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PURPOSE Human epidermal growth factor receptor 2 (HER2) is an effective therapeutic target in breast and gastric and gastroesophageal junction cancers. However, less is known about the prevalence of ERBB2 ( HER2) amplification and the efficacy of HER2-targeted treatment in other tumors. PATIENTS AND METHODS We assessed HER2 amplification status among 5,002 patients with advanced disease (excluding breast cancer) who underwent next-generation sequencing. We evaluated the clinical benefit of HER2-targeted therapy by measuring the time-dependent overall survival (OS) from the genomic testing results, progression-free survival (PFS), and PFS during HER2-targeted therapy (PFS2) compared with PFS during prior therapy (PFS1). RESULTS Overall, 122 patients (2.4%) had HER2 amplification, including patients with endometrial (5.3%), bladder (5.2%), biliary or gallbladder (4.9%), salivary (4.7%), and colorectal cancer (3.6%). Forty patients (38%) with nongastric, nongastroesophageal junction, or nonesophageal cancers received at least one line of HER2-targeted therapy. Patients receiving HER2-targeted therapy had a median OS of 18.6 months, compared with 10.9 months for patients who did not receive HER2-targeted therapy ( P = .070). On multivariable analysis, HER2-targeted therapy was significantly associated with increased OS (hazard ratio, 0.5; 95% CI, 0.27 to 0.93; P = .029), regardless of sex, age, or number of prior lines of treatment. The PFS2-to-PFS1 ratio was 1.3 or greater in 21 (57%) of 37 patients who received HER2-targeted therapy not in the first line of systemic treatment, and the median PFS2 and PFS1 times were 24 and 13 weeks, respectively ( P < .001). CONCLUSION HER2 amplifications using next-generation sequencing can be identified in a variety of tumor types. HER2-targeted therapy may confer clinical benefit in tumor types other than those for which HER2 inhibitors are approved.

Objective— Understanding the mechanisms regulating normal and pathological angiogenesis is of great scientific and clinical interest. In this report, we show that mutations in 2 different aminoacyl-transfer RNA synthetases, threonyl tRNA synthetase (tars y58 ) or isoleucyl tRNA synthetase (iars y68 ) , lead to similar increased branching angiogenesis in developing zebrafish. Approach and Results— The unfolded protein response pathway is activated by aminoacyl-transfer RNA synthetase deficiencies, and we show that unfolded protein response genes atf4, atf6 , and xbp1 , as well as the key proangiogenic ligand vascular endothelial growth factor (vegfaa) , are all upregulated in tars y58 and iars y68 mutants. Finally, we show that the protein kinase RNA-like endoplasmic reticulum kinase–activating transcription factor 4 arm of the unfolded protein response pathway is necessary for both the elevated vegfaa levels and increased angiogenesis observed in tars y58 mutants. Conclusions— Our results suggest that endoplasmic reticulum stress acts as a proangiogenic signal via unfolded protein response pathway–dependent upregulation of vegfaa.

PURPOSE Human epidermal growth factor receptor 2 (HER2) is an effective therapeutic target in breast and gastric and gastroesophageal junction cancers. However, less is known about the prevalence of ERBB2 (HER2) amplification and the efficacy of HER2-targeted treatment in other tumors. PATIENTS AND METHODS We assessed HER2 amplification status among 5,002 patients with advanced disease (excluding breast cancer) who underwent next-generation sequencing. We evaluated the clinical benefit of HER2-targeted therapy by measuring the time-dependent overall survival (OS) from the genomic testing results, progression-free survival (PFS), and PFS during HER2-targeted therapy (PFS2) compared with PFS during prior therapy (PFS1). RESULTS Overall, 122 patients (2.4%) had HER2 amplification, including patients with endometrial (5.3%), bladder (5.2%), biliary or gallbladder (4.9%), salivary (4.7%), and colorectal cancer (3.6%). Forty patients (38%) with nongastric, nongastroesophageal junction, or nonesophageal cancers received at least one line of HER2-targeted therapy. Patients receiving HER2-targeted therapy had a median OS of 18.6 months, compared with 10.9 months for patients who did not receive HER2-targeted therapy (P = .070). On multivariable analysis, HER2-targeted therapy was significantly associated with increased OS (hazard ratio, 0.5; 95% CI, 0.27 to 0.93; P = .029), regardless of sex, age, or number of prior lines of treatment. The PFS2-to-PFS1 ratio was 1.3 or greater in 21 (57%) of 37 patients who received HER2-targeted therapy not in the first line of systemic treatment, and the median PFS2 and PFS1 times were 24 and 13 weeks, respectively (P < .001). CONCLUSION HER2 amplifications using next-generation sequencing can be identified in a variety of tumor types. HER2-targeted therapy may confer clinical benefit in tumor types other than those for which HER2 inhibitors are approved.

