The Association Between Functional Variants in Long Non-coding RNAs and the Risk of Autism Spectrum Disorder Was Not Mediated by Gut Microbiota.

The effect of functional variants in long non-coding RNA (lncRNA) gene regions on autism spectrum disorder (ASD) remains unclear. The present study aimed to investigate the association of functional variants located in lncRNA genes with the risk of ASD and explore whether gut microbiota would mediate the relationship. A total of 87 cases and 71 healthy controls were enrolled in the study. MassARRAY platform and 16S rRNA sequencing were respectively applied to assess the genotype of candidate SNPs and gut microbiota of children. The logistic regression models showed that the association between rs2295412 and the risk of ASD was statistically significant after Bonferroni adjustments. The risk of ASD decreased by 19% for each additional C allele carried by children in multiplicative models (OR = 0.81, 95% CI, 0.69-0.94, P = 0.007). Although we identified significant correlations between rs8113922 polymorphisms, Bifidobacteriales, and ASD, the mediating effect of gut microbiota on the relationship of the polymorphisms with the risk of ASD was not significant. The findings demonstrated that functional variants in lncRNA genes play an important role in ASD and gut microbiota could not mediate the association. Future studies are warranted to verify the results and search for more possible mechanisms of variants located in lncRNA genes implicated in ASD.

NSUN5 is essential for proper cell proliferation and differentiation of mouse preimplantation embryos.

In brief: Proper early embryonic development in mammals relies on precise cellular signaling pathways. This study reveals that NSUN5 is crucial for the regulation of the Hippo pathway, ensuring normal proliferation and differentiation in mouse preimplantation embryos. Abstract: NOL1/NOP2/Sun domain family, member 5 (NSUN5) is an enzyme belonging to the 5-methylcytosine (m5C) writer family that modifies rRNA and mRNA. Our data revealed an upregulation of Nsun5 at the two-cell stage of mouse preimplantation development, suggesting its significance in early embryonic development. Given m5C's important role in stabilizing rRNA and mRNA and the Hippo signaling pathway's critical function in lineage segregation during embryogenesis, we hypothesized that NSUN5 controls cell differentiation by regulating the expression of components of the Hippo signaling pathway in mouse early embryos. To examine this hypothesis, we employed Nsun5-specific small interfering RNAs for targeted gene silencing in mouse preimplantation embryos. Nsun5 knockdown resulted in significant developmental impairments including reduced blastocyst formation, smaller size of blastocysts, and impaired hatching from the zona pellucida. Nsun5 knockdown also led to decreased cell numbers and increased apoptosis in embryos. We also observed diminished nuclear translocation of yes-associated protein 1 (YAP1) in Nsun5 knockdown embryos at the morula stage, indicating disrupted cell differentiation. This disruption was further evidenced by an altered ratio of CDX2-positive to OCT4-positive cells. Furthermore, Nsun5 depletion was found to upregulate the Hippo signaling-related key genes, Lats1 and Lats2 at the morula stage. Our findings underscore the essential role of Nsun5 in early embryonic development by affecting cell proliferation, YAP1 nuclear translocation, and the Hippo pathway.

Longitudinal Associations Between Physical Activity and Depressive Symptoms in Chinese Children: Evidence from the Tongji Mental Health Cohort Study.

BACKGROUND: We aimed to examine the associations between depressive symptoms and physical activity parameters (e.g., intensity, frequency, and duration) among Chinese school-aged children. METHOD: Participants in this study were extracted from the Tongji Mental Health Cohort Study. The baseline survey was conducted in June 2020 involving 2588 school-aged children from two primary schools in Hubei Province, China. A total of 2435 children were followed up successfully in December 2020. The Children's Depression Inventory Short Form (CDI-S) was applied to evaluate depressive symptoms among school-aged children. The Physical Activity Rating Scale-3 (PARS-3) was adopted to estimate children's physical activity parameters including the intensity, frequency, and duration. Generalized estimation equation models were used to explore the longitudinal associations between physical activity and depressive symptoms among school-aged children. RESULTS: Engaging in moderate levels of physical activity (OR, 0.800; 95%CI, 0.692-0.924) or high levels of physical activity (OR, 0.808; 95%CI, 0.689-0.947) in the baseline survey was associated with a reduced risk of developing depressive symptoms in the follow-up survey compared with children engaging in low levels of physical activity. Stratified analyses revealed that the associations between physical activity and depressive symptoms exhibited a significant correlation among boys and children in the older age group (11-12 years). Our findings showed that engaging in physical activity more than once a week, with each session lasting 20 min or longer, was related to significant reductions in depressive symptoms by 43.8% and 22.3%, respectively. CONCLUSION: Self-reported physical activity is positively associated with improved mental health among Chinese school-aged children, especially when considering parameters such as frequency and duration. The association between vigorous-intensity physical activity and depressive symptoms in children should be cautiously interpreted. Future research should continue to explore the effects of vigorous-intensity physical activity on depressive symptoms in children.

