Treatment Strategies for KRAS-Mutated Non-Small-Cell Lung Cancer

Activating mutations in KRAS are highly prevalent in solid tumours and are frequently found in 35% of lung, 45% of colorectal, and up to 90% of pancreatic cancers. Mutated KRAS is a prognostic factor for disease-free survival (DFS) and overall survival (OS) in NSCLC and is associated with a more aggressive clinical phenotype, highlighting the need for KRAS-targeted therapy. Once considered undruggable due to its smooth shallow surface, a breakthrough showed that the activated G12C-mutated KRAS isozyme can be directly inhibited via a newly identified switch II pocket. This discovery led to the development of a new class of selective small-molecule inhibitors against the KRAS G12C isoform. Sotorasib and adagrasib are approved in locally advanced or metastatic NSCLC patients who have received at least one prior systemic therapy. Currently, there are at least twelve KRAS G12C inhibitors being tested in clinical trials, either as a single agent or in combination. In this study, KRAS mutation prevalence, subtypes, rates of occurrence in treatment-resistant invasive mucinous adenocarcinomas (IMAs), and novel drug delivery options are reviewed. Additionally, the current status of KRAS inhibitors, multiple resistance mechanisms that limit efficacy, and their use in combination treatment strategies and novel multitargeted approaches in NSCLC are discussed.

Binding Immunoglobulin Protein (BIP) Inhibits TNF-α-Induced Osteoclast Differentiation and Systemic Bone Loss in an Erosive Arthritis Model

Objective

The association between inflammation and dysregulated bone remodeling is apparent in rheumatoid arthritis and is recapitulated in the human tumor necrosis factor transgenic (hTNFtg) mouse model. We investigated whether extracellular binding immunoglobulin protein (BiP) would protect the hTNFtg mouse from both inflammatory arthritis as well as extensive systemic bone loss and whether BiP had direct antiosteoclast properties in vitro.

Methods

hTNFtg mice received a single intraperitoneal administration of BiP at onset of arthritis. Clinical disease parameters were measured weekly. Bone analysis was performed by microcomputed tomography and histomorphometry. Mouse bone marrow macrophage and human peripheral blood monocyte precursors were used to study the direct effect of BiP on osteoclast differentiation and function in vitro. Monocyte and osteoclast signaling was analyzed by Western blotting, flow cytometry, and imaging flow cytometry.

Results

BiP-treated mice showed reduced inflammation and cartilage destruction, and histomorphometric analysis revealed a decrease in osteoclast number with protection from systemic bone loss. Abrogation of osteoclast function was also observed in an ex vivo murine calvarial model. BiP inhibited differentiation of osteoclast precursors and prevented bone resorption by mature osteoclasts in vitro. BiP also induced downregulation of CD115/c-Fms and Receptor Activator of NF-κB (RANK) messenger RNA and protein, causing reduced phosphorylation of the p38 mitogen-activated protein kinases, extracellular signal-regulated kinases 1/2 and p38, with suppression of essential osteoclast transcription factors, c-Fos and NFATc1. BiP directly inhibited TNF-α- or Receptor Activator of NF-κB Ligand (RANKL)-induced NF-κB nuclear translocation in THP-1 monocytic cells and preosteoclasts by the canonical and noncanonical pathways.

Conclusion

BiP combines an anti-inflammatory function with antiosteoclast activity, which establishes it as a potential novel therapeutic for inflammatory disorders associated with bone loss.

Association between circulating levels of heat-shock protein 27 and aggressive periodontitis

Heat-shock protein (Hsp) 27 is a major intracellular molecular chaperone and controller of intracellular responses to inflammatory signals. In the extracellular space, recombinant Hsp27 has been described to exert anti-inflammatory activities. The aim of this study was to assess the association between circulating levels of Hsp27 and different types of periodontitis. Pro- and anti-inflammatory cytokines and the stress proteins Hsp27 and Hsp60 with proposed anti- and pro-inflammatory properties, respectively, were measured by two-site ELISA in the serum of patients with aggressive periodontitis (AgP, n = 30), chronic periodontitis (CP, n = 29) and periodontally healthy controls (H, n = 28). Furthermore, Hsp27 and Hsp60 levels were also measured longitudinally in 12 AgP patients at 6 time points up to 3 months after treatment. AgP patients had lower levels of Hsp27 compared to CP patients and healthy subjects (adjusted one-way ANOVA, p < 0.001, followed by post hoc Tukey HSD comparisons), while no differences in levels of Hsp60 or cytokines between the three groups were detected. In CP patients and H subjects, the systemic Hsp27 levels correlated with Hsp60 (r = 0.43, p < 0.001; r = 0.59, p < 0.001, respectively) and with pro-inflammatory cytokines TNF-α (r = 0.48, p < 0.001; r = 0.55, p < 0.001, respectively) and IL-6 (r = 0.44, p < 0.01). However, no such correlations were detected in AgP cases. No consistent temporal patterns of changes of Hsp27 concentration were detected across AgP patients following periodontal treatment. This study provides the first evidence that Hsp27 may be differentially expressed and regulated in AgP patients as compared with CP patients and healthy individuals.

Extracellular cell stress (heat shock) proteins-immune responses and disease: an overview

Extracellular cell stress proteins are highly conserved phylogenetically and have been shown to act as powerful signalling agonists and receptors for selected ligands in several different settings. They also act as immunostimulatory 'danger signals' for the innate and adaptive immune systems. Other studies have shown that cell stress proteins and the induction of immune reactivity to self-cell stress proteins can attenuate disease processes. Some proteins (e.g. Hsp60, Hsp70, gp96) exhibit both inflammatory and anti-inflammatory properties, depending on the context in which they encounter responding immune cells. The burgeoning literature reporting the presence of stress proteins in a range of biological fluids in healthy individuals/non-diseased settings, the association of extracellular stress protein levels with a plethora of clinical and pathological conditions and the selective expression of a membrane form of Hsp70 on cancer cells now supports the concept that extracellular cell stress proteins are involved in maintaining/regulating organismal homeostasis and in disease processes and phenotype. Cell stress proteins, therefore, form a biologically complex extracellular cell stress protein network having diverse biological, homeostatic and immunomodulatory properties, the understanding of which offers exciting opportunities for delivering novel approaches to predict, identify, diagnose, manage and treat disease.This article is part of the theme issue 'Heat shock proteins as modulators and therapeutic targets of chronic disease: an integrated perspective'.

Climate change and pastoralism: impacts, consequences and adaptation

The authors discuss the main climate change impacts on pastoralist societies, including those on rangelands, livestock and other natural resources, and their extended repercussions on food security, incomes and vulnerability. The impacts of climate change on the rangelands of the globe and on the vulnerability of the people who inhabit them will be severe and diverse, and will require multiple, simultaneous responses. In higher latitudes, the removal of temperature constraints might increase pasture production and livestock productivity, but in tropical arid lands, the impacts are highly location specific, but mostly negative. The authors outline several adaptation options, ranging from implementing new technical practices and diversifying income sources to finding institutional support and introducing new market mechanisms, all of which are pivotal for enhancing the capacity of pastoralists to adapt to climate variability and change. Due to the dynamism of all the changes affecting pastoral societies, strategies that lock pastoral societies into specified development pathways could be maladaptive. Flexible and evolving combinations of practices and policies are the key to successful pastoral adaptation.

Generalization and fine mapping of European ancestry-based central adiposity variants in African ancestry populations

BACKGROUND/OBJECTIVES

Central adiposity measures such as waist circumference (WC) and waist-to-hip ratio (WHR) are associated with cardiometabolic disorders independently of body mass index (BMI) and are gaining clinically utility. Several studies report genetic variants associated with central adiposity, but most utilize only European ancestry populations. Understanding whether the genetic associations discovered among mainly European descendants are shared with African ancestry populations will help elucidate the biological underpinnings of abdominal fat deposition.

SUBJECTS/METHODS

To identify the underlying functional genetic determinants of body fat distribution, we conducted an array-wide association meta-analysis among persons of African ancestry across seven studies/consortia participating in the Population Architecture using Genomics and Epidemiology (PAGE) consortium. We used the Metabochip array, designed for fine-mapping cardiovascular-associated loci, to explore novel array-wide associations with WC and WHR among 15 945 African descendants using all and sex-stratified groups. We further interrogated 17 known WHR regions for African ancestry-specific variants.

