Genome-wide by environment interaction studies of maternal smoking and educational score in UK biobank.

PURPOSE: This study aimed to investigate the associations between maternal smoking (MS) and education score in adult offspring. METHODS: To better understand this link, we performed a two-stage genome-wide by environment interaction studies (GWEIS) of MS and offspring education score in UK Biobank cohort. Specifically, 276 996 subjects from England were enrolled in the discovery study, while 24 355 subjects from Scotland and 14 526 subjects from Wales were enrolled in the replication study. GWEIS were conducted by PLINK 2.0 with MS used as an environmental risk factor. RESULTS: Significant GWEIS associations ( P  < 0.0001) between MS and offspring education score in both the discovery cohort and two replicate cohorts (Scotland population and Wales population) were identified. GWEIS identified 2 independent significant single nucleotide polymorphism-MS interaction, with one variant located in the chromosomal 16 (rs72768988, Position: 22,768,798, P  = 1.22 × 10 -8 , ß = 6.7662) and the other one located in 2q32.3 region (2 : 196424612_GT_G, Position: 196 424 612, 3.60 × 10 -9 , ß = -0.4721). CONCLUSION: Our results suggested 2q32.3 region and HECW2 gene could negatively moderate the influence of MS on offspring's educational status.

Oral Submucous Fibrosis: Etiological Mechanism, Malignant Transformation, Therapeutic Approaches and Targets.

Oral submucosal fibrosis (OSF) is a chronic, progressive and potentially malignant oral disorder with a high regional incidence and malignant rate. With the development of the disease, the normal oral function and social life of patients are seriously affected. This review mainly introduces the various pathogenic factors and mechanisms of OSF, the mechanism of malignant transformation into oral squamous cell carcinoma (OSCC), and the existing treatment methods and new therapeutic targets and drugs. This paper summarizes the key molecules in the pathogenic and malignant mechanism of OSF, the miRNAs and lncRNAs with abnormal changes, and the natural compounds with therapeutic effects, which provides new molecular targets and further research directions for the prevention and treatment of OSF.

The alteration of urinary metabolomics profiles in Kashin-Beck disease in a three consecutive year study.

Kashin-Beck disease (KBD) is a serious, endemic chronic osteochondral disease characterized by symmetrical enlargement of the phalanges, brachydactyly, joint deformity, and even dwarfism. To investigate the urinary metabolomic profiles of KBD patients, we performed an untargeted metabolomics approach using liquid chromatography coupled with mass spectrometry (LC-MS). Adult urinary specimens were collected from 39 patients with KBD and 19 healthy subjects; the children's urinary specimens were collected from 5 patients with KBD, 25 suspected KBD cases and 123 healthy subjects in the KBD endemic area during a three consecutive year study. We identified 10 upregulated and 28 downregulated secondary level metabolites highly associated with aetiology and pathogenesis of KBD between adult KBD and adult controls. A total of 163, 967 and 795 metabolites were significantly different in the urine among children with KBD, suspected children with KBD cases and healthy child controls, respectively, for each year in three consecutive years. HT-2 toxin, Se-adenosylselenomethionine (AdoSeMet), the toxin T2 tetrol, and many kinds of amino acids were identified as differential metabolites in this study. Amino sugar and nucleotide sugar metabolism, fructose and mannose metabolism, arachidonic acid metabolism, D-glutamine and D-glutamate metabolism, ubiquinone and other terpenoid-quinone biosynthesis, and D-glutamine and D-glutamate metabolism were perturbed pathways in adult and child KBD patients. Our study provides new insight into the underlying mechanisms of KBD, and suggests that we should pay more attention to these differences in small-molecule metabolites and metabolic pathways in the environmental aetiology and pathogenesis of KBD.

Cleavage Stimulation Factor Subunit 2: Function Across Cancers and Potential Target for Chemotherapeutic Drugs.