Association between urinary BTEX metabolites and dyslexic odds among school-aged children.

Benzene, toluene, ethylbenzene, and xylene (BTEX) are ubiquitous in the environment, and all of them can cause neurotoxicity. However, the association between BTEX exposure and dyslexia, a disorder with language network-related regions in left hemisphere affected, remains unclear. We aimed to assess the relationship between BTEX exposure and dyslexic odds among school-aged children. A case-control study, including 355 dyslexics and 390 controls from three cities in China, was conducted. Six BTEX metabolites were measured in their urine samples. Logistic regression model was used to explore the association between the BTEX metabolites and the dyslexic odds. Urinary trans,trans-muconic acid (MU: a metabolite of benzene) was significantly associated with an increased dyslexic odds [odds ratio (OR) = 1.23, 95% confidence interval (CI): 1.01, 1.50], and the adjusted OR of the dyslexic odds in the third tertile was 1.72 (95% CI: 1.06, 2.77) compared to that in the lowest tertile regarding urinary MU concentration. Furthermore, the association between urinary MU level and the dyslexic odds was more pronounced among children from low-income families based on stratified analyses. Urinary metabolite levels of toluene, ethylbenzene, and xylene were not found to be associated with the dyslexic odds. In summary, elevated MU concentrations may be associated with an increased dyslexic odds. We should take measures to reduce MU related exposure among children, particularly those with low family income.

Association of exposure to phthalates and phthalate alternatives with dyslexia in Chinese primary school children.

Previous studies have shown associations between children's exposure to phthalates and neurodevelopmental disorders. Whereas the impact of exposure to phthalate alternatives is understudied. This study aimed to evaluate the association of exposure to phthalates/their alternatives with the risk of dyslexia. We recruited 745 children (355 dyslexia and 390 non-dyslexia) via the Tongji Reading Environment and Dyslexia Research Project, and their urine samples were collected. A total of 26 metabolites of phthalates/their alternatives were measured. Multivariate logistic regression and quantile-based g-computation were used to estimate the associations of exposure to the phthalates/their alternatives with dyslexia. More than 80% of the children had 17 related metabolites detected in their urine samples. After adjustment, the association between mono-2-(propyl-6-hydroxy-heptyl) phthalate (OH-MPHP) with the risk of dyslexia was observed. Compared with the lowest quartile of OH-MPHP levels, the odds of dyslexia for the third quartile was 1.93 (95% CI 1.06, 3.57). Regarding mixture analyses, it was found that OH-MPHP contributed the most to the association. Further analyses stratified by sex revealed that this association was only observed in boys. Our results suggested a significantly adverse association of di-2-propylheptyl phthalate exposure with children's language abilities. It highlights the necessity to prioritize the protection of children's neurodevelopment by minimizing their exposure to endocrine-disrupting chemicals like di-2-propylheptyl phthalate.

Dyslexia is associated with urinary polycyclic aromatic hydrocarbon metabolite concentrations of children from China: Data from the READ program.

It has been found that exposure to polycyclic aromatic hydrocarbons (PAHs) is associated with the risk of certain childhood neurodevelopmental disorders. However, no research has investigated the relationship between exposure to PAHs and children's dyslexia odds. The objective of this research was to investigate whether urinary mono-hydroxylated polycyclic aromatic hydrocarbons (OH-PAHs) are associated with increased dyslexia odds in Chinese children. We recruited 1,089 children (542 dyslexic children and 547 non-dyslexic children) for this case-control study. Ten OH-PAHs were measured in the participants' urine samples, which were collected between November 2017 and March 2023. Odds ratios (ORs) of the associations between the OH-PAHs and dyslexia were calculated using logistic regression models, after adjustment for the potential confounding factors. A significant association was found between urinary concentrations of 2-hydroxynaphthalene (2-OHNap) and the elevated odds of dyslexia. The children in the highest quartile of 2-OHNap had a higher OR of dyslexia (1.87, 95% CI: 1.07-3.27) than those in the lowest quartile (P-trend = 0.02) after adjustment for the covariates. After excluding children with maternal disorders during pregnancy, logistic regression analyses showed similar results. Our results suggested a possible association between PAH exposure and the elevated odds of dyslexia.