RESULTS

Of the 17 WHR loci, eight single-nucleotide polymorphisms (SNPs) located in four loci were replicated in the sex-combined or sex-stratified meta-analyses. Two of these eight independently associated with WHR after conditioning on the known variant in European descendants (rs12096179 in TBX15-WARS2 and rs2059092 in ADAMTS9). In the fine-mapping assessment, the putative functional region was reduced across all four loci but to varying degrees (average 40% drop in number of putative SNPs and 20% drop in genomic region). Similar to previous studies, the significant SNPs in the female-stratified analysis were stronger than the significant SNPs from the sex-combined analysis. No novel associations were detected in the array-wide analyses.

CONCLUSIONS

Of 17 previously identified loci, four loci replicated in the African ancestry populations of this study. Utilizing different linkage disequilibrium patterns observed between European and African ancestries, we narrowed the suggestive region containing causative variants for all four loci.

Climate change and pastoralism: impacts, consequences and adaptation

The authors discuss the main climate change impacts on pastoralist societies, including those on rangelands, livestock and other natural resources, and their extended repercussions on food security, incomes and vulnerability. The impacts of climate change on the rangelands of the globe and on the vulnerability of the people who inhabit them will be severe and diverse, and will require multiple, simultaneous responses. In higher latitudes, the removal of temperature constraints might increase pasture production and livestock productivity, but in tropical arid lands, the impacts are highly location specific, but mostly negative. The authors outline several adaptation options, ranging from implementing new technical practices and diversifying income sources to finding institutional support and introducing new market mechanisms, all of which are pivotal for enhancing the capacity of pastoralists to adapt to climate variability and change. Due to the dynamism of all the changes affecting pastoral societies, strategies that lock pastoral societies into specified development pathways could be maladaptive. Flexible and evolving combinations of practices and policies are the key to successful pastoral adaptation.

Abstract 3434: Neighborhood obesogenic environment and the risk of prostate cancer: The Multiethnic Cohort

Background: Obesity is a potentially modifiable risk factor for advanced prostate cancer (PCa). However, the role of the neighborhood obesogenic environment, characterized by obesity-related built and social environment measures, has not been evaluated in relation to PCa risk.

Objective: To examine the association of neighborhood obesogenic environment with PCa risk in African American (AA), Japanese American (JA), Latino (LA), and White (WH) men in the California component of the Multiethnic Cohort (MEC) Study.

Method: Individual-level sociodemographic data and health behaviors were linked with neighborhood measures of built and social environment for 42,850 men in the MEC, who predominately live in Los Angeles County. A principal components factor analysis was used to create indices based on 10 measures—neighborhood SES, population density, total businesses, recreational facilities, retail food environment, restaurant environment, parks, street connectivity, commuting by car, and traffic density—resulting in 4 obesogenic environment indices: physically active, low SES urban, businesses density, and unhealthy food. During a mean follow-up of 15 years and through linkage to the California Cancer Registry, 4,775 incident PCa cases were identified. Multivariable Cox proportional hazards regression was used to estimate hazard ratios (HR) and 95% confidence intervals (CI) for associations between each index and PCa risk, overall and stratified by race/ethnicity and disease aggressiveness. For Latinos, additional stratified analyses were conducted by nativity.

Results: Associations between the obesogenic indices and PCa risk varied by race/ethnicity. WH residing in low business environments experienced lower PCa risk (quintile [Q] 1 [low] vs. Q5 [high]: HR, 0.56 [95% CI, 0.41-0.77], p-trend: 0.0002). Among AA, unhealthy food environments were associated with greater risk of aggressive disease (advance stage or Gleason score &gt; = 7) (more vs. no: HR, 1.36 [95% CI, 1.09-1.70], p-trend: 0.0026). Among LA, living in Hispanic enclaves was associated with reduced risk (Q3-5 [high] vs. Q1-2 [low]: HR, 0.86 [95% CI, 0.75-0.98]), but living in high business environments was associated with increased risk of PCa (Q1 [low] vs. Q5 [high]: HR, 1.35 [95% CI, 1.05-1.73], p-trend: 0.0002) for those born in the US (p-trend: 0.0059). Lower SES urban environments were associated with a decreased risk of non-aggressive disease among LA (Q5 [low] vs. Q1 [high]: HR, 0.78 [95% CI, 0.63-0.98], p-trend: 0.0026), and was more marked among foreign-born (p trend = 0.0074) than US-born (p trend = 0.1211).

Conclusions: Built and social environment factors are associated with PCa risk, but their associations varied by race/ethnicity, nativity (among LA), and disease aggressiveness. An unhealthy food environment was strongly associated with the risk of aggressive prostate cancer in AA men, warranting further investigation into the underlying mechanisms.

Citation Format: Li Tao, Scarlett L. Gomez, Salma Shariff-Marco, Juan Yang, Song Yi Park, Cheryl Albright, Kristine Monroe, Brian Henderson, Laurence Kolonel, Loic Le Marchand, Lynne Wilkens, Iona Cheng. Neighborhood obesogenic environment and the risk of prostate cancer: The Multiethnic Cohort. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3434.

Leukocyte receptor expression in chronic periodontitis

BACKGROUND AND OBJECTIVE

Microbial recognition in the periodontium through specific leukocyte receptors gives rise to the response which in susceptible individuals can lead to periodontal diseases. The aim of this study was to explore the expression of leukocyte receptors in the gingival tissues of chronic periodontitis patients and to analyse differences between diseased and control sites (sites with probing pocket depth <4 mm).

MATERIAL AND METHODS

Thirty-seven chronic periodontitis patients were included in the study. Gingival biopsies were harvested from diseased and control sites and processed by flow cytometry for the determination of the expression of 16 leukocyte receptors (CD4, CD8, CD11b, CD14, CD16, CD19, CD25, CD28, CD49d, CD49e, CD62, CD71, CD80, CCR7, Ly6G and HLA-DR).

RESULTS

Expression of all studied receptors was higher in test compared with control sites (p < 0.005). Sampled sites with less bleeding on probing exhibited higher expression of CD16 and CD14 receptors (p = 0.020 and 0.011, respectively).

CONCLUSIONS

This study points towards considerable differences in the expression of leukocyte receptors between diseased and control sites in the same periodontal patients.

Closing system-wide yield gaps to increase food production and mitigate GHGs among mixed crop-livestock smallholders in Sub-Saharan Africa

In this study we estimate yield gaps for mixed crop-livestock smallholder farmers in seven Sub-Saharan African sites covering six countries (Kenya, Tanzania, Uganda, Ethiopia, Senegal and Burkina Faso). We also assess their potential to increase food production and reduce the GHG emission intensity of their products, as a result of closing these yield gaps. We use stochastic frontier analysis to construct separate production frontiers for each site, based on 2012 survey data prepared by the International Livestock Research Institute for the Climate Change, Agriculture and Food Security program. Instead of relying on theoretically optimal yields-a common approach in yield gap assessments-our yield gaps are based on observed differences in technical efficiency among farms within each site. Sizeable yield gaps were estimated to be present in all of the sites. Expressed as potential percentage increases in outputs, the average site-based yield gaps ranged from 28 to 167% for livestock products and from 16 to 209% for crop products. The emission intensities of both livestock and crop products registered substantial falls as a consequence of closing yield gaps. The relationships between farm attributes and technical efficiency were also assessed to help inform policy makers about where best to target capacity building efforts. We found a strong and statistically significant relationship between market participation and performance across most sites. We also identified an efficiency dividend associated with the closer integration of crop and livestock enterprises. Overall, this study reveals that there are large yield gaps and that substantial benefits for food production and environmental performance are possible through closing these gaps, without the need for new technology.

Increased percentages of regulatory T cells are associated with inflammatory and neuroendocrine responses to acute psychological stress and poorer health status in older men and women

RATIONALE

The percentage of regulatory T cells (TRegs)-a subtype of T lymphocyte that suppresses the immune response-appears to be reduced in a number of stress-related diseases. The role of the TReg in stress-disease pathways has not yet been investigated.

