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1.
Int J Cancer ; 2019 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-31265136

RESUMO

A small number of circulating proteins have been reported to be associated with breast cancer risk, with inconsistent results. Herein, we attempted to identify novel protein biomarkers for breast cancer via the integration of genomics and proteomics data. In the Breast Cancer Association Consortium (BCAC), with 122,977 cases and 105,974 controls of European descendants, we evaluated the associations of the genetically predicted concentrations of >1,400 circulating proteins with breast cancer risk. We used data from a large-scale protein quantitative trait loci (pQTL) analysis as our study instrument. Summary statistics for these pQTL variants related to breast cancer risk were obtained from the BCAC and used to estimate odds ratios (OR) for each protein using the inverse-variance weighted method. We identified 56 proteins significantly associated with breast cancer risk by instrumental analysis (false discovery rate <0.05). Of these, the concentrations of 32 were influenced by variants close to a breast cancer susceptibility locus (ABO, 9q34.2). Many of these proteins, such as insulin receptor, insulin-like growth factor receptor 1 and other membrane receptors (OR: 0.82-1.18, p values: 6.96 × 10-4 -3.28 × 10-8 ), are linked to insulin resistance and estrogen receptor signaling pathways. Proteins identified at other loci include those involved in biological processes such as alcohol and lipid metabolism, proteolysis, apoptosis, immune regulation and cell motility and proliferation. Consistent associations were observed for 22 proteins in the UK Biobank data (p < 0.05). The study identifies potential novel biomarkers for breast cancer, but further investigation is needed to replicate our findings.

2.
Cancer Res ; 79(18): 4592-4598, 2019 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-31337649

RESUMO

Several blood protein biomarkers have been associated with prostate cancer risk. However, most studies assessed only a small number of biomarkers and/or included a small sample size. To identify novel protein biomarkers of prostate cancer risk, we studied 79,194 cases and 61,112 controls of European ancestry, included in the PRACTICAL/ELLIPSE consortia, using genetic instruments of protein quantitative trait loci for 1,478 plasma proteins. A total of 31 proteins were associated with prostate cancer risk including proteins encoded by GSTP1, whose methylation level was shown previously to be associated with prostate cancer risk, and MSMB, SPINT2, IGF2R, and CTSS, which were previously implicated as potential target genes of prostate cancer risk variants identified in genome-wide association studies. A total of 18 proteins inversely correlated and 13 positively correlated with prostate cancer risk. For 28 of the identified proteins, gene somatic changes of short indels, splice site, nonsense, or missense mutations were detected in patients with prostate cancer in The Cancer Genome Atlas. Pathway enrichment analysis showed that relevant genes were significantly enriched in cancer-related pathways. In conclusion, this study identifies 31 candidates of protein biomarkers for prostate cancer risk and provides new insights into the biology and genetics of prostate tumorigenesis. SIGNIFICANCE: Integration of genomics and proteomics data identifies biomarkers associated with prostate cancer risk.

4.
J Natl Cancer Inst ; 2019 May 29.
Artigo em Inglês | MEDLINE | ID: mdl-31143935

RESUMO

BACKGROUND: DNA methylation plays a critical role in breast cancer development. Previous studies have identified DNA methylation marks in white blood cells as promising biomarkers for breast cancer. However, these studies were limited by low statistical power and potential biases. Utilizing a new methodology, we investigated DNA methylation marks for their associations with breast cancer risk. METHODS: Statistical models were built to predict levels of DNA methylation marks using genetic data and DNA methylation data from HumanMethylation450 BeadChip from the Framingham Heart Study (N=1,595). The prediction models were validated using data from the Women's Health Initiative (N=883). We applied these models to genome-wide association study (GWAS) data of 122,977 breast cancer cases and 105,974 controls to evaluate if the genetically predicted DNA methylation levels at CpGs are associated with breast cancer risk. All statistical tests were two-sided. RESULTS: Of the 62,938 CpG sites (CpGs) investigated, statistically significant associations with breast cancer risk were observed for 450 CpGs at a Bonferroni-corrected threshold of P<7.94 × 10-7, including 45 CpGs residing in 18 genomic regions which have not previously been associated with breast cancer risk. Of the remaining 405 CpGs located within 500 kilobase flaking regions of 70 GWAS-identified breast cancer risk variants, the associations for 11 CpGs were independent of GWAS-identified variants. Integrative analyses of genetic, DNA methylation and gene expression data found that 38 CpGs may affect breast cancer risk through regulating expression of 21 genes. CONCLUSION: Our new methodology can identify novel DNA methylation biomarkers for breast cancer risk and can be applied to other diseases.