Exposure to organophosphate, pyrethroid, and neonicotinoid insecticides and dyslexia: Association with oxidative stress.

Organophosphates (OPPs), pyrethroids (PYRs), and neonicotinoids (NNIs) are three major classes of insecticides used worldwide. They might compromise child neurodevelopment. However, few studies have explored the association between exposure to them and dyslexia. The present study aimed to investigate the association between dyslexia and exposure to the three classes of insecticides, as well as explore the potential role of oxidative stress in the association. A total of 355 dyslexic children and 390 controls were included in this study. The exposure biomarkers were determined by liquid chromatography-tandem mass spectrometry. Specifically, the exposure biomarkers included three typical metabolites of OPPs, three of PYRs, and nine of NNIs. Additionally, three typical oxidative stress biomarkers, namely, 8-hydroxy-2'-deoxyguanosine (8-OHdG) for DNA damage, 8-hydroxyguanosine (8-OHG) for RNA damage, and 4-hydroxy-2-nonenal-mercapturic acid (HNEMA) for lipid peroxidation were measured. The detection frequencies of the urinary biomarkers ranged from 83.9% to 100%. Among the target metabolites of the insecticides, a significant association was observed between urinary 3,5,6-trichloro-2-pyridinol (TCPy, the metabolite of chlorpyrifos, an OPP insecticide) and dyslexia. After adjusting for potential confounding variables, children in the highest quartile of TCPy levels had an increased odds of dyslexia (odds ratio [OR], 1.68; 95% confidence interval [CI]: 1.03, 2.75] in comparison to those in the lowest quartile. Among the three oxidative stress biomarkers, urinary HNEMA concentration showed a significant relationship with dyslexia. Children in the highest quartile of HNEMA levels demonstrated an increased dyslexic odds in comparison to those in the lowest quartile after multiple adjustments (OR, 1.64; 95% CI: 1.01, 2.65). Mediation analysis indicated a significant effect of HNEMA in the association between urinary TCPy and dyslexia, with an estimate of 17.2% (P < 0.01). In conclusion, this study suggested the association between urinary TCPy and dyslexia. The association could be attributed to lipid peroxidation partially.

Bidirectional Association Between Cardiovascular Disease and Lung Cancer in a Prospective Cohort Study.

INTRODUCTION: The study aimed to prospectively investigate the bidirectional association between cardiovascular disease (CVD) and lung cancer, and whether this association differs across genetic risk levels. METHODS: This study prospectively followed 455,804 participants from the United Kingdom Biobank cohort who were free of lung cancer at baseline. Cox proportional hazard models were used to estimate the hazard ratio (HR) for incident lung cancer according to CVD status. In parallel, similar approaches were used to assess the risk of incident CVD according to lung cancer status among 478,756 participants free of CVD at baseline. The bidirectional causal relations between these conditions were assessed using Mendelian randomization analysis. Besides, polygenic risk scores were estimated by integrating genome-wide association studies identified risk variants. RESULTS: During 4,007,477 person-years of follow-up, 2006 incident lung cancer cases were documented. Compared with participants without CVD, those with CVD had HRs (95% confidence interval [CI]) of 1.49 (1.30-1.71) for NSCLC, 1.80 (1.39-2.34) for lung squamous cell carcinoma (LUSC), and 1.25 (1.01-1.56) for lung adenocarcinoma (LUAD). After stratification by smoking status, significant associations of CVD with lung cancer risk were observed in former smokers (HR = 1.44, 95% CI: 1.20-1.74) and current smokers (HR = 1.38, 95% CI: 1.13-1.69), but not in never-smokers (HR = 0.98, 95% CI: 0.60-1.61). In addition, CVD was associated with lung cancer risk across each genetic risk level (pheterogeneity = 0.336). In the second analysis, 32,974 incident CVD cases were recorded. Compared with those without lung cancer, the HRs (95% CI) for CVD were 2.33 (1.29-4.21) in NSCLC, 3.66 (1.65-8.14) in LUAD, and 1.98 (0.64-6.14) in LUSC. In particular, participants with lung cancer had a high risk of incident CVD at a high genetic risk level (HR = 3.79, 95% CI: 1.57-9.13). No causal relations between these conditions were observed in Mendelian randomization analysis. CONCLUSIONS: CVD is associated with an increased risk of NSCLC including LUSC and LUAD. NSCLC, particularly LUAD, is associated with a higher CVD risk. Awareness of this bidirectional association may improve prevention and treatment strategies for both diseases. Future clinical demands will require a greater focus on cardiac oncology.