SUMMARY The integration of mass spectrometry-based proteomics with next-generation DNA and RNA sequencing profiles tumors more comprehensively. Here this “proteogenomics” approach was applied to 122 treatment-naive primary breast cancers accrued to preserve post-translational modifications, including protein phosphorylation and acetylation. Proteogenomics challenged standard breast cancer diagnoses, provided detailed analysis of the ERBB2 amplicon, defined tumor subsets that could benefit from immune checkpoint therapy, and allowed more accurate assessment of Rb status for prediction of CDK4/6 inhibitor responsiveness. Phosphoproteomics profiles uncovered novel associations between tumor suppressor loss and targetable kinases.Acetylproteome analysis highlighted acetylation on key nuclear proteins involved in the DNA damage response and revealed cross-talk between cytoplasmic and mitochondrial acetylation and metabolism. Our results underscore the potential of proteogenomics for clinical investigation of breast cancer through more accurate annotation of targetable pathways and biological features of this remarkably heterogeneous malignancy., In Brief Breast cancer is a highly heterogeneous disease with variable outcomes and subtype-driven treatment approaches, making precision medicine a considerable challenge. Proteogenomic analyses of 122 primary breast cancers provide insights into clinically relevant biology, including cell cycle dysregulation, tumor immunogenicity, aberrant metabolism, and heterogeneity in therapeutic target expression., Graphical Abstract

What would it be like if teacher candidates were prepared to negotiate difference as it exists in today's classrooms by learning to operate within collaborative communities of inclusive practice? What would it be like if teacher education modeled a truly inclusive form of educational practice where students "are not seen as disabled, defective, or disordered" but instead viewed as "different, complex, and whole" and "reflecting a diversity of cultural, social, racial, physical, and intellectual identities" (Christensen, 1996, p. 63)? What if teacher education programs helped future general and special education teachers to feel comfortable and capable with such complexity through a preparation model that promoted the merging of their areas of expertise (Altieri et al., 2012)? These were the philosophical questions that were driving us in 2006 as we began to think about transforming our teacher education model.We knew that co-teaching had proven to be an effective model for promoting the achievement of students with disabilities. Thousand, Villa, and Nevin (2006) and Scruggs, Mastropieri, and McDuffie (2007) cogently presented their meta-analyses and the documented benefits of collaborative partnerships and co-teaching for students, teachers, and schools. We also knew that, after more than 30 years of calls for collaborative teacher preparation in special and general education (e.g., Blanton &. Pugach, 2007; Winn &. Blanton, 2005), only a small number of programs had made significant, long-lasting changes to that end. We just had become a unified school of teacher education at Radford University in 2006, but there were still strong ties to program areas, and we were looking for ways to enhance collaboration but keep the distinct practitioner roles of general and special education. Blanton and Pugach's (2007) conceptual models for collaborative programs helped us think about how we could integrate our programs and merge expertise, rather than merge programs.We also were strongly influenced by the realities of the field of special education and those who chose it as a career. In 2008, when we proposed our 325T grant (Project MERGE: Merging Expertise for Results in the General Education Curriculum), a chronic shortage of special education teachers was a major problem in Virginia and the nation. In Virginia, 70% of school divisions anticipated "severe shortages" or "shortages" of teachers of students with "high incidence disabilities" (Virginia Department of Education, 2006).Program DescriptionThe purpose of our project was to improve the quality of services and results for children with disabilities, primarily through collaboration. Merging the expertise of our special education, general education, and content-area faculty served what was and continues to be our overarching vision: the preparation of special and general educators who create and sustain successful, equal partnerships to teach all students in the general curriculum.Through the 325T grant, we designed and implemented an integrated teacher education pilot program based around the Blanton and Pugach (2007) model of integrated teacher education and an expanded collaborative field experience based around the work of Kozleski, Pugach, and Yinger (2002). Our goals were (a) to revise curriculum and requirements so that graduates would meet highly-qualified teacher standards and would be prepared to meet the needs of students from all backgrounds; (b) to recruit, retain, and graduate 20 students per cohort, resulting in approximately 80 new teachers who successfully completed the improved program in Years 2 through 5 of the grant; and (c) to develop and implement collaborative induction and mentoring activities that would lend support to new teachers and create mutually beneficial opportunities for professional growth for current and former students, faculty, and cooperating professionals.The current iteration of the program works this way. …