5.
Cancer Res ; 79(13): 3192-3204, 2019 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-31101764

RESUMO

Genome-wide association study-identified prostate cancer risk variants explain only a relatively small fraction of its familial relative risk, and the genes responsible for many of these identified associations remain unknown. To discover novel prostate cancer genetic loci and possible causal genes at previously identified risk loci, we performed a transcriptome-wide association study in 79,194 cases and 61,112 controls of European ancestry. Using data from the Genotype-Tissue Expression Project, we established genetic models to predict gene expression across the transcriptome for both prostate models and cross-tissue models and evaluated model performance using two independent datasets. We identified significant associations for 137 genes at P < 2.61 × 10-6, a Bonferroni-corrected threshold, including nine genes that remained significant at P < 2.61 × 10-6 after adjusting for all known prostate cancer risk variants in nearby regions. Of the 128 remaining associated genes, 94 have not yet been reported as potential target genes at known loci. We silenced 14 genes and many showed a consistent effect on viability and colony-forming efficiency in three cell lines. Our study provides substantial new information to advance our understanding of prostate cancer genetics and biology. SIGNIFICANCE: This study identifies novel prostate cancer genetic loci and possible causal genes, advancing our understanding of the molecular mechanisms that drive prostate cancer.

6.
Artigo em Inglês | MEDLINE | ID: mdl-31028930

RESUMO

Copper (Cu) and cadmium (Cd) are two kinds of abundant toxic metals in aquatic ecosystem. The present study evaluated the effects of waterborne Cu and Cd on oxidative stress responses and histological alterations in female rare minnow (Gobiocypris rarus). Fish were exposed for 7 days to: (i) control (no added Cu or Cd), (ii) waterborne Cu (39.2 µg L-1), (iii) waterborne Cd (299.6 µg L-1), and (iv) Cu and Cd in mixture (19.6 and 149.8 µg L-1, respectively). Antioxidant enzyme activities and gene mRNA abundance in fish tissues (gills, liver, and ovaries) were induced by Cu and Cd exposures, both individually and in mixture, at day 1, but an asynchronous response was observed between most enzyme activities and gene mRNA abundance following 7 days exposure. Biochemical analysis and histological observation indicated that exposure to Cu and Cd, alone and in combination, caused evident damage to lipids and tissue structure in gills, liver and ovaries. Comparing with single Cu or Cd exposure, Cu and Cd co-exposure induced greater increase in the mRNA expression of most antioxidant genes and caused more severe lesions in fish tissues, which suggested that exposure to waterborne Cu and Cd in mixture might increase their individual toxicity. Furthermore, positive relationships between nuclear factor erythroid 2-related factor (Nrf2) expression and expression of manganese superoxide dismutase (Mn-SOD) and catalase (CAT) were also observed in the present study, which suggested that Cu or/and Cd induced expression of these antioxidant genes were might through activation of Nrf2.


Assuntos
Cádmio/toxicidade , Cobre/toxicidade , Cyprinidae/fisiologia , Doenças dos Peixes/induzido quimicamente , Estresse Oxidativo/efeitos dos fármacos , Animais , Cádmio/administração & dosagem , Cobre/administração & dosagem , Feminino , Regulação da Expressão Gênica/efeitos dos fármacos , Brânquias/efeitos dos fármacos , Glutationa , Fígado/efeitos dos fármacos , Malondialdeído , Ovário/efeitos dos fármacos , Testes de Toxicidade , Poluentes Químicos da Água/administração & dosagem , Poluentes Químicos da Água/toxicidade
7.
Int J Mol Sci ; 20(3)2019 Jan 29.
Artigo em Inglês | MEDLINE | ID: mdl-30699994

