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A Transcriptome-Wide Association Study (TWAS) Identifies Novel Candidate Susceptibility Genes for Pancreatic Cancer

J Natl Cancer Inst

2020 Peters, Ulrike; Thornquist, Mark D; White, J; Goodman, Gary E; Goodman, Phyllis J; Kooperberg, Charles L

BACKGROUND: Although 20 pancreatic cancer susceptibility loci have been identified through genome-wide association studies (GWAS) in individuals of European ancestry, much of its heritability remains unexplained and the genes responsible largely unknown. METHODS: To discover novel pancreatic cancer risk loci and possible causal genes, we performed a pancreatic cancer transcriptome-wide association study (TWAS) in Europeans using three approaches, FUSION, MetaXcan and SMulTiXcan. We integrated GWAS summary statistics from 9,040 pancreatic cancer cases and 12,496 controls, with gene expression prediction models built using transcriptome data from histologically normal pancreatic tissue samples (NCI Laboratory of Translational Genomics, LTG (n=95) and Genotype-Tissue Expression, GTEx v7 (n=174) datasets), and data from 48 different tissues (GTEx v7, n=74-421 samples). RESULTS: We identified 25 genes whose genetically predicted expression was statistically significantly associated with pancreatic cancer risk (FDR < 0.05), including 14 candidate genes at 11 novel loci (1p36.12: CELA3B; 9q31.1: SMC2, SMC2-AS1; 10q23.31: RP11-80H5.9; 12q13.13: SMUG1; 14q32.33: BTBD6; 15q23: HEXA; 15q26.1: RCCD1; 17q12:, PNMT, CDK12, PGAP3; 17q22: SUPT4H1; 18q11.22: RP11-888D10.3; and 19p13.11: PGPEP1) and 11 at 6 known risk loci (5p15.33: TERT, CLPTM1L, ZDHHC11B; 7p14.1: INHBA; 9q34.2: ABO; 13q12.2: PDX1; 13q22.1: KLF5; and 16q23.1: WDR59, CFDP1, BCAR1, TMEM170A). The association for 12 of these genes (CELA3B, SMC2, and PNMT at novel risk loci, and TERT, CLPTM1L, INHBA, ABO, PDX1, KLF5, WDR59, CFDP1 and BCAR1 at known loci) remained statistically significant after Bonferroni correction. CONCLUSIONS: By integrating gene expression and genotype data, we identified novel pancreatic cancer risk loci and candidate functional genes that warrant further investigation.

Endothelial activation, innate immune activation, and inflammation are associated with post-bronchodilator airflow limitation and obstruction among adolescents living with HIV

J Acquir Immune Defic Syndr

2020 Richardson, Barbra A; Chung, Michael H; Crothers, Kristina; Graham, Susan M; Triplette, Matthew A

BACKGROUND: Chronic inflammation, innate immune activation, T-cell imbalance and endothelial activation have been linked with lung diseases. We sought to determine whether markers of these pathophysiologic pathways were associated with spirometry and chest CT abnormalities among adolescents living with HIV (ALWH). SETTING: Coptic Hope Center for Infectious Diseases in Nairobi, Kenya METHODS:: We performed a cross-sectional study of ALWH (10-19 years old). Participants underwent chest CT, spirometry and venipuncture for serum biomarkers. We also collected demographic, anthropometric, T-cell subset, antiretroviral therapy, and exposure data. We compared characteristics and biomarkers by airflow obstruction (post-bronchodilator FEV1/FVC z-score [zFEV1/FVC] < -1.64). We used multivariable linear regression to determine associations of log10-transformed biomarkers and chest CT abnormalities with lower post-bronchodilator zFEV1/FVC (airflow limitation). We performed exploratory principal components analysis on biomarkers, and determined associations of factors with post-bronchodilator zFEV1/FVC and chest CT abnormalities. RESULTS: Of 47 participants with acceptable quality spirometry, 21 (45%) were female, median age was 13 years and 96% had perinatally-acquired HIV. Median CD4 was 672 cells/L. Overall, 28% had airflow obstruction and 78% had a chest CT abnormality; airflow obstruction was associated with mosaic attenuation (p=0.001). Higher endothelial activation (sVCAM-1, sICAM-1), inflammation and innate immune activation (SAA, sTREM-1, sCD163), and T-cell imbalance (lower CD4/CD8) markers were associated with airflow limitation. Factors comprising endothelial and innate immune activation were associated with airflow limitation. CONCLUSIONS: Endothelial activation, innate immune activation, T-cell imbalance, and chronic inflammation are associated with airflow limitation and obstruction, providing insights into chronic lung disease pathophysiology among ALWH.

