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Magaña J, Contreras MG, Keys KL, Risse-Adams O, Goddard PC, Zeiger AM, Mak ACY, Elhawary JR, Samedy-Bates LA, Lee E, Thakur N, Hu D, Eng C, Salazar S, Huntsman S, Hu T, Burchard EG, White MJ. An epistatic interaction between pre-natal smoke exposure and socioeconomic status has a significant impact on bronchodilator drug response in African American youth with asthma. BioData Min 2020; 13:7. [PMID: 32636926 PMCID: PMC7333373 DOI: 10.1186/s13040-020-00218-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/23/2020] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Asthma is one of the leading chronic illnesses among children in the United States. Asthma prevalence is higher among African Americans (11.2%) compared to European Americans (7.7%). Bronchodilator medications are part of the first-line therapy, and the rescue medication, for acute asthma symptoms. Bronchodilator drug response (BDR) varies substantially among different racial/ethnic groups. Asthma prevalence in African Americans is only 3.5% higher than that of European Americans, however, asthma mortality among African Americans is four times that of European Americans; variation in BDR may play an important role in explaining this health disparity. To improve our understanding of disparate health outcomes in complex phenotypes such as BDR, it is important to consider interactions between environmental and biological variables. RESULTS We evaluated the impact of pairwise and three-variable interactions between environmental, social, and biological variables on BDR in 233 African American youth with asthma using Visualization of Statistical Epistasis Networks (ViSEN). ViSEN is a non-parametric entropy-based approach able to quantify interaction effects using an information-theory metric known as Information Gain (IG). We performed analyses in the full dataset and in sex-stratified subsets. Our analyses identified several interaction models significantly, and suggestively, associated with BDR. The strongest interaction significantly associated with BDR was a pairwise interaction between pre-natal smoke exposure and socioeconomic status (full dataset IG: 2.78%, p = 0.001; female IG: 7.27%, p = 0.004)). Sex-stratified analyses yielded divergent results for females and males, indicating the presence of sex-specific effects. CONCLUSIONS Our study identified novel interaction effects significantly, and suggestively, associated with BDR in African American children with asthma. Notably, we found that all of the interactions identified by ViSEN were "pure" interaction effects, in that they were not the result of strong main effects on BDR, highlighting the complexity of the network of biological and environmental factors impacting this phenotype. Several associations uncovered by ViSEN would not have been detected using regression-based methods, thus emphasizing the importance of employing statistical methods optimized to detect both additive and non-additive interaction effects when studying complex phenotypes such as BDR. The information gained in this study increases our understanding and appreciation of the complex nature of the interactions between environmental and health-related factors that influence BDR and will be invaluable to biomedical researchers designing future studies.
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Affiliation(s)
- J. Magaña
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
| | - M. G. Contreras
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - K. L. Keys
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
- Berkeley Institute for Data Science, University of California, Berkeley, CA USA
| | - O. Risse-Adams
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
- Lowell Science Research Program, Lowell High School, San Francisco, CA USA
- Department of Biology, University of California, Santa Cruz, CA USA
| | - P. C. Goddard
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
- Department of Genetics, Stanford University, Stanford, CA USA
| | - A. M. Zeiger
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA USA
| | - A. C. Y. Mak
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
| | - J. R. Elhawary
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
| | - L. A. Samedy-Bates
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA USA
| | - E. Lee
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
| | - N. Thakur
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
| | - D. Hu
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
| | - C. Eng
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
| | - S. Salazar
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
| | - S. Huntsman
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
| | - T. Hu
- School of Computing, Queen’s University, Kingston, ON Canada
| | - E. G. Burchard
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA USA
| | - M. J. White
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
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Marker K, Vidaurre T, Tamayo L, Vásquez J, Florez RM, Casavilca S, Calderon M, Abugattas J, Gómez H, Fuentes H, Pimentel CM, Song S, Cherry D, Huntsman S, Hu D, Ziv E, Fejerman L. Abstract PR05: A genetic variant at 6q25 associated with estrogen receptor-negative breast cancer subtypes in Peruvian breast cancer patients. Cancer Epidemiol Biomarkers Prev 2020. [DOI: 10.1158/1538-7755.disp18-pr05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Background: We have previously identified a genetic variant, rs140068132, which has a strong protective effect on breast cancer risk. This variant is located near the estrogen receptor 1 gene (ESR1) on chromosome 6q25, a locus which has been repeatedly implicated in breast cancer risk. Women who carry two copies of the protective variant (GG) have 60-70% reduction in risk of developing breast cancer compared to women with none. The G variant has relatively high frequency in Latin American women (up to 23% in the 1000 Genomes Project Peruvians); it is only common in people of Indigenous American ancestry and almost absent in all other populations. We investigated whether the rs140068132-A/G polymorphism is associated with a specific breast cancer subtype among Peruvian women with breast cancer.