RESUMO

Cytoplasmic male sterility (CMS), which is controlled by mitochondrial genes, is an important trait for commercial hybrid seed production. So far, genes controlling this trait are still not clear in pepper. In this study, complete mitochondrial genomes were sequenced and assembled for the CMS line 138A and its maintainer line 138B. The genome size of 138A is 504,210 bp, which is 8618 bp shorter than that of 138B. Meanwhile, more than 214 and 215 open reading frames longer than 100 amino acids (aas) were identified in 138A and 138B, respectively. Mitochondrial genome structure of 138A was quite different from that of 138B, indicating the existence of recombination and rearrangement events. Based on the mitochondrial genome sequence and structure variations, mitochondrion of 138A and FS4401, a Korean origin CMS line, may have inherited from a common female ancestor, but their CMS traits did originate separately. Candidate gene selection was performed according to the published characteristics of the CMS genes, including the presence SNPs and InDels, located in unique regions, their chimeric structure, co-transcription, and transmembrane domain. A total of 35 ORFs were considered as potential candidate genes and 14 of these were selected, with orf300a and 0rf314a as strong candidates. A new marker, orf300a, was developed which did co-segregate with the CMS trait.


Assuntos
Capsicum/genética , Capsicum/fisiologia , Genoma Mitocondrial/genética , Infertilidade das Plantas/genética , Infertilidade das Plantas/fisiologia , Citoplasma/metabolismo , Proteínas de Plantas/genética
8.
Ecotoxicol Environ Saf ; 171: 475-483, 2019 Apr 30.
Artigo em Inglês | MEDLINE | ID: mdl-30639874

RESUMO

Bisphenol A (BPA), an environmental contaminant, has been shown to disturb the dynamics of Sertoli cell blood-testis barrier (BTB) in mammal testis. However, the effects of BPA on Sertoli cell barrier (SC barrier) were little known in fish to date. To evaluate the potential mechanism of reproductive toxicity of BPA, we studied the damage of SC barrier using in vivo models. In this study, male adult rare minnow Gobiocypris rarus were exposed to 15 µg/L BPA for 7-35 days. Gonadal histology and the integrity of SC barrier were analyzed. Meanwhile, the expressions of SC barrier -associated proteins, tumor necrosis factor (TNFα) content, and the mRNA expressions of genes in the mitogen activated protein kinase (MAPK) pathway were detected. Histological analysis demonstrated 15 µg/L BPA promoted the infiltration of inflammatory cells in fish testes after 7-days exposure. The biotin tracer assay showed that 7-days BPA exposure increased permeability for spermatid cysts. In addition, the BPA treatment caused increased TNFα in testis, which was reportedly related to SC barrier impairment. The expressions of Occludin and ß-Catenin protein were significantly decreased in the testes after 7- and 21-days exposure. BPA also altered the mRNA expressions of occludin, ß-catenin, p38 MAPK and JNK. Therefore, the detrimental effects of BPA on reproduction of male fish may attribute to the disturbed expressions of SC junction proteins.


Assuntos
Compostos Benzidrílicos/toxicidade , Barreira Hematotesticular/efeitos dos fármacos , Cyprinidae , Fenóis/toxicidade , Células de Sertoli/efeitos dos fármacos , Animais , Barreira Hematotesticular/metabolismo , Gônadas/efeitos dos fármacos , Gônadas/metabolismo , Masculino , Ocludina/genética , Ocludina/metabolismo , Células de Sertoli/metabolismo , Testículo/efeitos dos fármacos , Testículo/metabolismo , Fator de Necrose Tumoral alfa/efeitos dos fármacos , Fator de Necrose Tumoral alfa/metabolismo , beta Catenina/genética , beta Catenina/metabolismo
9.
Cancer Res ; 79(3): 505-517, 2019 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-30559148

RESUMO

DNA methylation is instrumental for gene regulation. Global changes in the epigenetic landscape have been recognized as a hallmark of cancer. However, the role of DNA methylation in epithelial ovarian cancer (EOC) remains unclear. In this study, high-density genetic and DNA methylation data in white blood cells from the Framingham Heart Study (N = 1,595) were used to build genetic models to predict DNA methylation levels. These prediction models were then applied to the summary statistics of a genome-wide association study (GWAS) of ovarian cancer including 22,406 EOC cases and 40,941 controls to investigate genetically predicted DNA methylation levels in association with EOC risk. Among 62,938 CpG sites investigated, genetically predicted methylation levels at 89 CpG were significantly associated with EOC risk at a Bonferroni-corrected threshold of P < 7.94 × 10-7. Of them, 87 were located at GWAS-identified EOC susceptibility regions and two resided in a genomic region not previously reported to be associated with EOC risk. Integrative analyses of genetic, methylation, and gene expression data identified consistent directions of associations across 12 CpG, five genes, and EOC risk, suggesting that methylation at these 12 CpG may influence EOC risk by regulating expression of these five genes, namely MAPT, HOXB3, ABHD8, ARHGAP27, and SKAP1. We identified novel DNA methylation markers associated with EOC risk and propose that methylation at multiple CpG may affect EOC risk via regulation of gene expression. SIGNIFICANCE: Identification of novel DNA methylation markers associated with EOC risk suggests that methylation at multiple CpG may affect EOC risk through regulation of gene expression.