Life Expectancy of Adult Survivors of Childhood Cancer Over 3 Decades

JAMA Oncol

2020 Leisenring, Wendy M

Importance: Advances in childhood and adolescent cancer treatment have been associated with increased rates of cure during the past 3 decades; however, improvement in adult life expectancy for these individuals has not yet been reported. Objectives: To project long-term survival and assess whether life expectancy will improve among adult survivors of childhood cancer who were treated in more recent decades. Design, Setting, and Participants: A microsimulation model of competing mortality risks was developed using data from the Childhood Cancer Survivor Study on 5-year survivors of childhood cancer diagnosed between 1970 and 1999. The model included (1) late recurrence, (2) treatment-related late effects (health-related [subsequent cancers, cardiac events, pulmonary conditions, and other] and external causes), and (3) US background mortality rates. Exposures: Treatment subgroups (no treatment or surgery only, chemotherapy alone, radiotherapy alone, and radiotherapy with chemotherapy) and individuals with acute lymphoblastic leukemia during childhood by era (1970-1979, 1980-1989, and 1990-1999). Main Outcomes and Measures: Conditional life expectancy (defined as the number of years a 5-year survivor can expect to live), cumulative cause-specific mortality risk, and 10-year mortality risks conditional on attaining ages of 30, 40, 50, and 60 years. Results: Among the hypothetical cohort of 5-year survivors of childhood cancer representative of the Childhood Cancer Survivor Study participants (44% female and 56% male; mean [SD] age at diagnosis, 7.3 [5.6] years), conditional life expectancy was 48.5 years (95% uncertainty interval [UI], 47.6-49.6 years) for 5-year survivors diagnosed in 1970-1979, 53.7 years (95% UI, 52.6-54.7 years) for those diagnosed in 1980-1989, and 57.1 years (95% UI, 55.9-58.1 years) for those diagnosed in 1990-1999. Compared with individuals without a history of cancer, these results represented a gap in life expectancy of 25% (95% UI, 24%-27%) (16.5 years [95% UI, 15.5-17.5 years]) for those diagnosed in 1970-1979, 19% (95% UI, 17%-20%) (12.3 years [95% UI, 11.3-13.4 years]) for those diagnosed in 1980-1989, and 14% (95% UI, 13%-16%) (9.2 years [95% UI, 8.3-10.4 years]) for those diagnosed in 1990-1999. During the 3 decades, the proportion of survivors treated with chemotherapy alone increased (from 18% in 1970-1979 to 54% in 1990-1999), and the life expectancy gap in this chemotherapy-alone group decreased from 11.0 years (95% UI, 9.0-13.1 years) to 6.0 years (95% UI, 4.5-7.6 years). In contrast, during the same time frame, only modest improvements in the gap in life expectancy were projected for survivors treated with radiotherapy (21.0 years [95% UI, 18.5-23.2 years] to 17.6 years [95% UI, 14.2-21.2 years]) or with radiotherapy and chemotherapy (17.9 years [95% UI, 16.7-19.2 years] to 14.8 years [95% UI, 13.1-16.7 years]). For the largest group of survivors by diagnosis-those with acute lymphoblastic leukemia-the gap in life expectancy decreased from 14.7 years (95% UI, 12.8-16.5 years) in 1970-1979 to 8.0 years (95% UI, 6.2-9.7 years). Conclusions and Relevance: Evolving treatment approaches are projected to be associated with improved life expectancy after treatment for pediatric cancer, in particular among those who received chemotherapy alone for their childhood cancer diagnosis. Despite improvements, survivors remain at risk for shorter lifespans, especially when radiotherapy was included as part of their childhood cancer treatment.