Methods: Blood samples and clinical data were collected from 441 women with breast cancer at the Instituto Nacional de Enfermedades Neoplasicas in Lima, Peru. Genotypic profiles were generated using the Affymetrix Precision Medicine Research Array. Four major breast cancer subtypes were identified based on immunohistochemical markers (luminal A, luminal B, triple-negative, and human epidermal growth factor receptor 2 (HER2) overexpressing). Quality control of the genotyped data was performed in PLINK. Genetic ancestry was determined for each individual using ADMIXTURE. ANOVAs were performed on the proportion of genetic ancestry and disease subtype. PLINK was used to perform a binary logistic regression on the rs140068132 variant and ER status (ER-negative versus-ER positive), with age and genetic ancestry as covariates.
Results: The breast cancer patients analyzed have the following average ancestry proportions: 77.3% Indigenous American, 17.4% European, 3.8% African and 1.5% East Asian. The frequency of the G allele in the Peruvian breast cancer patients is 14% (compared to 23% in healthy individuals from the 1000 Genomes Project). We found that the G allele of rs140068132 was associated with ER-negative status among cases (OR = 0.6443, P = 0.086) for both HER2 overexpressing and triple-negative. We also examined the proportions of ancestry in relation to subtypes of disease. The proportion of Indigenous American ancestry was associated with the HER2 overexpressing subtype (P = 0.06), with an average Indigenous American ancestry among these patients of 83.1% compared to 77.3% among all patients. The proportion of African ancestry was higher in women with the triple-negative subtype, with an average African ancestry of 4.8% among patients with the triple-negative subtype compared to a 3.8% average among all patients, but this trend was not statistically significant (P = 0.21).
Conclusions: The lower frequency of the variant in Peruvian breast cancer cases is consistent with a protective effect in this population. We have confirmed that the protective effect of the rs140068132 variant is stronger for ER-negative subtypes. Additional analyses are under way in a larger sample of Peruvian breast cancer patients.
This abstract is also being presented as Poster C051.
Citation Format: K.M. Marker, T. Vidaurre, L.I. Tamayo, J.N. Vásquez, R. Meza Florez, S. Casavilca, M. Calderon, J.E. Abugattas, H.L. Gómez, H.A. Fuentes, C.L. Monge Pimentel, S. Song, D. Cherry, S. Huntsman, D. Hu, E. Ziv, L. Fejerman. A genetic variant at 6q25 associated with estrogen receptor-negative breast cancer subtypes in Peruvian breast cancer patients [abstract]. In: Proceedings of the Eleventh AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2018 Nov 2-5; New Orleans, LA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl):Abstract nr PR05.