10.
Int J Epidemiol ; 2018 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-30277539

RESUMO

Background: In addition to the established association between general obesity and breast cancer risk, central obesity and circulating fasting insulin and glucose have been linked to the development of this common malignancy. Findings from previous studies, however, have been inconsistent, and the nature of the associations is unclear. Methods: We conducted Mendelian randomization analyses to evaluate the association of breast cancer risk, using genetic instruments, with fasting insulin, fasting glucose, 2-h glucose, body mass index (BMI) and BMI-adjusted waist-hip-ratio (WHRadj BMI). We first confirmed the association of these instruments with type 2 diabetes risk in a large diabetes genome-wide association study consortium. We then investigated their associations with breast cancer risk using individual-level data obtained from 98 842 cases and 83 464 controls of European descent in the Breast Cancer Association Consortium. Results: All sets of instruments were associated with risk of type 2 diabetes. Associations with breast cancer risk were found for genetically predicted fasting insulin [odds ratio (OR) = 1.71 per standard deviation (SD) increase, 95% confidence interval (CI) = 1.26-2.31, p = 5.09 × 10-4], 2-h glucose (OR = 1.80 per SD increase, 95% CI = 1.3 0-2.49, p = 4.02 × 10-4), BMI (OR = 0.70 per 5-unit increase, 95% CI = 0.65-0.76, p = 5.05 × 10-19) and WHRadj BMI (OR = 0.85, 95% CI = 0.79-0.91, p = 9.22 × 10-6). Stratified analyses showed that genetically predicted fasting insulin was more closely related to risk of estrogen-receptor [ER]-positive cancer, whereas the associations with instruments of 2-h glucose, BMI and WHRadj BMI were consistent regardless of age, menopausal status, estrogen receptor status and family history of breast cancer. Conclusions: We confirmed the previously reported inverse association of genetically predicted BMI with breast cancer risk, and showed a positive association of genetically predicted fasting insulin and 2-h glucose and an inverse association of WHRadj BMI with breast cancer risk. Our study suggests that genetically determined obesity and glucose/insulin-related traits have an important role in the aetiology of breast cancer.

11.
Biomed Pharmacother ; 107: 1210-1217, 2018 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-30257335

RESUMO

BACKGROUND AND AIM: Intrahepatic biliary epithelial cells (IBECs) of the bile duct in liver tissue of patients with hepatolithiasis promoted the development of diseases through epithelial-mesenchymal transition (EMT). This study investigated whether lipopolysaccharide (LPS), a cell-wall constituent of gram-negative bacteria, could induce EMT of IBECs and toll-like receptor 4 (TLR4) had a regulatory role via activating the nuclear factor-κB (NF-κB)/Snail signaling pathway during this process in vivo. METHODS: TLR4 short hairpin RNA (shRNA) adenovirus or negative control shRNA (NC shRNA) adenovirus (1 × 109 plaque-forming unit (PFU), respectively) was injected into the caudal vein of rats. After 96 h, 1 mg/kg LPS was infused retrogradely into the common bile duct for 48 h per rat. The effects of TLR4 shRNA on LPS-induced EMT were determined by evaluating the histopathological changes in IBECs using hematoxylin and eosin staining and the changes in the levels of EMT markers, TLR4, NF-κB p65, pNF-κB p65, and Snail using real-time polymerase chain reaction and Western blot analysis. RESULTS: Compared with normal saline treatment, a loss of epithelial cell markers (E-cadherin and cytokeratin 7) and a gain of mesenchymal cell markers (N-cadherin and matrix metalloproteinase 2) were revealed. The levels of TLR4, NF-κB phosphorylation, and Snail significantly increased after LPS treatment, whereas pretreatment with TLR4 shRNA inhibited the LPS-induced EMT by downregulating the NF-κB/Snail signaling pathway. CONCLUSIONS: LPS induced the EMT of IBECs by activating TLR4. The RNAi-mediated knockdown of TLR4 suppressed EMT occurrence via downregulating the NF-κB/Snail signaling pathway, implicating TLR4 as a new target for human hepatolithiasis.