Understanding the mechanisms that regulate angiogenesis and translating these into effective therapies are of enormous scientific and clinical interests. In this report, we demonstrate the central role of CDP-diacylglycerol synthetase (CDS) in the regulation of VEGFA signaling and angiogenesis. CDS activity maintains phosphoinositide 4,5 bisphosphate (PIP2) availability through resynthesis of phosphoinositides, whereas VEGFA, mainly through phospholipase Cγ1, consumes PIP2 for signal transduction. Loss of CDS2, 1 of 2 vertebrate CDS enzymes, results in vascular-specific defects in zebrafish in vivo and failure of VEGFA-induced angiogenesis in endothelial cells in vitro. Absence of CDS2 also results in reduced arterial differentiation and reduced angiogenic signaling. CDS2 deficit-caused phenotypes can be successfully rescued by artificial elevation of PIP2 levels, and excess PIP2 or increased CDS2 activity can promote excess angiogenesis. These results suggest that availability of CDS-controlled resynthesis of phosphoinositides is essential for angiogenesis.

Extensive genomic characterization of human cancers presents the problem of inference from genomic abnormalities to cancer phenotypes. To address this problem, we analysed proteomes of colon and rectal tumours characterized previously by The Cancer Genome Atlas (TCGA) and perform integrated proteogenomic analyses. Somatic variants displayed reduced protein abundance compared to germline variants. Messenger RNA transcript abundance did not reliably predict protein abundance differences between tumours. Proteomics identified five proteomic subtypes in the TCGA cohort, two of which overlapped with the TCGA 'microsatellite instability/CpG island methylation phenotype' transcriptomic subtype, but had distinct mutation, methylation and protein expression patterns associated with different clinical outcomes. Although copy number alterations showed strong cis- and trans-effects on mRNA abundance, relatively few of these extend to the protein level. Thus, proteomics data enabled prioritization of candidate driver genes. The chromosome 20q amplicon was associated with the largest global changes at both mRNA and protein levels; proteomics data highlighted potential 20q candidates, including HNF4A (hepatocyte nuclear factor 4, alpha), TOMM34 (translocase of outer mitochondrial membrane 34) and SRC (SRC proto-oncogene, non-receptor tyrosine kinase). Integrated proteogenomic analysis provides functional context to interpret genomic abnormalities and affords a new paradigm for understanding cancer biology.

The cerebral vasculature provides the massive blood supply that the brain needs to grow and survive. By acquiring distinctive cellular and molecular characteristics it becomes the blood-brain barrier (BBB), a selectively permeable and protective interface between the brain and the peripheral circulation that maintains the extracellular milieu permissive for neuronal activity. Accordingly, there is great interest in uncovering the mechanisms that modulate the formation and differentiation of the brain vasculature. By performing a forward genetic screen in zebrafish we isolated no food for thought (nft y72 ), a recessive late-lethal mutant that lacks most of the intracerebral central arteries (CtAs), but not other brain blood vessels. We found that the cerebral vascularization deficit of nft y72 mutants is caused by an inactivating lesion in reversion-inducing cysteine-rich protein with Kazal motifs [reck; also known as suppressor of tumorigenicity 15 protein (ST15)], which encodes a membrane-anchored tumor suppressor glycoprotein. Our findings highlight Reck as a novel and pivotal modulator of the canonical Wnt signaling pathway that acts in endothelial cells to enable intracerebral vascularization and proper expression of molecular markers associated with BBB formation. Additional studies with cultured endothelial cells suggest that, in other contexts, Reck impacts vascular biology via the vascular endothelial growth factor (VEGF) cascade. Together, our findings have broad implications for both vascular and cancer biology. Correction issued: http://dev.biologists.org/content/143/6/1055 Refereed/Peer-reviewed

