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  • 1
    In: G3 Genes|Genomes|Genetics, Oxford University Press (OUP), Vol. 5, No. 5 ( 2015-05-01), p. 719-740
    Abstract: The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.
    Type of Medium: Online Resource
    ISSN: 2160-1836
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2015
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  • 2
    In: Journal of the National Cancer Institute, Oxford University Press (OUP), Vol. 108, No. 11 ( 2016-11), p. djw153-
    Type of Medium: Online Resource
    ISSN: 0027-8874 , 1460-2105
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2016
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  • 3
    In: Lung Cancer, Elsevier BV, Vol. 152 ( 2021-02), p. 58-65
    Type of Medium: Online Resource
    ISSN: 0169-5002
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2021
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  • 4
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    Online Resource
    Elsevier BV ; 2000
    In:  Journal of the American Dietetic Association Vol. 100, No. 2 ( 2000-02), p. 198-204
    In: Journal of the American Dietetic Association, Elsevier BV, Vol. 100, No. 2 ( 2000-02), p. 198-204
    Type of Medium: Online Resource
    ISSN: 0002-8223
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2000
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  • 5
    In: Cancers, MDPI AG, Vol. 14, No. 17 ( 2022-08-30), p. 4221-
    Abstract: There is unmet need to develop circulating biomarkers that would enable earlier interception of lung cancer when more effective treatment options are available. Here, a set of 30 miRNAs, selected from a review of the published literature were assessed for their predictive performance in identifying lung cancer cases in the pre-diagnostic setting. The 30 miRNAs were assayed using sera collected from 102 individuals diagnosed with lung cancer within one year following blood draw and 212 controls matched for age, sex, and smoking status. The additive performance of top-performing miRNA candidates in combination with a previously validated four-protein marker panel (4MP) consisting of the precursor form of surfactant protein B (Pro-SFTPB), cancer antigen 125 (CA125), carcinoembryonic antigen (CEA) and cytokeratin-19 fragment (CYFRA21-1) was additionally assessed. Of the 30 miRNAs evaluated, five (miR-320a-3p, miR-210-3p, miR-92a-3p, miR-21-5p, and miR-140-3p) were statistically significantly (Wilcoxon rank sum test p 〈 0.05) elevated in case sera compared to controls, with individual AUCs ranging from 0.57–0.62. Compared to the 4MP alone, the combination of 3-miRNAs + 4MP improved sensitivity at 95% specificity by 19.1% ((95% CI of difference 0.0–28.6); two-sided p: 0.006). Our findings demonstrate utility for miRNAs for early detection of lung cancer in combination with a four-protein marker panel.
    Type of Medium: Online Resource
    ISSN: 2072-6694
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
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  • 6
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2020
    In:  Cancer Epidemiology, Biomarkers & Prevention Vol. 29, No. 9_Supplement ( 2020-09-01), p. A20-A20
    In: Cancer Epidemiology, Biomarkers & Prevention, American Association for Cancer Research (AACR), Vol. 29, No. 9_Supplement ( 2020-09-01), p. A20-A20
    Abstract: Hypomethylation of cg05575921 in the aryl-hydrocarbon receptor repressor (AHRR) gene is consistently and strongly associated with higher exposure to smoking (e.g., current smoking, greater number of pack years, and less time since quitting). Although cg05575921 hypomethylation has been reported to be associated with lung cancer risk and mortality, this has not been explored within heavy smokers or by histotype. We assessed cg05575921 methylation for associations with smoking behavior, prospective lung cancer risk, and mortality in 313 cases and controls from the Beta Carotene and Retinol Efficacy Trial (CARET) with ≥20 pack years of smoking and matched on age (±5 years), sex, race/ethnicity, enrollment year, smoking status, occupational asbestos exposure, and follow-up time. Methylation of cg05575921 in blood collected on average 4.3 years prior to diagnosis in cases was assayed using the 850K Illumina EPIC array. Quintiles of cg05575921 methylation were defined based on the control distribution, with the lowest quintile (Q1, referent) representing hypermethylation and the highest (Q5), hypomethylation. Among controls, increasing quintiles of cg05575921 hypomethylation were associated with current smoking status (Cochran-Armitage trend p=3.0 × 10-21), and with decreasing years since last smoked, increasing cigarettes per day, and decreasing body mass index (BMI) (ordinal ANOVA p=3.1 × 10-21, 1.3 × 10-17, and 