12.
Stat Med ; 37(30): 4758-4770, 2018 Dec 30.
Artigo em Inglês | MEDLINE | ID: mdl-30225919

RESUMO

Semicontinuous longitudinal data are characterized by within-subjects repeated measurements that either indicate absence of abnormality or reflect different amount of abnormality. Joint models for semicontinuous longitudinal data have been increasingly receiving attention in the literature. Such models permit flexible characterization of covariates-outcome associations. Order-restricted statistical inference has been well established in the literature but has not yet been applied to joint models for semicontinuous longitudinal data. We incorporate general order-restricted inference into the general joint models for semicontinuous longitudinal data previously proposed. We develop computational methods to address general order restrictions. Through simulations and a real-data example, we demonstrate the advantages of order-restricted inference in terms of increased power in hypothesis testing and increased precision in parameter estimation.

13.
Ecotoxicol Environ Saf ; 163: 514-520, 2018 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-30075455

RESUMO

Bisphenol A (BPA), an endocrine disrupting compound, is present in the aquatic environment. BPA can mimic estrogen and cause adverse effects on development and reproduction in different organisms. As epigenetic modifications due to BPA exposure have been reported, the interest on the effects of this chemical has increased. To assess the potential effects of maternal BPA exposure on offspring bone development, adult Gobiocypris rarus (G. rarus) females were exposed to 15 µg L-1 and 225 µg L-1 BPA for 21 days. Eggs were collected after artificial spawning and fertilized with the fresh milt of non-exposed male fish. The offspring were raised in clean water and randomly selected for examination at different development stages. Our results showed that specific effects including poor quality of the embryos, increased malformation (bent spine and tail), and delayed craniofacial cartilage ossification of the larvae. Additionally, the transcripts of ossification related genes were significantly downregulated in offspring, and the lysyloxidase activity decreased. The present study demonstrated the maternal-mediated skeleton toxicity of BPA and its adverse effects on G. rarus.


Assuntos
Compostos Benzidrílicos/toxicidade , Cartilagem/anormalidades , Cyprinidae/anormalidades , Disruptores Endócrinos/toxicidade , Fenóis/toxicidade , Poluentes Químicos da Água/toxicidade , Animais , Exposição Ambiental , Feminino , Masculino , Osteogênese/efeitos dos fármacos
14.
Cancer Epidemiol Biomarkers Prev ; 27(11): 1364-1370, 2018 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-30038052

RESUMO

Background: Pathogenic germline mutations in the CDKN2A tumor suppressor gene are rare and associated with highly penetrant familial melanoma and pancreatic cancer in non-Hispanic whites (NHW). To date, the prevalence and impact of CDKN2A rare coding variants (RCV) in racial minority groups remain poorly characterized. We examined the role of CDKN2A RCVs on the risk of pancreatic cancer among minority subjects.Methods: We sequenced CDKN2A in 220 African American (AA) pancreatic cancer cases, 900 noncancer AA controls, and 183 Nigerian controls. RCV frequencies were determined for each group and compared with that of 1,537 NHW patients with pancreatic cancer. Odds ratios (OR) and 95% confidence intervals (CI) were calculated for both a case-case comparison of RCV frequencies in AAs versus NHWs, and case-control comparison between AA cases versus noncancer AA controls plus Nigerian controls. Smaller sets of Hispanic and Native American cases and controls also were sequenced.Results: One novel missense RCV and one novel frameshift RCV were found among AA patients: 400G>A and 258_278del. RCV carrier status was associated with increased risk of pancreatic cancer among AA cases (11/220; OR, 3.3; 95% CI, 1.5-7.1; P = 0.004) compared with AA and Nigerian controls (17/1,083). Further, AA cases had higher frequency of RCVs: 5.0% (OR, 13.4; 95% CI, 4.9-36.7; P < 0.001) compared with NHW cases (0.4%).Conclusions: CDKN2A RCVs are more common in AA than in NHW patients with pancreatic cancer and associated with moderately increased pancreatic cancer risk among AAs.Impact: RCVs in CDKN2A are frequent in AAs and are associated with risk for pancreatic cancer. Cancer Epidemiol Biomarkers Prev; 27(11); 1364-70. ©2018 AACR.