MYC-MAX heterodimerization is essential for the induction of major zygotic genome activation and subsequent preimplantation development.

In mouse preimplantation development, zygotic genome activation (ZGA), which synthesizes new transcripts in the embryo, begins in the S phase at the one-cell stage, with major ZGA occurring especially at the late two-cell stage. Myc is a transcription factor expressed in parallel with ZGA, but its direct association with major ZGA has not been clarified. In this study, we found that developmental arrest occurs at the two-cell stage when mouse embryos were treated with antisense oligonucleotides targeting Myc or MYC-specific inhibitors from the one-cell stage. To identify when MYC inhibition affects development, we applied time-limited inhibitor treatment and found that inhibition of MYC at the one-cell, four-cell, and morula stages had no effect on preimplantation development, whereas inhibitor treatment at the two-cell stage arrested development at the two-cell stage. Furthermore, transcriptome analysis revealed that when MYC function was inhibited, genes expressed in the major ZGA phase were suppressed. These results suggest that MYC is essential for the induction of major ZGA and subsequent preimplantation development. Revealing the function of MYC in preimplantation development is expected to contribute to advances in assisted reproductive technology.

Association between urinary 2-hydroxyethyl mercapturic acid and dyslexia among school-aged children.

Ethylene oxide is commonly used in industrial synthesis and medical disinfection. It is a known human carcinogen and has neurotoxicity. However, the association between ethylene oxide exposure and neurodevelopmental disorders remains unclear. This study aimed to evaluate the association between urinary concentrations of 2-hydroxyethyl mercapturic acid (HEMA; metabolite of ethylene oxide) and dyslexia among school-aged children. A total of 355 dyslexic children and 390 controls from three cities in China were enrolled in this case-control study from November 2017 to December 2020. Urinary HEMA was detected in 100% of the urine samples, suggesting widespread exposure to ethylene oxide in the children. Notably, the children with dyslexia had higher concentrations of urinary HEMA compared to the controls (geometric mean: 2.92 vs. 2.47 ng/mL) (P = 0.004). In the multivariable-adjusted model, urinary concentrations of HEMA were significantly associated with dyslexia risk. The individuals within the highest HEMA concentration demonstrated a 1.97-fold increased odds of dyslexia compared to those within the lowest quartile (95% confidence interval: 1.20-3.23). Thus, these findings suggested the possible link between HEMA levels and the risk of dyslexia. Further studies are warranted to validate this finding and illustrate the underlying mechanism.

In Utero and Childhood/Adolescence Exposure to Tobacco Smoke, Genetic Risk, and Cancer Incidence in Adulthood: A Prospective Cohort Study.

