Faculty Bibliography
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171
A Transcriptome-Wide Association Study (TWAS) Identifies Novel Candidate Susceptibility Genes for Pancreatic Cancer
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.
PMID: 31917448
ISSN: 1460-2105
CID: 4257572
Genome-wide association study data reveal genetic susceptibility to chronic inflammatory intestinal diseases and pancreatic ductal adenocarcinoma risk
Registry-based epidemiologic studies suggest associations between chronic inflammatory intestinal diseases and pancreatic ductal adenocarcinoma (PDAC). As genetic susceptibility contributes to a large proportion of chronic inflammatory intestinal diseases, we hypothesize that the genomic regions surrounding established genome-wide associated variants for these chronic inflammatory diseases are associated with PDAC. We examined the association between PDAC and genomic regions (+/- 500 kb) surrounding established common susceptibility variants for ulcerative colitis, Crohn's disease, inflammatory bowel disease, celiac disease, chronic pancreatitis, and primary sclerosing cholangitis. We analyzed summary statistics from genome-wide association studies data for 8,384 cases and 11,955 controls of European descent from two large consortium studies using the summary data-based adaptive rank truncated product method to examine the overall association of combined genomic regions for each inflammatory disease group. Combined genomic susceptibility regions for ulcerative colitis, Crohn's disease, inflammatory bowel disease, and chronic pancreatitis were associated with PDAC at P-values < 0.05 (0.0040, 0.0057, 0.011, and 3.4 × 10-6, respectively). After excluding the 20 PDAC susceptibility regions (+/- 500 kb) previously identified by GWAS, the genomic regions for ulcerative colitis, Crohn's disease, and inflammatory bowel disease remained associated with PDAC (P-values = 0.0029, 0.0057, and 0.0098, respectively). Genomic regions for celiac disease (P-value = 0.22) and primary sclerosing cholangitis (P-value = 0.078) were not associated with PDAC. Our results support the hypothesis that genomic regions surrounding variants associated with inflammatory intestinal diseases, particularly, ulcerative colitis, Crohn's disease, inflammatory bowel disease, and chronic pancreatitis are associated with PDAC.
PMID: 32641412
ISSN: 1538-7445
CID: 4518002
Cancer epidemiology biomarkers & prevention. 2020:29(9):1784-1791.DOI: 10.1158/1055-9965.EPI-20-0275
Genome-wide gene-diabetes and gene-obesity interaction scan in 8,255 cases and 11,900 controls from the PanScan and PanC4 Consortia
BACKGROUND:Obesity and diabetes are major modifiable risk factors for pancreatic cancer. Interactions between genetic variants and diabetes/obesity have not previously been comprehensively investigated in pancreatic cancer at the genome-wide level. METHODS:We conducted a gene-environment interaction (GxE) analysis including 8,255 cases and 11,900 controls from four pancreatic cancer GWAS datasets (PanScan I-III and PanC4). Obesity (BMI=30 kg/m2) and diabetes (duration = 3 years) were the environmental variables of interest. Approximately 870,000 SNPs were analyzed. Case-control (CC), case-only (CO), and joint-effect test methods were used for SNP-level GxE analysis. As a complementary approach, gene-based GxE analysis was also performed. Age, sex, study site and principal components accounting for population substructure were included as covariates. Meta-analysis was applied to combine individual-GWAS summary statistics. RESULTS:No genome-wide significant interactions with diabetes or obesity were detected at the SNP level by the CC or CO approaches. The joint-effect test detected numerous genome-wide significant GxE signals in the GWAS main effects top hit regions but the significance diminished after adjusting for the GWAS top hits. In the gene-based analysis, a significant interaction of diabetes with variants in the FAM63A (family with sequence similarity 63 member A) gene (significance threshold P<1.25E-6) was observed in the meta-analysis (PGxE= 1.2E-6, PJoint= 4.2E-7). CONCLUSIONS:Our current analyses did not find significant GxE interactions at the SNP level but found one significant interaction with diabetes at the gene level. A larger sample size might unveil additional genetic factors via GxE scans. IMPACT/CONCLUSIONS:This study may contribute to discovering the mechanism of diabetes-associated pancreatic cancer.