15.
Calcif Tissue Int ; 2018 Jul 14.
Artigo em Inglês | MEDLINE | ID: mdl-30008090

RESUMO

Observational studies examining associations of smoking and alcohol consumption with bone mineral density (BMD) have generated inconsistent results and suffer from several methodological limitations. We aim to evaluate whether there are causal associations between smoking, alcohol consumption, and BMD using a Mendelian randomization (MR) design. Genetic variants associated with smoking status (n = 142), no. of cigarettes smoked per day (CPD) (n = 3), smoking initiation (n = 1), and alcohol consumption (n = 6) identified in published genome-wide association studies (GWAS) were used as instruments. Summary statistics data of 32735, 28498, 8143, and 445921 European subjects included in The GEnetic Factors for Osteoporosis Consortium or UK Biobank were used to generate associations of genetically predicted smoking or alcohol consumption with femoral neck (FN-BMD), lumbar spine (LS-BMD), forearm (FA-BMD), and heel BMD, respectively, by using the inverse-variance weighted method. The BMD was measured using either ultrasound (for heel) or Dual-energy X-ray Absorptiometry (for others). In our analyses, smoking status tended to be negatively associated with several types of BMD (heel BMD: ß = - 0.053, p = 0.003; FN-BMD: ß = - 0.139, p = 0.053; FA-BMD: ß = - 0.264, p = 0.077), although the association with LS-BMD was null. Smoking initiation was significantly inversely associated with heel BMD (ß = - 0.201, p = 3.60 × 10-8). CPD was associated with a lower FN-BMD (ß = - 0.014, p = 0.047) only. There was no clear association of genetically predicted alcohol consumption with BMD. Our study provided some evidence of a potential association between genetically predicted smoking and lower BMD, especially for heel BMD, but not for alcohol consumption. Considering the inconsistent findings with the different types of BMD and limitations of the current work, further studies are needed to better characterize the exact relationship between smoking, alcohol consumption, and BMD.

16.
Cancer Res ; 78(18): 5419-5430, 2018 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-30054336

RESUMO

Large-scale genome-wide association studies (GWAS) have identified approximately 35 loci associated with epithelial ovarian cancer (EOC) risk. The majority of GWAS-identified disease susceptibility variants are located in noncoding regions, and causal genes underlying these associations remain largely unknown. Here, we performed a transcriptome-wide association study to search for novel genetic loci and plausible causal genes at known GWAS loci. We used RNA sequencing data (68 normal ovarian tissue samples from 68 individuals and 6,124 cross-tissue samples from 369 individuals) and high-density genotyping data from European descendants of the Genotype-Tissue Expression (GTEx V6) project to build ovarian and cross-tissue models of genetically regulated expression using elastic net methods. We evaluated 17,121 genes for their cis-predicted gene expression in relation to EOC risk using summary statistics data from GWAS of 97,898 women, including 29,396 EOC cases. With a Bonferroni-corrected significance level of P < 2.2 × 10-6, we identified 35 genes, including FZD4 at 11q14.2 (Z = 5.08, P = 3.83 × 10-7, the cross-tissue model; 1 Mb away from any GWAS-identified EOC risk variant), a potential novel locus for EOC risk. All other 34 significantly associated genes were located within 1 Mb of known GWAS-identified loci, including 23 genes at 6 loci not previously linked to EOC risk. Upon conditioning on nearby known EOC GWAS-identified variants, the associations for 31 genes disappeared and three genes remained (P < 1.47 × 10-3). These data identify one novel locus (FZD4) and 34 genes at 13 known EOC risk loci associated with EOC risk, providing new insights into EOC carcinogenesis.Significance: Transcriptomic analysis of a large cohort confirms earlier GWAS loci and reveals FZD4 as a novel locus associated with EOC risk. Cancer Res; 78(18); 5419-30. ©2018 AACR.

17.
Nat Genet ; 50(7): 968-978, 2018 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-29915430

RESUMO

The breast cancer risk variants identified in genome-wide association studies explain only a small fraction of the familial relative risk, and the genes responsible for these associations remain largely unknown. To identify novel risk loci and likely causal genes, we performed a transcriptome-wide association study evaluating associations of genetically predicted gene expression with breast cancer risk in 122,977 cases and 105,974 controls of European ancestry. We used data from the Genotype-Tissue Expression Project to establish genetic models to predict gene expression in breast tissue and evaluated model performance using data from The Cancer Genome Atlas. Of the 8,597 genes evaluated, significant associations were identified for 48 at a Bonferroni-corrected threshold of P < 5.82 × 10-6, including 14 genes at loci not yet reported for breast cancer. We silenced 13 genes and showed an effect for 11 on cell proliferation and/or colony-forming efficiency. Our study provides new insights into breast cancer genetics and biology.