OBJECTIVE: To evaluate the association of early-life tobacco smoke exposure, especially interacting with cancer genetic variants, with adult cancer. PARTICIPANTS AND METHODS: We examined the associations of in utero tobacco smoke exposure, age of smoking initiation, and their interaction with genetic risk levels with cancer incidence in 393,081 participants from the UK Biobank. Information on tobacco exposure was obtained by self-reported questionnaires. A cancer polygenic risk score was constructed by weighting and integrating 702 genome-wide association studies-identified risk variants. Cox proportional hazards regression models were used to calculate hazard ratios (HRs) for overall cancer and organ-specific cancer incidence. RESULTS: During 11.8 years of follow-up, 23,450 (5.97%) and 23,413 (6.03%) incident cancers were included in the analyses of in utero exposure and age of smoking initiation, respectively. The HR (95% CI) for incident cancer in participants with in utero exposure to tobacco smoke was 1.04 (1.01-1.07) for overall cancer, 1.59 (1.44-1.75) for respiratory cancer, and 1.09 (1.03-1.17) for gastrointestinal cancer. The relative risk of incident cancer increased with earlier smoking initiation (Ptrend<.001), with the HR (95% CI) of 1.44 (1.36-1.51) for overall cancer, 13.28 (11.39-15.48) for respiratory cancer, and 1.72 (1.54-1.91) for gastrointestinal cancer in smokers with initiation in childhood compared with never smokers. Importantly, a positive additive interaction between age of smoking initiation and genetic risk was observed for overall cancer (Padditive=.04) and respiratory cancer (Padditive=.003) incidence. CONCLUSION: In utero exposure and earlier smoking initiation are associated with overall and organ-specific cancer, and age of smoking initiation interaction with genetic risk is associated with respiratory cancer.

Saturated fatty acid intake, genetic risk and colorectal cancer incidence: A large-scale prospective cohort study.

Previous investigations mainly focused on the associations of dietary fatty acids with colorectal cancer (CRC) risk, which ignored gene-environment interaction and mechanisms interpretation. We conducted a case-control study (751 cases and 3058 controls) and a prospective cohort study (125 021 participants) to explore the associations between dietary fatty acids, genetic risks, and CRC. Results showed that high intake of saturated fatty acid (SFA) was associated with a higher risk of CRC than low SFA intake (HR =1.22, 95% CI:1.02-1.46). Participants at high genetic risk had a greater risk of CRC with the HR of 2.48 (2.11-2.91) than those at low genetic risk. A multiplicative interaction of genetic risk and SFA intake with incident CRC risk was found (PInteraction = 7.59 × 10-20 ), demonstrating that participants with high genetic risk and high SFA intake had a 3.75-fold greater risk of CRC than those with low genetic risk and low SFA intake. Furthermore, incorporating PRS and SFA into traditional clinical risk factors improved the discriminatory accuracy for CRC risk stratification (AUC from 0.706 to 0.731). Multi-omics data showed that exposure to SFA-rich high-fat dietary (HFD) can responsively induce epigenome reprogramming of some oncogenes and pathological activation of fatty acid metabolism pathway, which may contribute to CRC development through changes in gut microbiomes, metabolites, and tumor-infiltrating immune cells. These findings suggest that individuals with high genetic risk of CRC may benefit from reducing SFA intake. The incorporation of SFA intake and PRS into traditional clinical risk factors will help improve high-risk sub-populations in individualized CRC prevention.

Identification of specific susceptibility loci for the early-onset colorectal cancer.

BACKGROUND: The incidence of early-onset colorectal cancer (EOCRC; patients < 50 years old) has been rising rapidly, whereas the EOCRC genetic susceptibility remains incompletely investigated. Here, we aimed to systematically identify specific susceptible genetic variants for EOCRC. METHODS: Two parallel GWASs were conducted in 17,789 CRC cases (including 1490 EOCRC cases) and 19,951 healthy controls. A polygenic risk score (PRS) model was built based on identified EOCRC-specific susceptibility variants by using the UK Biobank cohort. We also interpreted the potential biological mechanisms of the prioritized risk variant. RESULTS: We identified 49 independent susceptibility loci that were significantly associated with the susceptibility to EOCRC and the diagnosed age of CRC (both P < 5.0×10-4), replicating 3 previous CRC GWAS loci. There are 88 assigned susceptibility genes involved in chromatin assembly and DNA replication pathways, mainly associating with precancerous polyps. Additionally, we assessed the genetic effect of the identified variants by developing a PRS model. Compared to the individuals in the low genetic risk group, the individuals in the high genetic risk group have increased EOCRC risk, and these results were replicated in the UKB cohort with a 1.63-fold risk (95% CI: 1.32-2.02, P = 7.67×10-6). The addition of the identified EOCRC risk loci significantly increased the prediction accuracy of the PRS model, compared to the PRS model derived from the previous GWAS-identified loci. Mechanistically, we also elucidated that rs12794623 may contribute to the early stage of CRC carcinogenesis via allele-specific regulating the expression of POLA2. CONCLUSIONS: These findings will broaden the understanding of the etiology of EOCRC and may facilitate the early screening and individualized prevention.

