Citations

Abstract Targeted therapies and immunotherapies have led to significant improvements in the treatment of advanced cancers, including metastatic melanoma. However, new strategies are desperately needed to overcome therapeutic resistance to these agents, as well as to identify effective treatment approaches for cancer patients that fall outside major targetable mutational subtypes (e.g., non–V600 BRAF melanoma). One such strategy is to extend the paradigm of individually tailored, molecularly targeted therapy into a broader spectrum of melanoma patients, particularly those bearing tumors without commonly recognized therapeutic targets, as well as having failed or were ineligible for immunotherapy. In this nontreatment pilot study, next-generation sequencing (NGS) technologies were utilized, including whole genome and whole transcriptome sequencing, to identify molecular aberrations in patients with non–V600 BRAF metastatic melanoma. This information was then rationally matched to an appropriate clinical treatment from a defined pharmacopeia. Five patients with advanced non–V600 BRAF metastatic melanoma were enrolled. We demonstrated successful performance of the following during a clinically relevant time period: patient tumor biopsy, quality DNA/RNA extraction, DNA/RNA-based sequencing for gene expression analysis, analysis utilizing a series of data integration methodologies, report generation, and tumor board review with formulated treatment plan. Streamlining measures were conducted based on the experiences of enrolling, collecting specimens, and analyzing the molecular signatures of patients. We demonstrated the feasibility of using NGS to identify molecular aberrations and generate an individualized treatment plan in this patient population. A randomized treatment study utilizing lessons learned from the conduct of this pilot study is currently underway. Mol Cancer Ther; 14(8); 1962–71. ©2015 AACR.

We describe the development of rheumatoid factor-positive migratory polyarthritis in a 5-year-old male who had been administered bidaily oral mineral oil as a laxative since birth. Minor respiratory symptoms, radiographic and bronchoscopic findings were consistent with chronic lipoid pneumonia. We speculate that immune sensitization to mineral oil promoted the clinical syndrome of juvenile idiopathic arthritis.

Abstract Background. The increase in breast cancer risk during pregnancy and postpartum is well known; however, the molecular phenotype of breast cancers occurring shortly after pregnancy has not been well studied. Given this, we investigated whether nulliparity and the time interval since pregnancy among parous women affects the breast cancer phenotype in young women. Materials and Methods. We examined molecular phenotype in relation to time since pregnancy in a prospective cohort of 707 young women (aged ≤40 years) with breast cancer. Parity was ascertained from study questionnaires. Using tumor histologic grade on central review and biomarker expression, cancers were categorized as luminal A- or B-like, HER2 enriched, and triple negative. Results. Overall, 32% were luminal A-like, 41% were luminal B-like, 9% were HER2 enriched, and 18% were triple negative. Although, numerically, patients diagnosed >5 years after pregnancy had more luminal A-like subtypes than women with shorter intervals since pregnancy, there was no evidence of a relationship between these intervals and molecular subtypes once family history of breast cancer and age at diagnosis were considered. Conclusion. Distribution of breast cancer molecular phenotype did not differ significantly among young women by parity or time interval since parturition when important predictors of tumor phenotype such as age and family history were considered. Implications for Practice: Distribution of breast cancer molecular phenotype did not differ among parous young women by time interval since pregnancy. The implication of these findings for clinical practice suggests that pregnancy-associated breast cancers may be seen up to 5 years beyond parturition.

We aimed to determine variation in treatment of newly diagnosed infantile spasms, focusing on details of adrenocorticotropic hormone (ACTH) administration using a Redcap questionnaire sent to members of the Child Neurology Society. Two hundred fifty-seven members responded. Eighty-four percent prescribers used ACTH to treat infantile spasms. Seventy-six percent always admit patients. There is no difference between prescriber type (epileptologist or other) and prescriber location (state-funded or non-state-funded hospital) for decision to admit. Electroencephalographic (EEG) confirmation of spasms and education for injection were the commonest reasons to admit. Only 45% of prescribers accurately estimated the cost of ACTH. Participants in the hospital vial program were significantly more likely to always admit patients for ACTH than those who did not participate in such a program ( P = .02). Although having the hospital sample vial allows time to complete investigation of infantile spasms and eliminates delays in initiating ACTH, it adds significantly to the cost of therapy.