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Affiliation(s)
- K.M. Marker
- 1Division of Epidemiology, School of Public Health, University of California Berkeley, Berkeley, CA,
| | - T. Vidaurre
- 2Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru,
| | | | - J.N. Vásquez
- 2Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru,
| | - R. Meza Florez
- 2Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru,
| | - S. Casavilca
- 2Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru,
| | - M. Calderon
- 2Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru,
| | - J.E. Abugattas
- 2Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru,
| | - H.L. Gómez
- 2Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru,
| | - H.A. Fuentes
- 2Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru,
| | | | - S. Song
- 4Division of General Internal Medicine, Department of Medicine, Institute of Human Genetics, University of California San Francisco, San Francisco, CA,
| | - D. Cherry
- 5University of California San Diego, San Diego, CA
| | - S. Huntsman
- 4Division of General Internal Medicine, Department of Medicine, Institute of Human Genetics, University of California San Francisco, San Francisco, CA,
| | - D. Hu
- 4Division of General Internal Medicine, Department of Medicine, Institute of Human Genetics, University of California San Francisco, San Francisco, CA,
| | - E. Ziv
- 4Division of General Internal Medicine, Department of Medicine, Institute of Human Genetics, University of California San Francisco, San Francisco, CA,
| | - L. Fejerman
- 4Division of General Internal Medicine, Department of Medicine, Institute of Human Genetics, University of California San Francisco, San Francisco, CA,
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3
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Sherenian MG, Cho SH, Levin A, Min JY, Oh SS, Hu D, Galanter J, Sen S, Huntsman S, Eng C, Rodriguez-Santana JR, Serebrisky D, Avila PC, Kalhan R, Smith LJ, Borrell LN, Seibold MA, Keoki Williams L, Burchard EG, Kumar R. PAI-1 gain-of-function genotype, factors increasing PAI-1 levels, and airway obstruction: The GALA II Cohort. Clin Exp Allergy 2017; 47:1150-1158. [PMID: 28543872 DOI: 10.1111/cea.12958] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/27/2017] [Accepted: 04/27/2017] [Indexed: 01/05/2023]
Abstract
BACKGROUND PAI-1 gain-of-function variants promote airway fibrosis and are associated with asthma and with worse lung function in subjects with asthma. OBJECTIVE We sought to determine whether the association of a gain-of-function polymorphism in plasminogen activator inhibitor-1 (PAI-1) with airway obstruction is modified by asthma status, and whether any genotype effect persists after accounting for common exposures that increase PAI-1 level. METHODS We studied 2070 Latino children (8-21y) with genotypic and pulmonary function data from the GALA II cohort. We estimated the relationship of the PAI-1 risk allele with FEV1/FVC by multivariate linear regression, stratified by asthma status. We examined the association of the polymorphism with asthma and airway obstruction within asthmatics via multivariate logistic regression. We replicated associations in the SAPPHIRE cohort of African Americans (n=1056). Secondary analysis included the effect of the at-risk polymorphism on postbronchodilator lung function. RESULTS There was an interaction between asthma status and the PAI-1 polymorphism on FEV1 /FVC (P=.03). The gain-of-function variants, genotypes (AA/AG), were associated with lower FEV1 /FVC in subjects with asthma (β=-1.25, CI: -2.14,-0.35, P=.006), but not in controls. Subjects with asthma and the AA/AG genotypes had a 5% decrease in FEV1 /FVC (P<.001). In asthmatics, the risk genotype (AA/AG) was associated with a 39% increase in risk of clinically relevant airway obstruction (OR=1.39, CI: 1.01, 1.92, P=.04). These associations persisted after exclusion of factors that increase PAI-1 including tobacco exposure and obesity. CONCLUSIONS AND CLINICAL RELEVANCE The decrease in the FEV1 /FVC ratio associated with the risk genotype was modified by asthma status. The genotype increased the odds of airway obstruction by 75% within asthmatics only. As exposures known to increase PAI-1 levels did not mitigate this association, PAI-1 may contribute to airway obstruction in the context of chronic asthmatic airway inflammation.