The cleavage stimulation factor subunit complex is involved in the cleavage and polyadenylation of 3'-end pre-mRNAs that regulate mRNA formation and processing. However, cleavage stimulation factor subunit 2 (CSTF2) was found to play a more critical regulatory role across cancers. General cancer data sets from The Cancer Genome Atlas and Genotype-Tissue Expression project were thus downloaded for differential analysis, and the possible functions and mechanisms of CSTF2 in general cancer were analyzed using the Compartments database, cBioPortal database, Tumor Immune Single-cell Hub database, and Comparative Toxigenomics database using gene set enrichment analysis and R software. The results showed that CSTF2 could affect DNA repair and methylation in tumor cells. In addition, CSTF2 was associated with multiple tumor immune infiltrates in a wide range of cancers, and its high expression was associated with multiple immune checkpoints; therefore, it could serve as a potential target for many drug molecules. We also proved that CSTF2 promotes oral cell proliferation and migration. The high diagnostic efficacy of CSTF2 suggested that this gene may act as a new biomarker and personalized therapeutic target for a variety of tumors.

The first human induced pluripotent stem cell line of Kashin-Beck disease reveals involvement of heparan sulfate proteoglycan biosynthesis and PPAR pathway.

Kashin-Beck disease (KBD) is an endemic osteochondropathy. Due to a lack of suitable animal or cellular disease models, the research progress on KBD has been limited. Our goal was to establish the first disease-specific human induced pluripotent stem cell (hiPSC) cellular disease model of KBD, and to explore its etiology and pathogenesis exploiting transcriptome sequencing. HiPSCs were reprogrammed from dermal fibroblasts of two KBD and one healthy control donor via integration-free vectors. Subsequently, hiPSCs were differentiated into chondrocytes through three-week culture. Gene expression profiles in KBD, normal primary chondrocytes, and hiPSC-derived chondrocytes were defined by RNA sequencing. A Venn diagram was constructed to show the number of shared differentially expressed genes (DEGs) between KBD and normal. Gene oncology and Kyoto Encyclopedia of Genes and Genomes annotations were performed, and six DEGs were further validated in other individuals by RT-qPCR. KBD cellular disease models were successfully established by generation of hiPSC lines. Seventeen consistent and significant DEGs present in all compared groups (KBD and normal) were identified. RT-qPCR validation gave consistent results with the sequencing data. Glycosaminoglycan biosynthesis-heparan sulfate/heparin; PPAR signaling pathway; and cell adhesion molecules (CAMs) were identified to be significantly altered in KBD. Differentiated chondrocytes derived from KBD-origin hiPSCs provide the first cellular disease model for etiological studies of KBD. This study also provides new sights into the pathogenesis and etiology of KBD and is likely to inform the development of targeted therapeutics for its treatment.

Associations between electronic devices use and common mental traits: A gene-environment interaction model using the UK Biobank data.

BACKGROUND: Electronic devices use has been reported to be associated with depression. However, limited effort has been provided to elucidate the associations between electronic devices use and mental traits in interaction with genetic factors. METHODS: We first conducted an observational study consisting of 138 976-383 742 participants for TV watching, 29 636-38 599 participants for computer using and 118 61-330 985 participants for computer playing in the UK Biobank cohort. A linear regression model was used to evaluate the associations between common mental traits and electronic devices use. Subsequently, a genome-wide gene-environment interaction study (GWEIS) was performed by PLINK2.0 to estimate the interaction effects of genes and electronic devices use on the risks of the four mental traits. RESULTS: In the UK Biobank cohort, significant associations were observed between electronic devices use and mental traits (all P < 1.0 × 10-9 ), including depression score (B = 0.094 for TV watching), anxiety score (B = 0.051 for TV watching), cigarette smoking (B = 0.046 for computer using) and alcohol drinking (B = 0.010 for computer playing). GWEIS identified multiple mental traits associated loci, interacting with electronic devices use, such as DCDC2 (rs115986722, P = 4.10 × 10-10 ) for anxiety score and TV watching, PRKCE (rs56181965, P = 9.64 × 10-10 ) for smoking and computer using and FRMD4A (rs56227933, P = 7.42 × 10-11 ) for depression score and computer playing. CONCLUSIONS: Our findings suggested that electronic devices use was associated with common mental traits and provided new clues for understanding genetic architecture of mental traits.