Objective The purpose of this study was to evaluate the frequency of migraine headache in a large cohort of patients with fibromyalgia using a brief migraine headache‐screening tool. Background Several studies report a high prevalence of fibromyalgia among patients with migraine headaches, but there is a dearth of research evaluating the frequency of migraine headaches in patients with fibromyalgia, despite clinical observations suggesting that migraine headaches are common in patients with fibromyalgia. Design and Methods This was a cross‐sectional survey study. Patients (N = 3717) with a previous diagnosis of fibromyalgia who were members of the M ayo C linic F ibromyalgia R egistry were contacted by electronic survey and asked to complete a brief demographic and medical history questionnaire and the validated ID ‐ M igraine screener. Results A total of 1730 patients (46.5%) completed the electronic survey. The majority of participants were white (97.2%), female (92.5%), with a mean age of 56.2 (±13.1) years. Of the respondents, 966 (55.8%) met criteria for migraine headaches. Hypertension (309 [32.3%] vs 294 [40.1%], P = .004), asthma (312 [32.5%] vs 189 [25.9%], P = .011), irritable bowel syndrome (520 [54.6%] vs 348 [47.6], P = .017), chronic fatigue syndrome (486 [50.7%] vs 271 [37.1], P < .0001), depression (634 [66.5%] vs 413 [56.7%], P = .0002), anxiety (415 [43.5%] vs 252 [34.7%], P = .0011), and post‐traumatic stress disorder (172 [18.0%] vs 96 [13.2%], P = .006) were all significantly more common in those who met criteria for migraine headaches than those who did not. Conclusion The results of this study suggest that migraine headaches are common in patients with fibromyalgia. Clinicians who care for either population must be aware that these conditions commonly overlap and can significantly increase a patient's cumulative disease burden.

Abstract Purpose: The ultimate purpose of these studies and the proposed study is to use community-based interventions to increase overall use of mammographic services and to increase adherence with tribes' screening guidelines. Our immediate purposes by study: For Study 1, the purpose was to understand the risk and screening adherence profiles of women from four Bemidji Area tribes; for Study 2, the purpose was to ascertain whether non-adherent screeners and adherent screeners could be differentiated on any of six theoretical mediators of health behavior; in the proposed Study 3, the purpose is to use theoretical mediators that distinguish adherent and non-adherent screeners to design and test interventions to increase screening participation and adherence with tribes' screening guidelines. Experimental Procedures: All studies were designed to reflect principles of community-based participatory research. Study 1 was a chart review study that involved four tribes. Each tribe desired different levels of involvement that ranged from close control of all elements of the chart review to assigning the investigators to do the retrieval, review, and replacement of the medical records, and all elements of the analysis. All tribes managed the unique identifiers book which was a list of all women who were 40 years and older who had no prior history of breast cancer. Investigators retained only the unique identifiers and each individual's associated screening history and risk factors. Tribes received aggregated results from the study, but did not receive information on individual women's screening adherence or risk factors. Study 2, is guided by a community advisory committee that meets quarterly and involves one tribe. The study employs one tribal member and one tribal subcontractor, and has supported one student participant. The study team interviewed 55 women and used the results to develop a survey that is being administered to approximately 1400 women who are age 40 and older. Both the interviews and the survey are designed to examine the influence of six theoretical mediators (social norms, social networks, social support, health literacy, health beliefs, and theory of planned behavior) and demographic features on the behaviors of adherent and non-adherent mammographic screeners. Study 3 will involve four tribes and is designed to use the findings from Study 2 to develop and test interventions based on influential screening mediators. Each tribe has identified members who will serve on tribal research and advising units that will determine the specific interventions and receive training and mentoring to design and administer the interventions. The proposed interventions will be based on a case-control intervention design. Unpublished Data to Date: STUDY 1 showed that there were few significant differences (p = 0.05) based between adherent and non-adherent screeners based on risk factors. STUDY 2 interview results have shown some significant differences (p= 0.05) between adherent and non-adherent screeners related to self-efficacy (health beliefs model), perceived community support for annual mammograms (social norms), presence of 3rd degree relatives in social networks. There were no significant differences associated with health literacy, social support, and the theory of planned behavior. Conclusions: Findings in Study 2 show that potential differences between adherent and non-adherent screeners justify continuation to the survey phase. Should results of the survey demonstrate significant differences in the influential mediators of adherent compared to non-adherent screeners, follow-up with the intervention study (Study 3) will be an important next step. Citation Format: Wesley Petersen, Ann Nicometo, Robert Vierkant. Advancing toward interventions: Summary of two projects and a proposed intervention to improve mammography participation in Bemidji area native women. [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 B91. doi:10.1158/1538-7755.DISP13-B91

