Learning Agility of Learning & Development Professionals in the Life-Sciences Field during the Pandemic: An Empirical Study (Preprint)

Background

The COVID-19 pandemic has impacted the life sciences field worldwide. Life sciences organizations (eg, pharmaceutical and med-tech companies) faced a rapidly increasing need for vital medical products, patient support, and vaccine development. Learning and development (L&D) departments play a crucial role in life sciences organizations as they apply learning initiatives to organizational strategy within a constantly evolving sector. During the COVID-19 pandemic, the work of L&D professionals in life sciences organizations changed profoundly during the abrupt shift to remote work, since learning and training normally occur in a face-to-face environment. Given the complex and dynamic situation of the pandemic, both individuals and organizations needed to learn quickly and apply what they learned to solve new, unprecedented problems. This situation presents an opportunity to study how characteristics of learning agility were evidenced by life sciences organizations and individual employees in the remote working mode.

Objective

In collaboration with Life Sciences Trainers & Educators Networks (LTEN), this study investigated the responses and learning agility of L&D professionals and their organizational leadership within the life sciences sector to the work changes due to the pandemic. The study answered the following questions: (1) How did L&D professionals in the life sciences sector respond to the changes in their work environment during the COVID-19 pandemic? (2) How did L&D professionals in the life sciences sector demonstrate learning agility during remote working?

Methods

We adopted a mixed methods approach that included a semistructured interview and a survey. Participants who were life sciences or health care L&D practitioners and in relevant positions were recruited via email through the LTEN and its partner pharmaceutical, biotech, or medical devices organizations. Interviews with 12 L&D professionals were conducted between June and August 2020 through phone or online conferencing, covering 22 open-ended questions to stimulate ideas that could be explored further in the survey. The semistructured interview questions were grounded in theory on learning agility. In total, 4 themes were developed from the interviews, which formed the basis for developing the survey items. The subsequent survey regarding 4 specific themes was conducted from August to October 2020 using Qualtrics. Both interview and survey data were analyzed based on a learning agility framework.

Results

Findings revealed generally positive organizational and individual responses toward the changes brought about by the pandemic. Results also indicated that a disruptive crisis, such as the shift from working in the office to working from home (WFH), required professionals’ learning agility to both self-initiate their own learning and to support the learning agility of others in the organization.

Conclusions

This study was designed to better understand education and training in the life sciences field, particularly during the unique circumstances of the global COVID-19 pandemic. We put forward several directions for future research on the learning agility of L&D professionals in life sciences organizations.

Integrated Systems Biology Approach Identifies Novel Maternal and Placental Pathways of Preeclampsia

Preeclampsia is a disease of the mother, fetus, and placenta, and the gaps in our understanding of the complex interactions among their respective disease pathways preclude successful treatment and prevention. The placenta has a key role in the pathogenesis of the terminal pathway characterized by exaggerated maternal systemic inflammation, generalized endothelial damage, hypertension, and proteinuria. This sine qua non of preeclampsia may be triggered by distinct underlying mechanisms that occur at early stages of pregnancy and induce different phenotypes. To gain insights into these molecular pathways, we employed a systems biology approach and integrated different “omics,” clinical, placental, and functional data from patients with distinct phenotypes of preeclampsia. First trimester maternal blood proteomics uncovered an altered abundance of proteins of the renin-angiotensin and immune systems, complement, and coagulation cascades in patients with term or preterm preeclampsia. Moreover, first trimester maternal blood from preterm preeclamptic patients in vitro dysregulated trophoblastic gene expression. Placental transcriptomics of women with preterm preeclampsia identified distinct gene modules associated with maternal or fetal disease. Placental “virtual” liquid biopsy showed that the dysregulation of these disease gene modules originates during the first trimester. In vitro experiments on hub transcription factors of these gene modules demonstrated that DNA hypermethylation in the regulatory region of ZNF554 leads to gene down-regulation and impaired trophoblast invasion, while BCL6 and ARNT2 up-regulation sensitizes the trophoblast to ischemia, hallmarks of preterm preeclampsia. In summary, our data suggest that there are distinct maternal and placental disease pathways, and their interaction influences the clinical presentation of preeclampsia. The activation of maternal disease pathways can be detected in all phenotypes of preeclampsia earlier and upstream of placental dysfunction, not only downstream as described before, and distinct placental disease pathways are superimposed on these maternal pathways. This is a paradigm shift, which, in agreement with epidemiological studies, warrants for the central pathologic role of preexisting maternal diseases or perturbed maternal–fetal–placental immune interactions in preeclampsia. The description of these novel pathways in the “molecular phase” of preeclampsia and the identification of their hub molecules may enable timely molecular characterization of patients with distinct preeclampsia phenotypes.

Nutritional Correlates of Human Oral Microbiome

BACKGROUND

Despite many potential effects of the oral microbiome on oral and systemic health, scant information is available regarding the associations between diet and the oral microbiome.

METHODS

Oral rinse DNA samples from 182 participants in a population-based case-control study for colorectal cancer were used to amplify a V3-V4 region of bacterial 16S rRNA gene. The amplicons were sequenced using Illumina MiSeq paired end chemistry on 2 runs, yielding approximately 33 million filtered reads that were assigned to bacterial classes. Relative abundances of each class and family as well microbial diversity/richness indices were correlated with selected dietary intakes from a food frequency questionnaire.

RESULTS

Saturated fatty acids (SFAs) and vitamin C intakes were consistently correlated with alpha (within-subjects) diversity indexes in both richness and diversity. SFA intake was positively correlated with relative abundance of betaproteobacteria and fusobacteria. Vitamin C and other vitamins with correlated intakes-for example, the B vitamins and vitamin E-exhibited positive correlations with fusobacteria class, its family Leptotrichiaceae and a clostridia family Lachnospiraceae. In addition, glycemic load was positively correlated with Lactobacillaceae abundance.

CONCLUSION

The observed associations in this study were modest. However, the results suggest that the effects of diets are likely to be habitat specific, and observations from the gut microbiome are not transferrable to the oral microbiome. Further studies are warranted, incorporating a range of host biomarkers, such as cytohistological, molecular, or biochemical measurements, in order to address biological consequences of these dietary intakes in human oral health.

Abstract 5227: Molecular profiling in African American NSCLC patients to identify novel potential driver mutations

African Americans continue to have poorer 5 year survival after a lung cancer diagnosis than whites for reasons that remain to be fully characterized. This disparity remains even with advances in treatments targeting specific driver mutations that have improved outcomes for some patients. Although the relative frequency of these genetic alterations varies in subsets of individuals defined by sex, histologic subtype, smoking history and race, little is known about the occurrence of these mutations in African Americans. In this study, we characterize the spectrum of known driver mutations in 200 African American NSCLC patients and seek to identify novel somatic mutations in this population. Initially, the population was screened using the Sequenom LungCarta panel of 216 mutations in 24 genes known to contain alterations associated with lung cancer, RET and ROS1 fusion gene expression, and amplification of FGFR1. Whole-exome sequencing is being performed on tumors from those patients with no known somatic mutations. Paired normal and tumor DNA/RNA samples are being genotyped to distinguish germline from somatic mutations in both the screening and sequencing phases. Initial screening has been completed on 130 patients, with the remaining 70 underway. The mean age of the patients enrolled is 61.7 years, 58.5% are female, and 8.5% are never smokers. In profiling the first 130 African American patients, we find that only 28% of patients (N = 36) carry a known somatic mutation that is not present in the germline, far lower than the 41% reported in white patients in our previous studies. Of the identified mutations, approximately 23.8% are KRAS and 23.8% are PT53 alterations. The next most frequent somatic alterations are in EGFR (16.7%). The remaining alterations occurred in only 1 or 2 tumors and include EPHA3, ERBB2, FGFR1, MET, NOTCH1, NRAS, NTRK2, PIK3CA, PTEN, RET and STK11. Five percent of patients have tumors with two driver mutations. Half of the tumors carrying 2 driver mutations had concurrent alterations in KRAS and TP53. Patients with known genetic alterations were more likely to be female than patients with no known genetic alterations (p = 0.42), but did not differ in age, smoking status, pack-years, family history of lung cancer, history of COPD, stage at diagnosis or histology. Mutations in EGFR were responsible for the differences by sex. Exome sequencing is complete for the first 48 of the 92 patients with no known somatic mutations. Sequences are being aligned using Novoalign and GATK will be used for variant calling; results will be available soon. Genetic profiling of NSCLC in African Americans has the potential to both identify novel mutations, expanding the list of potential targets for tailored treatments, and aid clinical decision making in African American patients leading to improvements in outcomes.

Citation Format: Ann G. Schwartz, Angela S. Wenzlaff, Chrissy M. Lusk, Greg Dyson, Aliccia Bollig-Fischer, Susan Land, Sneh Lata, Michele L. Cote, Gerold Bepler, Shirish M. Gadgeel. Molecular profiling in African American NSCLC patients to identify novel potential driver mutations. [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 5227.

Oral microbiome and history of smoking and colorectal cancer

BACKGROUND

The equilibrium of oral microbiome may be altered by environmental factors, including cigarette smoking. Several recent studies also suggest that oral pathogens causing periodontal disease, such as Fusobacterium nucleatum, are involved in pathogenesis of colorectal cancer.