A phenome-wide association study (PheWAS) in the Population Architecture using Genomics and Epidemiology (PAGE) study reveals potential pleiotropy in African Americans

PLoS One

2019 Reiner, Alex P; Lin, Yi; Kooperberg, Charles L

We performed a hypothesis-generating phenome-wide association study (PheWAS) to identify and characterize cross-phenotype associations, where one SNP is associated with two or more phenotypes, between thousands of genetic variants assayed on the Metabochip and hundreds of phenotypes in 5,897 African Americans as part of the Population Architecture using Genomics and Epidemiology (PAGE) I study. The PAGE I study was a National Human Genome Research Institute-funded collaboration of four study sites accessing diverse epidemiologic studies genotyped on the Metabochip, a custom genotyping chip that has dense coverage of regions in the genome previously associated with cardio-metabolic traits and outcomes in mostly European-descent populations. Here we focus on identifying novel phenome-genome relationships, where SNPs are associated with more than one phenotype. To do this, we performed a PheWAS, testing each SNP on the Metabochip for an association with up to 273 phenotypes in the participating PAGE I study sites. We identified 133 putative pleiotropic variants, defined as SNPs associated at an empirically derived p-value threshold of p<0.01 in two or more PAGE study sites for two or more phenotype classes. We further annotated these PheWAS-identified variants using publicly available functional data and local genetic ancestry. Amongst our novel findings is SPARC rs4958487, associated with increased glucose levels and hypertension. SPARC has been implicated in the pathogenesis of diabetes and is also known to have a potential role in fibrosis, a common consequence of multiple conditions including hypertension. The SPARC example and others highlight the potential that PheWAS approaches have in improving our understanding of complex disease architecture by identifying novel relationships between genetic variants and an array of common human phenotypes.

Recombinant HIV-1 vaccine candidates based on replication-defective flavivirus vector

Sci Rep

2019 Gottardo, Raphael; Bennett, Chelsey L; McElrath, Julie; Mayer, Bryan T

Multiple approaches utilizing viral and DNA vectors have shown promise in the development of an effective vaccine against HIV. In this study, an alternative replication-defective flavivirus vector, RepliVax (RV), was evaluated for the delivery of HIV-1 immunogens. Recombinant RV-HIV viruses were engineered to stably express clade C virus Gag and Env (gp120TM) proteins and propagated in Vero helper cells. RV-based vectors enabled efficient expression and correct maturation of Gag and gp120TM proteins, were apathogenic in a sensitive suckling mouse neurovirulence test, and were similar in immunogenicity to recombinant poxvirus NYVAC-HIV vectors in homologous or heterologous prime-boost combinations in mice. In a pilot NHP study, immunogenicity of RV-HIV viruses used as a prime or boost for DNA or NYVAC candidates was compared to a DNA prime/NYVAC boost benchmark scheme when administered together with adjuvanted gp120 protein. Similar neutralizing antibody titers, binding IgG titers measured against a broad panel of Env and Gag antigens, and ADCC responses were observed in the groups throughout the course of the study, and T cell responses were elicited. The entire data demonstrate that RV vectors have the potential as novel HIV-1 vaccine components for use in combination with other promising candidates to develop new effective vaccination strategies.