We identified four mutants in two distinct loci exhibiting similar trunk vascular patterning defects in an F3 genetic screen for zebrafish vascular mutants. Initial vasculogenesis is not affected in these mutants, with proper specification and differentiation of endothelial cells. However, all four display severe defects in the growth and patterning of angiogenic vessels in the trunk, with ectopic branching and disoriented migration of intersegmental vessels. The four mutants are allelic to previously characterized mutants at the fused-somites (fss) and beamter (bea) loci, and they exhibit comparable defects in trunk somite boundary formation. The fss locus has been shown to correspond to tbx24; we show here that bea mutants are defective in the zebrafish dlC gene. Somitic expression of known vascular guidance factors efnb2a, sema3a1, and sema3a2 is aberrantly patterned in fss and bea mutants, suggesting that the vascular phenotype is due to loss of proper guidance cues provided by these factors. Developmental Dynamics 235:1753–1760, 2006. Published 2006 Wiley-Liss, Inc.

Recent successful drilling operations at Lake El'gygytgyn, NE Russia have recovered sediment cores back to 3.6Ma, representing the longest time-continuous sediment record of past climate change in the terrestrial Arctic. Analysis of the hydrogen isotopic ratio (δD) of specific organic biomarkers allows reconstruction of past hydrological conditions, thereby providing a powerful tool for reconstructing past Arctic climate changes. Compound specific isotopic analysis of sedimentary lipids from this remote basin provides new insights into the climate evolution of the Arctic, capturing the mechanisms and dynamics of the last two glacial-interglacial transitions, potentially enhancing the accuracy of modeled future climate change projections and presenting an opportunity to estimate past polar amplification of climate change. The results of this research document the first continuous, high fidelity continental record of reconstructed δD in precipitation from terrestrial plant leaf waxes in the High Arctic spanning the last 120 ka. The hydrogen isotopic composition of lipid biomarkers were determined from previously obtained Lake El'gygytgyn sediment cores and compared with other multi-proxy evidence of past climate change within the lake basin. The modern isotope hydrology and controls on the δD lipid signal were first established within the El'gygytgyn Basin from modern precipitation, stream and lake waters, ice cover as well as modern vegetation, water column and lake bottom surface sediments in order to provide a modern context to properly constrain and interpret paleoclimatic proxy data. Reconstructed δD records of paleoprecipitation and temperature at Lake El'gygytgyn lead other northern hemisphere climate records (e.g. North Greenland Ice Core Project, NGRIP δ18O records) and are in phase with other continental and Antarctic climate records, suggesting early high northern latitude continental warming prior to established glacial-interglacial transitions. The data set generated here leads to multiple avenues of future work and provides critical insights into Arctic paleoclimate and paleohydrology, contributing to our understanding of high latitude environmental change over geological timescales. Collectively, the results of this dissertation research will provide a context for paleoclimate reconstructions and future organic geochemical and stable isotope analysis. Future application of compound-specific H isotope analyses to long drill cores (recovered in 2009; ~315m of sediment) will potentially provide a quantitative high-resolution record of paleoclimatic and paleoenvironmental changes spanning the last 3.6 Ma.

Background Because of the structural and molecular similarities between the two systems, the lateral line, a fish and amphibian specific sensory organ, has been widely used in zebrafish as a model to study the development/biology of neuroepithelia of the inner ear. Both organs have hair cells, which are the mechanoreceptor cells, and supporting cells providing other functions to the epithelium. In most vertebrates (excluding mammals), supporting cells comprise a pool of progenitors that replace damaged or dead hair cells. However, the lack of regenerative capacity in mammals is the single leading cause for acquired hearing disorders in humans. Results In an effort to understand the regenerative process of hair cells in fish, we characterized and cloned an egfp transgenic stable fish line that trapped tnks1bp1, a highly conserved gene that has been implicated in the maintenance of telomeres' length. We then used this Tg(tnks1bp1:EGFP) line in a FACsorting strategy combined with microarrays to identify new molecular markers for supporting cells. Conclusions We present a Tg(tnks1bp1:EGFP) stable transgenic line, which we used to establish a transcriptional profile of supporting cells in the zebrafish lateral line. Therefore we are providing a new set of markers specific for supporting cells as well as candidates for functional analysis of this important cell type. This will prove to be a valuable tool for the study of regeneration in the lateral line of zebrafish in particular and for regeneration of neuroepithelia in general.