METHODS

For this study oral rinse DNA samples from 190 participants in a population-based case-control study for colorectal cancer were used to amplify a V3-V4 region of bacterial 16S rRNA gene. The amplicons were sequenced using Illumina MiSeq paired end chemistry on two runs, yielding approximately 35 million filtered reads which were assigned to bacterial phyla.

RESULTS

No association was found between Fusobacterium abundance or presence and colorectal cancer. However, adjusted for age and experimental batch, colorectal cancer history was associated with increased presence of genus Lactobacillus and increased relative abundance of Rothia by 28% and current smoking was associated with a 33% decrease in relative counts of Betaproteobacteria (primarily Neisseria) and 23% increase in relative abundance of Veillonellaceae family. We also found that smoking had significant effects on the 2^nd component scores and 2^nd coordinate distances in principal component and coordinate analyses.

CONCLUSIONS

It remains to be elucidated whether the observed differences can be translated into biochemical changes in oral environment, thus potentially affecting oral health.

Lead exposure induces changes in 5-hydroxymethylcytosine clusters in CpG islands in human embryonic stem cells and umbilical cord blood

Prenatal exposure to neurotoxicants such as lead (Pb) may cause stable changes in the DNA methylation (5mC) profile of the fetal genome. However, few studies have examined its effect on the DNA de-methylation pathway, specifically the dynamic changes of the 5-hydroxymethylcytosine (5hmC) profile. Therefore, in this study, we investigate the relationship between Pb exposure and 5mC and 5hmC modifications during early development. To study the changes in the 5hmC profile, we use a novel modification of the Infinium™ HumanMethylation450 assay (Illumina, Inc.), which we named HMeDIP-450K assay, in an in vitro human embryonic stem cell model of Pb exposure. We model Pb exposure-associated 5hmC changes as clusters of correlated, adjacent CpG sites, which are co-responding to Pb. We further extend our study to look at Pb-dependent changes in high density 5hmC regions in umbilical cord blood DNA from 48 mother-infant pairs from the Early Life Exposure in Mexico to Environmental Toxicants (ELEMENT) cohort. For our study, we randomly selected umbilical cord blood from 24 male and 24 female children from the 1st and 4th quartiles of Pb levels. Our data show that Pb-associated changes in the 5hmC and 5mC profiles can be divided into sex-dependent and sex-independent categories. Interestingly, differential 5mC sites are better markers of Pb-associated sex-dependent changes compared to differential 5hmC sites. In this study we identified several 5hmC and 5mC genomic loci, which we believe might have some potential as early biomarkers of prenatal Pb exposure.

Whole-exome sequencing reveals genetic variability among lung cancer cases subphenotyped for emphysema

Lung cancer continues to be a major public health challenge in the United States despite efforts to decrease the prevalence of smoking; outcomes are especially poor for African-American patients compared to other races/ethnicities. Chronic obstructive pulmonary disease (COPD) co-occurs with lung cancer frequently, but not always, suggesting both shared and distinct risk factors for these two diseases. To identify germline genetic variation that distinguishes between lung cancer in the presence and absence of emphysema, we performed whole-exome sequencing on 46 African-American lung cancer cases (23 with and 23 without emphysema frequency matched on age, sex, histology and pack years). Using conditional logistic regression, we found 6305 variants (of 168 150 varying sites) significantly associated with lung cancer subphenotype (P ≤ 0.05). Next, we validated 10 of these variants in an independent set of 612 lung cancer cases (267 with emphysema and 345 without emphysema) from the same population of inference as the sequenced cases. We found one variant that was significantly associated with lung cancer subphenotype in the validation sample. These findings contribute to teasing apart shared genetic factors from independent genetic factors for lung cancer and COPD.

Multigenerational epigenetic inheritance in humans: DNA methylation changes associated with maternal exposure to lead can be transmitted to the grandchildren

We report that the DNA methylation profile of a child’s neonatal whole blood can be significantly influenced by his or her mother’s neonatal blood lead levels (BLL). We recruited 35 mother-infant pairs in Detroit and measured the whole blood lead (Pb) levels and DNA methylation levels at over 450,000 loci from current blood and neonatal blood from both the mother and the child. We found that mothers with high neonatal BLL correlate with altered DNA methylation at 564 loci in their children’s neonatal blood. Our results suggest that Pb exposure during pregnancy affects the DNA methylation status of the fetal germ cells, which leads to altered DNA methylation in grandchildren’s neonatal dried blood spots. This is the first demonstration that an environmental exposure in pregnant mothers can have an epigenetic effect on the DNA methylation pattern in the grandchildren.

Phase II Trial of Carboplatin, Everolimus, and Prednisone in Metastatic Castration-resistant Prostate Cancer Pretreated With Docetaxel Chemotherapy: A Prostate Cancer Clinical Trial Consortium Study

OBJECTIVE

To conduct a phase II trial of the combination of carboplatin, prednisone, and everolimus in metastatic castrate-resistant prostate cancer (mCRPC) as mTOR inhibition can overcome resistance to chemotherapy in prostate cancer.

METHODS

Patients with progressive mCRPC pretreated with docetaxel-based regimen were eligible. Performance status of 0-1 and adequate bone marrow, renal, and liver function were required. Primary end point was time to progression. Treatment consisted of carboplatin (starting dose equal to area under the curve (AUC of 5) intravenously every 21 days along with oral everolimus 5 mg once daily and prednisone 5 mg twice daily.

RESULTS

Twenty-six patients were enrolled with median age of 69 years with 8 patients of African American origin. Grade 3 or 4 thrombocytopenia or neutropenia in 4 of 6 initial patients required dose adjustment of carboplatin to AUC of 4 for subsequent patients. There were no pharmacokinetic interactions between carboplatin and everolimus. The median time to progression was 2.5 months (90% confidence interval [CI], 1.8-4.3 months), and median overall survival was 12.5 months (90% CI, 7.7-18.7 months). Of 10 patients, 8 that demonstrated positive nuclear phosphorylated AKT (pAKT) staining on immunohistochemistry progressed within 9 weeks, whereas 2 patients with negative staining continued without progression for prolonged durations of 30 and 48 weeks. TSC1 gene mutations did not correlate with clinical outcome.

CONCLUSION

The addition of the mTOR inhibitor everolimus to carboplatin demonstrated minimal clinical efficacy in metastatic prostate cancer. pAKT testing warrants further evaluation as a predictive marker of response to everolimus therapy.

Early life lead exposure causes gender-specific changes in the DNA methylation profile of DNA extracted from dried blood spots

AIMS

In this paper, we tested the hypothesis that early life lead (Pb) exposure associated DNA methylation (5 mC) changes are dependent on the sex of the child and can serve as biomarkers for Pb exposure.

METHODS

In this pilot study, we measured the 5mC profiles of DNA extracted from dried blood spots (DBS) in a cohort of 43 children (25 males and 18 females; ages from 3 months to 5 years) from Detroit. Result & Discussion: We found that the effect of Pb-exposure on the 5-mC profiles can be separated into three subtypes: affected methylation loci which are conserved irrespective of the sex of the child (conserved); affected methylation loci unique to males (male-specific); and affected methylation loci unique to females (female-specific).

Evolutionary origins of the placental expression of chromosome 19 cluster galectins and their complex dysregulation in preeclampsia

INTRODUCTION

The dysregulation of maternal-fetal immune tolerance is one of the proposed mechanisms leading to preeclampsia. Galectins are key regulator proteins of the immune response in vertebrates and maternal-fetal immune tolerance in eutherian mammals. Previously we found that three genes in a Chr19 cluster encoding for human placental galectin-13 (PP13), galectin-14 and galectin-16 emerged during primate evolution and may confer immune tolerance to the semi-allogeneic fetus.

MATERIALS AND METHODS

This study involved various methodologies for gene and protein expression profiling, genomic DNA methylation analyses, functional assays on differentiating trophoblasts including gene silencing, luciferase reporter and methylation assays. These methods were applied on placental specimens, umbilical cord blood cells, primary trophoblasts and BeWo cells. Genomic DNA sequences were analyzed for transposable elements, transcription factor binding sites and evolutionary conservation.

RESULTS AND DISCUSSION

The villous trophoblastic expression of Chr19 cluster galectin genes is developmentally regulated by DNA methylation and induced by key transcription factors of villous placental development during trophoblast fusion and differentiation. This latter mechanism arose via the co-option of binding sites for these transcription factors through promoter evolution and the insertion of an anthropoid-specific L1PREC2 transposable element into the 5' untranslated region of an ancestral gene followed by gene duplication events. Among placental Chr19 cluster galectin genes, the expression of LGALS13 and LGALS14 is down-regulated in preterm severe preeclampsia associated with SGA. We reveal that this phenomenon is partly originated from the dysregulated expression of key transcription factors controlling trophoblastic functions and galectin gene expression. In addition, the differential DNA methylation of these genes was also observed in preterm preeclampsia irrespective of SGA.

CONCLUSIONS

These findings reveal the evolutionary origins of the placental expression of Chr19 cluster galectins. The complex dysregulation of these genes in preeclampsia may alter immune tolerance mechanisms at the maternal-fetal interface.

Apoptosis-Related Single Nucleotide Polymorphisms and the Risk of Non-Small Cell Lung Cancer in Women

BACKGROUND

Germline apoptosis-related single nucleotide polymorphisms (SNPs) have been shown to contribute to the risk of developing non-small cell lung cancer (NSCLC). However, very few studies have looked specifically at apoptosis-related SNPs in a racially-stratified analysis of white and African-American women.