Bioinformatics analysis of the role of CXC ligands in the microenvironment of head and neck tumor.

Chemokines play a significant role in cancer. CXC-motif chemokine ligands (CXCLs) are associated with the tumorigenesis and progression of head and neck squamous cell carcinoma (HNSC); however, their specific functions in the tumor microenvironment remain unclear. Here, we analyzed the molecular networks and transcriptional data of HNSC patients from the Oncomine, GEPIA, String, cBioPortal, Metascape, TISCH, and TIMER databases. To verify immune functions of CXCLs, their expression was analyzed in different immune cell types. To our knowledge, this is the first report on the correlation between CXCL9-12 and 14 expression and advanced tumor stage. CXCL2, 3, 8, 10, 13, and 16 were remarkably related to tumor immunity. Kaplan-Meier and TIMER survival analyses revealed that high expression of CXCL1, 2, 4, and 6-8 is correlated with low survival in HNSC patients, whereas high expression of CXCL9, 10, 13, 14, and 17 predicts high survival. Only CXCL13 and 14 were associated with overall survival in human papilloma virus (HPV)-negative patients. Single-cell datasets confirmed that CXCLs are associated with HNSC-related immune cells. Thus, CXCL1-6, 8-10, 12-14, and 17 could be prognostic targets for HNSC, and CXCL13 and 14 could be novel biomarkers of HPV-negative HNSC.

The Biological Function, Mechanism, and Clinical Significance of m6A RNA Modifications in Head and Neck Carcinoma: A Systematic Review.

Head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers, yet the molecular mechanisms underlying its onset and development have not yet been fully elucidated. Indeed, an in-depth understanding of the potential molecular mechanisms underlying HNSCC oncogenesis may aid the development of better treatment strategies. Recent epigenetic studies have revealed that the m6A RNA modification plays important roles in HNSCC. In this review, we summarize the role of m6A modification in various types of HNSCC, including thyroid, nasopharyngeal, hypopharyngeal squamous cell, and oral carcinoma. In addition, we discuss the regulatory roles of m6A in immune cells within the tumor microenvironment, as well as the potential molecular mechanisms. Finally, we review the development of potential targets for treating cancer based on the regulatory functions of m6A, with an aim to improving targeted therapies for HNSCC. Together, this review highlights the important roles that m6A modification plays in RNA synthesis, transport, and translation, and demonstrates that the regulation of m6A-related proteins can indirectly affect mRNA and ncRNA function, thus providing a novel strategy for reengineering intrinsic cell activity and developing simpler interventions to treat HNSCC.

Maternal smoking during pregnancy and risks to depression and anxiety in offspring: An observational study and genome-wide gene-environment interaction analysis in UK biobank cohort.

BACKGROUND: Maternal smoking during pregnancy (MSDP) has been reported to be associated with increased anxiety and depression behaviors in offspring. However, there is still scant evidence to support the link between MSDP and anxiety/depression. METHODS: Using the subjects from the UK Biobank cohort (n = 371,903-432,881). Logistic regression analyses were first conducted to test the correlation between MSDP and anxiety/depression in offspring. Second, genome-wide gene-environment interaction study (GWGEIS) analyses were conducted by PLINK, using MSDP as environmental factor. Genetic correlation analysis of anxiety/depression and smoking was conducted by the LDSC software using the published genome-wide association study (GWAS) summary data of four smoking traits (n = 337,334-1,232,091), anxiety (n = 31,880) and depression (n = 490,359). Finally, pathway enrichment analysis was carried out to detect the pathway involved in the development of offspring anxiety caused by the interaction of MSDP × SNPs. RESULTS: Observational analyses showed that anxiety and depression status in offspring were significantly associated with MSDP (all p < 0.0001). Further GWEGI analyses observed significant MSDP-gene interaction effects at UNC80 gene for anxiety (p = 9.09 × 10-9). LDSC did not detect significant genetic correlation between anxiety and smoking traits. Pathway analysis identified 19 significant pathways for anxiety, such as MANALO_HYPOXIA_UP (FDR = 5.50 × 10-4), REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS (FDR = 0.0304) and ONDER_CDH1_TARGETS_2_UP (FDR = 0.0371). CONCLUSION: Our study results suggested the important impact of MDSP on the risk of anxiety in offspring, partly attributing to environment-gene interactions effects.