Background: We developed and established a high depth targeted sequencing platform of 202 genes (all exons) to identify actionable DNA alterations in tumor samples. We aimed a minimum of 500x depth and defined actionable if the aberration had a direct link to an available clinical treatment or clinical trial. Our platform was optimized for FFPE specimens and low input DNA while the data analysis pipeline was designed to detect low frequency mutations and copy number alterations. Over 500 tumor samples and matched normal were analyzed using this platform. Methods: Libraries were made from a minimum of 170 ng of FFPE DNA (tumors) or blood DNA (matched normal). Capture of 202 genes (over 5,000 exons) was performed using Nimblegen probes to a minimum of 50x fold enrichment. Captured libraries were sequenced using Illumina HiSeq2000. Duplicate reads were removed from the raw data and the reads were mapped hg19 reference genome. We used VarScan2 for calling somatic, germline and loss of heterozygosity SNVs and short indels. Copy number variation was also reported when significant gain/loss on an exon was detected. Additionally, we used other tolls to annotate the functional consequence of the SNVs, such as CanDrA to predict if an SNV is driver or passenger event. Results: We sequenced over 500 tumor samples and their normal match (blood). The mean coverage for most of samples was over 1500x, which allowed us to detect low frequency mutations (5% or higher) with accuracy. The most common disease sites analyzed where we found genetic alterations were: breast, colon, brain, ovary, endometrial, skin, lung, prostate, head and neck, sarcoma, kidney and stomach. About 98% of all tumors analyzed had at least one somatic alteration (SNVs or copy number) and although the vast majority of the samples analyzed were derived from FFPE blocks, the number of samples that failed was less than 5%. Among the most common genes mutated are several “actionable genes” such as BRAF, EGFR and KRAS. The samples tested in this platform were also tested on ion torrent Ampliseq 46 gene panel (46 overlapping genes) in a CLIA certified laboratory at MD Anderson Cancer Center with a very high level of concordance. Conclusion: With a very low level of failure and high depth provided, our results indicate that this platform can be used for FFPE tumor samples with high level of accuracy and sensitivity, showing that this platform is reliable to be implemented in clinical settings. Citation Format: Karina Eterovic, Ken Chen, Hao Zhao, Funda Meric-Bernstam, Raja Luthra, Aldape Kenneth, Mark Routbort, Scott Kopetz, Michael Davies, John de Groot, Stacy Moulder, Yong Mao, Chacha Horombe, Lin-ya Tang, Song Ping, Zhang Qingxiu, Ezzeddine Nader, Lan Zhang, Kenna M. Shaw, John Mendelsohn, Gordon B. Mills. T200: a high depth targeted exome sequencing platform to identify actionable alterations in FFPE solid tumor samples. [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 4276. doi:10.1158/1538-7445.AM2014-4276

The FG nucleoporins are a conserved family of proteins, some of which bind to the nuclear localization sequence receptor, karyopherin. Distinct members of this family are found in each region of the nuclear pore complex (NPC), spanning from the cytoplasmically disposed filaments to the distal end of the nuclear basket. Movement of karyopherin from one FG nucleoporin to the next may be required for translocation of substrates across the NPC. So far, nothing is known about how the FG nucleoporins are localized within the NPC. To identify proteins that interact functionally with one member of this family, the Saccharomyces cerevisiae protein Nup1p, we previously identified 16 complementation groups containing mutants that are lethal in the absence of NUP1 These mutants were referred to as nle (Nup-lethal) mutants. Mutants in the nle3/nlel7 complementation group are lethal in combination with amino-terminal nup1 truncation mutants, which we have previously shown to be defective for localization to the NPC. Here we show that NLE3 (which is allelic to NUP170) encodes a protein with similarity to the mammalian nucleoporin Nup155. We show that Nle3p coprecipitates with glutathione S-transferase fusions containing the amino-terminal domain of Nup1p. Furthermore, a deletion of Nle3p leads to changes in the stoichiometry of several of the XFXFG nucleoporins, including the loss of Nup1p and Nup2p. These results suggest that Nle3p plays a role in localizing specific FG nucleoporins within the NPC. The broad spectrum of synthetic phenotypes observed with the nle3delta mutant provides support for this model. We also identify a redundant yeast homolog that can partially substitute for Nle3p and show that together these proteins are required for viability.