Status of disinfection byproducts research in India

India faces high incidents of waterborne disease outbreaks owing to their limited access to safe drinking water. In many ways, the effort to improve the quality of drinking water is performed, and it has been keenly monitored. Among those, the disinfection of drinking water is considered a necessary and important step as it controls the microbial population. Chlorination is the most practiced (greater than 80%) disinfection process in India, and it is known to generate various disinfection byproducts (DBPs). Although the toxicity and trend of DBPs are regularly monitored and investigated in most countries, still in India, the research is at the toddler level. This review summarizes i) the status of drinking water disinfection in India, ii) types of disinfection processes in centralized water treatment plants, iii) concentrations and occurrence patterns of DBPs in a different region of India, iv) a literature survey on the toxicity of DBPs, and v) removal methodologies or alternative technologies to mitigate the DBPs formation. Overall, this review may act as a roadmap to understand the trend of disinfection practices in India and their impacts on securing the goal of safe drinking water for all.

A deep learning approach to detect blood vessels in basal cell carcinoma

PURPOSE

Blood vessels called telangiectasia are visible in skin lesions with the aid of dermoscopy. Telangiectasia are a pivotal identifying feature of basal cell carcinoma. These vessels appear thready, serpiginous, and may also appear arborizing, that is, wide vessels branch into successively thinner vessels. Due to these intricacies, their detection is not an easy task, neither with manual annotation nor with computerized techniques. In this study, we automate the segmentation of telangiectasia in dermoscopic images with a deep learning U-Net approach.

METHODS

We apply a combination of image processing techniques and a deep learning-based U-Net approach to detect telangiectasia in digital basal cell carcinoma skin cancer images. We compare loss functions and optimize the performance by using a combination loss function to manage class imbalance of skin versus vessel pixels.

RESULTS

We establish a baseline method for pixel-based telangiectasia detection in skin cancer lesion images. An analysis and comparison for human observer variability in annotation is also presented.

CONCLUSION

Our approach yields Jaccard score within the variation of human observers as it addresses a new aspect of the rapidly evolving field of deep learning: automatic identification of cancer-specific structures. Further application of DL techniques to detect dermoscopic structures and handle noisy labels is warranted.

Modulating Androgen Receptor-Driven Transcription in Prostate Cancer with Selective CDK9 Inhibitors

Castration-resistant prostate cancers (CRPCs) lose sensitivity to androgen-deprivation therapies but frequently remain dependent on oncogenic transcription driven by the androgen receptor (AR) and its splice variants. To discover modulators of AR-variant activity, we used a lysate-based small-molecule microarray assay and identified KI-ARv-03 as an AR-variant complex binder that reduces AR-driven transcription and proliferation in prostate cancer cells. We deduced KI-ARv-03 to be a potent, selective inhibitor of CDK9, an important cofactor for AR, MYC, and other oncogenic transcription factors. Further optimization resulted in KB-0742, an orally bioavailable, selective CDK9 inhibitor with potent anti-tumor activity in CRPC models. In 22Rv1 cells, KB-0742 rapidly downregulates nascent transcription, preferentially depleting short half-life transcripts and AR-driven oncogenic programs. In vivo, oral administration of KB-0742 significantly reduced tumor growth in CRPC, supporting CDK9 inhibition as a promising therapeutic strategy to target AR dependence in CRPC.

Abstract 1771: Targeting oncogenic transcription in prostate cancer with a novel, oral bioavailable, and ultra-selective CDK9 inhibitor

Castration resistant prostate cancers (CRPCs) lose sensitivity to hormone therapy, but remain dependent on oncogenic transcription programs driven by the androgen receptor (AR) and other oncogenic transcription factors such as MYC. Using small molecule microarrays (SMMs), we screened HEK293 cellular lysates for compounds binding to exogenously expressed ARv7, a mutant splice form of AR that drives castration resistance. Although transcription factors like ARv7 and MYC are considered classically undruggable, SMMs are able to identify small molecule interactors of druggable co-factors and other proteins in complex with the target protein – in this case ARv7. SMM hits were triaged for the ability to selectively inhibit an AR dependent transcriptional reporter, and also for their ability to reduce proliferation in AR dependent tumor cells.