PMID: 32546605
ISSN: 1538-7755
CID: 4484782
The need for an independent evaluation of the COVID-19 response in Spain [Letter]
PMID: 32771082
ISSN: 1474-547x
CID: 4555882
Endocrine-disrupting chemicals: economic, regulatory, and policy implications
Endocrine-disrupting chemicals (EDCs) substantially cost society as a result of increases in disease and disability but-unlike other toxicant classes such as carcinogens-have yet to be codified into regulations as a hazard category. This Series paper examines economic, regulatory, and policy approaches to limit human EDC exposures and describes potential improvements. In the EU, general principles for EDCs call for minimisation of human exposure, identification as substances of very high concern, and ban on use in pesticides. In the USA, screening and testing programmes are focused on oestrogenic EDCs exclusively, and regulation is strictly risk-based. Minimisation of human exposure is unlikely without a clear overarching definition for EDCs and relevant pre-marketing test requirements. We call for a multifaceted international programme (eg, modelled on the International Agency for Research in Cancer) to address the effects of EDCs on human health-an approach that would proactively identify hazards for subsequent regulation.
PMID: 32707119
ISSN: 2213-8595
CID: 4539822
Influence of KRAS mutations, persistent organic pollutants, and trace elements on survival from pancreatic ductal adenocarcinoma
INTRODUCTION/BACKGROUND:Reasons why pancreatic ductal adenocarcinoma (PDAC) continues to have poor survival are only partly known. No previous studies have analyzed the combined influence of KRAS mutations, persistent organic pollutants (POPs), and trace elements upon survival in PDAC or in any other human cancer. OBJECTIVE:To analyze the individual and combined influence of KRAS mutations, POPs, and trace elements upon survival from PDAC. METHODS:Incident cases of PDAC (n = 185) were prospectively identified in five hospitals in Eastern Spain in 1992-1995 and interviewed face-to-face during hospital admission. KRAS mutational status was determined from tumour tissue through polymerase chain reaction and artificial restriction fragment length polymorphism. Blood and toenail samples were obtained before treatment. Serum concentrations of POPs were analyzed by high-resolution gas chromatography with electron-capture detection. Concentrations of 12 trace elements were determined in toenail samples by inductively coupled plasma mass spectrometry. Multivariable Cox proportional hazards regression was used to assess prognostic associations. RESULTS:Patients with a KRAS mutated tumor had a 70% higher risk of early death than patients with a KRAS wild-type PDAC (hazard ratio [HR] = 1.7, p = 0.026), adjusting for age, sex, and tumor stage. KRAS mutational status was only modestly and not statistically significantly associated with survival when further adjusting by treatment or by treatment intention. The beneficial effects of treatment remained unaltered when KRAS mutational status was taken into account, and treatment did not appear to be less effective in the subgroup of patients with a KRAS mutated tumor. POPs did not materially influence survival: the adjusted HR of the highest POP tertiles was near unity for all POPs. When considering the joint effect on survival of POPs and KRAS, patients with KRAS mutated tumors had modest and nonsignificant HRs (most HRs around 1.3 to 1.4). Higher concentrations of lead, cadmium, arsenic, vanadium, and aluminium were associated with better survival. When KRAS status, POPs, and trace elements were simultaneously considered along with treatment, only the latter was statistically significantly related to survival. CONCLUSIONS:In this study based on molecular, clinical, and environmental epidemiology, KRAS mutational status, POPs, and trace elements were not adversely related to PDAC survival when treatment was simultaneously considered; only treatment was independently related to survival. The lack of adverse prognostic effects of POPs and metals measured at the time of diagnosis provide scientific and clinical reassurance on the effects of such exposures upon survival of patients with PDAC. The weak association with KRAS mutations contributes to the scant knowledge on the clinical implications of a genetic alteration highly frequent in PDAC.