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Affiliation(s)
- M G Sherenian
- Division of Allergy-Immunology, Department of Pediatrics, Northwestern University, Chicago, IL, USA.,The Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - S H Cho
- Division of Allergy-Immunology, Department of Medicine, Northwestern University, Chicago, IL, USA.,Division of Allergy-Immunology, Department of Internal Medicine, University of South Florida, Tampa, FL, USA
| | - A Levin
- Department of Public Health Science, Henry Ford Health System, Detroit, MI, USA
| | - J-Y Min
- Department of Otolaryngology, Northwestern University, Chicago, IL, USA
| | - S S Oh
- Department of Medicine, University of California, San Francisco, CA, USA
| | - D Hu
- Department of Medicine, University of California, San Francisco, CA, USA
| | - J Galanter
- Department of Medicine, University of California, San Francisco, CA, USA
| | - S Sen
- Division of Biostatistics, Department of Preventive Medicine, UTHSC, Memphis, TN, USA
| | - S Huntsman
- Department of Medicine, University of California, San Francisco, CA, USA
| | - C Eng
- Department of Medicine, University of California, San Francisco, CA, USA
| | | | - D Serebrisky
- Pediatric Pulmonary Division, Jacobi Medical Center, Bronx, NY, USA
| | - P C Avila
- Division of Allergy-Immunology, Department of Medicine, Northwestern University, Chicago, IL, USA
| | - R Kalhan
- Division of Pulmonary Medicine, Department of Medicine, Northwestern University, Chicago, IL, USA
| | - L J Smith
- Division of Pulmonary Medicine, Department of Medicine, Northwestern University, Chicago, IL, USA
| | - L N Borrell
- Department of Health Sciences, Lehman College, CUNY, New York, NY, USA
| | - M A Seibold
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - L Keoki Williams
- Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA.,Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, MI, USA
| | - E G Burchard
- Department of Medicine, University of California, San Francisco, CA, USA
| | - R Kumar
- Division of Allergy-Immunology, Department of Pediatrics, Northwestern University, Chicago, IL, USA.,The Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
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4
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Shieh Y, Hu D, Huntsman S, Ma L, Gard CC, Leung JWT, Tice JA, Cummings SR, Kerlikowske K, Ziv E. Abstract P5-09-05: A model with polygenic risk score and mammographic density predicts interval cancers. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p5-09-05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction:
Interval breast cancers present with clinical symptoms following a normal screening mammogram. They are associated with unfavorable biological features and with dense breasts. Models predictive of aggressive phenotypes may facilitate tailored screening for women at elevated risk of interval cancers. Polygenic risk scores (PRS) represent the cumulative effects of multiple single nucleotide polymorphisms (SNPs) and can be used to risk-stratify women. In prior reports, PRS is preferentially associated with screen-detected rather than interval cancers. We investigated methods to refine the PRS to preferentially predict interval cancers, and tested the performance of the PRS in joint models with mammographic breast density (MBD).
Methods:
We used data from 1058 breast cancer cases from The Cancer Genome Atlas (TCGA) as the discovery set for our PRS. We selected 107 SNPs from genomewide association studies of breast cancer risk for testing against tumor status at last follow-up in TCGA. Presence of tumor indicated recurrence, progression, or positive margins after resection. Women with tumor present at <100 days of follow-up were excluded. Suggestive associations (p<0.2) were used to construct a PRS, calculated as the sum across all SNPs of the per-allele log-odds ratio multiplied by the number of risk alleles for each SNP. We tested the performance of the PRS in a nested case-control dataset with 471 cases (102 interval cancers, 369 screen detected) and 496 controls from the California Pacific Medical Center Research Institute cohort. Logistic regression was used to evaluate the association between PRS, MBD and interval cancers. Area under the receiver operating characteristic (AUROC) curve was used to measure discrimination.
Results:
Of 107 SNPs, 23 had suggestive associations with presence of tumor at last follow-up in TCGA. The 23-SNP PRS discriminated between women with interval cancers and controls, with AUROC 0.57 (95% CI 0.51-0.63). With the inclusion of MBD in the model, the AUROC was 0.68 (95% CI 0.62-0.74). Women in the highest PRS quintile had an unadjusted 2.07-fold odds (95% CI 1.05-4.07) of developing interval cancers compared with women in the lowest quintile; adjustment for MBD did not change the point estimate. The PRS also discriminated between women with interval and screen-detected cancers, although the findings did not reach statistical significance (AUROC 0.55, 95% CI 0.48-0.61). With the inclusion of MBD in the model, the AUROC was 0.63 (95% CI 0.57-0.69).