From this screen, we identified KI-ARv3, a potent and selective inhibitor of CDK9. CDK9 is a cyclin-dependent kinase (CDK) that functions primarily as a general co-factor in RNA Polymerase II (RNA Pol II) transcription elongation. CDK9 is a well-characterized and important cofactor for AR, MYC, and other oncogenic transcription factors. In prostate cancer, CDK9 has been shown to modulate and be required for AR-specific gene expression. More broadly, transcriptional CDK inhibitors including those selective for CDK9 have shown strong potential as therapeutic agents owing to their ability to selectively downregulate oncogenic transcription programs and target tumors addicted to transcription factors such as AR or MYC. However, as CDK9 also plays a global role in transcription, it is unclear whether there exists a sufficient therapeutic index for clinical benefit. Prior clinical investigation of transcriptional CDK inhibitors has also been confounded by off-target interactions with other kinases and especially other CDKs that also play important roles in transcription and the cell cycle.

We found that KI-ARv3 demonstrated excellent selectivity for CDK9 versus other CDKs and kinases, and further optimization of KI-ARv3 resulted in KB-00130742, an oral bioavailable CDK9 inhibitor with a biochemical IC50 of 15nM against CDK9 and greater than 50-fold selectivity for all profiled CDKs and greater than 100-fold selectivity against cell cycle CDKs. Both KI-ARv3 and KB-00130742 exhibited potent anti-tumor activity in CRPC models, as well as other models known to be dependent on MYC-driven transcription. In 22Rv1 CRPC cells, KB-00130742 rapidly downregulated nascent transcription, and preferentially depleted short half-life transcripts and AR driven oncogenic programs. In vivo, oral administration of KB-00130742 was well-tolerated and significantly reduced tumor growth in models of CRPC and leukemia. Overall these data support CDK9 inhibition using KB-00130742 as a therapeutic strategy to target AR dependence in CRPC and oncogenic transcription in other tumor types.

Citation Format: André Richters, David Freeman, Christina Lee, Florian Kabinger, Shelby Doyle, Becky Leifer, Peter Mikochik, Sajjeev Jagannathan, Jost Vrabic Koren, Kristen Karlin, Calla M. Olson, Christopher Wilfong, Charles Y. Lin, Doug Saffran, Joseph Vacca, Norbert Bischofberger, Marius Pop, Angela N. Koehler. Targeting oncogenic transcription in prostate cancer with a novel, oral bioavailable, and ultra-selective CDK9 inhibitor [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1771.

Random lasing from optical fibers with phase separated glass cores

A novel random laser, integrating a passive optical fiber with a phase separated aluminosilicate core-silica cladding as the feedback medium, is proposed and presented. The core exhibits greatly enhanced Rayleigh scattering, therefore requiring a significantly reduced length of scattering fiber (4 m) for lasing. With a Yb-doped fiber as the gain medium, the fiber laser operates at 1050 nm with low threshold power and possesses an output that can be amplified through conventional means. Furthermore, the laser was found to have a high degree of spatial coherence, spectral broadening with increasing input power, and temporal spectral variation. The facile setup and results herein pave the way for further study and applications based on low threshold random fiber lasers.

AP-1 activity induced by co-stimulation is required for chromatin opening during T cell activation

Activation of T cells is dependent on the organized and timely opening and closing of chromatin. Herein, we identify AP-1 as the transcription factor that directs most of this remodeling. Chromatin accessibility profiling showed quick opening of closed chromatin in naive T cells within 5 h of activation. These newly opened regions were strongly enriched for the AP-1 motif, and indeed, ChIP-seq demonstrated AP-1 binding at >70% of them. Broad inhibition of AP-1 activity prevented chromatin opening at AP-1 sites and reduced the expression of nearby genes. Similarly, induction of anergy in the absence of co-stimulation during activation was associated with reduced induction of AP-1 and a failure of proper chromatin remodeling. The translational relevance of these findings was highlighted by the substantial overlap of AP-1-dependent elements with risk loci for multiple immune diseases, including multiple sclerosis, inflammatory bowel disease, and allergic disease. Our findings define AP-1 as the key link between T cell activation and chromatin remodeling.

