Progressive multiple sclerosis exhibits decreasing glutamate and glutamine over two years

Background:

Few biomarkers of progressive multiple sclerosis (MS) are sensitive to change within the two-year time frame of a clinical trial.

Objective:

To identify biomarkers of MS disease progression with magnetic resonance spectroscopy (MRS) in secondary progressive MS (SPMS).

Methods:

Forty-seven SPMS subjects were scanned at baseline and annually for two years. Concentrations of N-acetylaspartate, total creatine, total choline, myo-inositol, glutamate, glutamine, and the sum glutamate+glutamine were measured in a single white matter voxel.

Results:

Glutamate and glutamine were the only metabolites to show an effect with time: with annual declines of (95% confidence interval): glutamate −4.2% (−6.2% to −2.2%, p < 10−4), glutamine −7.3% (−11.8% to −2.9%, p = 0.003), and glutamate+glutamine −5.2% (−7.6% to −2.8%, p < 10−4). Metabolite rates of change were more apparent than changes in clinical scores or brain atrophy measures.

Conclusions:

The high rates of change of both glutamate and glutamine over two years suggest they are promising new biomarkers of MS disease progression.

Abstract LB-179: Molecular biomarker profiling of archival primary breast cancers from a Phase 3 adjuvant study of capecitabine in early stage breast cancer patients

Current clinical practice stratifies patients for treatment and enrollment in clinical breast cancer studies based on ER, PR and HER2 status. Emerging data suggest that these three biomarkers do not fully capture the heterogeneity that exists within breast cancer. In addition, understanding the genetic landscape of breast cancer is critical for defining clinically actionable patient subsets that may derive benefit from targeted therapies. PIK3CA and TP53 mutations have previously been reported to be the most common mutations within breast cancer; however the prognostic significance of these alterations, as well as their overlap/exclusivity with other important biomarkers is poorly understood.

USON 01062 (O’Shaughnessy J, et al. Proc SABCS, 2010, abstract S4-2) is a phase III study that evaluated the addition of capecitabine to standard adjuvant chemotherapy. The study did not meet its primary endpoint of 5-year disease-free survival (HR 0.84, p=0.125), but showed improvement in overall survival (HR 0.68, p=0.011). FFPE primary breast cancers were obtained from approximately 2000 of the 2610 patients (pts) enrolled, and here we report results from our comprehensive biomarker analyses on 817 of these pts. Samples were profiled using a multiplexed PCR-based platform to determine somatic mutations in 6 key oncogenes, as well as assayed for 800 breast cancer-related genes encompassing a variety of signaling pathways and published breast cancer signatures. IHC for the proliferation marker Ki67 and the tumor suppressor PTEN was also performed.

Intrinsic subtyping analysis determined that 296 pts’ cancers were basal, 69 were HER2-enriched, 327 were luminal A, 124 were luminal B and 1 was normal-like. Approximately 80% of the triple negative breast cancers (TNBCs) were of the basal subtype, and 80% of the ER+ cancers were of the luminal A and B subtypes. The most heterogeneous group was the HER2-enriched group that was comprised of 60% HER2+ and 30% TN cancers. PIK3CA mutations were found at a frequency of 44% in luminal A, 24% in luminal B, 33% in HER2-enriched and 3% in the basal subtypes. Within the TNBC subset, 42% were basal like 1/2, 21% were immunomodulatory, 15% were mesenchymal stem-like, 13% were mesenchymal-like and 9% were luminal AR.

In conclusion, luminal A breast cancers were the most common subtype treated with chemotherapy on this adjuvant trial that evaluated the effectiveness of the anti-proliferative agent, capecitabine. Intrinsic subtyping and molecular profiling of pts’ primary breast cancer reveals the substantial heterogeneity of early breast cancers, highlighting the challenges in identifying patients who may benefit from adjuvant capecitabine based on standard clinical-pathologic features. Analysis of intrinsic subtyping, Ki67 levels and genomic alterations of these early breast cancer pts will be presented.