METHODS

We examined the risk of developing NSCLC associated with 98 germline SNPs in 32 apoptosis-related genes among women in a population-based case-control study from the Detroit metropolitan area. We examined 453 cases of NSCLC and 478 control subjects. We used an unconditional logistic regression with a dominant model, stratified by race, and adjusted for age, pack-years smoked, ever/never smoking status, family history of lung cancer, history of COPD, BMI and education.

RESULTS

Our logistic regression identified 3 significant apoptosis-related SNPs in whites (APAF-1, rs1007573; CD40 rs3765459, and CD40 rs1535045), and 7 significant SNPs (ATM, rs1801516; BAK1, rs513349; TNF, rs1800629; TP63, rs6790167; TP63, rs7613791, TP63, rs35592567 and TP63, rs3856775) in African-Americans. In a downstream analysis, these SNPs were further prioritized utilizing the False Positive Report Percentage (FPRP) methodology and backwards elimination. In whites, APAF-1 (rs1007573), CD40 (rs3765459) and CD40 (rs1535045) were all found to be significant by FPRP. In African-Americans, TP63 SNPs rs6790167 and rs7613791 were found to have a significant FPRP. In parallel, a backward elimination procedure was used on the 3 significant SNPs in whites and 7 significant SNPs in African-Americans. This procedure identified APAF-1 rs1007573 (OR=1.86, 95% CI: 1.17-2.95) and CD40 rs1535045 (OR=0.58, 95% CI: 0.40-0.84) as significant independent predictors of risk among whites, and ATM rs1801516 (OR=24.15, 95% CI: 3.50-166.55), TNF rs1800629 (OR= 0.42, 95% CI: 0.18-0.99) and TP63 rs6790167 (OR: 2.85, 95% CI: 1.33-6.09) as significant, independent predictors in African-Americans.

CONCLUSION

In whites, only SNPs APAF-1 rs1007573 and CD40 rs1535045 were significant by both FPRP and backwards elimination, while in African-Americans, only TP63 rs6790167 was significant by both methodologies. Thus, we have identified three promising variants associated with increased risk of NSCLC that warrant additional investigation in future studies.

Intronic non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees

Background

Previous whole-genome shotgun bisulfite sequencing experiments showed that DNA cytosine methylation in the honey bee (Apis mellifera) is almost exclusively at CG dinucleotides in exons. However, the most commonly used method, bisulfite sequencing, cannot distinguish 5-methylcytosine from 5-hydroxymethylcytosine, an oxidized form of 5-methylcytosine that is catalyzed by the TET family of dioxygenases. Furthermore, some analysis software programs under-represent non-CG DNA methylation and hydryoxymethylation for a variety of reasons. Therefore, we used an unbiased analysis of bisulfite sequencing data combined with molecular and bioinformatics approaches to distinguish 5-methylcytosine from 5-hydroxymethylcytosine. By doing this, we have performed the first whole genome analyses of DNA modifications at non-CG sites in honey bees and correlated the effects of these DNA modifications on gene expression and alternative mRNA splicing.

Results

We confirmed, using unbiased analyses of whole-genome shotgun bisulfite sequencing (BS-seq) data, with both new data and published data, the previous finding that CG DNA methylation is enriched in exons in honey bees. However, we also found evidence that cytosine methylation and hydroxymethylation at non-CG sites is enriched in introns. Using antibodies against 5-hydroxmethylcytosine, we confirmed that DNA hydroxymethylation at non-CG sites is enriched in introns. Additionally, using a new technique, Pvu-seq (which employs the enzyme PvuRts1l to digest DNA at 5-hydroxymethylcytosine sites followed by next-generation DNA sequencing), we further confirmed that hydroxymethylation is enriched in introns at non-CG sites.

Conclusions

Cytosine hydroxymethylation at non-CG sites might have more functional significance than previously appreciated, and in honey bees these modifications might be related to the regulation of alternative mRNA splicing by defining the locations of the introns.

Multiplex testing of driver mutations in non-small cell lung cancer (NSCLCs) of African-American (AA) patients

7561

Background: Recently driver genetic alterations have been identified in NSCLC that can be targeted for therapeutic interventions. Previous reports have suggested that rates of certain mutations may vary according to ethnic background. We conducted multiplex testing of NSCLCs of AA and white patients to assess variability in the mutation rates by race. Methods: We identified tumor tissues of 136 AA and 320 white NSCLC patients collected as part of three different institutional review board approved studies. Using the Sequenom MassArray system and a multiplexed panel, we analyzed tumor DNA for 214 oncogenic mutations in 26 genes previously identified in NSCLC. Estimated risk (Odds Ratios (OR)) of any mutation and specific gene mutations among AA patients compared to white patients were calculated after adjusting for age, sex, smoking status and histology (adenocarcinoma versus non-adenocarcinoma). Information on smoking status was unavailable on 46 patients and was not included in calculations of ORs for some genes (ORª). Results: The median age at diagnosis was 60 vs 66 years in AA vs white patients; 43% of AA patients and 66% of white patients were males; 69% of AA patients and 52% of white patients had adenocarcinoma; 66% of AA patients and 85% of white patients had stage I/II NSCLC and 10% of AA patients and 6% of white patients were never smokers. 43% of the AA patients and 47% of white patients had at least one mutation detected (OR = 0.78; 0.5-1.2). 19% of AA patients and 6% of white patients had more than 1 mutation detected (OR 2.3; 1.1-4.9). AA patients were more likely to harbor mutations in STK11 (LKB1) (OR=8.4; 3.2-21.8) and NOTCH1 (ORª=8.1; 2.2-30.8), and they were less likely to have MET mutations (ORª= 0.12; 0.02-0.9) then white patients. While not statistically significant, AA had lower prevalence of Kras mutations (OR=0.64, 0.3-1.4) and p53 mutations (OR= 0.82; 0.4-1.6). Conclusions: Our analysis of NSCLCs shows that AAs were more likely to have multiple genetic mutations than whites and the mutation profile differs by race.

Genes associated with prostate cancer are differentially expressed in African American and European American men

BACKGROUND

Despite more aggressive screening across all demographics and gradual declines in mortality related to prostate cancer (PCa) in the United States, disparities among populations persist. A substantial proportion of African American men (AAM) have a higher overall incidence, earlier age of onset, increased proportion of clinically advanced disease, and increased bone metastases and mortality from PCa compared to European American men (EAM). Limited early evidence indicates that underlying causes for disparities may be observed in tumor-specific gene expression programs.

METHODS

This study used microarray-based methods to measure expression levels for 517 genes that were previously associated with PCa in archived formalin-fixed paraffin embedded (FFPE) specimens; testing the hypothesis that gene expression features of functional consequence to cancer distinguish PCa from AAM and EAM. A t test was conducted comparing AAM to EAM expression levels for each probe on the array.

RESULTS

Analysis of 639 tumor samples (270 AAM, 369 EAM) showed that 95 genes were overexpressed specifically in PCa from AAM relative to EAM and 132 were overexpressed in PCa from EAM relative to AAM. Furthermore, systems-level analyses highlight the relevant signaling pathways and functions associated with the EAM- or AAM-specific overexpressed gene sets, for example, inflammation and lipid metabolism.

CONCLUSIONS

Results here bring further understanding to the potential for molecular differences for PCa in AAM versus EAM.

IMPACT

The results support the notion that therapeutic benefits will be realized when targeted treatments are designed to acknowledge and address a greater spectrum of PCa subtypes and molecular distinctions.

Variants in the Signaling Protein TSAd are Associated with Susceptibility to Ovarian Cancer in BRCA1/2 Negative High Risk Families

A substantial fraction of familial ovarian cancer cases cannot be attributed to specific genetic factors. The discovery of additional susceptibility genes will permit a more accurate assessment of hereditary cancer risk and allow for monitoring of predisposed women in order to intervene at the earliest possible stage. We focused on a population with elevated familial breast and ovarian cancer risk. In this study, we identified a SNP rs926103 whose minor allele is associated with predisposition to ovarian but not breast cancer in a Caucasian high-risk population without BRCA1/BRCA2 mutations. We have found that the allelic variation of rs926103, which alters amino acid 52 of the encoded protein SH2D2A/TSAd, results in differences in the activity of this protein involved in multiple signal transduction pathways, including regulation of immune response, tumor vascularization, cell growth, and differentiation. Our observation provides a novel candidate genetic biomarker of elevated ovarian cancer risk in members of high-risk families without BRCA1/2 mutations, as well as a potential therapeutic target, TSAd.

Interpreting genetic effects through models of cardiac electromechanics

Multiscale models of cardiac electromechanics are being increasingly focused on understanding how genetic variation and environment underpin multiple disease states. In this paper we review the current state of the art in both the development of specific models and the physiological insights they have produced. This growing research body includes the development of models for capturing the effects of changes in function in both single and multiple proteins in both specific expression systems and in vivo contexts. Finally, the potential for using this approach for ultimately predicting phenotypes from genetic sequence information is discussed.