0.002, respectively). We observed similar patterns in cases. We evaluated associations between cg05575921 methylation and lung cancer risk using logistic regression models conditioned on matching factors and adjusted for age, years since quit, and BMI. We evaluated cg05575921 methylation and lung cancer-specific mortality using Cox proportional hazards models adjusted for stage, age, sex, race, smoking status, intervention arm, asbestos exposure, and pack years smoked. We did not observe clear patterns of associations between cg05575921 methylation and lung cancer risk overall or by histotype. However, we found a linear relationship (p=0.03) between increasing cg05575921 hypomethylation and overall lung cancer mortality, with Q5 vs Q1 Hazard Ratio (HR)=1.60 (95% Confidence Interval (95% CI): 1.00-2.57) for mortality from lung cancer overall, and HR=2.09, 95% CI: 0.96-4.54 for adenocarcinoma (N=121). Our findings provide preliminary support that even among heavy smokers, cg05575921 hypomethylation is associated with more recent and extensive exposure to cigarette smoking, and that prediagnosis cg05575921 hypomethylation in lung cancer cases is associated with an increased hazard of death. However, since the CARET population represents a group who would largely qualify for lung cancer screening with annual low-dose computed tomography per the United States Preventive Task Force guidelines, our results do not provide support for the use of cg05575921 hypomethylation as an indicator for screening-based lung cancer risk stratification. Citation Format: Stefan Graw, Matt J. Barnett, Mark D. Thornquist, Gary E. Goodman, Chu Chen, Devin C. Koestler, Carmen J. Marsit, Jennifer A. Doherty, Laurie Grieshober. AHRR hypomethylation in heavy smokers: Associations with lung cancer risk and mortality [abstract]. In: Proceedings of the AACR Special Conference on Modernizing Population Sciences in the Digital Age; 2019 Feb 19-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(9 Suppl):Abstract nr A20.
    Type of Medium: Online Resource
    ISSN: 1055-9965 , 1538-7755
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2020
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  • 7
    In: BMC Cancer, Springer Science and Business Media LLC, Vol. 20, No. 1 ( 2020-12)
    Abstract: A low level of methylation at cg05575921 in the aryl-hydrocarbon receptor repressor ( AHRR ) gene is robustly associated with smoking, and some studies have observed associations between cg05575921 methylation and increased lung cancer risk and mortality. To prospectively examine whether decreased methylation at cg05575921 may identify high risk subpopulations for lung cancer screening among heavy smokers, and mortality in cases, we evaluated associations between cg05575921 methylation and lung cancer risk and mortality, by histotype, in heavy smokers. Methods The β-Carotene and Retinol Efficacy Trial (CARET) included enrollees ages 45–69 with ≥ 20 pack-year smoking histories and/or occupational asbestos exposure. A subset of CARET participants had cg05575921 methylation available from HumanMethylationEPIC assays of blood collected on average 4.3 years prior to lung cancer diagnosis in cases. Cg05575921 methylation β-values were treated continuously for a 10% methylation decrease and as quintiles, where quintile 1 (Q1, referent) represents high methylation and Q5, low methylation. We used conditional logistic regression models to examine lung cancer risk overall and by histotype in a nested case-control study including 316 lung cancer cases (diagnosed through 2005) and 316 lung cancer-free controls matched on age (±5 years), sex, race/ethnicity, enrollment year, current/former smoking, asbestos exposure, and follow-up time. Mortality analyses included 372 lung cancer cases diagnosed between 1985 and 2013 with available methylation data. We used Cox proportional hazards models to examine mortality overall and by histotype. Results Decreased cg05575921 methylation was strongly associated with smoking, even in our population of heavy smokers. We did not observe associations between decreased pre-diagnosis cg05575921 methylation and increased lung cancer risk, overall or by histotype. We observed linear increasing trends for lung cancer-specific mortality across decreasing cg05575921 methylation quintiles for adenocarcinoma and small cell carcinoma ( P -trends = 0.01 and 0.04, respectively). Conclusions In our study of heavy smokers, decreased cg05575921 methylation was strongly associated with smoking but not increased lung cancer risk. The observed association between cg05575921 methylation and increased mortality in adenocarcinoma and small cell histotypes requires further examination. Our results do not support using decreased cg05575921 methylation as a biomarker for lung cancer screening risk stratification.