Citation Format: Carol Lynn O'Brien, Tim R. Wilson, Jill M. Spoerke, Yuanyuan Xiao, Heidi Savage, Rachel Tam, Erica Schleifman, Rajesh Patel, Ling Huw, Hartmut Koeppen, Ling Fu, Teiko Sumiyoshi, Joyce O'Shaughnessy, Mark Lackner. Molecular biomarker profiling of archival primary breast cancers from a Phase 3 adjuvant study of capecitabine in early stage breast cancer patients. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-179. doi:10.1158/1538-7445.AM2014-LB-179

Profiling cancer gene mutations in clinical formalin-fixed, paraffin-embedded colorectal tumor specimens using targeted next-generation sequencing

PURPOSE

The success of precision oncology relies on accurate and sensitive molecular profiling. The Ion AmpliSeq Cancer Panel, a targeted enrichment method for next-generation sequencing (NGS) using the Ion Torrent platform, provides a fast, easy, and cost-effective sequencing workflow for detecting genomic "hotspot" regions that are frequently mutated in human cancer genes. Most recently, the U.K. has launched the AmpliSeq sequencing test in its National Health Service. This study aimed to evaluate the clinical application of the AmpliSeq methodology.

METHODS

We used 10 ng of genomic DNA from formalin-fixed, paraffin-embedded human colorectal cancer (CRC) tumor specimens to sequence 46 cancer genes using the AmpliSeq platform. In a validation study, we developed an orthogonal NGS-based resequencing approach (SimpliSeq) to assess the AmpliSeq variant calls.

RESULTS

Validated mutational analyses revealed that AmpliSeq was effective in profiling gene mutations, and that the method correctly pinpointed "true-positive" gene mutations with variant frequency >5% and demonstrated high-level molecular heterogeneity in CRC. However, AmpliSeq enrichment and NGS also produced several recurrent "false-positive" calls in clinically druggable oncogenes such as PIK3CA.

CONCLUSION

AmpliSeq provided highly sensitive and quantitative mutation detection for most of the genes on its cancer panel using limited DNA quantities from formalin-fixed, paraffin-embedded samples. For those genes with recurrent "false-positive" variant calls, caution should be used in data interpretation, and orthogonal verification of mutations is recommended for clinical decision making.

Next generation MUT-MAP, a high-sensitivity high-throughput microfluidics chip-based mutation analysis panel

Molecular profiling of tumor tissue to detect alterations, such as oncogenic mutations, plays a vital role in determining treatment options in oncology. Hence, there is an increasing need for a robust and high-throughput technology to detect oncogenic hotspot mutations. Although commercial assays are available to detect genetic alterations in single genes, only a limited amount of tissue is often available from patients, requiring multiplexing to allow for simultaneous detection of mutations in many genes using low DNA input. Even though next-generation sequencing (NGS) platforms provide powerful tools for this purpose, they face challenges such as high cost, large DNA input requirement, complex data analysis, and long turnaround times, limiting their use in clinical settings. We report the development of the next generation mutation multi-analyte panel (MUT-MAP), a high-throughput microfluidic, panel for detecting 120 somatic mutations across eleven genes of therapeutic interest (AKT1, BRAF, EGFR, FGFR3, FLT3, HRAS, KIT, KRAS, MET, NRAS, and PIK3CA) using allele-specific PCR (AS-PCR) and Taqman technology. This mutation panel requires as little as 2 ng of high quality DNA from fresh frozen or 100 ng of DNA from formalin-fixed paraffin-embedded (FFPE) tissues. Mutation calls, including an automated data analysis process, have been implemented to run 88 samples per day. Validation of this platform using plasmids showed robust signal and low cross-reactivity in all of the newly added assays and mutation calls in cell line samples were found to be consistent with the Catalogue of Somatic Mutations in Cancer (COSMIC) database allowing for direct comparison of our platform to Sanger sequencing. High correlation with NGS when compared to the SuraSeq500 panel run on the Ion Torrent platform in a FFPE dilution experiment showed assay sensitivity down to 0.45%. This multiplexed mutation panel is a valuable tool for high-throughput biomarker discovery in personalized medicine and cancer drug development.

Abstract 3462: High-throughput qRT-PCR expression profiling of estrogen receptor positive breast tumors

The class I phosphatidylinositol 3’ kinases (PI3K) play a major role in proliferation and survival in a wide variety of human cancers, and activation of the PI3K pathway is thought to be an important driver in estrogen receptor positive (ER+) breast cancer. A key factor in successful development of drugs targeting this pathway will be development in appropriate molecular subsets. Important questions relevant to PI3K inhibitor development in ER+ breast cancers are whether these inhibitors will work equally well in luminal A compared to luminal B tumors, and whether gene expression signatures of pathway activation may have additional utility in patient stratification beyond PIK3CA mutation status alone.