OBJECTIVES

The aim of the study was to investigate the association between biological responsivity to acute psychosocial stress and the percentage of TRegs in healthy older adults. The secondary purpose was to measure the associations between TReg percentage and psychological and physical well-being in the participants.

METHODS

Salivary cortisol and plasma interleukin (IL)-6 samples were obtained from 121 healthy older men and women from the Whitehall II cohort following acute psychophysiological stress testing. Three years later at a follow-up visit, we measured TReg percentages and psychological and physical well-being were recorded using the Short Form 36 Health Survey and the Center for Epidemiologic Studies Depression Scale.

RESULTS

Blunted cortisol responses (p = 0.004) and elevated IL-6 responses (p = 0.027) to acute psychophysiological stress were associated with greater TReg percentage independently of age, sex, BMI, smoking status, employment grade, time of testing, and baseline measures of cortisol and IL-6, respectively. Percentage of TRegs was associated cross-sectionally with lower physical (p = 0.043) and mental health status (p = 0.008), and higher levels of depressive symptoms (p = 0.002), independently of covariates.

CONCLUSIONS

Increased levels of TRegs may act as a defence against increased inflammation and may be a pre-indication for chronically stressed individuals on the cusp of clinical illness.

The contribution of rare variation to prostate cancer heritability

We report targeted sequencing of 63 known prostate cancer risk regions in a multi-ancestry study of 9,237 men and use the data to explore the contribution of low-frequency variation to disease risk. We show that SNPs with minor allele frequencies (MAFs) of 0.1-1% explain a substantial fraction of prostate cancer risk in men of African ancestry. We estimate that these SNPs account for 0.12 (standard error (s.e.) = 0.05) of variance in risk (∼42% of the variance contributed by SNPs with MAF of 0.1-50%). This contribution is much larger than the fraction of neutral variation due to SNPs in this class, implying that natural selection has driven down the frequency of many prostate cancer risk alleles; we estimate the coupling between selection and allelic effects at 0.48 (95% confidence interval [0.19, 0.78]) under the Eyre-Walker model. Our results indicate that rare variants make a disproportionate contribution to genetic risk for prostate cancer and suggest the possibility that rare variants may also have an outsize effect on other common traits.

Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for Thirteen Cancer Types

BACKGROUND

Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites.

METHODS

Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers.

RESULTS

GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, hl (2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (ρ = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (ρ = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (ρ = 0.51, SE =0.18), and bladder and lung (ρ = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures.

CONCLUSION

Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.

Cross Cancer Genomic Investigation of Inflammation Pathway for Five Common Cancers: Lung, Ovary, Prostate, Breast, and Colorectal Cancer

BACKGROUND

Inflammation has been hypothesized to increase the risk of cancer development as an initiator or promoter, yet no large-scale study of inherited variation across cancer sites has been conducted.

METHODS

We conducted a cross-cancer genomic analysis for the inflammation pathway based on 48 genome-wide association studies within the National Cancer Institute GAME-ON Network across five common cancer sites, with a total of 64 591 cancer patients and 74 467 control patients. Subset-based meta-analysis was used to account for possible disease heterogeneity, and hierarchical modeling was employed to estimate the effect of the subcomponents within the inflammation pathway. The network was visualized by enrichment map. All statistical tests were two-sided.

RESULTS

We identified three pleiotropic loci within the inflammation pathway, including one novel locus in Ch12q24 encoding SH2B3 (rs3184504), which reached GWAS significance with a P value of 1.78 x 10(-8), and it showed an association with lung cancer (P = 2.01 x 10(-6)), colorectal cancer (GECCO P = 6.72x10(-6); CORECT P = 3.32x10(-5)), and breast cancer (P = .009). We also identified five key subpathway components with genetic variants that are relevant for the risk of these five cancer sites: inflammatory response for colorectal cancer (P = .006), inflammation related cell cycle gene for lung cancer (P = 1.35x10(-6)), and activation of immune response for ovarian cancer (P = .009). In addition, sequence variations in immune system development played a role in breast cancer etiology (P = .001) and innate immune response was involved in the risk of both colorectal (P = .022) and ovarian cancer (P = .003).

CONCLUSIONS

Genetic variations in inflammation and its related subpathway components are keys to the development of lung, colorectal, ovary, and breast cancer, including SH2B3, which is associated with lung, colorectal, and breast cancer.

ABO blood group alleles and prostate cancer risk: Results from the breast and prostate cancer cohort consortium (BPC3)

BACKGROUND

ABO blood group has been associated with risk of cancers of the pancreas, stomach, ovary, kidney, and skin, but has not been evaluated in relation to risk of aggressive prostate cancer.

METHODS

We used three single nucleotide polymorphisms (SNPs) (rs8176746, rs505922, and rs8176704) to determine ABO genotype in 2,774 aggressive prostate cancer cases and 4,443 controls from the Breast and Prostate Cancer Cohort Consortium (BPC3). Unconditional logistic regression was used to calculate age and study-adjusted odds ratios and 95% confidence intervals for the association between blood type, genotype, and risk of aggressive prostate cancer (Gleason score ≥8 or locally advanced/metastatic disease (stage T3/T4/N1/M1).

RESULTS

We found no association between ABO blood type and risk of aggressive prostate cancer (Type A: OR = 0.97, 95%CI = 0.87-1.08; Type B: OR = 0.92, 95%CI =n0.77-1.09; Type AB: OR = 1.25, 95%CI = 0.98-1.59, compared to Type O, respectively). Similarly, there was no association between "dose" of A or B alleles and aggressive prostate cancer risk.

CONCLUSIONS

ABO blood type was not associated with risk of aggressive prostate cancer.

Abstract B25: Impact of neighborhood obesogenic factors on obesity in over 100,000 participants of the Multiethnic Cohort Study

Introduction: The obesity epidemic is a serious health priority with important consequences on obesity-associated cancers. Socioeconomic (SES) and “obesogenic” attributes of neighborhoods may promote obesity by providing a context where it is difficult to engage in physical activity and/or access healthy foods. This may be particularly relevant for minority populations that have limited neighborhood resources and experience higher levels of obesity. However, the extent to which these neighborhood factors translate into individual levels of body mass index (BMI) have been mixed among racial/ethnic groups. Therefore, leveraging the scale and racial/ethnic diversity of the Multiethnic Cohort (MEC) study, we examined the associations between neighborhood obesogenic factors and BMI among African Americans, Japanese Americans, Latinos, and Whites in California.

Methods: Study subjects included 107,697 MEC participants, ages 45-75, residing in California (93% from Los Angeles County) with geocoded addresses and data available on BMI at baseline questionnaire (1993-1996). Residential baseline addresses were geocoded to latitude and longitude coordinates and assigned to 1990 Census block groups to ascertain neighborhood levels of SES, population density, and commute patterns. In addition, geocodes were linked to business data to quantify neighborhood attributes of the retail/restaurant food environment, parks, recreational facilities, walkability, traffic density, and total businesses within a residential buffer area of one mile in radius. Polytomous logistic regression was conducted to examine the relationship between the obesogenic environment and BMI in kg/m2 (underweight: BMI&lt;18.5; normal weight: BMI=18.5-&lt;25 (reference); overweight BMI=25-&lt;30; obese BMI&gt;30) adjusting for age, sex, and race/ethnicity and including all neighborhood obesogenic factors. Stratified analyses were conducted by gender and race/ethnicity.