Ultraviolet Radiation Exposure and the Risk of Herpes Zoster in Three Prospective Cohort Studies

Mayo Clin Proc

2019 VoPham, Trang Minh

OBJECTIVE: To examine the association between ultraviolet radiation (UVR) exposure and the risk of herpes zoster (HZ) in 3 prospective cohorts. PATIENTS AND METHODS: We included 205,756 participants from the Health Professionals Follow-up Study (HPFS; 1986-2008), Nurses' Health Study (NHS; 1996-2012), and Nurses' Health Study II (NHS II; 1991-2013). Ambient UVR exposure was based on updated geocoded address histories linked with a high-resolution spatiotemporal ultraviolet model. Incident HZ cases were identified by self-reported clinician diagnosis. Sunburn history and medical, lifestyle, and dietary factors were assessed using biennial questionnaires. Multivariable Cox proportional hazards models were used. RESULTS: A total of 24,201 cases of HZ occurred during 3,626,131 person-years. Ambient UVR exposure was associated with a higher risk of HZ in men (HPFS: multivariable-adjusted hazard ratio [MVHR] comparing highest vs lowest quintiles, 1.14; 95% CI, 1.02-1.29; P=.03 for trend) but not in women (NHS: MVHR, 0.99; 95% CI, 0.93-1.05; NHS II: MVHR, 0.96; 95% CI, 0.90-1.03). A higher lifetime number of severe sunburns was associated with a higher risk of HZ in all cohorts (HPFS: MVHR for 10 sunburns vs none, 1.08; 95% CI, 0.96-1.20; P=.02 for trend; NHS: MVHR, 1.14; 95% CI, 1.05-1.22; P=.01 for trend; NHS II: MVHR, 1.13; 95% CI, 1.00-1.28; P<.001 for trend). CONCLUSION: Ambient UVR exposure was associated with a higher risk of HZ in men but not in women. A history of severe sunburn was associated with a modest increased risk of HZ in men and women, possibly because of immunosuppression from overexposure to the sun.

Circulating Levels of Insulin-like Growth Factor 1 and Insulin-like Growth Factor Binding Protein 3 Associate With Risk of Colorectal Cancer Based on Serologic and Mendelian Randomization Analyses

Gastroenterology

2019 Tangen, Catherine M; Banbury, Barbara L; Peters, Ulrike; Harrison, Tabitha; Huyghe, Jeroen R; Potter, Barney I; Sakoda, Lori; White, J; Hsu, Li; Li, Christopher I; Newcomb, Polly A; Phipps, Amanda I; Potter, John D; Qu, Conghui

BACKGROUND AIMS: Human studies examining associations between circulating levels of insulin-like growth factor 1 (IGF1) and insulin-like growth factor binding protein 3 (IGFBP3) and colorectal cancer risk have reported inconsistent results. We conducted complementary serologic and Mendelian randomization (MR) analyses to determine whether alterations in circulating levels of IGF1 or IGFBP3 are associated with colorectal cancer development. METHODS: Serum levels of IGF1 and other proteins were measured in blood samples collected from 397,380 participants from the UK Biobank, from 2006 through 2010. Incident cancer cases and cancer cases recorded first in death certificates were identified through linkage to national cancer and death registries. Complete follow up was available through March 31, 2016. For the MR analyses, we identified genetic variants associated with circulating levels of IGF1 and IGFBP3. The association of these genetic variants with colorectal cancer was examined with 2-sample MR methods using genome-wide association study consortia data (52,865 cases with colorectal cancer and 46,287 individuals without [controls]) RESULTS: After a median follow-up period of 7.1 years, 2665 cases of colorectal cancer were recorded. In a multivariable-adjusted model, circulating level of IGF1 level associated with colorectal cancer risk (hazard ratio per 1 standard deviation increment of IGF1, 1.11; 95% CI, 1.05-1.17). Similar associations were found by sex, follow-up time, and tumor subsite. In the MR analyses, a 1 standard deviation increment in IGF1 level, predicted based on genetic factors, was associated with a higher risk of colorectal cancer risk (odds ratio, 1.08; 95% CI, 1.03-1.12; P=3.3 x 10-4). Level of IGFBP3, predicted based on genetic factors, was associated with colorectal cancer risk (odds ratio per 1 standard deviation increment, 1.12; 95% CI, 1.06-1.18; P =4.2 x 10-5). Colorectal cancer risk was associated with only 1 variant in IGFBP3 (rs11977526), which also associated with anthropometric traits and circulating level of IGF2. CONCLUSIONS: In an analysis of blood samples from almost 400,000 participants in the UK Biobank, we found an association between circulating level of IGF1 and colorectal cancer. Using genetic data from 52,865 cases with colorectal cancer and 46,287 controls, a higher level of IGF1, determined by genetic factors, was associated with colorectal cancer. Further studies are needed to determine how this signaling pathway might contribute to colorectal carcinogenesis.