The goal of this study was to develop a methodology for high throughput profiling of ER+ breast cancers, in order to enable molecular subtyping of patients enrolled in clinical studies. To accomplish this, we developed an analysis platform to measure the relative expression of 90 breast cancer and PI3K pathway specific genes in formalin-fixed paraffin-embedded (FFPE) tissue. The content for this panel consists of genes known to be important for epithelial-mesenchymal biology, proliferation rate, and transcriptional output of the PI3K pathway. The 96 assay panel (including 6 housekeeping genes) was developed on the Fluidigm Biomark microfluidics platform and was extensively validated using well-characterized breast cancer cell lines and FFPE breast cancer samples of known subtypes based on immunohistochemistry for HER2, ER, and PR. All assays showed high levels of inter-and intra-chip reproducibility and were sensitive on standard curves down to 3ng RNA input.

Using this method we were able to separate breast cancers into distinct molecular subtypes, as well as identify more proliferative luminal B type tumors. In addition, PIK3CA mutation status, a potential biomarker, was determined using a highly specific and sensitive qRT-PCR mutation assay, in order to allow comparison with the PI3K pathway activation signature. We extended these analyses to a small cohort of patient samples consisting of matched primary and metastatic tumor tissues, and report here the correlation of primary and matched metastatic ER+ breast cancer FFPE tumor samples at both the gene expression and mutational levels. We found that the majority of matched pairs were concordant for both mutation status and gene expression, though a subset did show differences. Future studies will examine the prognostic significance and clinical relevance of this gene signature.

Citation Format: Erica B. Schleifman, Rupal M. Desai, Jill Spoerke, Cheryl Victoria Wong, Ilma Abbas, Carol O'Brien, Garret Hampton, Timothy Wilson, Hartmut Koeppen, Rajesh Patel, Teiko Sumiyoshi, Ling Fu, Rachel Tam, Rajiv Raja, Mark Lackner. High-throughput qRT-PCR expression profiling of estrogen receptor positive breast tumors. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3462. doi:10.1158/1538-7445.AM2013-3462

Abstract 1203: Molecular stratification of bladder cancer reveals distinct subtypes associated with unique clinical behaviors

Bladder cancer is a common malignancy, and in the US approximately 15,000 patients a year succumb to metastatic disease. The transition from the non-invasive to the lethal invasive variety is poorly understood, and this is reflected by the lack of efficacious treatment options for patients presenting with advanced disease. Notably, a significant fraction of superficial cancers can recur, requiring additional surgeries and conferring a higher risk for disease progression. Stratifying bladder cancers into molecular subtypes with defined clinical attributes could highlight non-invasive tumors with high risk of recurrence and reveal opportunities for therapeutic intervention in advanced disease. To this end, we molecularly characterized a collection of ∼200 clinically-annotated, formalin-fixed, paraffin-embedded tissues that represent non-invasive and invasive/advanced stage histopathologies. Tumors were assessed for mutation status at ∼100 mutation hotspots in key oncogenes as well as for the expression levels of ∼100 genes on a custom Fluidigm™ platform to interrogate key bladder cancer pathways, such as the FGFR3, PI3K and MAPK signaling axes. Integrative analysis of gene expression, mutation, and clinical data identified non-invasive subtypes that were FGFR3 mutation positive and exhibited a pathway up regulation gene expression signature. In contrast, invasive tumors were FGFR3 wild type and displayed less prominent pathway up regulation. As expected, invasive tumors had significantly worse disease-free survival (DFS) than their non-invasive counterparts (HR = 0.54; P = 0.03). On the molecular level, advanced tumors exhibited dysregulation of key pathways, including p53 and PI3K. Although similar histologically, and of common FGFR3 mutation status, tumors of the non-invasive type could be further classified into two distinct transcriptional subtypes associated with remarkably different DFS profiles (HR = 0.29; P = 0.004). Our molecular stratification of bladder cancer identified distinct subtypes associated with their respective clinical behaviors. In advanced disease, we defined molecular alterations that highlight opportunities for therapeutic intervention. We also identified a novel subtype of non-invasive malignancies associated with a surprisingly high risk of recurrence, highlighting the value of molecular stratification for identifying bladder cancer patients who might benefit from more aggressive treatment than the current standard of care.