Evaluate the effects of serum urate level on bone mineral density: a genome-wide gene-environment interaction analysis in UK Biobank cohort.

INTRODUCTION: Serum urate is associated with BMD and may be a protective factor. However, the exact association and mechanism are still unclear. We performed a genome-wide gene-environmental interaction study (GWGEIS) to explore the interaction effects between gene and urate on BMD, using data from the UK Biobank cohort. METHODS: A total of 4575 participants for femur total BMD, 4561 participants for L1-L4 BMD, and 237799 participants for heel BMD were included in the present study. Linear regression models were used to test for associations between urate and BMD (femur total BMD, L1-L4 BMD, heel BMD) by R software. GWGEIS was conducted by PLINK 2.0 using a generalize linear model, adjusted for age, sex, weight, smoking behavior, drinking behavior, physical activity and 10 principle components for population structure. RESULTS: Results showed that urate was positively associated with femur total BMD, L1-L4 BMD and heel BMD and similar findings were observed in both the male and female subgroups. GWGEIS identified 261 genome-wide significant (P < 5.00 × 10-8) SNP × urate interaction effects for femur total BMD (rs8192585 in NOTCH4, rs116080577 in PBX1, rs9409991 in COL5A1), 17 genome-wide significant SNP × urate interaction effects for heel BMD (rs145344540 in PDE11A and rs78485379 in DKK2), 17 suggestive genome-wide SNP × urate interaction effects (P < 1.00 × 10-5) for L1-L4 BMD (rs10977015 in PTPRD). We also detected genome-wide significant and suggestive SNP × urate interaction effects for BMD in both the male and female subgroups. CONCLUSIONS: This study reported several novel candidate genes, and strengthen the evidence of the interactive effects between gene and urate on the variations of BMD.

Integrating transcriptome-wide study and mRNA expression profiles yields novel insights into the biological mechanism of chondropathies.

BACKGROUND: Chondropathies are a group of cartilage diseases, which share some common pathogenetic features. The etiology of chondropathies is still largely obscure now. METHODS: A transcriptome-wide association study (TWAS) was performed using the UK Biobank genome-wide association study (GWAS) data of chondropathies (including 1314 chondropathy patients and 450,950 controls) with gene expression references of muscle skeleton (MS) and peripheral blood (YBL). The candidate genes identified by TWAS were further compared with three gene expression profiles of osteoarthritis (OA), cartilage tumor (CT), and spinal disc herniation (SDH), to confirm the functional relevance between the chondropathies and the candidate genes identified by TWAS. Functional mapping and annotation (FUMA) was used for the gene ontology enrichment analyses. Immunohistochemistry (IHC) was conducted to validate the accuracy of integrative analysis results. RESULTS: Integrating TWAS and mRNA expression profiles detected 84 candidate genes for knee OA, such as DDX20 (PTWAS YBL = 1.79 × 10- 3, fold change (FC) = 2.69), 10 candidate genes for CT, such as SRGN (PTWAS YBL = 1.46 × 10- 3, FC = 3.36), and 4 candidate genes for SDH, such as SUPV3L1 (PTWAS YBL = 3.59 × 10- 3, FC = 3.22). Gene set enrichment analysis detected 73 GO terms for knee OA, 3 GO terms for CT, and 1 GO term for SDH, such as mitochondrial protein complex (P = 7.31 × 10- 5) for knee OA, cytokine for CT (P = 1.13 × 10- 4), and ion binding for SDH (P = 3.55 × 10- 4). IHC confirmed that the protein expression level of DDX20 was significantly different between knee OA cartilage and healthy control cartilage (P = 0.0358). CONCLUSIONS: Multiple candidate genes and GO terms were detected for chondropathies. Our findings may provide a novel insight in the molecular mechanisms of chondropathies.

miRNA-21 promotes osteogenesis via the PTEN/PI3K/Akt/HIF-1α pathway and enhances bone regeneration in critical size defects.