The ability of single genes vs full genomes to resolve time and space in outbreak analysis

BMC Evol Biol

2019 Bedford, Trevor; Dudas, Gytis

BACKGROUND: Inexpensive pathogen genome sequencing has had a transformative effect on the field of phylodynamics, where ever increasing volumes of data have promised real-time insight into outbreaks of infectious disease. As well as the sheer volume of pathogen isolates being sequenced, the sequencing of whole pathogen genomes, rather than select loci, has allowed phylogenetic analyses to be carried out at finer time scales, often approaching serial intervals for infections caused by rapidly evolving RNA viruses. Despite its utility, whole genome sequencing of pathogens has not been adopted universally and targeted sequencing of loci is common in some pathogen-specific fields. RESULTS: In this study we highlighted the utility of sequencing whole genomes of pathogens by re-analysing a well-characterised collection of Ebola virus sequences in the form of complete viral genomes (19 kb long) or the rapidly evolving glycoprotein (GP, 2 kb long) gene. We have quantified changes in phylogenetic, temporal, and spatial inference resolution as a result of this reduction in data and compared these to theoretical expectations. CONCLUSIONS: We propose a simple intuitive metric for quantifying temporal resolution, i.e. the time scale over which sequence data might be informative of various processes as a quick back-of-the-envelope calculation of statistical power available to molecular clock analyses.

The association between DXA-derived body fat measures and breast cancer risk among postmenopausal women in the Women's Health Initiative

Cancer Med

2019 Neuhouser, Marian L; Reding, Kerryn W

BACKGROUND: Most studies demonstrating an association between excess adiposity and postmenopausal breast cancer have used anthropometric measures, particularly body mass index (BMI). However, more direct body fat measures may more accurately determine the relationship between body fat distribution and breast cancer risk. METHODS: Cox proportional hazards regression models were created to examine the associations of dual-energy x-ray absorptiometry (DXA) body fat measures (at baseline and during follow-up) with breast cancer risk among 10931 postmenopausal women from the Women's Health Initiative cohort. A total of 639 incident invasive breast cancer cases (including 484 estrogen receptor positive (ER+) cases) were ascertained after a median follow-up of 15.0years. RESULTS: Excess whole body fat mass and trunk fat mass were positively associated with risk invasive breast cancer risk. These associations persisted even after additional adjustment for standard anthropometric measures. In time-dependent analyses, we observed that both whole body fat mass and trunk fat mass, in the highest versus lowest category, were associated with a doubling of risk of invasive breast cancer overall (HR: 2.17; 95% CI: 1.54-3.05 and 2.20; 1.55-3.14, respectively) and of ER+ breast cancer (2.05; 1.37-3.05 and 2.03; 1.34-3.07, respectively). The remaining DXA measures were also positively associated with breast cancer risk in baseline and time-dependent analyses. CONCLUSION: These findings suggest that DXA-derived body fat measures are positively associated with breast cancer risk after adjustment for BMI and other conventional breast cancer risk factors.

Semiparametric isotonic regression analysis for risk assessment under nested case-control and case-cohort designs

Stat Methods Med Res

2019 Feng, Ziding

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