Results: Lower neighborhood SES was significantly associated with higher odds of being overweight and obese. For males, in comparison to the highest SES quintile (Q5), the odds ratios and 95% confidence intervals for obesity with decreasing SES quintiles were Q4: OR=1.36 (95% CI: 1.20-1.50), Q3: OR=1.59; (95% CI: 1.40-1.81), Q2: OR=1.70 (95% CI: 1.49-1.93), and Q1: OR=1.89 (95% CI: 1.63-2.19). For females, similar patterns of associations were seen although larger associations were observed (Q4: OR=1.52 (95% CI: 1.36-1.70), Q3: OR=2.11 (95% CI: 1.89-2.34), Q2: OR=2.72 (95% CI: 2.43-3.03), Q1: OR=3.34 (95% CI: 2.94-3.78)). All racial/ethnic groups demonstrated similar patterns of associations between SES and obesity. Neighborhoods with smaller density of businesses (i.e. fewer nearby walkable destinations) were significantly associated with higher odds of obesity (ORQ1 vs. Q5=1.24; 95% CI: 1.14-1.34). This association was consistently observed among African American males and females, U.S. born Latino males, foreign-born Latino females, and White females. For White males and females, residence in neighborhoods with lower levels of commuting by car or motorcycle were associated with lower odds of obesity in comparison to residence in neighborhoods at the highest level of commuting by car or motorcycle (males ORQ1 vs. Q5=0.51; 95% CI: 0.35-0.76; females ORQ1 vs. Q5=0.64; 95% CI: 0.48-0.84).

Conclusion: These findings demonstrate the impact of the neighborhood environment on obesity with complex relationships observed across gender and racial/ethnic groups. Future analyses will incorporate individual-level health behaviors such as dietary factors, physical activity and smoking, as well estimates of genetic ancestry. Our understanding of this relationship between the obesogenic environment and obesity provides a framework for future studies of neighborhood obesogenic factors and cancer risk.

Citation Format: Iona Cheng, Juan Yang, Andrew Hertz, Christina Clarke, Cheryl Albright, Loic Le Marchand, Laurence Kolonel, Brian Henderson, Kristine Monroe, Scarlett Lin-Gomez, Lynne Wilkens. Impact of neighborhood obesogenic factors on obesity in over 100,000 participants of the Multiethnic Cohort Study. [abstract]. In: Proceedings of the Seventh AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; Nov 9-12, 2014; San Antonio, TX. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2015;24(10 Suppl):Abstract nr B25.

Abstract 4611: Quantification and functional characterization of the shared heritability across multiple cancer sites: results from the GAME-ON Consortium

It is estimated that more than 1.6 million cancer diagnoses will occur in the US during 2014 and five common cancers_breast, colorectal, lung, ovarian and prostate cancer_together constitute more than 50% of new cancer diagnoses. Many cancers cluster within families and in some cases multiple tumor types affect one family. Quantifying the extent to which distinct cancer types share genetic predisposition will inform design for future genetic association studies and give insights to shared biological mechanisms underlying disease.

The GAME-ON consortium set out to conduct post-GWAS research for breast, colorectal, lung, ovarian and prostate cancer. Across the five cancer sites, a total of 51,725 cases and 62,155 controls were included as part of cancer-specific GWAS and summary statistics were shared between the cancer sites to conduct cross-cancer analysis. Using the recently developed LD score regression method, we leveraged these data to quantify the genetic correlation between these five cancers. In addition, we also estimated the genetic correlation between these cancers and 59 non-cancer traits using publically available GWAS summary statistics. Finally, we also functionally characterized the heritability across the five GAME-ON cancers.

We found a nominally significant positive genetic correlation between breast and lung cancer (rg = 0.26, p = 0.045), however this correlation did not remain significantly different from zero after adjusting for multiple testing. We found positive genetic correlations (all p&lt;0.003) between lung cancer and traits related to smoking (rg = 0.53-0.64) and adiposity (rg = 0.31-0.42). We also identified a positive genetic correlation between schizophrenia and breast cancer (rg = 0.16, p = 0.003) as well as a negative genetic correlation between adiposity and breast cancer (rg = -0.25, p = 0.01). However, these genetic correlations were not statistically significant after adjustment for number of tests performed.

In functional enrichment analysis across all cancers, we observed a 17-fold (se: 2.9) enrichment of heritability located within conserved regions. In addition, transcription factor binding sites (TFBS), super-enhancers and histone marks showed 6.6- (se: 1.2), 2.5- (se: 0.2) and 2.0-fold enrichments, respectively.

This is the first study to estimate the genetic correlation between these five common cancers in a population of unrelated individuals. Although we observe only modest evidence of a shared heritability of these cancers, the standard errors were large; larger samples will be needed to find modest, true genetic correlations. In addition, we found that conserved genetic regions are enriched for cancer heritability and future studies seeking to discover genetic variants associated with these cancers should focus on these regions.

Note: This abstract was not presented at the meeting.

Citation Format: Sara Lindstrom, Hilary Finucane, Brendan Bulik-Sullivan, Fredrick Schumacher, Christopher Amos, Stephen Gruber, Brian Henderson, David Hunter, Thomas Sellers, Benjamin Neale, Alkes Price, Peter Kraft, GAME-ON Consortium. Quantification and functional characterization of the shared heritability across multiple cancer sites: results from the GAME-ON Consortium. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4611. doi:10.1158/1538-7445.AM2015-4611

Genetic risk variants associated with in situ breast cancer

INTRODUCTION

Breast cancer in situ (BCIS) diagnoses, a precursor lesion for invasive breast cancer, comprise about 20 % of all breast cancers (BC) in countries with screening programs. Family history of BC is considered one of the strongest risk factors for BCIS.

METHODS

To evaluate the association of BC susceptibility loci with BCIS risk, we genotyped 39 single nucleotide polymorphisms (SNPs), associated with risk of invasive BC, in 1317 BCIS cases, 10,645 invasive BC cases, and 14,006 healthy controls in the National Cancer Institute's Breast and Prostate Cancer Cohort Consortium (BPC3). Using unconditional logistic regression models adjusted for age and study, we estimated the association of SNPs with BCIS using two different comparison groups: healthy controls and invasive BC subjects to investigate whether BCIS and BC share a common genetic profile.

RESULTS

We found that five SNPs (CDKN2BAS-rs1011970, FGFR2-rs3750817, FGFR2-rs2981582, TNRC9-rs3803662, 5p12-rs10941679) were significantly associated with BCIS risk (P value adjusted for multiple comparisons <0.0016). Comparing invasive BC and BCIS, the largest difference was for CDKN2BAS-rs1011970, which showed a positive association with BCIS (OR = 1.24, 95 % CI: 1.11-1.38, P = 1.27 x 10(-4)) and no association with invasive BC (OR = 1.03, 95 % CI: 0.99-1.07, P = 0.06), with a P value for case-case comparison of 0.006. Subgroup analyses investigating associations with ductal carcinoma in situ (DCIS) found similar associations, albeit less significant (OR = 1.25, 95 % CI: 1.09-1.42, P = 1.07 x 10(-3)). Additional risk analyses showed significant associations with invasive disease at the 0.05 level for 28 of the alleles and the OR estimates were consistent with those reported by other studies.

CONCLUSIONS

Our study adds to the knowledge that several of the known BC susceptibility loci are risk factors for both BCIS and invasive BC, with the possible exception of rs1011970, a putatively functional SNP situated in the CDKN2BAS gene that may be a specific BCIS susceptibility locus.

Identification of a common variant with potential pleiotropic effect on risk of inflammatory bowel disease and colorectal cancer

Although genome-wide association studies (GWAS) have separately identified many genetic susceptibility loci for ulcerative colitis (UC), Crohn's disease (CD) and colorectal cancer (CRC), there has been no large-scale examination for pleiotropy, or shared genetic susceptibility, for these conditions. We used logistic regression modeling to examine the associations of 181 UC and CD susceptibility variants previously identified by GWAS with risk of CRC using data from the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colon Cancer Family Registry. We also examined associations of significant variants with clinical and molecular characteristics in a subset of the studies. Among 11794 CRC cases and 14190 controls, rs11676348, the susceptibility single nucleotide polymorphism (SNP) for UC, was significantly associated with reduced risk of CRC (P = 7E-05). The multivariate-adjusted odds ratio of CRC with each copy of the T allele was 0.93 (95% CI 0.89-0.96). The association of the SNP with risk of CRC differed according to mucinous histological features (P heterogeneity = 0.008). In addition, the (T) allele was associated with lower risk of tumors with Crohn's-like reaction but not tumors without such immune infiltrate (P heterogeneity = 0.02) and microsatellite instability-high (MSI-high) but not microsatellite stable or MSI-low tumors (P heterogeneity = 0.03). The minor allele (T) in SNP rs11676348, located downstream from CXCR2 that has been implicated in CRC progression, is associated with a lower risk of CRC, particularly tumors with a mucinous component, Crohn's-like reaction and MSI-high. Our findings offer the promise of risk stratification of inflammatory bowel disease patients for complications such as CRC.

