In vitro anti-prostate adenocarcinoma and lung cancer studies of phenoxyaniline-block-poly(methyl methacrylate) based nanocomposites via controlled radical polymerization

A phenoxyaniline-based macroinitiator is utilized for the first time in order to produce phenoxyaniline-block-poly(methyl methacrylate) composites through single electron transfer-living radical polymerization (SET-LRP) under mild conditions. A different weight percentage of Cloisite 93A is added into the polymer mixtures in order to increase their biochemical properties. The prepared block copolymer nanocomposites are characterized using ATR-IR, UV-vis-spectroscopy, XRD, Raman, TGA, DSC, a particle size analyzer, contact angle measurements and SEM in order to characterize their structural, thermal, surface and morphological properties. Further, the developed polymeric nanocomposites are successfully applied in two different cancer cell lines (prostate adenocarcinoma and lung cancer), which show excellent anticancer properties. Also, acridine orange/ethidium bromide (AO/EtBr) dual staining is performed, which causes drastic cell death by apoptosis in both A549 and PC-3 cell lines, which indicated that the prepared polymeric nanocomposites effectively inhibit the cell proliferation and induce the apoptosis in both the cancer cells. Here nanoclay is used for cancer treatment because of its complete water solubility, which essentially causes the formation of a cationic complex between the clay and drug through electrostatic interactions. Hence, the exchange of ions between the clay and other ions in the biological environment leads to inhibition of the proliferation of prostate adenocarcinoma and lung cancer cells in the system.

All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons

Accurate discovery of somatic mutations in a cell is a challenge that partially lays in immaturity of dedicated analytical approaches. Approaches comparing a cell's genome to a control bulk sample miss common mutations, while approaches to find such mutations from bulk suffer from low sensitivity. We developed a tool, All2, which enables accurate filtering of mutations in a cell without the need for data from bulk(s). It is based on pair-wise comparisons of all cells to each other where every call for base pair substitution and indel is classified as either a germline variant, mosaic mutation, or false positive. As All2 allows for considering dropped-out regions, it is applicable to whole genome and exome analysis of cloned and amplified cells. By applying the approach to a variety of available data, we showed that its application reduces false positives, enables sensitive discovery of high frequency mutations, and is indispensable for conducting high resolution cell lineage tracing.

HuD Regulates mRNA-circRNA-miRNA Networks in the Mouse Striatum Linked to Neuronal Development and Drug Addiction

Simple Summary

Gene expression controls all aspects of life, including that of humans. Genes are expressed by copying the information stored in the DNA into RNA molecules, and this process is regulated in part by multiple RNA-binding proteins (RBPs). One such protein, HuD, plays a critical role in the development of neurons and has been implicated in childhood brain tumors, neurodegenerative disorders (Parkinson’s, Alzheimer’s, and ALS), and drug abuse. In addition, HuD participates in neuronal remodeling mechanisms in the mature brain and promotes regeneration of peripheral nerves. HuD primarily binds to transcribed messenger RNAs, which are then stabilized for translation into proteins. However, recent studies demonstrate that HuD also regulates the expression of non-coding RNAs, such as circular RNAs (circRNAs) and microRNAs (miRNAs). In this study, we examined the role of HuD in the control of non-coding RNA expression in the mouse striatum, a brain region associated both with normal behaviors and pathological conditions such as drug abuse. Our results show that HuD regulates mRNA-circRNA-miRNA networks involved in the expression of genes associated with brain development and remodeling of neuronal connections. These findings suggest the possibility of new mechanisms controlling brain development, neurodegenerative diseases, and substance use disorders.

Abstract

The RNA-binding protein HuD (a.k.a., ELAVL4) is involved in neuronal development and synaptic plasticity mechanisms, including addiction-related processes such as cocaine conditioned-place preference (CPP) and food reward. The most studied function of this protein is mRNA stabilization; however, we have recently shown that HuD also regulates the levels of circular RNAs (circRNAs) in neurons. To examine the role of HuD in the control of coding and non-coding RNA networks associated with substance use, we identified sets of differentially expressed mRNAs, circRNAs and miRNAs in the striatum of HuD knockout (KO) mice. Our findings indicate that significantly downregulated mRNAs are enriched in biological pathways related to cell morphology and behavior. Furthermore, deletion of HuD altered the levels of 15 miRNAs associated with drug seeking. Using these sets of data, we predicted that a large number of upregulated miRNAs form competing endogenous RNA (ceRNA) networks with circRNAs and mRNAs associated with the neuronal development and synaptic plasticity proteins LSAMP and MARK3. Additionally, several downregulated miRNAs form ceRNA networks with mRNAs and circRNAs from MEF2D, PIK3R3, PTRPM and other neuronal proteins. Together, our results indicate that HuD regulates ceRNA networks controlling the levels of mRNAs associated with neuronal differentiation and synaptic physiology.

Insights into the exceptional stability of the molecular precursor solution for Cu2ZnSnS4 solar absorber

Environment friendly molecular precursors are extensively studied for green, economical and scalable fabrication of inorganic thin films for various device applications. For compound semiconductors such as the chalcogenide solar absorber Cu₂ZnSnS₄ (CZTS), the stability of such precursor solution is highly sought after. The longer shelf life of the precursor could significantly improve the phase purity as well as the reproducibility of the resulting films, and also would aid the industrial scaling up of the fabrication process. Herein, the reason behind the exceptional stability shown by a precursor solution for CZTS is explored, by probing the nature of interaction between its various components. The unique combination of solvent and the sulfur source is shown as favorable for the stable bonds in the solution, especially the predominant bidentate bridging of sulfur source to the metal atoms. The insights elucidated through simple spectroscopic techniques can be handy when designing such sustainable precursors for other functional chalcogenides and technologically important inorganic compounds.