Direct Error-Driven Learning for Deep Neural Networks With Applications to Big Data

In this brief, heterogeneity and noise in big data are shown to increase the generalization error for a traditional learning regime utilized for deep neural networks (deep NNs). To reduce this error, while overcoming the issue of vanishing gradients, a direct error-driven learning (EDL) scheme is proposed. First, to reduce the impact of heterogeneity and data noise, the concept of a neighborhood is introduced. Using this neighborhood, an approximation of generalization error is obtained and an overall error, comprised of learning and the approximate generalization errors, is defined. A novel NN weight-tuning law is obtained through a layer-wise performance measure enabling the direct use of overall error for learning. Additional constraints are introduced into the layer-wise performance measure to guide and improve the learning process in the presence of noisy dimensions. The proposed direct EDL scheme effectively addresses the issue of heterogeneity and noise while mitigating vanishing gradients and noisy dimensions. A comprehensive simulation study is presented where the proposed approach is shown to mitigate the vanishing gradient problem while improving generalization by 6%.

Co-Stimulation–Induced AP-1 Activity is Required for Chromatin Opening During T Cell Activation

Activation of T cells is dependent on organized and timely opening and closing of chromatin. Herein, we identify AP-1 as the transcription factor that directs most of this remodeling. Chromatin accessibility profiling showed quick opening of closed chromatin in naïve T cells within 5 hours of activation. These newly open regions were strongly enriched for the AP-1 motif, and indeed, ChIP-seq demonstrated AP-1 binding at more than 70% of them. Broad inhibition of AP-1 activity prevented chromatin opening at AP-1 sites and reduced expression of nearby genes. Similarly, induction of anergy in the absence of co-stimulation during activation, was associated with reduced induction of AP-1 and a failure of proper chromatin remodeling. The translational relevance of these findings was highlighted by the substantial overlap of AP-1–dependent elements with risk loci for multiple immune diseases, most notably multiple sclerosis. Our findings define AP-1 as the key link between T cell activation and chromatin remodeling.

Microbiota-sensitive epigenetic signature predicts inflammation in Crohn's disease

Altered response to the intestinal microbiota strongly associates with inflammatory bowel disease (IBD); however, how commensal microbial cues are integrated by the host during the pathogenesis of IBD is not understood. Epigenetics represents a potential mechanism that could enable intestinal microbes to modulate transcriptional output during the development of IBD. Here, we reveal a histone methylation signature of intestinal epithelial cells isolated from the terminal ilea of newly diagnosed pediatric IBD patients. Genes characterized by significant alterations in histone H3-lysine 4 trimethylation (H3K4me3) showed differential enrichment in pathways involving immunoregulation, cell survival and signaling, and metabolism. Interestingly, a large subset of these genes was epigenetically regulated by microbiota in mice and several microbiota-sensitive epigenetic targets demonstrated altered expression in IBD patients. Remarkably though, a substantial proportion of these genes exhibited H3K4me3 levels that correlated with the severity of intestinal inflammation in IBD, despite lacking significant differential expression. Collectively, these data uncover a previously unrecognized epigenetic profile of IBD that can be primed by commensal microbes and indicate sensitive targets in the epithelium that may underlie how microbiota predispose to subsequent intestinal inflammation and disease.