BACKGROUND: Functional reconstruction of maxillofacial bone defects is a considerable clinical challenge. Many studies have emphasized the osteogenic and angiopoietic abilities of stem cells for tissue regeneration. We previously showed that microRNA-21 (miRNA-21) can promote angiogenesis in human umbilical cord blood-derived mesenchymal stem cells (UCBMSCs). In the present study, the role of miRNA-21 in osteogenic differentiation of bone marrow-derived stem cells (BMSCs) was investigated. METHODS: Western blotting and qPCR were performed to investigate the influences of miRNA-21 on osteogenic differentiation of BMSCs. The effects of miRNA-21 on PTEN/PI3K/Akt/HIF-1α pathway were also assessed using western blotting. To further evaluate the roles of miRNA-21 in osteogenesis in vivo, we conducted animal experiments in rat and canine. New bone formation was assessed using micro-CT and histological methods. RESULTS: In the present study, we found that miRNA-21 promotes the migration and osteogenic differentiation of bone marrow-derived stem cells (BMSCs) in vitro. Using gain- and loss-of-function studies, we found that miRNA-21 promoted the osteogenic ability of BMSCs by increasing P-Akt and HIF-1α activation. Finally, we verified the essential role of miRNA-21 in osteogenesis by implanting a miRNA-21-modified BMSCs/ß-tricalcium phosphate (ß-TCP) composite into critical size defects. Radiography, micro-CT, and histology revealed significantly greater volume of new bone formation in the miRNA-21 group than in the control group. CONCLUSION: In conclusion, our study demonstrated an essential role of miRNA-21 in promoting maxillofacial bone regeneration via the PTEN/PI3K/Akt/HIF-1α pathway.

Functional reconstruction of critical-sized load-bearing bone defects using a Sclerostin-targeting miR-210-3p-based construct to enhance osteogenic activity.

A considerable amount of research has focused on improving regenerative therapy strategies for repairing defects in load-bearing bones. The enhancement of tissue regeneration with microRNAs (miRNAs) is being developed because miRNAs can simultaneously regulate multiple signaling pathways in an endogenous manner. In this study, we developed a miR-210-based bone repair strategy. We identified a miRNA (miR-210-3p) that can simultaneously up-regulate the expression of multiple key osteogenic genes in vitro. This process resulted in enhanced bone formation in a subcutaneous mouse model with a miR-210-3p/poly-l-lactic acid (PLLA)/bone marrow-derived stem cell (BMSC) construct. Furthermore, we constructed a model of critical-sized load-bearing bone defects and implanted a miR-210-3p/ß-tricalcium phosphate (ß-TCP)/bone mesenchymal stem cell (BMSC) construct into the defect. We found that the load-bearing defect was almost fully repaired using the miR-210-3p construct. We also identified a new mechanism by which miR-210-3p regulates Sclerostin protein levels. This miRNA-based strategy may yield novel therapeutic methods for the treatment of regenerative defects in vital load-bearing bones by utilizing miRNA therapy for tissue engineering. STATEMENT OF SIGNIFICANCE: The destroyed maxillofacial bone reconstruction is still a real challenge for maxillofacial surgeon, due to that functional bone reconstruction involved load-bearing. Base on the above problem, this paper developed a novel miR-210-3p/ß-tricalcium phosphate (TCP)/bone marrow-derived stem cell (BMSC) construct (miR-210-3p/ß-TCP/BMSCs), which lead to functional reconstruction of critical-size mandible bone defect. We found that the load-bearing defect was almost fully repaired using the miR-210-3p construct. In addition, we also found the mechanism of how the delivered microRNA activated the signaling pathways of endogenous stem cells, leading to the defect regeneration. This miRNA-based strategy can be used to regenerate defects in vital load-bearing bones, thus addressing a critical challenge in regenerative medicine by utilizing miRNA therapy for tissue engineering.

Serum and Hair Zinc Levels in Patients with Endemic Osteochondropathy in China: A Meta-analysis.