    Type of Medium: Online Resource
    ISSN: 1471-2407
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
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  • 8
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 81, No. 13_Supplement ( 2021-07-01), p. 774-774
    Abstract: Epigenetic alterations, including changes in DNA methylation, and telomere length (TL) are established molecular markers of aging, morbidity, and mortality. We hypothesized that older methylation-derived biologic age (meAge) measured prior to lung cancer diagnoses would be associated with increased post-diagnosis mortality in high risk heavy smokers. Our study included 372 lung cancer cases from the β-Carotene and Retinol Efficacy Trial (CARET), a unique population of heavy smokers at high risk for lung cancer. Genome-wide DNA methylation data (Illumina MethylationEPIC) and TL were assayed in blood collected on average 4.9 years prior to diagnosis. We estimated meAge using scores developed by Hannum (leukocytes; 65/71 CpGs), Horvath (pan tissue; 335/353 CpGs), and Levine (DNAm PhenoAge, whole blood; 513 CpGs). We assessed Pearson correlations between meAge, age at blood draw, and log2-transformed TL, and we defined meAge acceleration (ΔmeAge) as the difference between each meAge and age. We examined associations between ΔmeAge, with and without TL adjustment, and all-cause mortality after lung cancer diagnoses using Cox proportional hazards models adjusted for age, sex, smoking status, pack years, time between blood draw and diagnosis, and methylation-estimated blood cell counts, including a strata variable for early (I/II), late (III/IV), or unknown stage. We assessed mortality in those with both old meAge and short TL (dichotomized at the medians) compared to those with both young meAge and long TL. We modeled all cases and by histotype (adenocarcinoma N=148, squamous cell N=115, small cell N=81). In our study population, mean age (64.3) was underestimated by Hannum and Levine meAges (52.4 and 57.0, respectively) and overestimated by Horvath meAge (70.3). Age was positively correlated with meAges (Hannum r=0.55, P=1E-30; Horvath r=0.49, P=2E-24; Levine r=0.41, P=2E-16), as were meAges with each other (all r≥0.66, P≤3E-48). TL was negatively correlated with age (r=-0.13, P=0.01) and meAges (Hannum r=-0.20, P=0.0001; Horvath r=-0.17, P=0.001; Levine r=-0.15, P=0.003). While each year of age was associated with 3% higher mortality in all cases (95% confidence interval (CI): 1.01-1.06), we did not observe an independent association with ΔmeAge (Hannum 0.99, 0.97-1.01; Horvath 1.00, 0.99-1.02; Levine 1.00, 0.99-1.01) regardless of TL adjustment or histotype. Shorter TL was associated with increased mortality in those who developed small cell lung cancer, as we reported previously; here, we observed that this association was independent of ΔmeAge. Combined old meAge and short TL was not associated with mortality. Though prospectively collected ΔmeAge has been reported to predict all-cause mortality in population-based studies, we did not observe that pre-diagnosis ΔmeAge, nor combined meAge-TL, were associated with mortality in a group of heavy smokers who went on to develop lung cancer. Citation Format: Laurie Grieshober, Stefan Graw, Matt J. Barnett, Mark D. Thornquist, Gary E. Goodman, Chu Chen, Devin C. Koestler, Carmen J. Marsit, Jennifer A. Doherty. Methylation-derived biologic age, telomere length, and lung cancer mortality in heavy smokers from CARET [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 774.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2021
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  • 9
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2023
    In:  Cancer Research Vol. 83, No. 7_Supplement ( 2023-04-04), p. 3005-3005