Two susceptibility loci identified for prostate cancer aggressiveness

Most men diagnosed with prostate cancer will experience indolent disease; hence, discovering genetic variants that distinguish aggressive from nonaggressive prostate cancer is of critical clinical importance for disease prevention and treatment. In a multistage, case-only genome-wide association study of 12,518 prostate cancer cases, we identify two loci associated with Gleason score, a pathological measure of disease aggressiveness: rs35148638 at 5q14.3 (RASA1, P=6.49 × 10(-9)) and rs78943174 at 3q26.31 (NAALADL2, P=4.18 × 10(-8)). In a stratified case-control analysis, the SNP at 5q14.3 appears specific for aggressive prostate cancer (P=8.85 × 10(-5)) with no association for nonaggressive prostate cancer compared with controls (P=0.57). The proximity of these loci to genes involved in vascular disease suggests potential biological mechanisms worthy of further investigation.

A genome-wide pleiotropy scan for prostate cancer risk

BACKGROUND

No single-nucleotide polymorphisms (SNPs) specific for aggressive prostate cancer have been identified in genome-wide association studies (GWAS).

OBJECTIVE

To test if SNPs associated with other traits may also affect the risk of aggressive prostate cancer.

DESIGN, SETTING, AND PARTICIPANTS

SNPs implicated in any phenotype other than prostate cancer (p≤10(-7)) were identified through the catalog of published GWAS and tested in 2891 aggressive prostate cancer cases and 4592 controls from the Breast and Prostate Cancer Cohort Consortium (BPC3). The 40 most significant SNPs were followed up in 4872 aggressive prostate cancer cases and 24,534 controls from the Prostate Cancer Association Group to Investigate Cancer Associated Alterations in the Genome (PRACTICAL) consortium.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

Odds ratios (ORs) and 95% confidence intervals (CIs) for aggressive prostate cancer were estimated.

RESULTS AND LIMITATIONS

A total of 4666 SNPs were evaluated by the BPC3. Two signals were seen in regions already reported for prostate cancer risk. rs7014346 at 8q24.21 was marginally associated with aggressive prostate cancer in the BPC3 trial (p=1.6×10(-6)), whereas after meta-analysis by PRACTICAL the summary OR was 1.21 (95% CI 1.16-1.27; p=3.22×10(-18)). rs9900242 at 17q24.3 was also marginally associated with aggressive disease in the meta-analysis (OR 0.90, 95% CI 0.86-0.94; p=2.5×10(-6)). Neither of these SNPs remained statistically significant when conditioning on correlated known prostate cancer SNPs. The meta-analysis by BPC3 and PRACTICAL identified a third promising signal, marked by rs16844874 at 2q34, independent of known prostate cancer loci (OR 1.12, 95% CI 1.06-1.19; p=4.67×10(-5)); it has been shown that SNPs correlated with this signal affect glycine concentrations. The main limitation is the heterogeneity in the definition of aggressive prostate cancer between BPC3 and PRACTICAL.

CONCLUSIONS

We did not identify new SNPs for aggressive prostate cancer. However, rs16844874 may provide preliminary genetic evidence on the role of the glycine pathway in prostate cancer etiology.

PATIENT SUMMARY

We evaluated whether genetic variants associated with several traits are linked to the risk of aggressive prostate cancer. No new such variants were identified.

Vitamin D metabolic pathway genes and pancreatic cancer risk

Evidence on the association between vitamin D status and pancreatic cancer risk is inconsistent. This inconsistency may be partially attributable to variation in vitamin D regulating genes. We selected 11 vitamin D-related genes (GC, DHCR7, CYP2R1, VDR, CYP27B1, CYP24A1, CYP27A1, RXRA, CRP2, CASR and CUBN) totaling 213 single nucleotide polymorphisms (SNPs), and examined associations with pancreatic adenocarcinoma. Our study included 3,583 pancreatic cancer cases and 7,053 controls from the genome-wide association studies of pancreatic cancer PanScans-I-III. We used the Adaptive Joint Test and the Adaptive Rank Truncated Product statistic for pathway and gene analyses, and unconditional logistic regression for SNP analyses, adjusting for age, sex, study and population stratification. We examined effect modification by circulating vitamin D concentration (≤50, >50 nmol/L) for the most significant SNPs using a subset of cohort cases (n = 713) and controls (n = 878). The vitamin D metabolic pathway was not associated with pancreatic cancer risk (p = 0.830). Of the individual genes, none were associated with pancreatic cancer risk at a significance level of p<0.05. SNPs near the VDR (rs2239186), LRP2 (rs4668123), CYP24A1 (rs2762932), GC (rs2282679), and CUBN (rs1810205) genes were the top SNPs associated with pancreatic cancer (p-values 0.008-0.037), but none were statistically significant after adjusting for multiple comparisons. Associations between these SNPs and pancreatic cancer were not modified by circulating concentrations of vitamin D. These findings do not support an association between vitamin D-related genes and pancreatic cancer risk. Future research should explore other pathways through which vitamin D status might be associated with pancreatic cancer risk.

Subgingival microbiota in health compared to periodontitis and the influence of smoking

The etiology of periodontitis has traditionally been associated to a consortium of three bacterial species—the so-called “red-complex” of periodontal disease—which has been the target for most diagnostic and therapeutic strategies. However, other species have also been found to correlate with disease severity. In addition, the influence of smoking on periodontal microbiota is poorly understood. In the current manuscript, the composition of the subgingival microbiota in healthy individuals vs. patients with chronic periodontitis has been investigated using 16S pyrosequencing and the influence of smoking on periodontal composition has been examined. Subgingival bacterial communities were sampled from 82 patients: 22 non-smoking healthy controls, 28 non-smoking periodontal patients, and 32 smoking periodontal patients. Bacterial diversity was higher in periodontal patients than in healthy subjects, which could be interpreted as the consequence of a nutritionally richer environment or a reduced immune competence. Periodontal patients showed a significantly higher prevalence/relative abundance of “established” periopathogens but also other taxa whose role is not well-established and that should be targets for future research. These include Anaeroglobus, Bulleidia, Desulfobulbus, Filifactor, Mogibacterium, Phocaeicola, Schwartzia or TM7. The microbial community of smoking-associated periodontitis is less diverse and distinct from that of non-smokers, indicating that smoking has an influence on periodontal ecology. Interestingly, the high sequencing coverage allowed the detection at low proportions of periodontal pathogens in all healthy individuals, indicating that chronic periodontitis cannot be strictly considered an infectious disease but the outcome of a polymicrobial dysbiosis, where changes in the proportions of microbial consortia trigger the inflammatory and tissue-degradation responses of the host.

Age-related clonal hematopoiesis associated with adverse outcomes

BACKGROUND

The incidence of hematologic cancers increases with age. These cancers are associated with recurrent somatic mutations in specific genes. We hypothesized that such mutations would be detectable in the blood of some persons who are not known to have hematologic disorders.

METHODS

We analyzed whole-exome sequencing data from DNA in the peripheral-blood cells of 17,182 persons who were unselected for hematologic phenotypes. We looked for somatic mutations by identifying previously characterized single-nucleotide variants and small insertions or deletions in 160 genes that are recurrently mutated in hematologic cancers. The presence of mutations was analyzed for an association with hematologic phenotypes, survival, and cardiovascular events.

RESULTS

Detectable somatic mutations were rare in persons younger than 40 years of age but rose appreciably in frequency with age. Among persons 70 to 79 years of age, 80 to 89 years of age, and 90 to 108 years of age, these clonal mutations were observed in 9.5% (219 of 2300 persons), 11.7% (37 of 317), and 18.4% (19 of 103), respectively. The majority of the variants occurred in three genes: DNMT3A, TET2, and ASXL1. The presence of a somatic mutation was associated with an increase in the risk of hematologic cancer (hazard ratio, 11.1; 95% confidence interval [CI], 3.9 to 32.6), an increase in all-cause mortality (hazard ratio, 1.4; 95% CI, 1.1 to 1.8), and increases in the risks of incident coronary heart disease (hazard ratio, 2.0; 95% CI, 1.2 to 3.4) and ischemic stroke (hazard ratio, 2.6; 95% CI, 1.4 to 4.8).