Identifying treatment options for BRAFV600 wild-type metastatic melanoma: A SU2C/MRA genomics-enabled clinical trial

Although combination BRAF and MEK inhibitors are highly effective for the 40-50% of cutaneous metastatic melanomas harboring BRAFV600 mutations, targeted agents have been ineffective for BRAFV600wild-type (wt) metastatic melanomas. The SU2C Genomics-Enabled Medicine for Melanoma Trial utilized a Simon two-stage optimal design to assess whether comprehensive genomic profiling improves selection of molecular-based therapies for BRAFV600wt metastatic melanoma patients who had progressed on standard-of-care therapy, which may include immunotherapy. Of the response-evaluable patients, binimetinib was selected for 20 patients randomized to the genomics-enabled arm, and nine were treated on the alternate treatment arm. Response rates for 27 patients treated with targeted recommendations included one (4%) partial response, 18 (67%) with stable disease, and eight (30%) with progressive disease. Post-trial genomic and protein pathway activation mapping identified additional drug classes that may be considered for future studies. Our results highlight the complexity and heterogeneity of metastatic melanomas, as well as how the lack of response in this trial may be associated with limitations including monotherapy drug selection and the dearth of available single and combination molecularly-driven therapies to treat BRAFV600wt metastatic melanomas.

Comprehensive identification of somatic nucleotide variants in human brain tissue

BACKGROUND

Post-zygotic mutations incurred during DNA replication, DNA repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. However, detecting mosaic variants in DNA from non-cancerous somatic tissues poses significant challenges, particularly if the variants only are present in a small fraction of cells.

RESULTS

Here, the Brain Somatic Mosaicism Network conducts a coordinated, multi-institutional study to examine the ability of existing methods to detect simulated somatic single-nucleotide variants (SNVs) in DNA mixing experiments, generate multiple replicates of whole-genome sequencing data from the dorsolateral prefrontal cortex, other brain regions, dura mater, and dural fibroblasts of a single neurotypical individual, devise strategies to discover somatic SNVs, and apply various approaches to validate somatic SNVs. These efforts lead to the identification of 43 bona fide somatic SNVs that range in variant allele fractions from ~ 0.005 to ~ 0.28. Guided by these results, we devise best practices for calling mosaic SNVs from 250× whole-genome sequencing data in the accessible portion of the human genome that achieve 90% specificity and sensitivity. Finally, we demonstrate that analysis of multiple bulk DNA samples from a single individual allows the reconstruction of early developmental cell lineage trees.

CONCLUSIONS

This study provides a unified set of best practices to detect somatic SNVs in non-cancerous tissues. The data and methods are freely available to the scientific community and should serve as a guide to assess the contributions of somatic SNVs to neuropsychiatric diseases.

Complex mosaic structural variations in human fetal brains

Somatic mosaicism, manifesting as single nucleotide variants (SNVs), mobile element insertions, and structural changes in the DNA, is a common phenomenon in human brain cells, with potential functional consequences. Using a clonal approach, we previously detected 200-400 mosaic SNVs per cell in three human fetal brains (15-21 wk postconception). However, structural variation in the human fetal brain has not yet been investigated. Here, we discover and validate four mosaic structural variants (SVs) in the same brains and resolve their precise breakpoints. The SVs were of kilobase scale and complex, consisting of deletion(s) and rearranged genomic fragments, which sometimes originated from different chromosomes. Sequences at the breakpoints of these rearrangements had microhomologies, suggesting their origin from replication errors. One SV was found in two clones, and we timed its origin to ∼14 wk postconception. No large scale mosaic copy number variants (CNVs) were detectable in normal fetal human brains, suggesting that previously reported megabase-scale CNVs in neurons arise at later stages of development. By reanalysis of public single nuclei data from adult brain neurons, we detected an extrachromosomal circular DNA event. Our study reveals the existence of mosaic SVs in the developing human brain, likely arising from cell proliferation during mid-neurogenesis. Although relatively rare compared to SNVs and present in ∼10% of neurons, SVs in developing human brain affect a comparable number of bases in the genome (∼6200 vs. ∼4000 bp), implying that they may have similar functional consequences.

ACValidator: A novel assembly-based approach for in silico verification of circular RNAs

Circular RNAs (circRNAs) are evolutionarily conserved RNA species that are formed when exons "back-splice" to each other. Current computational algorithms to detect these back-splicing junctions produce divergent results, and hence there is a need for a method to distinguish true-positive circRNAs. To this end, we developed Assembly based CircRNA Validator (ACValidator) for in silico verification of circRNAs. ACValidator extracts reads from a user-defined window on either side of a circRNA junction and assembles them to generate contigs. These contigs are aligned against the circRNA sequence to find contigs spanning the back-spliced junction. When evaluated on simulated datasets, ACValidator achieved over ∼80% sensitivity on datasets with an average of 10 circRNA-supporting reads and with read lengths of at least 100 bp. In experimental datasets, ACValidator produced higher verification percentages for samples treated with ribonuclease R compared to nontreated samples. Our workflow is applicable to non-polyA-selected RNAseq datasets and can also be used as a candidate selection strategy for prioritizing experimental validations. All workflow scripts are freely accessible on our GitHub page https://github.com/tgen/ACValidator along with detailed instructions to set up and run ACValidator.