Abstract Background: Common genetic variants identified by genome-wide association studies and follow-up genotyping initiatives only explain a small proportion of the heritability of epithelial ovarian cancer (EOC). We hypothesized that some of the missing heritability may be explained by rare (minor allele frequency (MAF) &lt;0.5%) and low-frequency (MAF 0.5-5%) protein-coding variants that are not well captured by genotyping arrays that focus on common variants. Methods: To examine the association between uncommon variants and EOC susceptibility, we genotyped 7,060 EOC cases and 6,712 controls from the Ovarian Cancer Association Consortium using the Affymetrix Axiom Exome Genotyping Array. This platform contains 300,785 putative functional coding variants selected from exome sequences of 12,000+ individuals representing multiple ethnicities and complex traits. After performing quality control (QC), we used unconditional logistic regression treating the number of minor alleles carried as an ordinal variable (log-additive model) to evaluate SNP-EOC risk associations. Genotype cluster plots were visually inspected for top-ranking variants to determine assay success, and allele frequencies of samples from the 1000 Genomes Project and other cohorts were evaluated for QC purposes. Results: A total of 13,318 samples (97%) passed QC, and 12,779 eligible samples (6,293 invasive serous and endometrioid cases and 6,486 controls) were included in the analyses. 280,737 (93%) of the 300,785 attempted markers were successfully genotyped and had call rates &gt;90%. After removing 31,436 monomorphic markers, the 249,301 remaining markers were included in association analyses. We confirmed variants at previously reported EOC susceptibility loci (9p22, 3q25, 17cen-q21.3, and 8q24), with p-values between 10-5 and 10-11. Several correlated low-frequency non-synonymous variants (MAF=5%) residing in a novel EOC susceptibility gene at 3q25.31 were risk-associated. The most significant variant at 3q25.31 had an OR=1.36 and p = 5.58x10-8. Also noteworthy is a rare variant at 15q15.1-q21.1 (MAF=0.5%) that introduces a stop codon in a gene belonging to the tyrosine kinase family (OR=0.39, CI=0.26-0.58, p = 4.52x10-6). We also identified a more common synonymous coding variant in a phosphatase at 6q21.3 that was associated with increased risk (OR=1.22, CI=1.13-1.33, p = 1.84x10-6, MAF=9.6%). Population stratification and gene-based analyses are underway to further examine the impact of the newly-identified variants on EOC risk. A meta-analysis to include data from an additional 2104 EOC cases and 2516 controls genotyped with Illumina's HumanExome Beadchip rare variant array is also underway. Functional analysis of the most promising variants will follow. Conclusions: Preliminary data from this large-scale study reveals novel rare and low-frequency variants that may influence susceptibility to epithelial ovarian cancer. Citation Format: Jennifer Permuth-Wey, Y. Ann Chen, Zhihua Chen, Andrew Berchuck, Georgia Chenevix-Trench, Jennifer Doherty, Simon Gayther, Ellen L. Goode, Edwin Iversen, Alvaro N.A. Monteiro, Leigh Pearce, Paul D.P. Pharoah, Catherine M. Phelan, Ailith Pirie, Susan Ramus, Mary Ann Rossing, Joellen M. Schildkraut, Thomas A. Sellers, on behalf of the Ovarian Cancer Association Consortium. Exome genotyping array identifies rare and low-frequency variants that may be associated with ovarian cancer risk. [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 946. doi:10.1158/1538-7445.AM2014-946