CONCLUSIONS

Age-related clonal hematopoiesis is a common condition that is associated with increases in the risk of hematologic cancer and in all-cause mortality, with the latter possibly due to an increased risk of cardiovascular disease. (Funded by the National Institutes of Health and others.).

Risk factors for endometrial cancer in black and white women: a pooled analysis from the Epidemiology of Endometrial Cancer Consortium (E2C2)

PURPOSE

Endometrial cancer (EC) is the most common gynecologic cancer in the USA. Over the last decade, the incidence rate has been increasing, with a larger increase among blacks. The aim of this study was to compare risk factors for EC in black and white women.

METHODS

Data from seven cohort and four case-control studies were pooled. Unconditional logistic regression was used to estimate adjusted odds ratios (OR) and 95 % confidence intervals for each risk factor in blacks and whites separately.

RESULTS

Data were pooled for 2,011 black women (516 cases and 1,495 controls) and 19,297 white women (5,693 cases and 13,604 controls). BMI ≥ 30 was associated with an approximate threefold increase in risk of EC in both black and white women (ORblack 2.93, 95 % CI 2.11, 4.07 and ORwhite 2.99, 95 % CI 2.74, 3.26). Diabetes was associated with a 30-40 % increase in risk among both groups. Increasing parity was associated with decreasing risk of EC in blacks and whites (p value = 0.02 and <0.001, respectively). Current and former smoking was associated with decreased risk of EC among all women. Both black and white women who used oral contraceptives for 10 +years were also at reduced risk of EC (OR 0.49, 95 % CI 0.27, 0.88 and OR 0.69, 95 % CI 0.58, 0.83, respectively). Previous history of hypertension was not associated with EC risk in either group.

CONCLUSIONS

The major known risk factors for EC exert similar effects on black and white women. Differences in the incidence rates between the two populations may be due to differences in the prevalence of risk factors.

Abstract B25: Characterizing the neighborhood environment for studies of cancer risk: The Multiethnic Cohort

Introduction: While considerable progress has been made in identifying individual-level risk factors for cancer etiology, the contextual features of the neighborhood environments, where these factors operate have yet to be thoroughly investigated. This is particularly relevant for minority and low socioeconomic populations that have limited neighborhood resources and experience higher levels of obesity, smoking, and other high risk behaviors. Recognizing the need for neighborhood studies of cancer in minority populations, we have linked the well-characterized resources of the Multiethnic Cohort Study (MEC) and the California Neighborhoods Data System to enable prospective studies of the neighborhood environment and cancer risk. The objective of this analysis was to characterize the contextual features of the neighborhood environments of MEC participants, residing in California at baseline, and assess the relationship between these neighborhood characteristics, demographic factors, and health behaviors.

Methods: Study subjects included 111,697 MEC participants, ages 45-75, residing in California (93% from Los Angeles County) that completed a baseline questionnaire from 1993-1996. Residential baseline addresses were geocoded to latitude and longitude coordinates and assigned 1990 Census block groups to characterize their neighborhood social (e.g., socioeconomic status (SES) distributed into quintiles based on statewide distribution, racial/ethnic composition, percent foreign-born) and built environment (e.g., population density, urbanicity, street connectivity, housing) characteristics using the California Neighborhoods Data System. Linear regression and Cochran-Mantel-Haenszel tests were conducted adjusting for age, sex, race/ethnicity to examine the relationship between neighborhood characteristics, demographic factors, and health behaviors at baseline.

Results: Ninety-eight percent of California residences of MEC participants at baseline (n=109,682, 30.3% African Americans, 41.3% Latinos, 13.1% Whites, 11.3% Japanese Americans; and 42.8% men and 57.2% women) were successfully geocoded and linked to 7,947 Census block groups, our neighborhood unit. African Americans and Latinos were more likely to reside in low SES neighborhoods (67% and 61%, respectively, in quintiles 1 and 2). In contrast, Whites and Japanese Americans were less likely to reside in low SES neighborhoods (27% and 19%, respectively, in quintiles 1 and 2). Higher levels of neighborhood SES were significantly associated with higher levels of education, higher mean intake of fruits (g/kcal/day), lower mean intake of red meat (g/kcal/day), higher alcohol intake (g/day), lower proportions of smoking, higher mean levels of moderate/vigorous activity, and lower mean levels of body mass index (BMI) in comparison to low SES neighborhoods (Ps&lt;0.001). Higher levels of population density were significantly associated with lower education, lower mean intake of fruits (g/kcal/day), higher mean intake of red meat (g/kcal/day), and lower mean levels of moderate physical activity in comparison to low population density neighborhoods (Ps&lt;0.001). Residing in neighborhoods with higher levels of commuting by car or motorcycle were significantly associated with higher mean levels of moderate and moderate/vigorous physical activity and lower mean intake of vegetables compared to residing in neighborhoods with less commuting by car or motorcycle (Ps&lt;0.001). Residing in neighborhoods of higher levels of Hispanic acculturation were significantly associated with lower mean levels of moderate physical activity, lower mean intake of fruits (g/kcal/day), higher mean intake of red meat (g/kcal/day), and higher mean levels of BMI in comparison to residing in neighborhoods of low levels of Hispanic acculturation (Ps&lt;0.001).

Conclusion: These findings demonstrate the complex relationships between specific social and built environment features and several health behaviors among MEC participants, residing primarily in Los Angeles County at baseline. Future work will evaluate additional neighborhood characteristics such as retail and restaurant food environments, parks, and traffic density. The diversity and range of neighborhood exposures of MEC participants coupled with our understanding of the relationship between these exposures and individual-level factors establish the framework for future studies of their independent and joint effects on cancer risk.

Citation Format: Iona Cheng, Salma Shariff-Marco, Juan Yang, Andrew Hertz, Jana Koerte, Hang Le Galanis, Myles Cockburn, Christina Clarke, Clayton Schupp, Cheryl Albright, Loic Le Marchand, Laurence Kolonel, Brian Henderson, Scarlett Lin-Gomez, Kristine Monroe, Lynne Wilkens. Characterizing the neighborhood environment for studies of cancer risk: The Multiethnic Cohort. [abstract]. In: Proceedings of the Sixth AACR Conference: The Science of Cancer Health Disparities; Dec 6–9, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2014;23(11 Suppl):Abstract nr B25. doi:10.1158/1538-7755.DISP13-B25

Abstract LB-299: Genome wide association study of breast cancer in Latinas identifies protective variants of Indigenous American origin on 6q25

Background: Multiple breast cancer genome-wide association studies (GWAS) have been conducted, with most samples analyzed being of European or Asian origin. No GWAS has been published to date on US Latinas or Latin American women. Previous studies have demonstrated that among Latina women, those with the highest Indigenous American ancestry are protected from breast cancer. We performed the first genome-wide association study of breast cancer in Latinas in a total of 1523 cases and 3221 controls and validated the strongest associations in an additional 977 Latina cases and 1158 controls.

Methods: For the discovery phase, samples were genotyped with either the 6.0 Affymetrix array or Illumina Infinitum 660W/Omni 2.5 arrays. Additional genotypes were imputed from 1000 genomes and the final analysis included ∼7 million SNPs. SNPs for replication were genotyped using Sequenom. Logistic regression analyses included the first 10 principal components as covariates.