Association of perchlorate, thiocyanate, and nitrate with dyslexic risk.

Perchlorate, thiocyanate, and nitrate are sodium iodide symporter (NIS) inhibitors that disturb iodide uptake into the thyroid and have been implicated in child development. However, no data are available on the association between exposure to/related with them and dyslexia. Here, we examined the association of exposure to/related with the three NIS inhibitors with the risk of dyslexia in a case-control study. The three chemicals were detected in urine samples of 355 children with dyslexia and 390 children without dyslexia from three cities in China. The adjusted odds ratios for dyslexia were examined using logistic regression models. The detection frequencies of all the targeted compounds were 100%. After adjusting for multiple covariates, urinary thiocyanate was significantly associated with the risk of dyslexia (P-trend = 0.02). Compared with the lowest quartile, children within the highest quartile had a 2.66-fold risk of dyslexia (95% confidence interval: 1.32, 5.36]. Stratified analyses showed that the association between urinary thiocyanate level and the risk of dyslexia was more pronounced among boys, children with fixed reading time, and those without maternal depression or anxiety during pregnancy. Urinary perchlorate and nitrate levels were not associated with the risk of dyslexia. This study suggests the possible neurotoxicity of thiocyanate or its parent compounds in dyslexia. Further investigation is warranted to confirm our findings and clarify the potential mechanisms.

Birthweight, genetic risk, and gastrointestinal cancer incidence: a prospective cohort study.

BACKGROUND: The epidemiologic studies investigating the association of birthweight and genetic factors with gastrointestinal cancer remain scarce. The study aimed to prospectively assess the interactions and joint effects of birthweight and genetic risk levels on gastrointestinal cancer incidence in adulthood. METHODS: A total of 254,997 participants were included in the UK Biobank study. We used multivariate restricted cubic splines and Cox regression models to estimate the hazard ratios (HRs) and 95% confidential intervals (CI) for the association between birthweight and gastrointestinal cancer risk, then constructed a polygenic risk score (PRS) to assess its interaction and joint effect with birthweight on the development of gastrointestinal cancer. RESULTS: We documented 2512 incident cases during a median follow-up of 8.88 years. Compare with participants reporting a normal birthweight (2.5-4.5 kg), multivariable-adjusted HR of gastrointestinal cancer incidence for participants with high birthweight (≥4.5 kg) was 1.17 (95%CI: 1.01-1.36). Such association was remarkably observed in pancreatic cancer, with an HR of 1.82 (95%CI: 1.26-2.64). No statistically significant association was observed between low birth weight and gastrointestinal cancers. Participants with high birthweight and high PRS had the highest risk of gastrointestinal cancer (HR: 2.95, 95%CI: 2.19-3.96). CONCLUSION: Our findings highlight that high birthweight is associated with a higher incidence of gastrointestinal cancer, especially for pancreatic cancer. Benefits would be obtained from birthweight control, particularly for individuals with a high genetic risk.KEY MESSAGESThe epidemiologic studies investigating the association of birthweight and genetic factors with gastrointestinal cancer remain scarce.This cohort study of 254,997 adults in the United Kingdom found an association of high birthweight with the incidence of gastrointestinal cancer, especially for pancreatic cancer, and also found that participants with high birthweight and high polygenic risk score had the highest risk of gastrointestinal cancer.Our data suggests a possible effect of in utero or early life exposures on adulthood gastrointestinal cancer, especially for those with a high genetic risk.

Combining multi-omics approaches to prioritize the variant-regulated functional long non-coding RNAs in autism spectrum disorder.