AP-1 transcription factor remodels chromatin during T cell activation

Upon encountering an antigen, naïve T helper cells activate, differentiate into several lineages and contribute to immune response. Epigenetic changes at cytokine and other effector genes during activation have been described, but the underlying mechanism is not understood. We profiled open chromatin during human T cell activation using ATAC-Seq and identified regions of epigenetic changes genome-wide. Open chromatin correlated with expression at nearby genes, which were enriched for functions related to T cell activation and immune response. As AP-1 and NFAT motifs were enriched in these newly open chromatin regions, we profiled their binding using ChIP-Seq. AP-1 was present at the majority of activation-specific open chromatin regions, which were often co-bound by both transcription factors. Notably, super enhancer formation was associated with AP-1 binding and chromatin opening during T cell activation. We also found that autoimmune disease-associated SNPs were significantly enriched in the newly open chromatin regions. Our data suggest that AP-1 activity contributes to the formation of the activated T cell epigenome and that mutations at the activation-specific open chromatin regions may contribute to autoimmune diseases.

Genomic integration of Wnt/β-catenin and BMP/Smad1 signaling coordinates foregut and hindgut transcriptional programs

Digestive system development is orchestrated by combinatorial signaling interactions between endoderm and mesoderm, but how these signals are interpreted in the genome is poorly understood. Here we identified the transcriptomes of Xenopus foregut and hindgut progenitors, which are conserved with mammals. Using RNA-seq and ChIP-seq we show that BMP/Smad1 regulates dorsal-ventral gene expression in both the endoderm and mesoderm, whereas Wnt/β-catenin acts as a genome-wide toggle between foregut and hindgut programs. Unexpectedly, β-catenin and Smad1 binding were associated with both transcriptional activation and repression, with Wnt-repressed genes often lacking canonical Tcf DNA binding motifs, suggesting a novel mode of direct repression. Combinatorial Wnt and BMP signaling was mediated by Smad1 and β-catenin co-occupying hundreds of cis-regulatory DNA elements, and by a crosstalk whereby Wnt negatively regulates BMP ligand expression in the foregut. These results extend our understanding of gastrointestinal organogenesis and of how Wnt and BMP might coordinate genomic responses in other contexts.

CD28 co-stimulatory signaling and AP-1 transcription factor are involved in the establishment of open chromatin during T cell activation

Upon encountering an antigen, naïve T helper (Th) cells are activated, differentiate into several lineages and contribute to immune response. Epigenetic changes at several cytokine and other effector genes during activation has been described previously, but the mechanism behind these changes is not understood. Here, we have profiled open chromatin during human T cell activation using ATAC-Seq approach and identified the regions where epigenetic changes take place genome-wide. Open chromatin formation correlated with induction of gene expression at nearby genes. This gene set was also enriched for functions related to T cell activation and immune response in GO analysis. T cell activation requires antigen signaling via T cell receptor and co-stimulation via CD28 which in turn result in nuclear translocation of NFAT and AP-1 transcription factors. For this reason, we profiled genome-wide distribution of these proteins during activation by ChIP-Seq. Our results show that 73% of activation-induced open chromatin loci contain binding sites for AP-1, whereas 39% of them bind NFAT. Over 90 % of the binding sites for NFAT were shared with AP-1 binding sites. We and others have previously shown that the lack of co-stimulation results in reduction or delay of AP-1 translocation into the nucleus. In order to confirm the role of AP-1 in establishment of the open chromatin structure during activation we mapped open chromatin in the cells that were activated without co-stimulation. Our data showed that ATAC signal was reduced at the open chromatin sites bound by AP-1 in the absence of co-stimulation, suggesting that CD28 signaling and AP-1 transcription factor are involved in open chromatin formation during T cell activation.

Molecular chaperone GRP78 enhances aggresome delivery to autophagosomes to promote drug resistance in multiple myeloma