Results: We identified two new variants, located 5’ of the ESR1 gene (6q25 region), which are strongly associated with breast cancer in this population. The minor allele for these variants is strongly protective (rs140068132: OR 0.61, 95%CI 0.48-0.75, p=3x10-13 & rs147157845: OR 0.63 95% CI 0.49-0.76; p =2x10-12). These alleles are present only in Latinos, correlate with Indigenous American ancestry, and are uncorrelated with previously reported risk variants in the ESR1 region. We found a strong association for both ER-positive and ER-negative breast cancer, but significantly more protection for ER-negative disease (p=0.014). The rs140068132 variant is also associated with breast density. The average breast density among women who are homozygous for the protective allele is approximately half of that of women homozygous for the common allele [Mean (sd) density for Homozygous GG = 9 (8); Homozygous AA = 17 (14), p 0.0009]. rs140068132, is located within a putative binding region for multiple transcription factors. MAPPER predicts disruption of putative transcription factor binding sites for the rare allele at rs140068132 but not rs147157845. Electromotility shift assays showed differential binding of the two alleles at the rs140068132 locus, with the protective allele (G) showing substantially reduced binding affinity compared to the common A allele.

Conclusions: The variants at this locus represent, to our knowledge, the strongest genome wide effect size on breast cancer for a common variant (frequency &gt;0.05 in any major population). These results may help in understanding the previous observations of lower breast cancer risk among Latina women with more Indigenous American ancestry and highlight the importance of conducting GWAS in diverse populations.

Citation Format: Laura Fejerman, Nasim Ahmadiyeh, Donglei Hu, Scott Huntsman, Kenneth Beckman, Jennifer Caswell, Esther M. John, Gabriela Torres-Mejia, Luis Carvajal-Carmona, Magdalena Echeverry, Anna Marie Tuazon, Carolina Ramirez, COLUMBUS Consortium, Christopher Gignoux, Celeste Eng, Esteban Gonzalez-Burchard, Brian Henderson, Loic Le Marchand, Eliseo J. Perez-Stable, Christopher A. Haiman, Elad Ziv. Genome wide association study of breast cancer in Latinas identifies protective variants of Indigenous American origin on 6q25. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-299. doi:10.1158/1538-7445.AM2014-LB-299

The RpfC (Rv1884) atomic structure shows high structural conservation within the resuscitation-promoting factor catalytic domain

The first structure of the catalytic domain of RpfC (Rv1884), one of the resuscitation-promoting factors (RPFs) from Mycobacterium tuberculosis, is reported. The structure was solved using molecular replacement once the space group had been correctly identified as twinned P21 rather than the apparent C2221 by searching for anomalous scattering sites in P1. The structure displays a very high degree of structural conservation with the previously published structures of the catalytic domains of RpfB (Rv1009) and RpfE (Rv2450). This structural conservation highlights the importance of the versatile domain composition of the RPF family.

Prostate cancer (PCa) risk variants and risk of fatal PCa in the National Cancer Institute Breast and Prostate Cancer Cohort Consortium

BACKGROUND

Screening and diagnosis of prostate cancer (PCa) is hampered by an inability to predict who has the potential to develop fatal disease and who has indolent cancer. Studies have identified multiple genetic risk loci for PCa incidence, but it is unknown whether they could be used as biomarkers for PCa-specific mortality (PCSM).

OBJECTIVE

To examine the association of 47 established PCa risk single-nucleotide polymorphisms (SNPs) with PCSM.

DESIGN, SETTING, AND PARTICIPANTS

We included 10 487 men who had PCa and 11 024 controls, with a median follow-up of 8.3 yr, during which 1053 PCa deaths occurred.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

The main outcome was PCSM. The risk allele was defined as the allele associated with an increased risk for PCa in the literature. We used Cox proportional hazards regression to calculate the hazard ratios of each SNP with time to progression to PCSM after diagnosis. We also used logistic regression to calculate odds ratios for each risk SNP, comparing fatal PCa cases to controls.

RESULTS AND LIMITATIONS

Among the cases, we found that 8 of the 47 SNPs were significantly associated (p<0.05) with time to PCSM. The risk allele of rs11672691 (intergenic) was associated with an increased risk for PCSM, while 7 SNPs had risk alleles inversely associated (rs13385191 [C2orf43], rs17021918 [PDLIM5], rs10486567 [JAZF1], rs6465657 [LMTK2], rs7127900 (intergenic), rs2735839 [KLK3], rs10993994 [MSMB], rs13385191 [C2orf43]). In the case-control analysis, 22 SNPs were associated (p<0.05) with the risk of fatal PCa, but most did not differentiate between fatal and nonfatal PCa. Rs11672691 and rs10993994 were associated with both fatal and nonfatal PCa, while rs6465657, rs7127900, rs2735839, and rs13385191 were associated with nonfatal PCa only.

CONCLUSIONS

Eight established risk loci were associated with progression to PCSM after diagnosis. Twenty-two SNPs were associated with fatal PCa incidence, but most did not differentiate between fatal and nonfatal PCa. The relatively small magnitudes of the associations do not translate well into risk prediction, but these findings merit further follow-up, because they may yield important clues about the complex biology of fatal PCa.

PATIENT SUMMARY

In this report, we assessed whether established PCa risk variants could predict PCSM. We found eight risk variants associated with PCSM: One predicted an increased risk of PCSM, while seven were associated with decreased risk. Larger studies that focus on fatal PCa are needed to identify more markers that could aid prediction.

Insulin-like growth factor pathway genetic polymorphisms, circulating IGF1 and IGFBP3, and prostate cancer survival

BACKGROUND

The insulin-like growth factor (IGF) signaling pathway has been implicated in prostate cancer (PCa) initiation, but its role in progression remains unknown.

METHODS

Among 5887 PCa patients (704 PCa deaths) of European ancestry from seven cohorts in the National Cancer Institute Breast and Prostate Cancer Cohort Consortium, we conducted Cox kernel machine pathway analysis to evaluate whether 530 tagging single nucleotide polymorphisms (SNPs) in 26 IGF pathway-related genes were collectively associated with PCa mortality. We also conducted SNP-specific analysis using stratified Cox models adjusting for multiple testing. In 2424 patients (313 PCa deaths), we evaluated the association of prediagnostic circulating IGF1 and IGFBP3 levels and PCa mortality. All statistical tests were two-sided.

RESULTS

The IGF signaling pathway was associated with PCa mortality (P = .03), and IGF2-AS and SSTR2 were the main contributors (both P = .04). In SNP-specific analysis, 36 SNPs were associated with PCa mortality with P trend less than .05, but only three SNPs in the IGF2-AS remained statistically significant after gene-based corrections. Two were in linkage disequilibrium (r 2 = 1 for rs1004446 and rs3741211), whereas the third, rs4366464, was independent (r 2 = 0.03). The hazard ratios (HRs) per each additional risk allele were 1.19 (95% confidence interval [CI] = 1.06 to 1.34; P trend = .003) for rs3741211 and 1.44 (95% CI = 1.20 to 1.73; P trend < .001) for rs4366464. rs4366464 remained statistically significant after correction for all SNPs (P trend.corr = .04). Prediagnostic IGF1 (HRhighest vs lowest quartile = 0.71; 95% CI = 0.48 to 1.04) and IGFBP3 (HR = 0.93; 95% CI = 0.65 to 1.34) levels were not associated with PCa mortality.

CONCLUSIONS

The IGF signaling pathway, primarily IGF2-AS and SSTR2 genes, may be important in PCa survival.

Genetic dysbiosis: the role of microbial insults in chronic inflammatory diseases

Thousands of bacterial phylotypes colonise the human body and the host response to this bacterial challenge greatly influences our state of health or disease. The concept of infectogenomics highlights the importance of host genetic factors in determining the composition of human microbial biofilms and the response to this microbial challenge. We hereby introduce the term ‘genetic dysbiosis’ to highlight the role of human genetic variants affecting microbial recognition and host response in creating an environment conducive to changes in the normal microbiota. Such changes can, in turn, predispose to, and influence, diseases such as: cancer, inflammatory bowel disease, rheumatoid arthritis, psoriasis, bacterial vaginosis and periodontitis. This review presents the state of the evidence on host genetic factors affecting dysbiosis and microbial misrecognition (i.e. an aberrant response to the normal microbiota) and highlights the need for further research in this area.