A large number of studies have shown growing interest in the zinc (Zn) levels of serum and hair samples collected from patients with Kashin-Beck disease (KBD), an endemic chronic osteochondral disease. However, inconsistent conclusions regarding the serum and hair Zn levels have been made. The aim of this study is to assess and to explore the change in serum and hair Zn levels among KBD patients. Multiple databases, including PubMed, Web of Science, Chinese National Knowledge Infrastructure (CNKI), Wanfang database and Technology of Chongqing (VIP), were carefully searched for available studies up to January 13, 2017 in this integrated analysis. Standard mean difference (SMD) with a 95% confidence interval (95% CI) was calculated using STATA 11.0. A total of 18 studies, involving 978 KBD cases and 1116 healthy controls, were collected in this analysis. Pooled analysis found the KBD patients had a higher hair Zn level and a lower serum Zn level than the healthy controls (hair Zn (µg/g), SMD = 0.030, 95% CI = -0.315, 0.376; serum Zn (mg/L), SMD = -0.069, 95%CI = -0.924, 0.785). Meta-regression method and sensitivity analysis were utilized to analyze the heterogeneity of data. Positive correlations were separately identified between hair Zn level in KBD patients (r = 0.4639, P = 0.032) and controls (r = 0.4743, P = 0.012) and the survey year. No evidence of publication bias was observed. The available results suggest that increased hair Zn level and decreased serum Zn level are commonly found in KBD patients; however, the role of Zn in the etiology and pathogenesis of KBD could not yet be confirmed.

GWAS summary-based pathway analysis correcting for the genetic confounding impact of environmental exposures.

Genome-wide association study (GWAS)-based pathway association analysis is a powerful approach for the genetic studies of human complex diseases. However, the genetic confounding effects of environment exposure-related genes can decrease the accuracy of GWAS-based pathway association analysis of target diseases. In this study, we developed a pathway association analysis approach, named Mendelian randomization-based pathway enrichment analysis (MRPEA), which was capable of correcting the genetic confounding effects of environmental exposures, using the GWAS summary data of environmental exposures. After analyzing the real GWAS summary data of cardiovascular disease and cigarette smoking, we observed significantly improved performance of MRPEA compared with traditional pathway association analysis (TPAA) without adjusting for environmental exposures. Further, simulation studies found that MRPEA generally outperformed TPAA under various scenarios. We hope that MRPEA could help to fill the gap of TPAA and identify novel causal pathways for complex diseases.

Diagnostic value of circulating microRNAs for osteosarcoma in Asian populations: a meta-analysis.

A large number of studies have provided new insights into the diagnostic value of circulating microRNAs (miRNA) for osteosarcoma (OS), one of the most common primary malignancies in adolescents. However, inconsistent conclusions on the diagnostic performance of various kinds of miRNAs have been made. To assess the true diagnostic value of circulating miRNA for the early detection of OS in this meta-analysis, multiple databases, including PubMed, EMBASE, Web of Science, Chinese National Knowledge Infrastructure (CNKI), and Technology of Chongqing (VIP), were carefully searched for available studies up to October 30, 2015. The quality of each study was scored using the quality assessment of diagnostic accuracy studies-2 (QUADAS-2). Sensitivity and specificity was pooled using a random-effects model. Positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and the area under the curve (AUC) were used to measure the diagnostic values. Subgroup and meta-regression analyses were used to find potential sources of heterogeneity. Publication bias was tested with the Deeks' funnel plot asymmetry test. Eight articles with 741 OS patients and 479 healthy controls were finally included in this meta-analysis. The pooled estimations indicated circulating miRNAs has a high accuracy for diagnosing OS, with sensitivity of 0.94, specificity of 0.80, PLR of 4.75, NLR of 0.07, DOR of 69, and AUC of 0.94. In addition, subgroup and meta-regression analyses revealed that the expression patterns of miRNAs obtained from plasma are more credible diagnostic biomarkers than those from serum. In conclusion, as noninvasive biomarkers, circulating miRNAs have a promising future for the diagnosis of OS in Asian populations.