to-date meta-analysis of prospective studies to assess observational association, and then conducted MR analysis to make causal inference based on the genetic predisposition to alcohol consumption ("drinks per week") and pathological drinking behaviours ("alcohol use disorder" and "problematic alcohol use"), as well as genetically predicted DNA methylation at by alcohol-related CpG sites in blood. We found an observational dose-response association between alcohol intake and breast cancer incidence with an additional risk of 4% for per 10 g/day increase in alcohol consumption. Genetic predisposition to alcohol consumption ("drinks per week") was not causally associated with breast cancer incidence at the OR of 1.01 (95% CI 0.84, 1.23), but problematic alcohol use (PAU) was linked to a higher breast cancer risk at the OR of 1.76 (95% CI 1.04, 2.99) when conditioning on alcohol consumption. Epigenetic MR analysis identified four CpG sites, cg03260624 near CDC7 gene, cg10816169 near ZNF318 gene, cg03345232 near RIN3 gene, and cg26312998 near RP11-867G23.13 gene, where genetically predicted epigenetic modifications were associated with an increased breast cancer incidence risk. Our findings re-affirmed that alcohol consumption is of high risk for breast cancer incidence even at a very low dose, and the pathogenic effect of alcohol on breast cancer could be due to pathological drinking behaviour and epigenetic modification at several CpG sites, which could be potential intervention targets for breast cancer prevention.


Subject(s)
Breast Neoplasms , Alcohol Drinking/epidemiology , Breast Neoplasms/epidemiology , Breast Neoplasms/genetics , Breast Neoplasms/pathology , Cell Cycle Proteins/genetics , DNA Methylation , Female , Genetic Predisposition to Disease , Humans , Mendelian Randomization Analysis , Prospective Studies , Protein Serine-Threonine Kinases , Risk Factors
19.
Nanoscale ; 14(24): 8858-8864, 2022 Jun 23.
Article in English | MEDLINE | ID: mdl-35697049

ABSTRACT

We present a wearable device with III-V nanowires in a flexible polymer, which is used for active mechanical tuning of the second-harmonic generation intensity. An array of vertical GaAs nanowires was grown with metalorganic vapour-phase epitaxy, then embedded in polydimethylsiloxane and detached from the rigid substrate with mechanical peel off. Experimental results show a tunability of the second-harmonic generation intensity by a factor of two for 30% stretching which matches the simulations including the distribution of sizes. We studied the impact of different parameters on the band dispersion and tunability of the second-harmonic generation, such as the pitch, the length, and the diameter. We predict at least three orders of magnitude active mechanical tuning of the nonlinear signal intensity for nanowire arrays. The flexibility of the array together with the resonant wavelength engineering make such structures perspective platforms for future bendable or stretchable nanophotonic devices as light sources or sensors.

20.
Int J Cancer ; 151(1): 83-94, 2022 07 01.
Article in English | MEDLINE | ID: mdl-35102554

ABSTRACT

Alcohol consumption is thought to be one of the modifiable risk factors for colorectal cancer (CRC). However, the causality and mechanisms by which alcohol exerts its carcinogenic effect are unclear. We evaluated the association between alcohol consumption and CRC risk by analyzing data from 32 cohort studies and conducted two-sample Mendelian randomization (MR) analysis to examine for casual relationship. To explore the effect of alcohol related DNA methylation on CRC risk, we performed an epigenetic MR analysis with data from an epigenome-wide association study (EWAS). We additionally performed gene-alcohol interaction analysis nested in the UK Biobank to assess effect modification between alcohol consumption and susceptibility genes. We discovered distinct effects of alcohol on CRC incidence and mortality from the meta-analyses, and genetic predisposition to alcohol drinking was causally associated with an increased CRC risk (OR = 1.79, 95% CI: 1.23-2.61) using two-sample MR approaches. In epigenetic MR analysis, two alcohol-related CpG sites (cg05593667 and cg10045354 mapped to COLCA1/COLCA2 gene) were identified causally associated with an increased CRC risk (P < 8.20 × 10-4 ). Gene-alcohol interaction analysis revealed that carriage of the risk allele of the eQTL (rs3087967) and mQTL (rs11213823) polymorphism of COLCA1/COLCA2 would interact with alcohol consumption to increase CRC risk (PInteraction  = .027 and PInteraction  = .016). Our study provides comprehensive evidence to elucidate the role of alcohol in CRC and highlights that the pathogenic effect of alcohol on CRC could be partly attributed to DNA methylation by regulating the expression of COLCA1/COLCA2 gene.


Subject(s)
Alcohol Drinking , Colorectal Neoplasms , DNA Methylation , Mendelian Randomization Analysis , Alcohol Drinking/epidemiology , Alcohol Drinking/genetics , Alcohol Drinking/metabolism , Cohort Studies , Colorectal Neoplasms/epidemiology , Colorectal Neoplasms/genetics , Colorectal Neoplasms/metabolism , Genome-Wide Association Study , Humans , Mendelian Randomization Analysis/methods , Neoplasm Proteins/genetics , Neoplasm Proteins/metabolism , Polymorphism, Single Nucleotide
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