Monocyte cytokine synthesis in response to extracellular cell stress proteins suggests these proteins exhibit network behaviour

Human peripheral blood monocytes were exposed to single or pairs of cell stress proteins (CSPs), specifically Hsp10, Hsp27, Hsp60 and Hsp70-the former two having anti-inflammatory actions while the latter pair being assumed to be pro-inflammatory in activity. This study was to test if these proteins exhibited any network behaviour. To control for possible lipopolysaccharide contamination, polymyxin B was used. Surprisingly, at concentrations higher than 1 μg/ml, polymyxin B itself could induce cytokine synthesis. A number of commercial sources of the molecular chaperones were tested, and marked variations in monocyte cytokine synthesis were found. All four CSPs stimulated the same profile of IL-1/IL-6 synthesis and IL-10/TNF-α synthesis although the kinetics of production of these two pairs of cytokines were very different. A key question was whether extracellular molecular chaperones exhibited network behaviour. To test this, monocytes were cultured with suboptimal concentrations of single CSP and pairs of CSP to look for additive, synergistic or antagonistic cell responses. The major finding was that pairs of molecular chaperones, including chaperones thought to stimulate monocyte cytokine synthesis, could produce significant antagonistic cellular responses. This demonstrates that extracellular CSPs constitute an additional potent layer within the complex cytokine network and furthermore suggests that monocytes have evolved to dampen their immune responses upon exposure to extracellular networks of CSPs-perhaps as a mechanism for protecting cells against detrimental cellular stress responses.

Special topics--Mitigation of methane and nitrous oxide emissions from animal operations: I. A review of enteric methane mitigation options

The goal of this review was to analyze published data related to mitigation of enteric methane (CH4) emissions from ruminant animals to document the most effective and sustainable strategies. Increasing forage digestibility and digestible forage intake was one of the major recommended CH4 mitigation practices. Although responses vary, CH4 emissions can be reduced when corn silage replaces grass silage in the diet. Feeding legume silages could also lower CH4 emissions compared to grass silage due to their lower fiber concentration. Dietary lipids can be effective in reducing CH4 emissions, but their applicability will depend on effects on feed intake, fiber digestibility, production, and milk composition. Inclusion of concentrate feeds in the diet of ruminants will likely decrease CH4 emission intensity (Ei; CH4 per unit animal product), particularly when inclusion is above 40% of dietary dry matter and rumen function is not impaired. Supplementation of diets containing medium to poor quality forages with small amounts of concentrate feed will typically decrease CH4 Ei. Nitrates show promise as CH4 mitigation agents, but more studies are needed to fully understand their impact on whole-farm greenhouse gas emissions, animal productivity, and animal health. Through their effect on feed efficiency and rumen stoichiometry, ionophores are likely to have a moderate CH4 mitigating effect in ruminants fed high-grain or mixed grain-forage diets. Tannins may also reduce CH4 emissions although in some situations intake and milk production may be compromised. Some direct-fed microbials, such as yeast-based products, might have a moderate CH4-mitigating effect through increasing animal productivity and feed efficiency, but the effect is likely to be inconsistent. Vaccines against rumen archaea may offer mitigation opportunities in the future although the extent of CH4 reduction is likely to be small and adaptation by ruminal microbes and persistence of the effect is unknown. Overall, improving forage quality and the overall efficiency of dietary nutrient use is an effective way of decreasing CH4 Ei. Several feed supplements have a potential to reduce CH4 emission from ruminants although their long-term effect has not been well established and some are toxic or may not be economically feasible.

Do reciprocal interactions between cell stress proteins and cytokines create a new intra-/extra-cellular signalling nexus?

Cytokine biology began in the 1950s, and by 1988, a large number of cytokines, with a myriad of biological actions, had been discovered. In 1988, the basis of the protein chaperoning function of the heat shock, or cell stress, proteins was identified, and it was assumed that this was their major activity. However, since this time, evidence has accumulated to show that cell stress proteins are secreted by cells and can stimulate cellular cytokine synthesis with the generation of pro- and/or anti-inflammatory cytokine networks. Cell stress can also control cytokine synthesis, and cytokines are able to induce, or even inhibit, the synthesis of selected cell stress proteins and may also promote their release. How cell stress proteins control the formation of cytokines is not understood and how cytokines control cell stress protein synthesis depends on the cellular compartment experiencing stress, with cytoplasmic heat shock factor 1 (HSF1) having a variety of actions on cytokine gene transcription. The endoplasmic reticulum unfolded protein response also exhibits a complex set of behaviours in terms of control of cytokine synthesis. In addition, individual intracellular cell stress proteins, such as Hsp27 and Hsp90, have major roles in controlling cellular responses to cytokines and in controlling cytokine synthesis in response to exogenous factors. While still confusing, the literature supports the hypothesis that cell stress proteins and cytokines may generate complex intra- and extra-cellular networks, which function in the control of cells to external and internal stressors and suggests the cell stress response as a key parameter in cytokine network generation and, as a consequence, in control of immunity.

Fine Mapping and Identification of BMI Loci in African Americans

Genome-wide association studies (GWASs) primarily performed in European-ancestry (EA) populations have identified numerous loci associated with body mass index (BMI). However, it is still unclear whether these GWAS loci can be generalized to other ethnic groups, such as African Americans (AAs). Furthermore, the putative functional variant or variants in these loci mostly remain under investigation. The overall lower linkage disequilibrium in AA compared to EA populations provides the opportunity to narrow in or fine-map these BMI-related loci. Therefore, we used the Metabochip to densely genotype and evaluate 21 BMI GWAS loci identified in EA studies in 29,151 AAs from the Population Architecture using Genomics and Epidemiology (PAGE) study. Eight of the 21 loci (SEC16B, TMEM18, ETV5, GNPDA2, TFAP2B, BDNF, FTO, and MC4R) were found to be associated with BMI in AAs at 5.8 × 10(-5). Within seven out of these eight loci, we found that, on average, a substantially smaller number of variants was correlated (r(2) > 0.5) with the most significant SNP in AA than in EA populations (16 versus 55). Conditional analyses revealed GNPDA2 harboring a potential additional independent signal. Moreover, Metabochip-wide discovery analyses revealed two BMI-related loci, BRE (rs116612809, p = 3.6 × 10(-8)) and DHX34 (rs4802349, p = 1.2 × 10(-7)), which were significant when adjustment was made for the total number of SNPs tested across the chip. These results demonstrate that fine mapping in AAs is a powerful approach for both narrowing in on the underlying causal variants in known loci and discovering BMI-related loci.

Special topics--Mitigation of methane and nitrous oxide emissions from animal operations: I. A review of enteric methane mitigation options

The goal of this review was to analyze published data related to mitigation of enteric methane (CH4) emissions from ruminant animals to document the most effective and sustainable strategies. Increasing forage digestibility and digestible forage intake was one of the major recommended CH4 mitigation practices. Although responses vary, CH4 emissions can be reduced when corn silage replaces grass silage in the diet. Feeding legume silages could also lower CH4 emissions compared to grass silage due to their lower fiber concentration. Dietary lipids can be effective in reducing CH4 emissions, but their applicability will depend on effects on feed intake, fiber digestibility, production, and milk composition. Inclusion of concentrate feeds in the diet of ruminants will likely decrease CH4 emission intensity (Ei; CH4 per unit animal product), particularly when inclusion is above 40% of dietary dry matter and rumen function is not impaired. Supplementation of diets containing medium to poor quality forages with small amounts of concentrate feed will typically decrease CH4 Ei. Nitrates show promise as CH4 mitigation agents, but more studies are needed to fully understand their impact on whole-farm greenhouse gas emissions, animal productivity, and animal health. Through their effect on feed efficiency and rumen stoichiometry, ionophores are likely to have a moderate CH4 mitigating effect in ruminants fed high-grain or mixed grain-forage diets. Tannins may also reduce CH4 emissions although in some situations intake and milk production may be compromised. Some direct-fed microbials, such as yeast-based products, might have a moderate CH4-mitigating effect through increasing animal productivity and feed efficiency, but the effect is likely to be inconsistent. Vaccines against rumen archaea may offer mitigation opportunities in the future although the extent of CH4 reduction is likely to be small and adaptation by ruminal microbes and persistence of the effect is unknown. Overall, improving forage quality and the overall efficiency of dietary nutrient use is an effective way of decreasing CH4 Ei. Several feed supplements have a potential to reduce CH4 emission from ruminants although their long-term effect has not been well established and some are toxic or may not be economically feasible.