Identification of Circular RNAs using RNA Sequencing

Circular RNAs (circRNAs) are a class of non-coding RNAs involved in functions including micro-RNA (miRNA) regulation, mediation of protein-protein interactions, and regulation of parental gene transcription. In classical next generation RNA sequencing (RNA-seq), circRNAs are typically overlooked as a result of poly-A selection during construction of mRNA libraries, or are found at very low abundance, and are therefore difficult to isolate and detect. Here, a circRNA library construction protocol was optimized by comparing library preparation kits, pre-treatment options and various total RNA input amounts. Two commercially available whole transcriptome library preparation kits, with and without RNase R pre-treatment, and using variable amounts of total RNA input (1 to 4 µg), were tested. Lastly, multiple tissue types; including liver, lung, lymph node, and pancreas; as well as multiple brain regions; including the cerebellum, inferior parietal lobe, middle temporal gyrus, occipital cortex, and superior frontal gyrus; were compared to evaluate circRNA abundance across tissue types. Analysis of the generated RNA-seq data using six different circRNA detection tools (find_circ, CIRI, Mapsplice, KNIFE, DCC, and CIRCexplorer) revealed that a stranded total RNA library preparation kit with RNase R pre-treatment and 4 µg RNA input is the optimal method for identifying the highest relative number of circRNAs. Consistent with previous findings, the highest enrichment of circRNAs was observed in brain tissues compared to other tissue types.

2D-BCNO with Eu3+: partial energy transfer and direct natural white light for LEDs

2D-BCNO transfers some energy to excite Eu³⁺ ions and together they generate white light.

Identification of therapeutic targets in chordoma through comprehensive genomic and transcriptomic analyses

Chordoma is a rare, orphan cancer arising from embryonal precursors of bone. Surgery and radiotherapy (RT) provide excellent local control, often at the price of significant morbidity because of the structures involved and the need for relatively high doses of RT; however, recurrence remains high. Although our understanding of the genetic changes that occur in chordoma is evolving rapidly, this knowledge has yet to translate into treatments. We performed comprehensive DNA (paired tumor/normal whole-exome and shallow whole-genome) and RNA (tumor whole-transcriptome) next-generation sequencing analyses of archival sacral and clivus chordoma specimens. Incorporation of transcriptomic data enabled the identification of gene overexpression and expressed DNA alterations, thus providing additional support for potential therapeutic targets. In three patients, we identified alterations that may be amenable to off-label FDA-approved treatments for other tumor types. These alterations include FGFR1 overexpression (ponatinib, pazopanib) and copy-number duplication of CDK4 (palbociclib) and ERBB3 (gefitinib). In a third patient, germline DNA demonstrated predicted pathogenic changes in CHEK2 and ATM, which may have predisposed the patient to developing chordoma at a young age and may also be associated with potential sensitivity to PARP inhibitors because of homologous recombination repair deficiency. Last, in the fourth patient, a missense mutation in IGF1R was identified, suggesting potential activity for investigational anti-IGF1R strategies. Our findings demonstrate that chordoma patients present with aberrations in overlapping pathways. These results provide support for targeting the IGF1R/FGFR/EGFR and CDK4/6 pathways as treatment strategies for chordoma patients. This study underscores the value of comprehensive genomic and transcriptomic analysis in the development of rational, individualized treatment plans for chordoma.

Factors affecting high-density lipoprotein cholesterol in HIV-infected patients on nevirapine-based antiretroviral therapy

Background & objectives:

Cardiovascular disease (CVD) risk with low high-density lipoprotein cholesterol (HDL-C) and high triglycerides is common in the general population in India. As nevirapine (NVP)-based antiretroviral therapy (ART) tends to increase HDL-C, gene polymorphisms associated with HDL-C metabolism in HIV-infected adults on stable NVP-based ART were studied.

Methods:

A cross-sectional study was conducted between January 2013 and July 2014 among adults receiving NVP-based ART for 12-15 months. Blood lipids were estimated and gene polymorphisms in apolipoprotein C3 (APOC3), cholesteryl ester transfer protein (CETP) and lipoprotein lipase (LPL) genes were analyzed by real-time polymerase chain reaction. Framingham's 10-yr CVD risk score was estimated. Logistic regression was done to show factors related to low HDL-C levels.

Results:

Of the 300 patients included (mean age: 38.6±8.7 yr; mean CD4 count 449±210 cell/μl), total cholesterol (TC) >200 mg/dl was observed in 116 (39%) patients. Thirty nine per cent males and 47 per cent females had HDL-C levels below normal while 32 per cent males and 37 per cent females had TC/HDL ratio of 4.5 and 4.0, respectively. Body mass index [adjusted odds ratio (aOR)=1.70, 95% confidence interval (CI) 1.01-2.84, P=0.04] and viral load (aOR=3.39, 95% CI: 1.52-7.52, P=0.003) were negatively associated with serum HDL-C levels. The 10-yr risk score of developing CVD was 11-20 per cent in 3 per cent patients. Allelic variants of APOC3 showed a trend towards low HDL-C.

Interpretation & conclusions:

High-risk lipid profiles for atherosclerosis and cardiovascular disease were common among HIV-infected individuals, even after 12 months of NVP-based ART. Targeted interventions to address these factors should be recommended in the national ART programmes.