PMID: 32791343
ISSN: 1096-0953
CID: 4556662
Repositioning of the global epicentre of non-optimal cholesterol
High blood cholesterol is typically considered a feature of wealthy western countries. However, dietary and behavioural determinants of blood cholesterol are changing rapidly throughout the world and countries are using lipid-lowering medications at varying rates. These changes can have distinct effects on the levels of high-density lipoprotein (HDL) cholesterol and non-HDL cholesterol, which have different effects on human health4,5. However, the trends of HDL and non-HDL cholesterol levels over time have not been previously reported in a global analysis. Here we pooled 1,127 population-based studies that measured blood lipids in 102.6 million individuals aged 18 years and older to estimate trends from 1980 to 2018 in mean total, non-HDL and HDL cholesterol levels for 200 countries. Globally, there was little change in total or non-HDL cholesterol from 1980 to 2018. This was a net effect of increases in low- and middle-income countries, especially in east and southeast Asia, and decreases in high-income western countries, especially those in northwestern Europe, and in central and eastern Europe. As a result, countries with the highest level of non-HDL cholesterol-which is a marker of cardiovascular risk-changed from those in western Europe such as Belgium, Finland, Greenland, Iceland, Norway, Sweden, Switzerland and Malta in 1980 to those in Asia and the Pacific, such as Tokelau, Malaysia, The Philippines and Thailand. In 2017, high non-HDL cholesterol was responsible for an estimated 3.9 million (95% credible interval 3.7 million-4.2 million) worldwide deaths, half of which occurred in east, southeast and south Asia. The global repositioning of lipid-related risk, with non-optimal cholesterol shifting from a distinct feature of high-income countries in northwestern Europe, north America and Australasia to one that affects countries in east and southeast Asia and Oceania should motivate the use of population-based policies and personal interventions to improve nutrition and enhance access to treatment throughout the world.
PMID: 32494083
ISSN: 1476-4687
CID: 4481132
Public Health Is Not Afraid of Pleasure [Editorial]
PMID: 31913673
ISSN: 1541-0048
CID: 4258372
Concentrations of trace elements and KRAS mutations in pancreatic ductal adenocarcinoma
Trace elements are a possible risk factor for pancreatic ductal adenocarcinoma (PDAC). However, their role in the occurrence and persistence of KRAS mutations remains unstudied. There appear to be no studies analyzing biomarkers of trace elements and KRAS mutations in any human cancer. We aimed to determine whether patients with KRAS mutated and nonmutated tumors exhibit differences in concentrations of trace elements. Incident cases of PDAC were prospectively identified in five hospitals in Spain. KRAS mutational status was determined through polymerase chain reaction from tumor tissue. Concentrations of 12 trace elements were determined in toenail samples by inductively coupled plasma mass spectrometry. Concentrations of trace elements were compared in 78 PDAC cases and 416 hospital-based controls (case-control analyses), and between 17 KRAS wild-type tumors and 61 KRAS mutated tumors (case-case analyses). Higher levels of iron, arsenic, and vanadium were associated with a statistically nonsignificant increased risk of a KRAS wild-type PDAC (OR for higher tertile of arsenic = 3.37, 95% CI 0.98-11.57). Lower levels of nickel and manganese were associated with a statistically significant higher risk of a KRAS mutated PDAC (OR for manganese = 0.34, 95% CI 0.14-0.80). Higher levels of selenium appeared protective for both mutated and KRAS wild-type PDAC. Higher levels of cadmium and lead were clear risk factors for both KRAS mutated and wild-type cases. This is the first study analyzing biomarkers of trace elements and KRAS mutations in any human cancer. Concentrations of trace elements differed markedly between PDAC cases with and without mutations in codon 12 of the KRAS oncogene, thus suggesting a role for trace elements in pancreatic and perhaps other cancers with such mutations. Environ. Mol. Mutagen., 60:693-703, 2019. © 2019 Wiley Periodicals, Inc.
PMCID:6786909
PMID: 31066938
ISSN: 1098-2280
CID: 4214332
Multiple sessions of transcranial direct current stimulation (tDCS) combined with aerobic physical activity improves walking speed [Meeting Abstract]
Background: Walking impairments are one of the most impactful consequences of multiple sclerosis (MS). Recently, physical rehabilitation research has focused on developing synergistic protocols to enhance clinical benefit. Recent studies have shown that transcranial direct current stimulation (tDCS) and aerobic physical activity (PA) have converging activation pathways and when completed simultaneously, they may promote cortical neuroplasticity.