Despite the clinical benefit of the proteasome inhibitor bortezomib, multiple myeloma (MM) patients invariably relapse through poorly defined mechanisms. Myeloma cells inevitably develop chemoresistance that leads to disease relapse and patient-related deaths. Studies in tumor cell lines and biopsies obtained from patients refractory to therapy have revealed that myeloma cells adapt to stress by inducing expression of glucose-regulated protein 78 (GRP78), an endoplasmic reticulum (ER) chaperone with anti-apoptotic properties. Treatment of myeloma cells with bortezomib increased GRP78 levels and activated GRP78-dependent autophagy. Expression profiling indicated that GRP78-encoding HSPA5 was significantly upregulated in bortezomib-resistant cells. Co-treatment with the anti-diabetic agent metformin suppressed GRP78 and enhanced the anti-proliferative effect of bortezomib. Bortezomib treatment led to GRP78 co-localization with proteotoxic protein aggregates, known as aggresomes. Pharmacologic suppression, genetic ablation or mutational inactivation of GRP78 followed by bortezomib treatment led to the accumulation of aggresomes but impaired autophagy and enhanced anti-myeloma effect of bortezomib. GRP78 was co-immunoprecipitated with the KDEL receptor, an ER quality control regulator that binds proteins bearing the KDEL motif to mediate their retrieval from the Golgi complex back to the ER. Taken together, we demonstrate that inhibition of GRP78 functional activity disrupts autophagy and enhances the anti-myeloma effect of bortezomib.

Abstract A18: MicroRNA-29b replacement inhibits proteasomes and disrupts the aggresome-autophagy pathway to enhance the antimyeloma benefit of bortezomib

Purpose: The goal of the present study was to identify and functionally characterize novel microRNAs (miRNAs) that inhibit the ubiquitin+proteasome system (UPS) and also disrupt the aggresome+autophagy pathway for anti-myeloma benefit.

Background: Evading apoptosis is a cancer hallmark that remains a serious obstacle in current treatment approaches. Drug resistance accounts for the majority of tumor relapses and cancer-related deaths. Functional blockade of the UPS using targeted therapeutics has translated into clinical success and transformed the management of MM. However, drug resistance emerges through induction of the aggresome+autophagy pathway as a compensatory protein clearance mechanism leading to treatment failure, disease relapse and ultimately fatal outcome.

Experimental Procedures: Myeloma cells were exposed to the proteasome inhibitors bortezomib, carfilzomib or ixazomib to generate cells with acquired drug resistance. Genome-wide, microarray-based profiling was performed to identify miRNAs significantly deregulated in the drug-resistant myeloma cells relative to parental drug-naïve cells. Based upon the miRNA profiling, we identified a curated panel of miRNAs that were significantly reduced in drug-resistant cells. To determine the effect of individual miRNAs, synthetic miRNA replacements were transfected into myeloma cells. Individual miRNA replacements were also transfected into human embryonic kidney (HEK) cells that expressed a short-lived green fluorescent protein that is degraded by the proteasome. The effect of individual miRNAs on the UPS was then quantitated in HEK cells by confocal microscopy and fluorescent imaging.

Results: MiRNA-29b was significantly downregulated in the myeloma cells generated with acquired resistance to bortezomib, carfilzomib and ixazomib relative to the parental cells. MiRNA-29b was also downregulated in MM patient tumor cells relative to plasma cells form healthy individuals. MiRNA-29b targeted PSME4 which encodes the proteasome activator PA200. Transfection of synthetically-engineered miRNA-29b replacements reduced the viability of myeloma cells and patient tumor cells and synergistically enhanced the cytotoxic effect of proteasome inhibitors. The miRNA-29b replacement also reduced the growth of myeloma xenografts in mouse models in vivo. MiRNA-29b replacements decreased expression of PSME4 and the protein product PA200, a proteasome activator. Reduction in PA200 reduced the proteasome's chymotrypsin-like peptidase activity and inhibited ornithine decarboxylase turnover, a proteasome substrate degraded through Ub-independent mechanisms. Following proteasome inhibition, perinuclear aggregates of insoluble ubiquitinated proteins, termed aggresomes, accumulate and are degraded by the autophagy pathway. Importantly, in contrast to bortezomib, miRNA-29b replacement inhibited proteasome activity but did not induce the formation of perinuclear aggresomes or autophagosomes. Rather, immunofluorescence studies indicated that miRNA-29b replacement promoted the accumulation of small, ubiquitinated protein aggregates that were dispersed throughout the cytoplasm but were not transported by microtubules and were not coalesced into mature aggresomes. The ubiquitinated proteins also were not detected in autophagosomes.