Circular RNA expression and regulatory network prediction in posterior cingulate astrocytes in elderly subjects

Background

Circular RNAs (circRNAs) are a novel class of endogenous, non-coding RNAs that form covalently closed continuous loops and that are both highly conserved and abundant in the mammalian brain. A role for circRNAs in sponging microRNAs (miRNAs) has been proposed, but the circRNA-miRNA-mRNA interaction networks in human brain cells have not been defined. Therefore, we identified circRNAs in RNA sequencing data previously generated from astrocytes microdissected from the posterior cingulate (PC) of Alzheimer’s disease (AD) patients (N = 10) and healthy elderly controls (N = 10) using four circRNA prediction algorithms - CIRI, CIRCexplorer, find_circ and KNIFE.

Results

Overall, utilizing these four tools, we identified a union of 4438 unique circRNAs across all samples, of which 70.3% were derived from exonic regions. Notably, the widely reported CDR1as circRNA was detected in all samples across both groups by find_circ. Given the putative miRNA regulatory function of circRNAs, we identified potential miRNA targets of circRNAs, and further, delineated circRNA-miRNA-mRNA networks using in silico methods. Pathway analysis of the genes regulated by these miRNAs identified significantly enriched immune response pathways, which is consistent with the known function of astrocytes as immune sensors in the brain.

Conclusions

In this study, we performed circRNA detection on cell-specific transcriptomic data and identified potential circRNA-miRNA-mRNA regulatory networks in PC astrocytes. Given the known function of astrocytes in cerebral innate immunity and our identification of significantly enriched immune response pathways, the circRNAs we identified may be associated with such key functions. While we did not detect recurrent differentially expressed circRNAs in the context of healthy controls or AD, we report for the first time circRNAs and their potential regulatory impact in a cell-specific and region-specific manner in aged subjects. These predicted regulatory network and pathway analyses may help provide new insights into transcriptional regulation in the brain.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4670-5) contains supplementary material, which is available to authorized users.

Oligomeric amyloid β preferentially targets neuronal and not glial mitochondrial-encoded mRNAs

INTRODUCTION

Our laboratories have demonstrated that accumulation of oligomeric amyloid β (OAβ) in neurons is an essential step leading to OAβ-mediated mitochondrial dysfunction.

METHODS

Alzheimer's disease (AD) and matching control hippocampal neurons, astrocytes, and microglia were isolated by laser-captured microdissection from the same subjects, followed by whole-transcriptome sequencing. Complementary in vitro work was performed in OAβ-treated differentiated SH-SY5Y, followed by the use of a novel CoQ₁₀ analogue for protection. This compound is believed to be effective both in suppressing reactive oxygen species and also functioning in mitochondrial electron transport.

RESULTS

We report decreases in the same mitochondrial-encoded mRNAs in Alzheimer's disease laser-captured CA1 neurons and in OAβ-treated SH-SY5Y cells, but not in laser-captured microglia and astrocytes. Pretreatment with a novel CoQ₁₀ analogue, protects neuronal mitochondria from OAβ-induced mitochondrial changes.

DISCUSSION

Similarity of expression changes in neurons from Alzheimer's disease brain and neuronal cells treated with OAβ, and the effect of a CoQ₁₀ analogue on the latter, suggests a pretreatment option to prevent OAβ toxicity, long before the damage is apparent.

Unveiling the multifunctional roles of hitherto known capping ligand oleic acid as blue emitter and sensitizer in tuning the emission colour to white in red-emitting phosphors

Multifunctional roles of oleic acid as capping ligand, blue emitter and sensitizer are revealed in obtaining white light emission from Eu³⁺-based red phosphors.

Phenotypic Variability and mTOR Pathway Gene Aberrations in Familial Tuberous Sclerosis

Tuberous sclerosis complex (TSC) is an autosomal dominant disorder that demonstrates variable severity, such that affected family members may have mild or severe disease. We performed exome and RNA sequencing of blood leukocytes from mild and severe cases across four families to identify mTOR pathway aberrations that may underlie phenotypic variability. In each family, we identified TSC1/TSC2 aberrations along with different mTOR pathway gene alterations, including base substitutions, deletions, and skewed allelic frequencies. Here, we describe the first reported DNA and RNA analysis of TSC families demonstrating mTOR pathway aberrations in mild and severe forms of the disease.

Laser-captured microglia in the Alzheimer's and Parkinson's brain reveal unique regional expression profiles and suggest a potential role for hepatitis B in the Alzheimer's brain

Expression array data from dozens of laboratories, including our own, show significant changes in expression of many genes in Alzheimer's disease (AD) patients compared with normal controls. These data typically rely on brain homogenates, and information about transcripts specific to microglia and other central nervous system (CNS) cell types, which far outnumber microglia-specific transcripts, is lost. We therefore used single-cell laser capture methods to assess the full range of microglia-specific expression changes that occur in different brain regions (substantia nigra and hippocampus CA1) and disease states (AD, Parkinson's disease, and normal controls). Two novel pathways, neuronal repair and viral processing were identified. Based on KEGG analysis (Kyoto Encyclopedia of Genes and Genomes, a collection of biological pathways), one of the most significant viruses was hepatitis B virus (HBV) (false discovery rate < 0.00000001). Immunohistochemical analysis using HBV-core antibody in HBV-positive control, amnestic mild cognitive impairment, and HBV-positive AD cases show increased HBV immunoreactivity as disease pathology increases. These results are the first, to our knowledge, to show regional differences in human microglia. In addition, these data reveal new functions for microglia and suggest a novel risk factor for AD.