Abstract INTRODUCTION Next generation sequencing (NGS) of patients has significantly changed our ways to study cancer genomics as it provides precise estimates of gene expression, fusion transcripts, expressed single nucleotide variants (eSNVs), splice variants and copy number variants. The Breast Cancer Genome Guided Therapy (BEAUTY) is an ongoing clinical study in which RNA sequencing (RNAseq) and whole exome sequencing (WES) are performed prior to, during and after neoadjuvant chemotherapy. Here we report the use of these sequencing technologies to investigate gene expression levels and mutational profiles in a triple negative breast cancer (TNBC) patient enrolled in BEAUTY whose disease did not respond to neoadjuvant paclitaxel and anthracycline/cycphosphamide. METHODS Computational approaches were used to integrate WES and RNAseq data obtained before therapy (V1T), after 12 weekly paclitaxel treatments (V2T) and after anthracycline-based regimen at surgical resection (V3T) to study a single patient with persistent TNBC disease after neoadjuvant chemotherapy. RESULTS Using RNA-Seq data, we identified an inter-chromosomal fusion transcript between chromosome 20 and 22 (GNAS-TTC38) that was highly expressed at V1T, V2T and V3T. We also identified intra-chromosomal fusion transcripts that were expressed at two time points, such as fusion transcript (KANSL1-ARL17A) on chromosome 17 for V1T and V2T and fusion transcript (RBM12B-LINC00535) on chromosome 8 for V2T and V3T time points. Several gene expression changes were also observed. Gene expression analysis of V1T, V2T and V3T tumors was performed. Differential temporal gene expression profiles of 9884 genes that were significant and varying at different time points were obtained for pathway analysis. Pathway analysis of 9884 genes identified up regulation and down regulation of several transcription factors with a fold change of 2x or more. When compared to blood, DNA tumor and RNA-Seq data, we identified 81 common somatic eSNVs that were expressed in both V1T and V2T time points and we are in the process of investigating V3T data. We found alterations of key transporter domains (CD225, Coatamer_beta_C, DUF2435, Dynamitin, EI24, GLTP, LMF1, Porin_3, V-ATPase_C) in our V1T and V2T SNV data. Similar to gene expression analysis, we are in the process of obtaining the list of mutations at various time points to identify driver and passenger mutation candidate genes for this specific TNBC patient. CONCLUSIONS Our initial time-series analysis of eSNV, fusion transcripts and gene expression data demonstrate that intensive analysis for individual patients is feasible. Further investigation of drug transporters and transcription regulators may help develop personalized treatment strategies for patients with disease resistant to current regimens. Citation Format: Krishna R. Kalari, Xiaojia Tang, Kevin J. Thompson, Douglas W. Mahoney, Poulami Barman, Jason P. Sinnwell, Hugues Sicotte, Peter Vedell, Steven N. Hart, Travis J. Dockter, Katie N. Jones, Amy L. Conners, Ann M. Moyer, Daniel W. Visscher, Jia Yu, Bowen Gao, Sarah A. McLaughlin, John A. Copland, Alvaro Moreno-Aspitia, Donald W. Northfelt, Richard J. Gray, Vera J. Suman, Jeanette E. Eckel Passow, Jean-Pierre A. Kocher, Eric D. Wieben, Gianrico Farrugia, Cloann G. Schultz, James N. Ingle, Richard Weinshilboum, Matthew P. Goetz, Liewei Wang, Judy C. Boughey. Analysis of sequencing data to identify potential drug targets for an individual newly diagnosed with basal breast cancer who failed to respond to current standard neoadjuvant chemotherapy. [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 4185. doi:10.1158/1538-7445.AM2014-4185