FGFR1 amplification in squamous cell lung cancers

7063

Background: Squamous cell carcinoma of the lung (SqCCL) is the second most common type of lung cancer. There are currently no established targeted therapies that take advantage of SqCCL-specific genetic abnormalities. Amplification of the fibroblast growth factor receptor type 1 gene (FGFR1) has been identified as a driver event in breast cancers and in SqCCL. The demographic characteristics and prognosis of patients with these tumors remains to be defined. Methods: DNA from 123 surgically resected, fresh frozen, and clinically annotated SqCCLs was extracted using a resin-based or phenol-based methodology. DNA quantity and quality was assessed using the Quantifiler kit (ABI). Specimen histology was validated, and the proportion of tumor cells was >60%. Copy number variation (CNV) analysis was performed using quantitative PCR with primers specific for exons 12 and 16 of FGFR1 and data analysis using CopyCaller (ABI). Samples with a predicted CNV of at 2 or greater in at least one exon were scored as amplified. Chi-squared tests were used to examine clinical and demographic differences between patients with and without amplification of FGFR1. Survival differences were examined by Kaplan Meier and Cox regression models. Results: Men comprised the majority of the population (n=91, 74%) and most cases were pathological stage I (n=75, 61%) or stage II (n=32, 26%). Thirty (24.4%) tumors showed amplification of FGFR1. There was no association between amplification and sex (p=0.18) or stage (p=0.37). The majority of the patients were white (n=114, 92.7%), but the proportion of tumors that were amplified was higher among non-whites (5/9, 55.5%) than whites (25/114, 21.9%, p=0.02). Overall, median survival was 32.2 months. In univariate survival analysis, amplification was associated with an increased hazard of death (HR=1.55, Wilcoxon p=0.03). Tumor stage at diagnosis was also associated with increased risk of death (HR=1.67, p=0.0009). Only stage remained a significant predictor of death in the multivariate survival models (HR=1.65, p=0.004). Conclusions: Somatic amplification of FGFR1 is a relatively common event in SqCCL and may be associated with race and overall survival.

Abstract 4599: Comprehensive molecular oncogenomic profiling & miRNA analysis of prostate cancer

Background: Comprehensive molecular oncogenomic and microRNA (miRNA) profiling of tumors can provide tumor specific oncogenomic and miRNA signatures which can be useful to improve diagnostic accuracy, refine prognostic and predictive capabilities, and may serve as therapeutic targets. In prostate cancer (PCa) such a comprehensive analysis has not been reported. Design: DNA and RNA obtained from scant amounts of fresh frozen PCa tumor tissue samples (n=36) were profiled by (1) Mutation analysis: Sequenom Massarray & OncoCarta VI panel that profiles 238 common cancer mutations in 19 oncogenes (known predictors of response or resistance to targeted therapies);(2) Whole-genome gene expression Microarrays: Illumina Chip;(3) Single Nucleotide Polymorphisms (SNP) with genome-wide coverage:Illumina Omni microarrays. (4)miRNA analysis was done on RNA from FFPE PCa tumor tissues (n=126) using RT-PCR. Data was statistically analyzed & correlated with clinical & pathologic variables. Results: Massarray analysis identified a MET oncogene mutation, variant T992I, in a 49 year old patient with Gleason score 7 (4+3) tumor. Of the 47,224 genes analyzed by gene expression microarrays, 74 genes were significant predictors of high tumor grade by ordinal regression analysis (p<0.0001). TGIF1 was the most significant gene. Of the 731,442 SNP's analyzed, 638 significantly predicted high tumor grade by logistic regression analysis (p<0.0001). There was significant interaction between gene and SNPs in 531 SNP/gene pairs (p<0.05). Ingenuity Pathway analysis revealed the significant predictor genes (p<0.05) were involved in biological pathways for Gene Expression, Cell Cycle, Cancer,” “Inflammatory Response, Cell Death, Infection Mechanism & Cellular Assembly, Organization, Gene Expression, Cancer. P53 gene was found to be at the center hub of significant predicting pathways. Loss of miR-34a expression was found in PCa tissues consistent with the central role of p53. Conclusions: Using high throughput genomic profiling & miRNA analysis of small amounts of fresh-frozen and FFPE PCa tumor samples, we identified clinically relevant hot spot mutation in MET oncogene and several significant genes & SNPs to predict tumor grade. P53 gene is at the center hub of all significant pathways. Loss of miR-34a was consistent with p53 function in PCa. MET oncogene mutation is a novel finding, not previously reported in PCa against which small molecule inhibitors are under development. These molecular signatures may have a significant clinical impact on improving diagnostic and predictive capabilities & in designing targeted therapies to achieve the goal of personalized medicine.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4599. doi:1538-7445.AM2012-4599

A Bayesian Shrinkage Model for Incomplete Longitudinal Binary Data with Application to the Breast Cancer Prevention Trial

We consider inference in randomized longitudinal studies with missing data that is generated by skipped clinic visits and loss to follow-up. In this setting, it is well known that full data estimands are not identified unless unverified assumptions are imposed. We assume a non-future dependence model for the drop-out mechanism and partial ignorability for the intermittent missingness. We posit an exponential tilt model that links non-identifiable distributions and distributions identified under partial ignorability. This exponential tilt model is indexed by non-identified parameters, which are assumed to have an informative prior distribution, elicited from subject-matter experts. Under this model, full data estimands are shown to be expressed as functionals of the distribution of the observed data. To avoid the curse of dimensionality, we model the distribution of the observed data using a Bayesian shrinkage model. In a simulation study, we compare our approach to a fully parametric and a fully saturated model for the distribution of the observed data. Our methodology is motivated by, and applied to, data from the Breast Cancer Prevention Trial.

Volume of white matter hyperintensities in healthy adults: contribution of age, vascular risk factors, and inflammation-related genetic variants

Aging is associated with appearance of white matter hyperintensities (WMH) on MRI scans. Vascular risk and inflammation, which increase with age, may contribute to white matter deterioration and proliferation of WMH. We investigated whether circulating biomarkers and genetic variants associated with elevated vascular risk and inflammation are associated with WMH volume in healthy adults (144 volunteers, 44-77 years of age). We examined association of WMH volume with age, sex, hypertension, circulating levels of total plasma homocysteine (tHcy), cholesterol (low-density lipoprotein), and C-reactive protein (CRP), and four polymorphisms related to vascular risk and inflammation: Apolipoprotein ε (ApoE ε2,3,4), Angiotensin-Converting Enzyme insertion/deletion (ACE I/D), methylenetetrahydrofolate reductase (MTHFR) C677T, C-reactive protein (CRP)-286C>A>T, and interleukin-1β (IL-1β) C-511T. We found that larger WMH volume was associated with advanced age, hypertension, and elevated levels of homocysteine and CRP but not with low-density lipoprotein levels. Homozygotes for IL-1β-511T allele and carriers of CRP-286T allele that are associated with increased inflammatory response had larger WMH than the other allelic combinations. Carriers of the APOE ε2 allele had larger frontal WMH than ε3 homozygotes and ε4 carriers did. Thus, in healthy adults, who are free of neurological and vascular disease, genetic variants that promote inflammation and elevated levels of vascular risk biomarkers can contribute to brain abnormalities. This article is part of a Special Issue entitled: Imaging Brain Aging and Neurodegenerative disease.

Analysis of positional candidate genes in the AAA1 susceptibility locus for abdominal aortic aneurysms on chromosome 19

BACKGROUND

Abdominal aortic aneurysm (AAA) is a complex disorder with multiple genetic risk factors. Using affected relative pair linkage analysis, we previously identified an AAA susceptibility locus on chromosome 19q13. This locus has been designated as the AAA1 susceptibility locus in the Online Mendelian Inheritance in Man (OMIM) database.

METHODS

Nine candidate genes were selected from the AAA1 locus based on their function, as well as mRNA expression levels in the aorta. A sample of 394 cases and 419 controls was genotyped for 41 SNPs located in or around the selected nine candidate genes using the Illumina GoldenGate platform. Single marker and haplotype analyses were performed. Three genes (CEBPG, PEPD and CD22) were selected for DNA sequencing based on the association study results, and exonic regions were analyzed. Immunohistochemical staining of aortic tissue sections from AAA and control individuals was carried out for the CD22 and PEPD proteins with specific antibodies.

RESULTS

Several SNPs were nominally associated with AAA (p < 0.05). The SNPs with most significant p-values were located near the CCAAT enhancer binding protein (CEBPG), peptidase D (PEPD), and CD22. Haplotype analysis found a nominally associated 5-SNP haplotype in the CEBPG/PEPD locus, as well as a nominally associated 2-SNP haplotype in the CD22 locus. DNA sequencing of the coding regions revealed no variation in CEBPG. Seven sequence variants were identified in PEPD, including three not present in the NCBI SNP (dbSNP) database. Sequencing of all 14 exons of CD22 identified 20 sequence variants, five of which were in the coding region and six were in the 3'-untranslated region. Five variants were not present in dbSNP. Immunohistochemical staining for CD22 revealed protein expression in lymphocytes present in the aneurysmal aortic wall only and no detectable expression in control aorta. PEPD protein was expressed in fibroblasts and myofibroblasts in the media-adventitia border in both aneurysmal and non-aneurysmal tissue samples.

CONCLUSIONS

Association testing of the functional positional candidate genes on the AAA1 locus on chromosome 19q13 demonstrated nominal association in three genes. PEPD and CD22 were considered the most promising candidate genes for altering AAA risk, based on gene function, association evidence, gene expression, and protein expression.