Discussion:
A PRS associated with presence of tumor at last follow-up was independently predictive of interval cancers relative to controls. Models with PRS and MBD discriminated between interval and screen-detected cancers, although MBD provided most of the predictive power. Our findings are limited by the size and low number of recurrences in TCGA. It is possible that tumor status largely reflects treatment received, and may only partially represent the biological pathways of interval cancers. Our results suggest that SNPs may potentially identify women at risk for developing interval breast cancer, although further validation is required.
Citation Format: Shieh Y, Hu D, Huntsman S, Ma L, Gard CC, Leung JWT, Tice JA, Cummings SR, Kerlikowske K, Ziv E. A model with polygenic risk score and mammographic density predicts interval cancers [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P5-09-05.
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Affiliation(s)
- Y Shieh
- University of California, San Francisco; New Mexico State University; University of Texas MD Anderson Cancer Center; San Francisco Coordinating Center; San Francisco Veterans Affairs Medical Center
| | - D Hu
- University of California, San Francisco; New Mexico State University; University of Texas MD Anderson Cancer Center; San Francisco Coordinating Center; San Francisco Veterans Affairs Medical Center
| | - S Huntsman
- University of California, San Francisco; New Mexico State University; University of Texas MD Anderson Cancer Center; San Francisco Coordinating Center; San Francisco Veterans Affairs Medical Center
| | - L Ma
- University of California, San Francisco; New Mexico State University; University of Texas MD Anderson Cancer Center; San Francisco Coordinating Center; San Francisco Veterans Affairs Medical Center
| | - CC Gard
- University of California, San Francisco; New Mexico State University; University of Texas MD Anderson Cancer Center; San Francisco Coordinating Center; San Francisco Veterans Affairs Medical Center
| | - JWT Leung
- University of California, San Francisco; New Mexico State University; University of Texas MD Anderson Cancer Center; San Francisco Coordinating Center; San Francisco Veterans Affairs Medical Center
| | - JA Tice
- University of California, San Francisco; New Mexico State University; University of Texas MD Anderson Cancer Center; San Francisco Coordinating Center; San Francisco Veterans Affairs Medical Center
| | - SR Cummings
- University of California, San Francisco; New Mexico State University; University of Texas MD Anderson Cancer Center; San Francisco Coordinating Center; San Francisco Veterans Affairs Medical Center
| | - K Kerlikowske
- University of California, San Francisco; New Mexico State University; University of Texas MD Anderson Cancer Center; San Francisco Coordinating Center; San Francisco Veterans Affairs Medical Center
| | - E Ziv
- University of California, San Francisco; New Mexico State University; University of Texas MD Anderson Cancer Center; San Francisco Coordinating Center; San Francisco Veterans Affairs Medical Center
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Schabath M, Dalvi T, Dai H, Crim A, Midha A, Shire N, Walker J, Greenawalt D, Lawrence D, Rigas J, Brody R, Potter D, Kumar N, Huntsman S, Gray J. P1.01-042 Molecular Epidemiology of Programmed Cell Death 1-Ligand 1 (PD-L1) Protein Expression in Non-Small Cell Lung Cancer. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2016.11.566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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6