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 83, No. 7_Supplement ( 2023-04-04), p. 3005-3005
    Abstract: Pre-diagnosis circulating leukocyte profiles, including higher white blood cell (WBC) counts and neutrophil-to-lymphocyte ratios (NLR), have been reported to be associated with non-small cell lung cancer (NSCLC) risk. Higher neutrophil levels were recently reported to drive NSCLC-WBC count associations, implicating the innate immune response in NSCLC risk and etiology. Though not directly measurable in bio-banked blood, leukocyte subtype proportions can be estimated using established deconvolution algorithms applied to genome-wide DNA methylation data. We previously reported that NSCLC risk was elevated in heavy smokers with greater pre-diagnosis methylation-derived NLR (mdNLR). Here, we examine the influence of each pre-diagnosis mdNLR leukocyte subtype (neutrophils, and lymphocytes: B, Natural Killer, CD8+T, and CD4+T cells), separately on NSCLC risk. In our nested case-control study from the Beta Carotene and Retinol Efficacy Trial of heavy smokers (≥20 pack years), 243 NSCLC cases were 1:1 matched to controls on age (±5 years), sex, race and ethnicity, enrollment (±2 years), smoking status (ever/never), asbestos exposure, and follow-up time. Methylation was assayed on the Illumina EPIC array in whole blood collected on average 4.4 years (range 0.1-10.1) before diagnosis in NSCLC cases. We assessed conditional logistic regression models for each mdNLR-related leukocyte subtype, dichotomized at the median in controls, and further adjusted for continuous age and smoking pack years at blood draw. We evaluated NSCLC risk overall, and in subgroup strata: histotype, sex, smoking status, asbestos exposure, stage at diagnosis, age at blood draw, age at diagnosis, and time between blood draw and diagnosis. A greater than median level of neutrophils was suggestively associated with NSCLC risk (OR=1.40, 95% CI: 0.93-2.12); this association was restricted to squamous cell carcinoma (SCC n=103 pairs; 2.00, 1.03-3.86), with no association for adenocarcinoma (n=132 pairs; 0.99, 0.57-1.73). SCC-neutrophil associations were strongest among former smokers (n=26 pairs; 6.81, 1.48-31.3), cases with ≤ 4.4 years between blood draw and diagnosis (n=48 pairs; 3.00, 1.10-8.14), cases aged & gt; 64.8 years at blood draw (n=56 pairs; 2.66, 1.05-6.73), and cases diagnosed at stage III or IV (n=61 pairs; 2.21, 0.92-5.30). Greater than median lymphocyte levels were suggestively associated with reduced NSCLC (0.71, 0.47-1.08) and SCC risk (0.62, 0.32-1.21), but less so for adenocarcinoma (0.85, 0.48-1.50). Though statistically imprecise, SCC-lymphocyte associations were strongest for CD4+T cells (0.56, 0.28-1.12). Our results indicate that greater pre-diagnosis neutrophil levels may be a biomarker for SCC, but not adenocarcinoma, in heavy smokers. Given the descriptive nature of this analysis, small sample size, and multiple testing, additional research is needed to replicate these findings. Citation Format: Laurie Grieshober, Stefan Graw, Matt J. Barnett, Gary E. Goodman, Chu Chen, Devin C. Koestler, Carmen J. Marsit, Jennifer A. Doherty. Pre-diagnostic methylation-based leukocyte profiles and non-small cell lung cancer risk in heavy smokers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3005.
    Type of Medium: Online Resource
    ISSN: 1538-7445
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2023
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  • 10
    In: Journal of Thoracic Oncology, Elsevier BV, Vol. 14, No. 9 ( 2019-09), p. 1594-1607
    Type of Medium: Online Resource
    ISSN: 1556-0864
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2019
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