Plasma levels of resistin-like molecule beta in humans

BACKGROUND

Resistin-like molecules (RELM) are expressed in many tissues and among those, RELMβ is most abundantly expressed in the colon. Based on animal studies, RELMβ is induced by high fat diets, obesity, and intestinal microflora and may play a role in insulin resistance and intestinal inflammation. In the present study, we evaluated whether RELMβ could be measured in human plasma and the influence of selected host and behavioral factors on RELMβ levels, including known risk factors for colorectal cancer.

METHODS

The subjects for this pilot study were derived from healthy controls who participated in a population-based case-control study of colorectal cancer in Metropolitan Detroit. The subjects were 45-80 years of age without history of cancer or colorectal resection.

RESULTS

RELMβ was present in human plasma, with levels in the range of 0.08-0.26 ng/mL. Lower RELMβ levels were found in subjects with non-Caucasian race, lower pack-years of smoking, and higher physical activity index scores. Other variables such as dietary intakes, gender, obesity, use of non-steroidal anti-inflammatory agents and history of polyps were not associated with RELMβ levels.

CONCLUSIONS

The direct association of RELMβ with smoking and inverse association with physical activity, both of which are risk factors for colon cancer, indicates that RELMβ may be involved in mediating the effects of these two lifestyle factors on risk of colon cancer.

Functional polymorphisms to modulate luminal lipid exposure and risk of colorectal cancer

PURPOSE

Fat absorption may play a crucial role in colorectal carcinogenesis by determining intra-colonic exposure to potentially carcinogenic lipid metabolites.

METHODS

We conducted a population-based case-control study that included 1163 cases and 1501 controls to examine whether individuals who carry genetic variants associated with lower lipid absorption have a higher risk of colorectal cancer. Using Taqman assay, we determined FABP2 alanine (A)/threonine (T) polymorphism at codon 54 in exon-2 and APOE isoforms. Multivariable odds ratios (OR) and 95% confidence intervals (CI) were calculated by unconditional logistic regression models, assuming FABP2 A54 and APO non-E4 as high risk alleles.

RESULTS

We found no associations with either of the polymorphisms. The OR associated with FABP2 A54 homozygotes compared with the others was 1.01 (95% CI; 0.86-1.45) and that for non-ApoE4 carriers compared with carries was 0.95 (95% CI; 0.80-1.13). However, there was a statistically significant negative interaction between total fat intake and FABP2 AA genotypes (p=0.025), indicating that the risk of colorectal cancer associated with this polymorphism is higher in the subjects with lower fat intake.

CONCLUSIONS

These results suggest that these SNPs may not be useful in predicting colorectal cancer risk in populations with high fat intake.

DNA/RNA markers for colorectal cancer risk in preserved stool specimens: a pilot study

AIMS AND BACKGROUND

Exfoliated cells in human stool offer excellent opportunities to non-invasively detect molecular markers associated with colorectal tumorigenesis, and to evaluate the effects of exposures to exogenous and endogenous carcinogenic or chemopreventive substances. This pilot study investigated the feasibility of determining DNA methylation and RNA expression simultaneously in stool specimens treated with a single type of nucleic acid preservatives.

METHODS

Stool specimens from 56 volunteers that were preserved up to a week with RNA later were used in this study. Bisulfite sequencing was used to determine methylation at 27 CpG loci on the estrogen receptor 1 (ESR1) promoter. Taqman assay was used for quantitative reverse transcription polymerase chain reactions to measure cyclooxygenase 2 (COX2) and epidermal growth factor receptor (EGFR) mRNA expression. Subjects' basic demographic and other selected risk factors for colorectal cancer were captured through questionnaires and correlated with the levels of these markers.

RESULTS

Less than 10% of the samples failed in individual assays. Overall, 24.0% of the CpG loci on the ESR1 promoter were methylated. COX2 expression and alcohol use were positively correlated; an inverse association was present between EGFR expression and cigarette smoking; and subjects using anti-diabetic medication had higher ESR1 methylation. In addition, higher EGFR expression levels were marginally associated with history of polyps and family history of colorectal cancer.

CONCLUSIONS

The present study demonstrates that simultaneous analyses for DNA and RNA markers are feasible in stool samples treated with a single type of nucleotide preservatives. Among several associations observed, the association between EGFR expression and polyps deserves further investigation as a potential target for colorectal cancer screening. Larger studies are warranted to confirm some of our observations.

Cytokine and cytokine receptor single-nucleotide polymorphisms predict risk for non-small cell lung cancer among women

Studies on the relationships between inflammatory pathway genes and lung cancer risk have not included African-Americans and have only included a handful of genes. In a population-based case-control study on 198 African-American and 744 Caucasian women, we examined the association between 70 cytokine and cytokine receptor single-nucleotide polymorphisms (SNPs) and risk of non-small cell lung cancer (NSCLC). Unconditional logistic regression was used to estimate odds ratios and 95% confidence intervals in a dominant model adjusting for major risk factors for lung cancer. Separate analyses were conducted by race and by smoking history and history of chronic obstructive pulmonary disease among Caucasians. Random forest analysis was conducted by race. On logistic regression analysis, IL6 (interleukin 6), IL7R, IL15, TNF (tumor necrosis factor), and IL10 SNP were associated with risk of non-small cell lung cancer among African-Americans; IL7R and IL10 SNPs were also associated with risk of lung cancer among Caucasians. Although random forest analysis showed IL7R and IL10 SNPs as being associated with risk for lung cancer among African-Americans, it also identified TNFRSF10A SNP as an important predictor. On random forest analysis, an IL1A SNP was identified as an important predictor of lung cancer among Caucasian women. Inflammatory SNPs differentially predicted risk for NSCLC according to race, as well as based on smoking history and history of chronic obstructive pulmonary disease among Caucasian women. Pathway analysis results are presented. Inflammatory pathway genotypes may serve to define a high risk group; further exploration of these genes in minority populations is warranted.

Routine preventive care and cancer surveillance in long-term survivors (LTS) of colorectal cancer: Results from NSABP Protocol LTS-01

6500

Background: Little is known about the use of routine preventive care and cancer surveillance in long-term colorectal cancer survivors. NSABP LTS-01 is a study that examines the use of such services in long-term colorectal cancer survivors previously treated in NSABP adjuvant trials. Methods: Long-term colorectal cancer survivors (≥ 5 years) were recruited from five completed NSABP treatment trials (Protocols C-05, C-06, C-07, R-02, R-03) at 65 study sites. A survey battery for long-term survivors of colorectal cancer (LTS-01) was developed. A 1:4 comparison cohort case-matched by age, gender, race, and education was created from the 2005 National Health Interview Survey. Contingency tables and multivariate models were used to compare cohorts and determine predictors of preventive care and cancer surveillance. Results: 649 LTS-01 patients (625 colon, 24 rectal) completed the interview; 57% male, mean age 66.1yr (SD 10.5), median survival 8 yrs. LTS-01 patients were more likely to have a usual source of healthcare than the NHIS cohort (98% vs. 93%, p < 0.0001). The number of ER visits in the previous 12 months was not significantly different between the two groups. LTS-01 patients were more likely to have received a flu shot in the past 12 months (68% vs. 42%, p < 0.0001) and were also more likely to have undergone cancer screening by Pap smear (67% vs. 54%, p < 0.001), mammogram (85% vs. 71%, p < 0.001), and PSA test (84% vs. 75%, p < 0.001). For CRC surveillance, 3% did not have a colonoscopy, 13% had not had a CEA test, and 34% did not have a CT scan in the last 5 years. The best predictor of the receipt of these cancer screening tests was the presence of health insurance (OR 2.6–4.5). No factor was uniformly associated with colorectal cancer surveillance. Conclusions: Long-term survivors of colorectal cancer achieve better routine preventive care including cancer screening than the general population. However in these stage II and stage III cancer patients cancer surveillance is variably performed.

No significant financial relationships to disclose.

African American-preponderant single nucleotide polymorphisms (SNPs) and risk of breast cancer

BACKGROUND

African American women more often present with more aggressive types of breast cancer than Caucasian women, but little is known whether genetic polymorphisms specific to or disproportionate in African Americans are associated with their risk of breast cancer.

METHODS

A population-based case-control study was conducted including 194 cases identified through the Metropolitan Detroit Cancer Surveillance System and 189 controls recruited through random digit dialing to examine polymorphisms in genes involved in estrogen metabolism and action.

RESULTS

The African American-specific CYP1A1 5639C allele was associated with an increased risk of breast cancer (odds ratio (OR)=2.34, 95% confidence interval (CI) 1.23-4.44) and this association with the CYP1A1 5639 locus was dependent on another polymorphism in the CYP3A4 gene (P=0.043 for the interaction). In addition, African American-predominant CYP1B1 432 Val allele was significantly more often found in the cases than in the controls overall and the HSD17B1 312 Gly allele was specifically associated with premenopausal breast cancer risk (OR=3.00, 95%CI 1.29-6.99).

CONCLUSION

These observations need to be confirmed in larger studies due to the limited statistical power of the study based on a small number of cases.