OBJECTIVE: Rising evidence has indicated that long non-coding RNA (lncRNA) may play an essential role in the development of autism spectrum disorder (ASD). However, identifying the lncRNAs associated with ASD and the risk loci on them remains a major challenge. This study aims to identify potential causative variants and explore the related mechanisms. METHODS: By leveraging differential expression analysis, WGCNA analysis and cis-expression quantitative analysis, our study mined functional SNPs with the regulated long non-coding RNA genes in brain tissues. We recruited 611 ASD children and 645 healthy children in the case-control study. RESULTS: Total 68 different expressed lncRNAs were validated by calculating the brain tissue-specific expression using RNA-seq data. By the WGCNA method, 9 functional lncRNAs classified as e-lncRNA were found to interact with 976 ASD risk genes. Furthermore, we mined functional SNPs regulated long non-coding RNAs in brain tissues. We analyzed the association between candidate SNPs and ASD risks in Chinese children, which showed BDNF-AS rs1565228 allele G to C reduced the risk of ASD (OR = 0.81, 95%CI: 0.66-0.98). Further bioinformatics analysis showed that the variant rs1565228 C>G with the low binding affinity of transcription factor SRF caused the decreased expression of lncRNA BDNF-AS. Our study revealed that rs2295412 in the non-coding sequence of the lncRNA gene region was significantly associated with the risk of ASD. DISCUSSION: These findings suggested that the SNPs in the non-coding region of lncRNA may play important roles in the genetic susceptibility of ASD, which may facilitate the early screening of ASD.

In Utero and Childhood/Adolescence Exposure to Tobacco Smoke, Genetic Risk, and Lung Cancer Incidence and Mortality in Adulthood.

Rationale: The individual effects of early-life tobacco smoke exposure and its interactions with genetic factors on lung cancer in adulthood remain unclear. Objectives: To investigate the associations of early-life tobacco exposures as well as their interactions with polygenic risk scores (PRSs) with lung cancer incidence and mortality. Methods: A total of 432,831 participants from the UK Biobank study were included. We estimated the associations of in utero exposure to tobacco smoke, the age of smoking initiation and their interactions with PRSs with lung cancer incidence and mortality in adulthood using Cox proportional hazard models. Measurements and Main Results: Lung cancer incidence (hazard ratio [HR]: 1.59, 95% confidence interval [CI], 1.44-1.76) increased among participants with in utero tobacco exposure. Multivariable-adjusted HRs (with 95% CIs) of lung cancer incidence for smoking initiation in adulthood, adolescence, and childhood (versus never-smokers) were 6.10 (5.25-7.09), 9.56 (8.31-11.00), and 15.15 (12.90-17.79) (Ptrend < 0.001). Similar findings were observed in lung cancer mortality. Participants with high PRSs and in utero tobacco exposure (versus low PRSs participants without in utero exposure) had an HR of 2.35 for lung cancer incidence (95% CI, 1.97-2.80, Pinteraction = 0.089) and 2.43 for mortality (95% CI, 2.05-2.88, Pinteraction = 0.032). High PRSs with smoking initiation in childhood (versus never-smokers with low PRSs) had HRs of 18.71 for incidence (95% CI, 14.21-24.63, Pinteraction = 0.004) and 19.74 for mortality (95% CI, 14.98-26.01, Pinteraction = 0.033). Conclusions: In utero and childhood/adolescence exposure to tobacco smoke and its interaction with genetic factors may substantially increase the risks of lung cancer incidence and mortality in adulthood.

Systematic analysis on expression quantitative trait loci identifies a novel regulatory variant in ring finger and WD repeat domain 3 associated with prognosis of pancreatic cancer.

BACKGROUND: Pancreatic adenocarcinoma (PAAD) is an extremely lethal malignancy. Identification of the functional genes and genetic variants related to PAAD prognosis is important and challenging. Previously identified prognostic genes from several expression profile analyses were inconsistent. The regulatory genetic variants that affect PAAD prognosis were largely unknown. METHODS: Firstly, a meta-analysis was performed with seven published datasets to systematically explore the candidate prognostic genes for PAAD. Next, to identify the regulatory variants for those candidate genes, expression quantitative trait loci analysis was implemented with PAAD data resources from The Cancer Genome Atlas. Then, a two-stage association study in a total of 893 PAAD patients was conducted to interrogate the regulatory variants and find the prognostic locus. Finally, a series of biochemical experiments and phenotype assays were carried out to demonstrate the biological function of variation and genes in PAAD progression process. RESULTS: A total of 128 genes were identified associated with the PAAD prognosis in the meta-analysis. Fourteen regulatory loci in 12 of the 128 genes were discovered, among which, only rs4887783, the functional variant in the promoter of Ring Finger and WD Repeat Domain 3 ( RFWD3 ), presented significant association with PAAD prognosis in both stages of the population study. Dual-luciferase reporter and electrophoretic mobility shift assays demonstrated that rs4887783-G allele, which predicts the worse prognosis, enhanced the binding of transcript factor REST, thus elevating RFWD3 expression. Further phenotypic assays revealed that excess expression of RFWD3 promoted tumor cell migration without affecting their proliferation rate. RFWD3 was highly expressed in PAAD and might orchestrate the genes in the DNA repair process. CONCLUSIONS: RFWD3 and its regulatory variant are novel genetic factors for PAAD prognosis.