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Abid Z, Oh SS, Hu D, Sen S, Huntsman S, Eng C, Farber HJ, Rodriguez-Cintron W, Rodriguez-Santana JR, Serebrisky D, Avila PC, Thyne SM, Kim KYA, Borrell LN, Williams LK, Seibold MA, Burchard EG, Kumar R. Maternal age and asthma in Latino populations. Clin Exp Allergy 2016; 46:1398-1406. [PMID: 27238356 DOI: 10.1111/cea.12765] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/02/2016] [Accepted: 05/16/2016] [Indexed: 12/27/2022]
Abstract
BACKGROUND Younger maternal age at birth is associated with increased risk of asthma in offspring in European descent populations, but has not been studied in Latino populations. OBJECTIVES We sought to examine the relationship between maternal age at birth and prevalence of asthma in a nationwide study of Latino children. METHODS We included 3473 Latino children aged 8-21 years (1696 subjects with physician-diagnosed asthma and 1777 healthy controls) from five US centres and Puerto Rico recruited from July 2008 through November 2011. We used multiple logistic regression models to examine the effect of maternal age at birth on asthma in offspring overall and in analyses stratified by ethnic subgroup (Mexican American, Puerto Rican and other Latino). Secondary analyses evaluated the effects of siblings, acculturation and income on this relationship. RESULTS Maternal age < 20 years was significantly associated with decreased odds of asthma in offspring, independent of other risk factors (OR = 0.73, 95% CI: 0.57-0.93). In subgroup analyses, the protective effect of younger maternal age was observed only in Mexican Americans (OR = 0.53, 95% CI: 0.36, 0.79). In Puerto Ricans, older maternal age was associated with decreased odds of asthma (OR = 0.65, 95% CI: 0.44-0.97). In further stratified models, the protective effect of younger maternal age in Mexican Americans was seen only in children without older siblings (OR = 0.44, 95% CI: 0.23-0.81). CONCLUSION AND CLINICAL RELEVANCE In contrast to European descent populations, younger maternal age was associated with decreased odds of asthma in offspring in Mexican American women. Asthma is common in urban minority populations but the factors underlying the varying prevalence among different Latino ethnicities in the United States is not well understood. Maternal age represents one factor that may help to explain this variability.
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Affiliation(s)
- Z Abid
- Division of Allergy-Immunology, Department of Medicine, Northwestern University, Chicago, IL, USA
| | - S S Oh
- Department of Medicine, University of California, San Francisco, CA, USA
| | - D Hu
- Department of Medicine, University of California, San Francisco, CA, USA
| | - S Sen
- Department of Biostatistics, University of California, San Francisco, CA, USA
| | - S Huntsman
- Department of Medicine, University of California, San Francisco, CA, USA
| | - C Eng
- Department of Medicine, University of California, San Francisco, CA, USA
| | - H J Farber
- Department of Pediatrics, Section of Pulmonology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | | | | | - D Serebrisky
- Pediatric Pulmonary Division, Jacobi Medical Center, Bronx, NY, USA
| | - P C Avila
- Division of Allergy-Immunology, Department of Medicine, Northwestern University, Chicago, IL, USA
| | - S M Thyne
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - K-Y A Kim
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - L N Borrell
- Department of Health Sciences, Lehman College, CUNY, New York, NY, USA
| | - L K Williams
- Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA.,Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, MI, USA
| | - M A Seibold
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - E G Burchard
- Department of Medicine, University of California, San Francisco, CA, USA
| | - R Kumar
- Division of Allergy-Immunology, Department of Pediatrics, Northwestern University, Chicago, IL, USA. .,The Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA.