Genetic and vascular modifiers of age-sensitive cognitive skills: effects of COMT, BDNF, ApoE, and hypertension

Several single nucleotide polymorphisms have been linked to neural and cognitive variation in healthy adults. We examined contribution of three polymorphisms frequently associated with individual differences in cognition (Catechol-O-Methyl-Transferase Val158Met, Brain-Derived-Neurotrophic-Factor Val66Met, and Apolipoprotein E epsilon4) and a vascular risk factor (hypertension) in a sample of 189 volunteers (age 18-82). Genotypes were determined from buccal culture samples, and cognitive performance was assessed in 4 age-sensitive domains?fluid intelligence, executive function (inhibition), associative memory, and processing speed. We found that younger age and COMT Met/Met genotype, associated with low COMT activity and higher prefrontal dopamine content, were independently linked to better performance in most of the tested domains. Homozygotes for Val allele of BDNF polymorphism exhibited better associative memory and faster speed of processing than the Met allele carriers, with greater effect for women and persons with hypertension. Carriers of ApoE epsilon4 allele evidenced steeper age-related increase in costs of Stroop color interference, but showed no negative effects on memory. The findings indicate that age-related cognitive performance is differentially affected by distinct genetic factors and their interactions with vascular health status.

Synergistic effects of the MTHFR C677T polymorphism and hypertension on spatial navigation

Navigation skills deteriorate with age, but the mechanisms of the decline are poorly understood. Part of the decrement may be due to age-related vascular risk factors. The T allele in a C677T variant in methylenetetrahydrofolate reductase (MTHFR) gene is associated with elevated plasma homocysteine, which is detrimental to vascular integrity and has been linked to cognitive decline. We inquired if a combination of physiological (hypertension) and genetic (MTHFR 677T) vascular risks has a synergistic negative impact on cognitive performance in otherwise healthy adults. We tested 160 participants (18-80 years old) on a virtual water maze. Advanced age, female sex, and hypertension were associated with poorer performance. However, hypertensive carriers of the T allele performed significantly worse than the rest of the participants at all ages. These findings indicate that hypertension combined with a genetic vascular risk factor may significantly increase risk for cognitive impairment.

Differential effects of Th1, monocyte/macrophage and Th2 cytokine mixtures on early gene expression for molecules associated with metabolism, signaling and regulation in central nervous system mixed glial cell cultures

BACKGROUND

Cytokines secreted by immune cells and activated glia play central roles in both the pathogenesis of and protection from damage to the central nervous system (CNS) in multiple sclerosis (MS).

METHODS

We have used gene array analysis to identify the initial direct effects of cytokines on CNS glia by comparing changes in early gene expression in CNS glial cultures treated for 6 hours with cytokines typical of those secreted by Th1 and Th2 lymphocytes and monocyte/macrophages (M/M).

RESULTS

In two previous papers, we summarized effects of these cytokines on immune-related molecules, and on neural and glial related proteins, including neurotrophins, growth factors and structural proteins. In this paper, we present the effects of the cytokines on molecules involved in metabolism, signaling and regulatory mechanisms in CNS glia. Many of the changes in gene expression were similar to those seen in ischemic preconditioning and in early inflammatory lesions in experimental autoimmune encephalomyelitis (EAE), related to ion homeostasis, mitochondrial function, neurotransmission, vitamin D metabolism and a variety of transcription factors and signaling pathways. Among the most prominent changes, all three cytokine mixtures markedly downregulated the dopamine D3 receptor, while Th1 and Th2 cytokines downregulated neuropeptide Y receptor 5. An unexpected finding was the large number of changes related to lipid metabolism, including several suggesting a switch from diacylglycerol to phosphatidyl inositol mediated signaling pathways. Using QRT-PCR we validated the results for regulation of genes for iNOS, arginase and P glycoprotein/multi-drug resistance protein 1 (MDR1) seen at 6 hours with microarray.

CONCLUSION

Each of the three cytokine mixtures differentially regulated gene expression related to metabolism and signaling that may play roles in the pathogenesis of MS, most notably with regard to mitochondrial function and neurotransmitter signaling in glia.

Somatic alterations in brain tumors

Mutations in TP53 and RB1 have been shown to participate in the development of malignant brain tumors. Emerging evidence shows that mutations are involved in LGI1 in brain tumor progression. Herein we present data from the sequencing of a series of high- and low-grade gliomas with matched normal DNA. We report on 35 unique missense mutations in TP53, RB1 and LGI1 genes and use available information for each mutation in order to classify them as likely to be 'driver' or 'passenger' mutations. The identification of putatively deleterious mutations in LGI1 supports the notion that this locus may play a role in brain cancer development.

Integration of expression profiles and genetic mapping data to identify candidate genes in intracranial aneurysm

Intracranial aneurysm (IA) is a complex genetic disease for which, to date, 10 loci have been identified by linkage. Identification of the risk-conferring genes in the loci has proven difficult, since the regions often contain several hundreds of genes. An approach to prioritize positional candidate genes for further studies is to use gene expression data from diseased and nondiseased tissue. Genes that are not expressed, either in diseased or nondiseased tissue, are ranked as unlikely to contribute to the disease. We demonstrate an approach for integrating expression and genetic mapping data to identify likely pathways involved in the pathogenesis of a disease. We used expression profiles for IAs and nonaneurysmal intracranial arteries (IVs) together with the 10 reported linkage intervals for IA. Expressed genes were analyzed for membership in Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathways. The 10 IA loci harbor 1,858 candidate genes, of which 1,561 (84%) were represented on the microarrays. We identified 810 positional candidate genes for IA that were expressed in IVs or IAs. Pathway information was available for 294 of these genes and involved 32 KEGG biological function pathways represented on at least 2 loci. A likelihood-based score was calculated to rank pathways for involvement in the pathogenesis of IA. Adherens junction, MAPK, and Notch signaling pathways ranked high. Integration of gene expression profiles with genetic mapping data for IA provides an approach to identify candidate genes that are more likely to function in the pathology of IA.

Association of Kallikrein Gene Polymorphisms With Intracranial Aneurysms

Background and Purpose— Genomewide DNA linkage analysis identified a susceptibility locus for intracranial aneurysm (IA) on chromosome 19q13 in the Finnish population, a region including the kallikrein gene cluster. We investigated the association of single nucleotide polymorphisms (SNPs) in the kallikrein gene cluster with IA in the Finnish population.

Methods— We genotyped 18 haplotype-tagging SNPs spanning a 244 kbp region in the kallikrein gene cluster for 266 Finnish IA cases and 290 Finnish control subjects. In a second phase, we genotyped 2 SNPs (rs1722561 and rs1701946) in an additional set of 102 Finnish IA cases and 102 Finnish control subjects; and in a third phase, we genotyped these 2 SNPs in 156 Russian IA cases and 186 Russian control subjects. Both single-marker and haplotype-based tests of association were performed.

Results— In phase I, SNPs rs1722561 and rs1701946 were significantly associated with IA in the Finnish population for single locus models (rs1722561: P =0.0395; rs1701946: P =0.0253). A 2-SNP haplotype block (rs1722561–rs1701946) identified in phase I was also associated with IA in the expanded Finnish (phase II) data set (asymptotic P =0.012; empirical P =0.019). In the Finnish and Russian combined data set (phase III) with 524 cases and 578 control subjects, the same 2 SNPs (OR: 1.35, 95% CI: 1.14, 1.60; P =0.0005 for rs1722561 and OR: 1.32, 95% CI: 1.12, 1.57; P =0.0011 for rs1701946) were significantly associated with IA. These SNPs are located in the intronic region of KLK8 , although linkage disequilibrium could extend from rs268912–rs2250066, a ≈76-kbp region that includes KLK5–KLK10.

Conclusions— Polymorphisms within the kallikrein gene cluster are associated with IA suggesting that the kallikreins are important candidate genes for IA.

Long-term outcomes after invasive breast tumor recurrence (IBTR) in women with DCIS in NSABP B-17 and B-24

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Background: DCIS patients treated with lumpectomy have a very favorable outcome but are at risk for IBTR. Local control is improved by radiotherapy (RT) and adjuvant tamoxifen (TAM). Local failures, specifically invasive IBTRs (I-IBTR), may impact on long-term outcome. We present long-term outcome results from a cohort of DCIS patients from two NSABP randomized trials. Patients and Methods: A total of 2,615 women with primary DCIS from NSABP B-17 and B-24 (randomized from 1985 to 1994) were included. Median follow-up was > 12 yrs. In B-17 treatment was lumpectomy (LO, 403) or lumpectomy with whole breast irradiation (LRT, 410). In B-24 patients received LRT (901) or LRT plus TAM [901]. Hazard ratio and cumulative incidence of IBTR were examined by treatment. Mortality hazard was evaluated in relation to prior IBTR. Results: IBTR was a first failure in 465 patients (243 invasive, 222 noninvasive). The 12 year cumulative incidence of all IBTRs was 32.9% for LO, 15.8% LRT, and 12.5% LRT+TAM. RT significantly reduced I-IBTR (LRT/LO hazard ratio (HR) = 0.39; 95% confidence interval (CI) =0.26 to 0.59). TAM conferred additional benefit on I-IBTR (LRT+TAM/LRT HR=0.68; 95% CI= 0.48 to 0.97). Overall mortality was low. Women with I-IBTR had a two-fold greater mortality risk relative to those without I-IBTR (HR=2.08; 95% CI = 1.46 to 2.98). The effect was greater for LRT patients (HR=3.04; 95% CI= 1.92 to 4.84) than for LO patients (HR=1.17; 95% CI = 0.57 to 2.39). For LRT+TAM patients, the effect was similar to that for LRT patients HR=1.91; 95% CI= 0.76 to 4.78). Conclusions: As in cases of I- IBTR after an invasive index tumor, the occurrence of an I-IBTR with a DCIS index tumor, particularly after RT, confers increased risk for subsequent mortality.