Objective(s): To harness cortical plasticity to improve gait for individuals with MS.
Aim(s): To investigate the effects of multiple sessions of PA with simultaneously administered tDCS on walking abilities.
Method(s): MS participants (EDSS: 1-6.5, Relapsing-Remitting or Secondary-Progressive subtype) with clinically significant gait deviations were recruited for a randomized controlled trial of 10 sessions of either active or sham tDCS paired with unloaded cycling for 20 minutes. Stimulation was administered over the primary motor cortex (2.5 mA-2.0 mA; anode over C3/cathode over FP2). Walking speed was assessed quantitatively by using a single inertial sensor placed on the lower back and perceived walking abilities were evaluated using the 12-Item MS Walking Scale (MSWS-12), a self-report questionnaire. Measurements were collected at baseline, the end of tDCS intervention, and 4-weeks post-intervention. Two-way repeated measures-ANOVA (Time, Treatment) was performed to investigate differences between active and sham conditions.
Result(s): Thirty-two participants were enrolled in the study, 22 underwent active treatment. No demographic differences were detected between active and sham groups (active:EDSS 4.3+/-1.2, age 55.5+/-10.3; sham:EDSS 4.5+/-1.5, age 49.7+/-13.9). Statistical analysis showed significant Treatment by Time interactions for gait speed and MSWS-12 score. Post-hoc analysis revealed that gait speed increased significantly after active treatment (Baseline vs. End Treatment, 0.98 vs. 1.16 m/s, p< 0.001; Baseline vs. Follow-up, 0.98 vs. 1.20 m/s, p< 0.001). Active group further reported significant improvement in self-report measure (Baseline vs. End Treatment, 58.04 vs. 49.73, p< 0.05). No significant difference was detected after sham stimulation.
Conclusion(s): Our results indicate that multiple sessions of tDCS administered simultaneously with PA induce cumulative and selfreport improvement in walking and benefits persisted until 4-week post-intervention
Objective(s): To harness cortical plasticity to improve gait for individuals with MS.
Aim(s): To investigate the effects of multiple sessions of PA with simultaneously administered tDCS on walking abilities.
Method(s): MS participants (EDSS: 1-6.5, Relapsing-Remitting or Secondary-Progressive subtype) with clinically significant gait deviations were recruited for a randomized controlled trial of 10 sessions of either active or sham tDCS paired with unloaded cycling for 20 minutes. Stimulation was administered over the primary motor cortex (2.5 mA-2.0 mA; anode over C3/cathode over FP2). Walking speed was assessed quantitatively by using a single inertial sensor placed on the lower back and perceived walking abilities were evaluated using the 12-Item MS Walking Scale (MSWS-12), a self-report questionnaire. Measurements were collected at baseline, the end of tDCS intervention, and 4-weeks post-intervention. Two-way repeated measures-ANOVA (Time, Treatment) was performed to investigate differences between active and sham conditions.
Result(s): Thirty-two participants were enrolled in the study, 22 underwent active treatment. No demographic differences were detected between active and sham groups (active:EDSS 4.3+/-1.2, age 55.5+/-10.3; sham:EDSS 4.5+/-1.5, age 49.7+/-13.9). Statistical analysis showed significant Treatment by Time interactions for gait speed and MSWS-12 score. Post-hoc analysis revealed that gait speed increased significantly after active treatment (Baseline vs. End Treatment, 0.98 vs. 1.16 m/s, p< 0.001; Baseline vs. Follow-up, 0.98 vs. 1.20 m/s, p< 0.001). Active group further reported significant improvement in self-report measure (Baseline vs. End Treatment, 58.04 vs. 49.73, p< 0.05). No significant difference was detected after sham stimulation.
Conclusion(s): Our results indicate that multiple sessions of tDCS administered simultaneously with PA induce cumulative and selfreport improvement in walking and benefits persisted until 4-week post-intervention
EMBASE:631450545
ISSN: 1352-4585
CID: 4385732