ANK1 is up-regulated in laser captured microglia in Alzheimer's brain; the importance of addressing cellular heterogeneity

Recent epigenetic association studies have identified a new gene, ANK1, in the pathogenesis of Alzheimer’s disease (AD). Although strong associations were observed, brain homogenates were used to generate the data, introducing complications because of the range of cell types analyzed. In order to address the issue of cellular heterogeneity in homogenate samples we isolated microglial, astrocytes and neurons by laser capture microdissection from CA1 of hippocampus in the same individuals with a clinical and pathological diagnosis of AD and matched control cases. Using this unique RNAseq data set, we show that in the hippocampus, ANK1 is significantly (p<0.0001) up-regulated 4-fold in AD microglia, but not in neurons or astrocytes from the same individuals. These data provide evidence that microglia are the source of ANK1 differential expression previously identified in homogenate samples in AD.

Abstract 3389: Integrated genomic analyses reveal frequent TERT aberrations in acral melanoma

Genomic analyses of cutaneous melanoma (CM) have yielded biological and therapeutic insights, but understanding of non-ultraviolet (UV)-derived CMs remains limited. Deeper analysis of acral lentiginous melanoma (ALM), a rare sun-shielded melanoma subtype associated with worse survival than CM, is needed to delineate non-UV oncogenic mechanisms. We thus performed comprehensive genomic and transcriptomic analysis of 34 ALM patients. Unlike CM, somatic alterations were dominated by structural variation and absence of UV-derived mutation signatures. Only 38% of patients demonstrated driver BRAF/NRAS/NF1 mutations. Contrasting with CM, we observed PAK1 copy gains in 15% of patients, and somatic TERT translocations, copy gains, and missense and promoter mutations, or germline events, in 41% of patients. We further show that in vitro TERT inhibition has cytotoxic effects on primary ALM cells. These findings provide insight into the role of TERT in ALM tumorigenesis, and reveal preliminary evidence that TERT inhibition represents a potential therapeutic strategy in ALM.

Citation Format: Winnie S. Liang, William Hendricks, Jeffrey Kiefer, Jessica Schmidt, Shobana Sekar, John Carpten, David W. Craig, Jonathan Adkins, Lori Cuyugan, Zarko Manojlovic, Rebecca F. Halperin, Adrienne Helland, Sara Nasser, Christophe Legendre, Laurence H. Hurley, Karthigayini Sivaprakasam, Douglas B. Johnson, Holly Crandall, Klaus J. Busam, Victoria Zismann, Valerie De Luca, Jeeyun Lee, Aleksandar Sekulic, Charlotte E. Ariyan, Jeffrey Sosman, Jeffrey Trent. Integrated genomic analyses reveal frequent TERT aberrations in acral melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3389. doi:10.1158/1538-7445.AM2017-3389

Integrated genomic analyses reveal frequent TERT aberrations in acral melanoma

Genomic analyses of cutaneous melanoma (CM) have yielded biological and therapeutic insights, but understanding of non-ultraviolet (UV)-derived CMs remains limited. Deeper analysis of acral lentiginous melanoma (ALM), a rare sun-shielded melanoma subtype associated with worse survival than CM, is needed to delineate non-UV oncogenic mechanisms. We thus performed comprehensive genomic and transcriptomic analysis of 34 ALM patients. Unlike CM, somatic alterations were dominated by structural variation and absence of UV-derived mutation signatures. Only 38% of patients demonstrated driver BRAF/NRAS/NF1 mutations. In contrast with CM, we observed PAK1 copy gains in 15% of patients, and somatic TERT translocations, copy gains, and missense and promoter mutations, or germline events, in 41% of patients. We further show that in vitro TERT inhibition has cytotoxic effects on primary ALM cells. These findings provide insight into the role of TERT in ALM tumorigenesis and reveal preliminary evidence that TERT inhibition represents a potential therapeutic strategy in ALM.

Anisotropic optical and conductive properties of oriented 1D-nanoparticle thin films made by spray-assisted self-assembly

We report on the fabrication of oriented anisotropic metal nanoparticle thin films made by Grazing Incidence Spraying (GIS) and on the anisotropic plasmonic properties of the resulting thin films. Gold nanorods of two different aspect ratios and silver nanowires were self-assembled as a uniaxially aligned monolayer with the GIS approach. In particular, we examine the influence of the nanowire/nanorod length and diameter on the degree of ordering determined by electron microscopy pictures. Furthermore, we show that the anisotropy of the optical properties (probed by polarized UV-visible-near infrared spectroscopy) strongly depend on the quality of alignment. The prepared monolayer thin films have an orientation order parameter of up to 0.83 for silver nanowires, which is reflected in an optical anisotropy of 0.57 in the UV-visible and 0.76 in the near infrared through the selective excitation of transverse and longitudinal surface plasmon resonance modes. The electronic transport in oriented silver nanowire monolayers is also shown to be highly directional, with the sheet resistance varying over almost an order of magnitude depending on the transport direction. Such anisotropic conductive plasmonic thin films may find applications in various fields like biochemical sensing, energy transport and harvesting or optoelectronic devices.

Abstract LB-176: Identification of mutations in histone modification genes in Hodgkin lymphoma

Background: Understanding genetic aberrations in cancer has led to discoveries of new targets for cancer therapies. The genomic landscape of Hodgkin lymphoma (HL) has not been fully described.

Methods: We performed targeted next generation sequencing (NGS) on 13 archival tumor samples from patients with relapsed/refractory HL treated in the phase I clinical trial with the mTOR inhibitor sirolimus and the HDAC inhibitor vorinostat using the Foundation One NGS panel (Foundation One, Foundation Medicine, MA). Subsequently, we performed whole exome and RNA sequencing on pre- and post-treatment tumor biopsies from 3 patients treated in the same study.