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7
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Dai H, Wenham RM, Kumar N, Mitchell M, Crim A, Welsh E, Berglund AE, Huntsman S, Cristescu R, Nebozhyn M, Loboda A, Sullivan D, Dalton WS. Prognostic and predictive signature discovery and validation in ovarian cancer utilizing the total-cancer-care (TCC) data warehouse. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.e22167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | | | | | | | - Eric Welsh
- Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
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8
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Almhanna K, Sullivan D, Mitchell M, Springett GM, Kalebic T, Wyant T, Danaee H, Trepicchio WL, Jump H, Daniels D, Brass S, Urdialis M, Hawkins K, Huntsman S, Dalton WS. Enhancing enrollment using cohort surveillance for phase II biomarkers driven studies in patients with gastric/GEJ and pancreatic cancer. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.e15017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | | | | | | | - Tim Wyant
- Takeda Pharmaceuticals International Company, Cambridge, MA
| | - Hadi Danaee
- Translational Medicine, Millennium Pharmaceuticals, Inc., Cambridge, MA
| | | | - Helen Jump
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
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Dai H, Fishman MN, Ching KA, Williams JA, Teer JK, English PA, Zhang Y, Murray BW, Kumar N, Huntsman S, Berglund AE, Dalton WS, Matczak E, Martini JF. Identification of tumor biomarkers for sunitinib in advanced renal cell carcinoma (RCC). J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.7_suppl.470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
470 Background: Sunitinib is a standard of care for advanced RCC. Despite efforts to identify predictive molecular markers for patient selection, none are available, likely due to multiple resistance mechanisms. Using the Total Cancer Care (TCC) database, which integrates patient clinical, molecular, and biospecimen data, we devised a tumor genomics and transcriptomics experiment to identify differences between RCC patients who derive prolonged clinical benefit from sunitinib versus those who are resistant. Methods: A discovery set of 34 RCC patients treated with sunitinib at the approved regimen were identified in the TCC database (n=16 treated for ≤6 months, having primarily discontinued for reasons other than tolerability; n=18 treated for ≥18 months). Tumor samples were analyzed by whole exome sequencing (WES) and by parallel 400-gene expression profiling. Following gene mutation identification and supervised gene expression analysis, molecular differences between the two groups were identified and tested for potential association with treatment duration. Results: Of the 34 cases identified, 24 remained for analysis following sample QC failure and clinical review (n=10 and 14 treated for ≤6 and ≥18 months, respectively). Gene expression analysis revealed a 37-gene signature associated with treatment duration: MAPK8 (JNK1) was a leading candidate biomarker (Pearson correlation with log [treatment duration]=–0.70; p=0.06 after Bonferroni multiplicity correction). Pathway-based WES analyses identified 25 potential variants of interest, none remaining statistically significant after correction. However, following genome-wide analysis, a single variant in an intronic region of ING3 was statistically associated with treatment duration (p=0.02). Conclusions: Activation of the PI3K/AKT pathway was a marker of resistance to sunitinib. In contrast, activation of the angiogenic, NOTCH, or JAK-STAT pathways was, to some degree, associated with sensitivity to therapy. However, neither VHL alteration nor lack of expression, nor alteration in chromatin-rearrangement genes, was associated with sunitinib treatment duration. These findings require further validation in a larger and independent cohort.
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Scherer ML, Nalls MA, Pawlikowska L, Ziv E, Mitchell G, Huntsman S, Hu D, Sutton-Tyrrell K, Lakatta EG, Hsueh WC, Newman AB, Tandon A, Kim L, Kwok PY, Sung A, Li R, Psaty B, Reiner AP, Harris T. Admixture mapping of ankle-arm index: identification of a candidate locus associated with peripheral arterial disease. J Med Genet 2009; 47:1-7. [PMID: 19586928 DOI: 10.1136/jmg.2008.064808] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Peripheral arterial disease (PAD) is associated with significant morbidity and mortality, and has a higher prevalence in African Americans than Caucasians. Ankle-arm index (AAI) is the ratio of systolic blood pressure in the leg to that in the arm, and, when low, is a marker of PAD. METHODS The authors used an admixture mapping approach to search for genetic loci associated with low AAI. Using data from 1040 African American participants in the observational, population based Health, Aging, and Body Composition Study who were genotyped at 1322 single nucleotide polymorphisms (SNPs) that are informative for African versus European ancestry and span the entire genome, we estimated genetic ancestry in each chromosomal region and then tested the association between AAI and genetic ancestry at each locus. RESULTS The authors found a region of chromosome 11 that reaches its peak between 80 and 82 Mb associated with low AAI (p<0.001 for rs12289502 and rs9665943, both within this region). 753 African American participants in the observational, population based Cardiovascular Health Study were genotyped at rs9665943 to test the reproducibility of this association, and this association was also statistically significant (odds ratio (OR) for homozygous African genotype 1.59, 95% confidence interval (CI) 1.12 to 2.27). Another candidate SNP (rs1042602) in the same genomic region was tested in both populations, and was also found to be significantly associated with low AAI in both populations (OR for homozygous African genotype 1.89, 95% CI 1.29 to 2.76). CONCLUSION This study identifies a novel region of chromosome 11 representing an area with a potential candidate gene associated with PAD in African Americans.