Abstract GNE-317 is a dual PI3K/mTOR inhibitor with excellent blood-brain barrier penetration. In this study, the efficacy of GNE-317 was evaluated in the Mayo panel of primary glioblastoma multiforme (GBM) xenografts. Based on the concept of oncogene addiction, we hypothesized that GNE-317 would be most efficacious in EGFR-hyper-activated and/or PTEN-deficient lines. In a CyQUANT cell proliferation assay, the inhibitory concentration of 50% cell number (IC50) for GBM6, 10, 22, and 84 were 0.59±0.50, 0.72±0.40, 0.26±0.14, and 3.49±1.64 microM, respectively. In these selected lines, there was a poor correlation between EGFR or PTEN status and in vitro response. The efficacy of GNE-317 also was evaluated in 10 lines in an orthotopic xenograft model. Mice with established tumors were randomized to daily dosing with GNE-317 (30 mg/kg) or placebo until moribund. Similar to in vitro data, there was a spectrum of response to GNE-317 (Table 1). The survival benefit ratio (ratio of median survival) did not correlate with EGFR amplification (P=0.78), EGFR mutation (P=0.25), or PTEN (P=0.55) status when analyzed singly. However, GNE-317 did extend survival in 4 of 5 lines in which either EGFR or PTEN were deregulated. To evaluate potentially clinically relevant combinations, the efficacy of GNE-317 combined with bevacizumab (BEV) was tested in the same orthotopic model in GBM8, 10, and 59. In GBM10, GNE-317/BEV provided a significant increase in survival compared to the most effective single agent (P&lt;0.0001). In GBM8, 10, and 59, the ratio of median survival for GNE-317/BEV vs. placebo were 1.47, 1.75, and 1.74, respectively (all P≤0.01). In conclusion, there may be a correlation between deregulation of the EGFR/PTEN signaling network and GNE-317 efficacy, and the efficacy of GNE-317 in some models can be extended when combined with bevacizumab. Table 1:Molecular Characteristics and Efficacy of GNE-317 in Mayo Primary GBM XenograftsEGFR AmplifiedEGFR vIII MutatedPTEN MutatedGNE-317 Responder*Benefit Ratio** of GNE-317GBM6YesYesWTYes1.35GBM8YesNoYes, HDYes1.19GBM10NoNoYes, HDYes1.47GBM22NoNoWTNo0.85GBM59YesYesYes, HDYes1.27GBM84YesNoYes, del Exon 1No1.02GBM115NoNoTBDNo0.86GBM116NoNoTBDNo1.05GBM117NoNoTBDYes1.38GBM122YesNoTBDNo0.99Abbreviations: HD=homozygous deleted; del=deletion in; TBD=to be determined; WT=wild type.* If in vivo survival difference reached P&lt;0.05 by Log-rank Kaplan-Meier method between the GNE-317 treated and placebo groups, the GBM line was classified as a responder to GNE-317.** The benefit ratio equals to median survival of the GNE-317 treated group, divided by that of the placebo group. Note: This abstract was not presented at the meeting. Citation Format: Terence T. Sio, Jenny L. Pokorny, Ann C. Mladek, Brett L. Carlson, Mark A. Schroeder, Dennis O. Iyekegbe, Katrina Bakken, Laurent Salphati, Heidi Phillips, Jann N. Sarkaria. Preclinical efficacy of GNE-317, a dual PI3K/mTOR inhibitor, with or without bevacizumab in EGFR and/or PTEN-mutated glioblastoma multiforme. [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 2617. doi:10.1158/1538-7445.AM2014-2617