Results: In archival samples from 13 HL patients tested using the Foundation One panel, a total of 21 gene aberrations across 13 genes were detected; 12 (92%) tumor samples had mutations in genes involved in immune response, apoptosis, and cell proliferation pathways (SOCS1, PIM1, MCL1, BRCA1, TP53, TNFAIP3, B2M, XPO1, BCL6) and 7 (54%) samples had mutations in DNA repair pathway genes (TP53, BRCA1, ATM, PIM1). In addition, whole exome and RNA sequencing of pre- and post-treatment tumor and germline (peripheral blood mononuclear cells) samples from HL patients treated with sirolimus and vorinostat (complete response, n = 1; stable disease for 3 months, n = 1; progression, n = 1) identified missense point mutations in key histone modification genes not included in the Foundation One panel, including HDAC8 (histone deacetylase 8), JMJD1C (jumonji domain containing 1C), and KDM2A (lysine-specific demethylase 2A) in the patient who progressed on therapy. This same patient additionally had a B2M missense mutation (M1R) affecting the same residue as the B2M event (M1I) identified in the archival cohort. Furthermore, there was a trend towards increased burden of molecular aberrations (median, 67 aberrations) in pre- and post- tumor samples of the patient who progressed compared to the other 2 patients (median, 6 aberrations), who did not progress.

Conclusion: While analysis of additional HL specimens is needed, our data suggest that testing for molecular aberrations with NGS is feasible and somatic missense mutations in HDAC8, JMJD1C, and KDM2A may be associated with lack of clinical response to sirolimus and vorinostat.

Citation Format: Winnie S. Liang, Bodour Salhia, Adrienne Helland, Shobana Sekar, Ignacio Garrido-Laguna, Michelle Fanale, Yasuhiro Oki, Jason R. Westin, R. Eric Davis, Funda Meric-Bernstam, Filip Janku. Identification of mutations in histone modification genes in Hodgkin lymphoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-176. doi:10.1158/1538-7445.AM2015-LB-176

Evidence of a two-step process and pathway dependency in the thermodynamics of poly(diallyldimethylammonium chloride)/poly(sodium acrylate) complexation

Recent studies have pointed out the importance of polyelectrolyte assembly in the elaboration of innovative nanomaterials. Beyond their structures, many important questions on the thermodynamics of association remain unanswered. Here, we investigate the complexation between poly(diallyldimethylammonium chloride) (PDADMAC) and poly(sodium acrylate) (PANa) chains using a combination of three techniques: isothermal titration calorimetry (ITC), static and dynamic light scattering and electrophoresis. Upon addition of PDADMAC to PANa or vice-versa, the results obtained by the different techniques agree well with each other, and reveal a two-step process. The primary process is the formation of highly charged polyelectrolyte complexes of size 100 nm. The secondary process is the transition towards a coacervate phase made of rich and poor polymer droplets. The binding isotherms measured are accounted for using a phenomenological model that provides the thermodynamic parameters for each reaction. Small positive enthalpies and large positive entropies consistent with a counterion release scenario are found throughout this study. Furthermore, this work stresses the importance of the underestimated formulation pathway or mixing order in polyelectrolyte complexation.

Alzheimer's disease is associated with altered expression of genes involved in immune response and mitochondrial processes in astrocytes

Alzheimer's disease (AD) is characterized by deficits in cerebral metabolic rates of glucose in the posterior cingulate (PC) and precuneus in AD subjects, and in APOEε4 carriers, decades before the onset of measureable cognitive deficits. However, the cellular and molecular basis of this phenotype remains to be clarified. Given the roles of astrocytes in energy storage and brain immunity, we sought to characterize the transcriptome of AD PC astrocytes. Cells were laser capture microdissected from AD (n = 10) and healthy elderly control (n = 10) subjects for RNA sequencing. We generated >5.22 billion reads and compared sequencing data between controls and AD patients. We identified differentially expressed mitochondria-related genes including TRMT61B, FASTKD2, and NDUFA4L2, and using pathway and weighted gene coexpression analyses, we identified differentially expressed immune response genes. A number of these genes, including CLU, C3, and CD74, have been implicated in beta amyloid generation or clearance. These data provide key insights into astrocyte-specific contributions to AD, and we present this data set as a publicly available resource.

Poly(ethylene) glycol-capped silver and magnetic nanoparticles: synthesis, characterization, and comparison of bactericidal and cytotoxic effects

Silver and magnetic (Fe3O4) nanoparticles have attracted wide attention as novel antimicrobial agents due to their unique chemical and physical properties. In order to study the comparative effects on antibacterial and animal cytotoxicity, Staphylococcus aureus and NIH 3T3 fibroblasts were used, respectively. Both nanoparticles were synthesized via a novel matrix-mediated method using poly(ethylene) glycol. Formation of silver nanoparticles was confirmed by fluorescence and ultraviolet-visible spectroscopic techniques. The poly(ethylene) glycol-coated silver and Fe3O4 nanoparticles were characterized by scanning electron microscope, transmission electron microscope, zeta potential, particle size analysis, Fourier-transform infrared, X-ray diffraction, and X-ray photoelectron spectroscopy. The antimicrobial results indicate that both poly(ethylene) glycol-coated silver and Fe3O4 nanoparticles inhibited S. aureus growth at the concentrations of 5 and 10 µg/mL at all time points without showing any significant cytotoxicity on NIH 3T3 fibroblasts. The particle size of both the poly(ethylene) glycol-coated silver and Fe3O4 nanoparticles dominated in the range 10-15 nm, obtained by particle size analyzer. The poly(ethylene) glycol coating on the particles showed less aggregation of nanoparticles, as observed by scanning electron microscope and transmission electron microscope. The overall obtained results indicated that these two nanoparticles were stable and could be used to develop a magnetized antimicrobial scaffolds for biomedical applications.