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Affiliation(s)
- M L Scherer
- Laboratory of Epidemiology, Demography and Biometry, National Institute on Aging, Bethesda, MD 20892-9205, USA
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11
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Vitale L, Lenzi L, Huntsman S, Canaider S, Frabetti F, Casadei R, Facchin F, Carinci P, Zannotti M, Coppola D, Strippoli P. Differential expression of alternatively spliced mRNA forms of the insulin-like growth factor 1 receptor in human neuroendocrine tumors. Oncol Rep 2006. [DOI: 10.3892/or.15.5.1249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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12
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Centeno BA, Enkemann SA, Coppola D, Huntsman S, Bloom G, Yeatman TJ. Classification of human tumors using gene expression profiles obtained after microarray analysis of fine-needle aspiration biopsy samples. Cancer 2005; 105:101-9. [PMID: 15643601 DOI: 10.1002/cncr.20737] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Gene expression profiling using gene-discovery, high-density microarray technologies is a powerful tool. One potential application is the development of tumor classifiers that predict the site of origin. For this technology to be relevant, however, it must be applicable to tumor biopsy samples, which most often are fine-needle aspiration biopsy (FNAB) samples. METHODS Surgically resected tumors were sampled by FNAB using different gauge needles. A portion of the excised tumor was also collected. RNA samples were extracted using standard techniques and the quality and quantity of the RNA samples were measured for each sample. Thirteen representative FNAB samples and two representative tissue samples were submitted for microarray analysis and then subjected to a tumor classifier. RESULTS Fourteen of 18 samples analyzed for quantity and quality of RNA yielded an adequate amount of RNA (> 1 microg total RNA). Tumor type contributed to the RNA yield because one of the four inadequate samples was retrieved from a patient with lobular carcinoma of the breast and the other three samples were retrieved from patients with retroperitoneal sarcomas. Of the 13 samples submitted for microarray analysis, 9 were classified correctly as to tumor type using a tissue-based tumor classifier. CONCLUSIONS The authors demonstrated that FNABs reproducibly obtained an adequate amount of RNA for microarray analysis when a standardized collection procedure was used. Furthermore, the samples generated interpretable gene expression profiles that could be matched accurately with a tumor classifier established on tissue specimens. The current study showed that FNAB produced adequate material for microarray analysis when utilizing a standardized collection procedure.
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Affiliation(s)
- Barbara A Centeno
- Department of Interdisciplinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33609, USA.
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Abstract
The algal osmolyte dimethylsulphoniopropionate (DMSP) and its enzymatic cleavage product dimethylsulphide (DMS) contribute significantly to the global sulphur cycle, yet their physiological functions are uncertain. Here we report results that, together with those in the literature, show that DMSP and its breakdown products (DMS, acrylate, dimethylsulphoxide, and methane sulphinic acid) readily scavenge hydroxyl radicals and other reactive oxygen species, and thus may serve as an antioxidant system, regulated in part by enzymatic cleavage of DMSP. In support of this hypothesis, we found that oxidative stressors, solar ultraviolet radiation, CO(2) limitation, Fe limitation, high Cu(2+) (ref. 9) and H(2)O(2) substantially increased cellular DMSP and/or its lysis to DMS in marine algal cultures. Our results indicate direct links between such stressors and the dynamics of DMSP and DMS in marine phytoplankton, which probably influence the production of DMS and its release to the atmosphere. As oxidation of DMS to sulphuric acid in the atmosphere provides a major source of sulphate aerosols and cloud condensation nuclei, oxidative stressors--including solar radiation and Fe limitation--may be involved in complex ocean atmosphere feedback loops that influence global climate and hydrological cycles.
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Affiliation(s)
- W Sunda
- Beaufort Laboratory, National Oceanic and Atmospheric Administration, Beaufort, North Carolina 28516, USA.
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