18.
Lifetime Data Anal ; 2018 Jun 08.
Artigo em Inglês | MEDLINE | ID: mdl-29948579

RESUMO

In HIV vaccine studies, longitudinal immune response biomarker data are often left-censored due to lower limits of quantification of the employed immunological assays. The censoring information is important for predicting HIV infection, the failure event of interest. We propose two approaches to addressing left censoring in longitudinal data: one that makes no distributional assumptions for the censored data-treating left censored values as a "point mass" subgroup-and the other makes a distributional assumption for a subset of the censored data but not for the remaining subset. We develop these two approaches to handling censoring for joint modelling of longitudinal and survival data via a Cox proportional hazards model fit by h-likelihood. We evaluate the new methods via simulation and analyze an HIV vaccine trial data set, finding that longitudinal characteristics of the immune response biomarkers are highly associated with the risk of HIV infection.

19.
Reprod Sci ; : 1933719118776788, 2018 May 30.
Artigo em Inglês | MEDLINE | ID: mdl-29848177

RESUMO

OBJECTIVE: To identify novel susceptibility genes for age at natural menopause (ANM). METHODS: Using transcription data generated in tissues from normal hypothalami (n = 73) and ovaries (n = 68) and high-density genotyping data provided by the Genotype-Tissue Expression (GTEx) database, we built 16 164 genetic models to predict gene expression across the transcriptome in these tissues. We used these models and summary statistics data from genome-wide association studies (GWAS) of ANM generated in 69 360 women of European ancestry to identify genes with their predicted expression related to ANM. RESULTS: We found the predicted expression of 34 genes to be significantly associated with ANM at a Bonferroni-corrected threshold of P < 3.09 ×10-6. These include 4 genes located more than 1 Mb away from any previously GWAS-identified ANM-associated variants, 24 genes that reside in known GWAS-identified loci but have not been previously implicated, and 6 genes previously implicated as ANM-associated genes. CONCLUSION: Results from this transcriptome-wide association study, which integrated Expression quantitative trait loci (eQTL) data with summary statistics of GWAS of ANM, improves our understanding of the genetics and biology of female reproductive aging.

20.
Theor Appl Genet ; 131(9): 1861-1872, 2018 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-29855672

RESUMO

KEY MESSAGE: Based on genome resequencing, a strong candidate gene Capana02g002096 was identified in this study. Capana02g002096 encodes a homolog of AtDYT1 which is a bHLH transcription factor and involves in the early tapetal development. Genic male-sterile line is an efficient tool for commercial hybrid seed production in pepper; however, so far, only few genes controlling this trait have been cloned. A spontaneous genic male-sterile mutant, msc-1, had been identified and widely used in China, of which the male-sterile trait was proved to be controlled by a single recessive locus. For cloning the gene(s) underlying the msc-1 locus, genome resequencing and comparison analyses were performed between male-sterile and male-fertile lines. According to the genomic variations and genes' annotations, Capana02g002096 was selected as a candidate gene underlying the msc-1 locus. Capana02g002096 encodes a homolog of AtDYT1, which is a bHLH transcription factor and involves in the early tapetal development. Moreover, a 7-bp deletion was identified in the exon of Capana02g002096, which led to a premature stop codon and may cause a loss-of-function mutation. Further genotyping in the 16C1369AB population containing 1110 plants, a F2 population consisting of 510 plants and 46 inbreed lines revealed that the male-sterile phenotype was co-segregated with the 7-bp deletion. Additionally, real-time PCR analysis revealed that Capana02g002096 was an anther-specific gene and repression of the gene's expression through VIGS led to male-sterile phenotype. Therefore, based on the evidence at genetic, genomic, transcriptional and posttranscriptional levels, Capana02g002096 was considered as a strong candidate gene underlying the msc-1 locus in pepper and was renamed Msc-1.


Assuntos
Fatores de Transcrição de Zíper de Leucina e Hélice-Alça-Hélix Básicos/genética , Capsicum/genética , Genes de Plantas , Infertilidade das Plantas/genética , Sequência de Aminoácidos , Clonagem Molecular , Códon sem Sentido , Inativação Gênica , Fenótipo , Deleção de Sequência
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