A novel cross-linked human amniotic membrane for corneal implantations

The aim of this study was to evaluate the efficacy of Al2(SO4)3 cross-linked human amniotic membrane for ocular surface reconstruction using tissue culture techniques. The human amniotic membrane was cross-linked with Al2(SO4)3, and the cross-linked human amniotic membrane was characterized for its mechanical properties, percentage of swelling in water, sterility, infrared spectroscopy and scanning electron microscopy. The potential of cross-linked human amniotic membrane to support the attachment and proliferation of corneal limbal epithelial cells was assessed in vitro, using static culture system. About 125% increase in the tensile strength was observed in the cross-linked human amniotic membrane compared to human amniotic membrane. Infrared spectroscopy studies have confirmed the cross-linking of human amniotic membrane with Al2(SO4)3. The cross-linked human amniotic membrane was found to be sterile up to 1 year. In culture studies, confluent sheets of epithelial cells were seen at the end of 14th day resembling the morphological features of limbal epithelia. The cross-linked human amniotic membrane has exhibited improved mechanical properties, and the tissue culture studies have shown its feasibility to be used as a limbal transplant. It was concluded that the crosslinked human amniotic membrane with its improved mechanical properties could be used on par with human amniotic membrane.

Subchronic memantine induced concurrent functional disconnectivity and altered ultra-structural tissue integrity in the rodent brain: revealed by multimodal MRI

BACKGROUND

An effective NMDA antagonist imaging model may find key utility in advancing schizophrenia drug discovery research. We investigated effects of subchronic treatment with the NMDA antagonist memantine by using behavioural observation and multimodal MRI.

METHODS

Pharmacological MRI (phMRI) was used to map the neuroanatomical binding sites of memantine after acute and subchronic treatment. Resting state fMRI (rs-fMRI) and diffusion MRI were used to study the changes in functional connectivity (FC) and ultra-structural tissue integrity before and after subchronic memantine treatment. Further corroborating behavioural evidences were documented.

RESULTS

Dose-dependent phMRI activation was observed in the prelimbic cortex following acute doses of memantine. Subchronic treatment revealed significant effects in the hippocampus, cingulate, prelimbic and retrosplenial cortices. Decreases in FC amongst the hippocampal and frontal cortical structures (prelimbic, cingulate) were apparent through rs-fMRI investigation, indicating a loss of connectivity. Diffusion kurtosis MRI showed decreases in fractional anisotropy and mean diffusivity changes, suggesting ultra-structural changes in the hippocampus and cingulate cortex. Limited behavioural assessment suggested that memantine induced behavioural effects comparable to other NMDA antagonists as measured by locomotor hyperactivity and that the effects could be reversed by antipsychotic drugs.

CONCLUSION

Our findings substantiate the hypothesis that repeated NMDA receptor blockade with nonspecific, noncompetitive NMDA antagonists may lead to functional and ultra-structural alterations, particularly in the hippocampus and cingulate cortex. These changes may underlie the behavioural effects. Furthermore, the present findings underscore the utility and the translational potential of multimodal MR imaging and acute/subchronic memantine model in the search for novel disease-modifying treatments for schizophrenia.

Preparation and evaluation of biocomposites as wound dressing material

Collagen was isolated from the chrome containing leather waste (CCLW) which is a major solid waste in leather industry. Composite films were made using sago starch (SG), soya protein (SY), and collagen (C) and were cross linked with glutaraldehyde (G).The films prepared were characterized for their physico chemical properties like tensile strength, infrared spectra, thermogravimetric analysis, surface morphology, and water absorption studies. Better mechanical properties and surface morphology were observed for SG-SY-G-C films compared to other films prepared using collagen. The composite films prepared were used as wound dressing material on the experimental wounds of rats and healing pattern was evaluated using planimetric, biochemical, and histopathological studies. These studies have revealed better wound healing capacity of SG-SY-G-C film and utilization of CCLW in the preparation of value added product like wound dressing material.

Evaluation of biocomposite films containing alginate and sago starch impregnated with silver nano particles

In recent years, the metal nanoparticles/polymer composites have created lot of attraction due to their wide range of applications. In the present study, the composite films of alginate (AL) and sago starch (SG) impregnated with silver nano particles (AgNP) with and without antibiotic gentamicin (G) were prepared by solvent casting method. The films prepared were characterized for thermo gravimetric analysis, SEM, TEM and mechanical properties and the results have shown the composite nature of the films. AL-SG-AgNP and AL-SG-AgNP-G composites were used as wound dressing materials in experimental wounds of rats. The healing pattern of the wounds was evaluated by planimetric studies, macroscopic observations, biochemical studies and histopathological observations. The results have shown faster healing pattern in the wounds treated with AL-SG-AgNP and AL-SG-AgNP-G composites compared to untreated control. This study revealed that AL-SG-AgNP film might be a potential and economical wound dressing material.