Citation Format: Doris Kim, YJ Choi, Dorothy French, Rajesh Patel, Ling Fu, Cheryl Wong, Ilma Abbas, Rachel Tam, Erica Schleifman, Teiko Sumiyoshi, Anna Faarborg, Bob Yauch, Garret Hampton, Lukas Amler, Rajiv Raja, Omar Kabbarah. Molecular stratification of bladder cancer reveals distinct subtypes associated with unique clinical behaviors. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1203. doi:10.1158/1538-7445.AM2013-1203

Mutation scanning using MUT-MAP, a high-throughput, microfluidic chip-based, multi-analyte panel

Targeted anticancer therapies rely on the identification of patient subgroups most likely to respond to treatment. Predictive biomarkers play a key role in patient selection, while diagnostic and prognostic biomarkers expand our understanding of tumor biology, suggest treatment combinations, and facilitate discovery of novel drug targets. We have developed a high-throughput microfluidics method for mutation detection (MUT-MAP, mutation multi-analyte panel) based on TaqMan or allele-specific PCR (AS-PCR) assays. We analyzed a set of 71 mutations across six genes of therapeutic interest. The six-gene mutation panel was designed to detect the most common mutations in the EGFR, KRAS, PIK3CA, NRAS, BRAF, and AKT1 oncogenes. The DNA was preamplified using custom-designed primer sets before the TaqMan/AS-PCR assays were carried out using the Biomark microfluidics system (Fluidigm; South San Francisco, CA). A cross-reactivity analysis enabled the generation of a robust automated mutation-calling algorithm which was then validated in a series of 51 cell lines and 33 FFPE clinical samples. All detected mutations were confirmed by other means. Sample input titrations confirmed the assay sensitivity with as little as 2 ng gDNA, and demonstrated excellent inter- and intra-chip reproducibility. Parallel analysis of 92 clinical trial samples was carried out using 2-100 ng genomic DNA (gDNA), allowing the simultaneous detection of multiple mutations. DNA prepared from both fresh frozen and formalin-fixed, paraffin-embedded (FFPE) samples were used, and the analysis was routinely completed in 2-3 days: traditional assays require 0.5-1 µg high-quality DNA, and take significantly longer to analyze. This assay can detect a wide range of mutations in therapeutically relevant genes from very small amounts of sample DNA. As such, the mutation assay developed is a valuable tool for high-throughput biomarker discovery and validation in personalized medicine and cancer drug development.

Identification of the MBF1 heat-response regulon of Arabidopsis thaliana

Brief periods of heat stress of even a few days can have a detrimental effect on yield production worldwide, causing devastating economic and societal impacts. Here we report on the identification of a new heat-response regulon in plants controlled by the multiprotein bridging factor 1c (MBF1c) protein of Arabidopsis thaliana. Members of the highly conserved MBF1 protein family function as non-DNA-binding transcriptional co-activators involved in regulating metabolic and development pathways in different organisms from yeast to humans. Nonetheless, our studies suggest that MBF1c from Arabidopsis functions as a transcriptional regulator which binds DNA and controls the expression of 36 different transcripts during heat stress, including the important transcriptional regulator DRE-binding protein 2A (DREB2A), two heat shock transcription factors (HSFs), and several zinc finger proteins. We further identify CTAGA as a putative response element for MBF1c, demonstrate that the DNA-binding domain of MBF1c has a dominant-negative effect on heat tolerance when constitutively expressed in plants, and show that constitutive expression of MBF1c in soybean enhances yield production in plants grown under controlled growth conditions without causing adverse effects on growth. Our findings could have a significant impact on improving heat tolerance and yield of different crops subjected to heat stress.

The plant NADPH oxidase RBOHD mediates rapid systemic signaling in response to diverse stimuli

Cell-to-cell communication and long-distance signaling play a key role in the response of plants to pests, mechanical wounding, and extreme environmental conditions. Here, we report on a rapid systemic signal in Arabidopsis thaliana that traveled at a rate of 8.4 centimeters per minute and was dependent on the respiratory burst oxidase homolog D (RbohD) gene. Signal propagation was accompanied by the accumulation of reactive oxygen species (ROS) in the extracellular spaces between cells and was inhibited by the suppression of ROS accumulation at locations distant from the initiation site. The rapid systemic signal was triggered by wounding, heat, cold, high-intensity light, and salinity stresses. Our results reveal the profound role that ROS play in mediating rapid, long-distance, cell-to-cell propagating signals in plants.

Fabrication of strong long-period gratings in hydrogen-free fibers with 157-nm F2-laser radiation

Long-period gratings were fabricated in standard telecommunication fiber (Corning SMF-28) by use of what is believed to be record short-wavelength light from a 157-nm F(2) laser. Strong loss peaks were formed without the need for enhancement techniques such as hydrogen loading. The magnitude of the attenuation peak was sensitive to the single-pulse laser fluence, decreasing with increasing pulse fluence as a result of nonuniform 157-nm laser interaction with both the fiber cladding and core. The long-period fiber gratings have good wavelength stability (Dlambda~7 nm) under thermal annealing at 150 degrees C.