No significant financial relationships to disclose.

The response of IFNAR2 to high-dose IFNα2b during a neoadjuvant clinical trial

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Background: The appropriate subgroup of melanoma patients to select for high-dose IFNa2b (HDI) adjuvant therapy has been undefined since approval of this modality in 1996. A biomarker appropriate for clinical practice and relevant to the biological effects of this agent would be of great importance. IFNAR2 is required for type I IFN-dependent signaling. Therefore, the response of IFNAR2 during HDI was evaluated during a prospective neoadjuvant clinical trial of HDI. Methods: Following diagnostic biopsy and before definitive surgery, HDI was administered as a neoadjuvant therapy for patients with stage IIIB melanoma, in the context of an IRB-approved protocol UPCI 00- 008, separately reported. Immunohistochemical analysis of IFNAR2 was performed on fixed paired biopsies of 8 patients. Paired-sample permutation tests and two-sample permutation tests were used to evaluate the findings of this study. Mean values of the percentage of IFNAR2 positive cells are presented with standard errors (SE). Results: HDI down-regulates IFNAR2 in both responders and non- responders, from 86.875 ± 5.82 (pre-treatment) to 34.375 ± 9.919 (post-treatment), p = 0.0145. However, the decrease in IFNAR2 differs between responders (25.0 ± 12.583) and non-responders (69.0 ± 3.588), p = 0.021. Conclusions: HDI down-regulates IFNAR2 expression, and may provide a biomarker relevant to HDI benefit, given differences between patients with and without response to neoadjuvant therapy. A larger clinical trial is needed to evaluate these pilot data.

No significant financial relationships to disclose.

Phase II study of short course CHOP-rituximab (R) followed by ibritumomab tiuxetan (IT) as first-line treatment for follicular lymphoma (FL)

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Background: Therapy with CHOP-R and radioimmunotherapy (RIT) is a promising treatment for untreated FL. Press reports complete responses (CR) of 69% in FL patients (pts.) with 6 cycles of CHOP followed by I-131 tositumomab. We report efficacy and safety using 3 cycles of CHOP-R followed by IT and extended R. Methods: Eligibility criteria include symptomatic or grade 3 untreated FL. 60 pts. have been accrued and 47 evaluated. The treatment consists of two phases: CHOP-R for 3 cycles followed by IT. One week after IT, pts receive R weekly × 4. Bone marrow (BM) biopsies and fusion PET-CT scans are obtained at baseline, after CHOP-R, and 12 weeks post RIT. The primary endpoint is CR rate. CR requires a neg. PET scan and conventional Working Group criteria. Results: Toxicity data are available for 47 pts of median age 56 (range, 39–78), 44 of whom completed both phases of therapy and are evaluated for response. Characteristics and CR rates after IT are shown: 3 pts. did not receive RIT (1 second malignancy, 1 non-compliance, 1 septic death). Of the 44, CR after CHOP-R is 41%. After IT, CR improved to 89%. Of the 5 pts who did not achieve CR, 3 had neg. PET scans (2 with PR, 1 with SD by CT), and 2 had residual disease by PET with PR by CT. At a mean follow-up of 16 months (range, 6–33 months), there are 4 relapses: 3 who achieved CR by PET-CT, 1 with PR by PET-CT. Toxicity was predominantly myelosuppression. There was 1 episode of febrile neutropenia after RIT. Conclusions: 3 cycles of CHOP-R followed by IT and R achieve a high CR in previously-untreated pts. with FL. Addition of RIT increased CR from 41% to 89%. Data will be presented on the affect of bulky disease, positive BM, grade 2 or 3 histology, and high FLIPI score on CR. Further follow-up is necessary to evaluate response duration and determine whether there is a correlation with early or late CR.

[Table: see text] [Table: see text]

Global analysis of gene expression in the estrogen induced pituitary tumor of the F344 rat

The F344 rat rapidly forms large prolactinomas in response to chronic estrogen treatment. To identify genes expressed in the course of this estrogen induced pituitary tumor growth, we performed microarray analysis on the F344 rat pituitary after chronic estrogen treatment and on untreated controls. At a significance level set to minimize type I error, some 72 genes were found to be differentially expressed between estrogen treated and untreated. Of those genes, 70 have not been reported previously as being affected by estrogen in the F344 rat pituitary. Since many other investigators have studied the effect of estrogen on specific gene expression in rat pituitary, we also examined the mRNA expression of the 36 genes that have been previously reported as having their expression affected by estrogen in the rat pituitary. Of these, 13 were found to have their expression affected by estrogen treatment in the same direction as had been reported by others.

Differential effects of Th1, monocyte/macrophage and Th2 cytokine mixtures on early gene expression for immune-related molecules by central nervous system mixed glial cell cultures

Cytokines secreted within the central nervous system (CNS) are important in the development of multiple sclerosis (MS) lesions. The balance between Th1, monocyte/macrophage (M/M) and Th2 cytokines in the CNS may be pivotal in determining the outcome of lesion development. We examined the effects of mixtures of cytokines on gene expression by CNS glial cells, as mixtures of cytokines are present in MS lesions, which in turn contain mixtures of glial cells. In this initial analysis by gene array, we examined changes at 6 hours to identify early changes in gene expression that represent primary responses to the cytokines. Rat glial cells were incubated with mixtures of Th1, M/M and Th2 cytokines for 6 hours and examined for changes in early gene expression employing microarray gene chip technology. A minimum of 814 genes were differentially regulated by one or more of the cytokine mixtures in comparison to controls, including changes in expression in a large number of genes for immune system-related proteins. Expression of the proteins for these genes likely influences development and inhibition of MS lesions as well as protective and regenerative processes. Analysing gene expression for the effects of various combinations of exogenous cytokines on glial cells in the absence of the confounding effects of inflammatory cells themselves should increase our understanding of cytokine-induced pathways in the CNS.

Imaging results after CHOP-rituximab followed by 90Y ibritumomab tiuxetan and rituximab (R) in patients with previously-untreated follicular lymphoma (FL)

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Background: There has been some question regarding the predictive value of 111In scans in FL. We report imaging results with fusion PET-CT scans and 111In scans in a single-institution, non-randomized, phase II trial in patients with FL treated with CHOP-R followed by 90Y ibritumomab tiuxetan (Zevalin (Z)) and R. Methods: Eligible patients have CD20 positive FL, Grade 1–3 or transformed, Stage II-IV, no prior treatment with monoclonal antibody or chemotherapy, and symptomatic disease (if grade 1–2). CHOP-R is given every 21 days for 3 cycles. Four weeks after the last dose of CHOP-R, patients receive the Zevalin regimen, which includes 111In imaging and 90Y therapy. One week after Z, patients receive R 375 mg/m2 IV weekly for 4 doses. Bone marrow examination and fusion PET-CT scans are performed at baseline, after CHOP-R, and 12 weeks after Z. The primary endpoint is CR, and responses are reported using the International Working Group (IWG) criteria with the additional requirement of a negative PET scan for CR/CRu. Results: Thirty-six FL patients have been accrued, and 16 patients have completed therapy and follow-up studies. One patient did not have a positive PET scan at baseline. Following therapy, the proportion with a negative PET scan improved from 8 of 15 (53.3%) after CHOP-R to 15 of 15 (100%) after Z. Using IWG criteria in combination with PET scan results, the CR rate increased from 4 of 15 (26.7%) after CHOP-R to 12 of 15 (80%) after Z. Five of 6 patients (83%) with tumor uptake by 111In scan and 7 of 9 (78%) with a 111In scan negative for tumor achieved a CR. Conclusions: There was no significant difference in CR between those patients with 111In tumor uptake versus patients with a negative 111In scan. Functional imaging with PET-CT may be a more sensitive method than CT alone in determining residual disease in FL. This trial continues to accrue patients, and more time is needed to determine the duration of response and time to next therapy.

No significant financial relationships to disclose.

Early results of modified fludarabine, cyclophosphamide, and rituximab (mFCR) for patients with previously untreated advanced chronic lymphocytic leukemia (CLL)

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Background: Recent data reporting results of FCR therapy in previously untreated advanced CLL patients (F-25 mg/m2 d1–3 q 4wk; C-250 mg/m2 d 1–3 q 4wk; R-500 mg/m2 d1 q 4wk for 6 cycles) demonstrated complete remission (CR) of 70% and overall response (OR) of 95% (J Clin Oncol 2005;23:4079). The major toxicity was grade 3/4 neutropenia during 52% of courses. One approach to decrease neutropenia without compromising efficacy could be by reducing the doses of F and C and increasing the dose of R as high-dose R has been reported to be more efficacious in CLL. Methods: We conducted a phase II study for previously untreated advanced CLL patients treated with mFCR (F-20mg/m2 d1–3 q 4 wk; C-150 mg/m2 d1–3 q 4 wk; R-500mg/m2 d1 and d14 q 4wks; maintenance R-500 mg/m2 q 3 months until progression). A Simon two-stage design was used where 15 patients were accrued in the first stage and because of acceptable toxicity and response rate in stage I an additional 35 patients will be treated. The primary endpoint was response rate. Results: Twenty patients (13 male, 7 female), age 36–85 years (median 59) were treated with a total of 105 mFCR courses. All 20 patients were evaluable for toxicity. Grade 3/4 neutropenia occurred during 11(10.5%) courses. There were no episodes of neutropenic fever. Grade 3/4 thrombocytopenia occurred during 4 (3.8%) courses. Two patients are currently on study and not evaluable for response and among the 18 evaluable patients, the CR was 68%, PR was 32% with an OR of 100%. Eleven of the 12 CR patients had no evidence of CD5+/CD19+ coexpressing cells in their bone marrow after therapy and one had <1%; all 12 were NED by CT scan. Conclusions: Our preliminary results suggest mFCR is highly effective with considerably less grade 3/4 neutropenia than standard FCR. Complete responders had minimal residual disease in their bone marrow following mFCR.