Preparation, characterization and evaluation of biocomposite films containing chitosan and sago starch impregnated with silver nanoparticles

The positive attributes of excellent biocompatibility and biodegradability of biopolymers with versatile biological activities have provided ample opportunities for further development of functional biomaterials of high potential in various fields. The biopolymers used in this study, i.e. chitosan and sago starch are abundantly available in nature and can be used in various biomedical applications. In the present study, the composite films of chitosan (Ch) and sago starch (SG) impregnated with silver nanoparticles (AgNP) with and without antibiotic gentamicin (G) were prepared by solvent casting method. The films prepared were characterized for their physic-chemical properties using conventional methods. The results obtained showed that with the increase of chitosan content in the composite results in decrease in its water absorption capacity. The FTIR and SEM studies have shown the composite nature of the films prepared. Ch-SG-AgNP and Ch-SG-AgNP-G composites were used as wound dressing materials in experimental wounds of rats. The healing pattern of the wounds was evaluated by planimetric studies, macroscopic observations, biochemical studies and histopathological observations. The results have shown faster healing pattern in the wounds treated with Ch-SG-AgNP and Ch-SG-AgNP-G composites compared to untreated control. This study suggests that Ch-SG-AgNP film may be a potential candidate as a dressing material for wound healing applications.

Fabrication of novel biofibers by coating silk fibroin with chitosan impregnated with silver nanoparticles

Nanoparticle based agents often applied as coatings on biomaterials have shown promise in delivering the improved sterility against variety of microbes. In the present study, silk fibers (SF) were coated with chitosan impregnated with silver nanoparticles (Ag-C-SF). These Ag-C-SF fibers were characterized using scanning electron microscopy (SEM) with energy dispersive X-ray analysis, atomic force microscopy (AFM), Infra Red spectroscopy, Thermogravimetric Analysis and Microbiological assay techniques. AFM studies have confirmed the nano sized silver particles in chitosan solution; SEM pictures have exhibited the coating of chitosan along with silver nanoparticles on the silk fibroin. The modified fibers have also shown anti-microbial activity and improved thermal stability. The Ag-C-SF fibers may be explored as wound dressing and tendon reconstruction material in future.

7-Meth-oxy-3,4-dihydro-naphthalen-1(2H)-one

In the title compound, C(11)H(12)O(2), the six-membered ketone ring fused to the 7-meth-oxy benzene ring adopts a slightly distorted envelope configuration with the central methyl-ene C atom being the flap. The crystal packing is stabilized by weak inter-molecular C-H⋯O and C-H⋯π inter-actions, which lead to supra-molecular layers in the bc plane.

Magnetic nanowires generated via the waterborne desalting transition pathway

We report a simple and versatile waterborne synthesis of magnetic nanowires following the innovative concept of electrostatic "desalting transition". Highly persistent superparamagnetic nanowires are generated from the controlled assembly of oppositely charged nanoparticles and commercially available polyelectrolytes. The wires have diameters around 200 nm and lengths between 1 μm and 0.5 mm, with either positive or negative charges on their surface. Beyond, we show that this soft-chemistry assembly approach is a general phenomenon independent of the feature of the macromolecular building blocks, opening significant perspectives for the design of multifunctional materials.

Photoinduced electron transfer from phycoerythrin to colloidal metal semiconductor nanoparticles

Phycoerythrin is a water soluble pigment which absorbs in the visible region at 563 nm. The interaction of phycoerythrin with colloidal metal semiconductors was studied by absorption, FT-IR and fluorescence spectroscopy. Phycoerythrin adsorbed strongly on the surface of TiO(2) nanoparticles, the apparent association constant for the association between colloidal metal-TiO(2) nanoparticles and phycoerythrin was determined from fluorescence quenching data. The free energy change (DeltaG(et)) for electron transfer process has been calculated by applying Rehm-Weller equation.

Cyanobacterial chlorophyll as a sensitizer for colloidal TiO2

Chlorophyll has been extracted from cyanobacteria. The adsorption of chlorophyll on the surface of colloidal TiO(2) through electrostatic interaction was observed. The apparent association constant (K(app)) of chlorophyll-TiO(2) obtained from absorption spectra is 3.78x10(4)M(-1). The K(app) value of chlorophyll-TiO(2) as determined from fluorescence spectra is 1.81x10(4)M(-1), which matches well with that determined from the absorption spectra changes. These data indicate that there is an interaction between chlorophyll and colloidal TiO(2) nanoparticle surface. The dynamics of photoinduced electron transfer from chlorophyll to the conduction band of colloidal TiO(2) nanoparticle has been observed and the mechanism of electron transfer has been confirmed by the calculation of free energy change (DeltaG(et)) by applying Rehm-Weller equation as well as energy level diagram. Lifetime measurements gave the rate constant (k(et)) for electron injection from the excited state chlorophyll into the conduction band of TiO(2) is 4.2x10(8)s(-1).

Growth of hydroxyapatite on physiologically clotted fibrin capped gold nanoparticles

The growth of hydroxyapatite (HAp) on physiologically clotted fibrin (PCF)-gold nanoparticles is presented for the first time by employing a wet precipitation method. Fourier transform infrared (FTIR) spectroscopy confirmed the characteristic functionalities of PCF and HAp in the PCF-Au-HAp nanocomposite. Scanning electron microscopy (SEM) images have shown cuboidal nanostructures having a size in the range of 70-300 nm of HAp, whereas 2-50 nm sized particles were visualized in high-resolution transmission electron microscopy (TEM). Energy-dispersive x-ray (EDX) and x-ray diffraction (XRD) studies have confirmed the presence of HAp. These results show that gold nanoparticles with PCF acted as a matrix for the growth of HAp, and that PCF-Au-HAp nanocomposite is expected to have better osteoinductive properties.

Prenatal diagnosis of complete heart block

Two cases of complete heart block diagnosed prenatally are presented. Proper evaluation of such cases by fetal echocardiography is necessary. In the absence of obstetric complication, vaginal delivery of such cases can be expected with biophysical and biochemical monitoring of the fetus in a tertiary care center.