Aberrant RNA Splicing Is a Primary Link between Genetic Variation and Pancreatic Cancer Risk.

Understanding the genetic variation underlying transcript splicing is essential for fully dissecting the molecular mechanisms of common diseases. The available evidence from splicing quantitative trait locus (sQTL) studies using pancreatic ductal adenocarcinoma (PDAC) tissues have been limited to small sample sizes. Here we present a genome-wide sQTL analysis to identify SNP that control mRNA splicing in 176 PDAC samples from TCGA. From this analysis, 16,175 sQTLs were found to be significantly enriched in RNA-binding protein (RBP) binding sites and chromatin regulatory elements and overlapped with known loci from PDAC genome-wide association studies (GWAS). sQTLs and expression quantitative trait loci (eQTL) showed mostly nonoverlapping patterns, suggesting sQTLs provide additional insights into the etiology of disease. Target genes affected by sQTLs were closely related to cancer signaling pathways, high mutational burden, immune infiltration, and pharmaceutical targets, which will be helpful for clinical applications. Integration of a large-scale population consisting of 2,782 patients with PDAC and 7,983 healthy controls identified an sQTL variant rs1785932-T allele that promotes alternative splicing of ELP2 exon 6 and leads to a lower level of the ELP2 full-length isoform (ELP2_V1) and a higher level of a truncated ELP2 isoform (ELP2_V2), resulting in decreased risk of PDAC [OR = 0.83; 95% confidence interval (CI), 0.77-0.89; P = 1.16 × 10-6]. The ELP2_V2 isoform functioned as a potential tumor suppressor gene, inhibiting PDAC cell proliferation by exhibiting stronger binding affinity to JAK1/STAT3 than ELP2_V1 and subsequently blocking the pathologic activation of the phosphorylated STAT3 (pSTAT3) pathway. Collectively, these findings provide an informative sQTL resource and insights into the regulatory mechanisms linking splicing variants to PDAC risk. SIGNIFICANCE: In pancreatic cancer, splicing quantitative trait loci analysis identifies a rs1785932 variant that contributes to decreased risk of disease by influencing ELP2 mRNA splicing and blocking the STAT3 oncogenic pathway.

Genome-wide gene-bisphenol A, F and triclosan interaction analyses on urinary oxidative stress markers.

BACKGROUND: Bisphenols and triclosan (TCS) are common endocrine disrupters (EDCs) that may induce oxidative stress. However, there is limited information as to whether these EDCs interact with genetic variants to modify the levels of oxidative stress on a genome-wide scale. METHODS: We first performed a genome-wide scan among a Chinese population and also measured three urinary EDCs, including bisphenol A (BPA), bisphenol F (BPF) and TCS, and three urinary oxidative stress markers [4-hydroxy-2-nonenal-mercapturic acid (HNE-MA), 8-iso-prostaglandin-F2α (8-isoPGF2α) and 8-hydroxy-deoxyguanosine (8-OHdG)]. Subsequently, we examined interactions between three urinary EDCs and nearly 4.6 million genetic variants for three urinary oxidative stress markers by the general linear model. RESULTS: Urinary BPA, BPF and TCS were positively associated with HNE-MA, 8-isoPGF2α and 8-OHdG. Significant rs6855040 (4p15.32/between SNORA75B and QDPR)-BPA, rs1112943 (4q35.1/SNX25)-TCS interactions were associated with the 8-isoPGF2α levels (all P < 5 × 10-8). In addition, rs4656116 (1p22.3/CACL1), rs16958760 (17p11.2/between USP43 and DHRS7C) and rs11651078 (17p11.2/LOC339260) showed significant gene-TCS interactions with 8-OHdG (all P < 5 × 10-8). The gene-level analysis found significant interaction between SNX25 and TCS for 8-isoPGF2α levels (P < 2.12 × 10-6). CONCLUSION: Our results identify several gene-EDCs interactions for oxidative stress, highlighting that EDCs may modify the effect of genetic variants on oxidative stress.