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TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

The TRANSFAC database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel on composite elements have been further enhanced on various levels. A new web interface with different search options and integrated versions of Match and Patch provides increased functionality for TRANSFAC. The list of databases which are linked to the common GENE table of TRANSFAC and TRANSCompel has been extended by: Ensembl, UniGene, EntrezGene, HumanPSD and TRANSPRO. Standard gene names from HGNC, MGI and RGD, are included for human, mouse and rat genes, respectively. With the help of InterProScan, Pfam, SMART and PROSITE domains are assigned automatically to the protein sequences of the transcription factors. TRANSCompel contains now, in addition to the COMPEL table, a separate table for detailed information on the experimental EVIDENCE on which the composite elements are based. Finally, for TRANSFAC, in respect of data growth, in particular the gain of Drosophila transcription factor binding sites (by courtesy of the Drosophila DNase I footprint database) and of Arabidopsis factors (by courtesy of DATF, Database of Arabidopsis Transcription Factors) has to be stressed. The here described public releases, TRANSFAC 7.0 and TRANSCompel 7.0, are accessible under http://www.gene-regulation.com/pub/databases.html.

Genetic analysis of polymorphisms in biologically relevant candidate genes in patients with abdominal aortic aneurysms

BACKGROUND

Abdominal aortic aneurysms (AAAs) are characterized by histologic signs of chronic inflammation, destructive remodeling of extracellular matrix, and depletion of vascular smooth muscle cells. We investigated the process of extracellular matrix remodeling by performing a genetic association study with polymorphisms in the genes for matrix metalloproteinases (MMPs), tissue inhibitors of metalloproteinases (TIMPs), and structural extracellular matrix molecules in AAA. Our hypothesis was that genetic variations in one or more of these genes contribute to greater or lesser activity of these gene products, and thereby contribute to susceptibility for developing AAAs.

METHODS

DNA samples from 812 unrelated white subject (AAA, n = 387; controls, n = 425) were genotyped for 14 polymorphisms in 13 different candidate genes: MMP1(nt-1607), MMP2(nt-955), MMP3(nt-1612), MMP9(nt-1562), MMP10(nt+180), MMP12(nt-82), MMP13(nt-77), TIMP1(nt+434), TIMP1(rs2070584), TIMP2(rs2009196), TIMP3(nt-1296), TGFB1(nt-509), ELN(nt+422), and COL3A1(nt+581). Odds ratios and P values adjusted for gender and country of origin using logistic regression and stratified by family history of AAA were calculated to test for association between genotype and disease status. Haplotype analysis was carried out for the two TIMP1 polymorphisms in male subjects.

RESULTS

Analyses with one polymorphism per test without interactions showed an association with the two TIMP1 gene polymorphisms (nt+434, P = .0047; rs2070584, P = .015) in male subjects without a family history of AAA. The association remained significant when analyzing TIMP1 haplotypes (chi 2 P = .014 and empirical P = .009). In addition, we found a significant interaction between the polymorphism and gender for MMP10 ( P = .037) in cases without a family history of AAA, as well as between the polymorphism and country of origin for ELN ( P = .0169) and TIMP3 ( P = .0023) in cases with a family history of AAA.

CONCLUSIONS

These findings suggest that genetic variations in TIMP1, TIMP3, MMP10, and ELN genes may contribute to the pathogenesis of AAAs. Further work is needed to confirm the findings in an independent set of samples and to study the functional role of these variants in AAA. It is noteworthy that contrary to a previous study, we did not find an association between the MMP9 (nt-1562) polymorphism and AAA, suggesting genetic heterogeneity of the disease.

CLINICAL RELEVANCE

Abdominal aortic aneurysms (AAAs) are an important cardiovascular disease, but the genetic and environmental risk factors, which contribute to individual's risk to develop an aneurysm, are poorly understood. Histologically, AAAs are characterized by signs of chronic inflammation, destructive remodeling of the extracellular matrix, and depletion of vascular smooth muscle cells. We hypothesized that genes involved in these events could harbor changes that make individuals more susceptible to developing aneurysms. This study identified significant genetic associations between DNA sequence changes in tissue inhibitor of metalloproteinase 1 (TIMP1), TIMP3, matrix metalloproteinase 10 (MMP10) and elastin (ELN) genes, and AAA. The results will require confirmation using an independent set of samples. After replication it is possible that these sequence changes in combination with other risk factors could be used in the future to identify individuals who are at increased risk for developing an AAA.

Influence of Maternal-Fetal Histocompatibility and MHC Zygosity on Maternal Microchimerism

To investigate the relationship between maternal-fetal histocompatibility and maternal microchimerism, we developed a sensitive quantitative PCR assay for the neomycin resistance gene (neoR), and, in a mouse model system, used neoR as a noninherited maternal allele marker of maternal cells to detect and quantitate maternal microchimerism in tissues of neoR(-/-) N2 backcross progeny of (neoR(+/-))F(1) females mated with neoR(-/-) males. Using this approach, we obtained evidence for the presence of chimeric maternal cells in the brain, spleen, and thymus of all weanling and adult mice so tested. The numbers of chimeric maternal cells present in the spleen did not differ significantly from those in the thymus regardless of age or maternal-fetal histocompatibility. At all ages, brain tissue had higher level of maternal microchimerism than lymphoid tissue in mice MHC identical with their mothers, but the levels were similar in mice MHC disparate with their mothers. The levels of chimeric maternal cells in both brain and lymphoid tissue of mice with homozygous syngenicity and maternal allogenicity were similar, and tended to be higher than tissue-specific levels in mice with either combined maternal-fetal allogenicity or heterozygous syngenicity. Thus, MHC homozygous progeny had higher levels of maternal microchimerism than MHC heterozygous progeny. We conclude that normal mice possess small numbers of maternal cells in spleen, thymus, brain, and probably most other tissues, and that maternal-fetal histocompatibility influences the levels of these cells by mechanisms related to MHC zygosity of the progeny.

Microsatellite alterations in african americans with head and neck cancer

OBJECTIVE

To determine the genetic differences between African Americans (AA) and Non-African Americans (NAA) with head and neck squamous cell carcinoma (HNSCC).

METHODS

DNA was obtained from tumor tissues and peripheral blood from 18 AA and 19 NAA patients with HNSCC. Microsatellite analysis using a fluorescent technique was performed on chromosomal arms 1p, 3p, 4q, 9p, 13q, and 17p. Statistical analyses were performed on the molecular and clinical outcome data.

RESULTS

Based on the Surveillance, Epidemiologic, and End Result (SEER) data from southeast Michigan, the incidence rate of HNSCC in AA has been higher than for NAA, and the overall 5-year relative survival rate is lower for AA than NAA (36.2% vs. 47.6%). In this study, we found that the rate of loss of heterozygosity of chromosomal arms 1p, 3p, 4q, 9p, 13q, and 17p ranged from 68.8% to 83.3% for HNSCC in AA and from 66.7% to 90.0% in NAA. The difference in the rates of microsatellite alterations in chromosomal arms 3p, 4q, and 9p between AA and NAA were between 12.5% and 20% and were not statistically significant.

CONCLUSION

The incidence and clinical outcomes for AA with HNSCC are different from that of NAA in southeast Michigan. In our group of patients with HNSCC, differences in rates of microsatellite alterations and survival were found between AA and NAA; however, these differences were not statistically significant. We conclude that genetic difference, as determined by the rates of microsatellite alterations, is not predictive of outcome difference between AA and NAA HNSCC patients.

Gene expression profiles predict survival and progression of pleural mesothelioma

PURPOSE

Clinical outcomes for malignant pleural mesothelioma (MPM) patients having surgery are imprecisely predicted by histopathology and intraoperative staging. We hypothesized that gene expression profiles could predict time to progression and survival in surgically cytoreduced pleural mesothelioma of all stages.

EXPERIMENTAL DESIGN

Gene expression analyses from 21 MPM patients having cytoreductions and identical postoperative adjuvant therapy were performed using the U95 Affymetrix gene chip. Using both dChip and SAM, neural networks constructed a common 27 gene classifier, which was associated with either the high-risk and low-risk group of patients. Data were validated using real-time PCR and immunohistochemical staining. The 27 gene classifier was also used for validation in a separate set of 17 MPM patients from another institution.

RESULTS

The groups predicted by the gene classifier recapitulated the actual time to progression and survival of the test set with 95.2% accuracy using 10-fold cross-validation. Clinical outcomes were independent of histology, and heterogeneity of progression and survival in early stage patients was defined by the classifier. The gene classifier had a 76% accuracy in the separate validation set of MPMs.

CONCLUSIONS

These data suggest that pretherapy gene expression analysis of mesothelioma biopsies may predict which patients may benefit from a surgical approach.