Conclusions: MiRNA-29b replacement represents the first-in-class miRNA-based agent to inhibit proteasomes and uncouple the UPS from the aggresome-autophagy pathway. Taken together, our study highlights the potential of miRNA replacement therapy to synergistically enhance the anti-myeloma effect of PIs.

Citation Format: Sajjeev Jagannathan, Nikhil Vad, Mohamed Abdel-Malek, Ehsan Malek, James Driscoll. MicroRNA-29b replacement inhibits proteasomes and disrupts the aggresome-autophagy pathway to enhance the antimyeloma benefit of bortezomib. [abstract]. In: Proceedings of the AACR Special Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; Sep 20-23, 2014; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(17 Suppl):Abstract nr A18.

Abstract 153: Long non-coding RNAs deregulated in Multiple Myeloma impact therapeutic response to proteasome inhibitors

Multiple Myeloma (MM) is a complex disease that frequently leads to fatal outcome and accurate risk classification to optimize the choice of therapy may have impact on clinical outcomes. MM stratification based upon cytogenetic abnormalities and protein-coding gene expression does not adequately correlate with the depth or durability of therapeutic response. Therefore, the new class of molecular effectors, non-coding RNAs (ncRNAs), may enhance the basic understanding of myelomagenesis, drug resistance and provide better stratification of myeloma subtypes. NcRNAs include long ncRNAs (lncRNAs) and microRNAs (miRNAs) that may act as positive or negative regulators of gene expression to control cell proliferation, apoptosis and drug resistance. We hypothesized that lncRNAs commonly deregulated in the 3 resistant cell lines would have significant overlap to the deregulated lncRNA in MM patients. To investigate the role of lncRNAs in resistance to proteasome inhibitors (PIs), we compared global lncRNA profiling in drug-naïve cells to cells with acquired resistance to the PIs bortezomib, carfilzomib and ixazomib. RPMI 8226 cells resistant to each of the three PIs were generated through successive exposure to bortezomib, carfilzomib or ixazomib. Total RNA was isolated and genome-wide ncRNA expression profiling was performed using Affymetrix 3.0 microarray chips LncRNA expression profiles from drug-resistant cells were compared to that of drug-naïve cells treated with vehicle alone. MM patients’ bone marrow aspirates were obtained after UCCOM IRB-approval. Bioinformatic analysis identified a panel of 18 lncRNAs that were significantly (>100-fold) deregulated in all three drug-resistant cell lines relative to drug-naïve cells. Strikingly, the majority of the deregulated lncRNAs exhibited a similar expression pattern in all 3 PI-resistant cell lines (Figure 2a). RPMI 8226 cells carry a t(14,16) and none of the deregulated lncRNAs detected localized to chromosomes 14 or 16, suggestive of a cytogenetic-independent mechanism of drug resistance. We also identified lncRNAs deregulated in MM patient samples relative to plasma cells from healthy age-matched individuals. We found a significant overlap (>90%) between deregulated lncRNAs in PI-resistant cells and MM cells. The lncRNA COL4A-2A was upregulated >5,000-fold in resistant cells and displayed extensive sequence complementarity to miRNA-29 that was downregulated in resistant cells. Taken together, we identified a curated panel of deregulated lncRNAs in common within myeloma cells generated with acquired resistant to three different clinically-relevant proteasome inhibitors and MM patients. Further investigation is warranted to shed light on the role of these lncRNAs in the development of MM, to identify their targets and to define their role in drug resistance.

Note: This abstract was not presented at the meeting.

Citation Format: Ehsan Malek, Rebekah Karns, Anil G. Jegga, Sajjeev Jagannathan, Nikhil Vad, Mohamed A.Y Abdel Malek, James J. Driscoll. Long non-coding RNAs deregulated in Multiple Myeloma impact therapeutic response to proteasome inhibitors. [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 153. doi:10.1158/1538-7445.AM2015-153

Abstract 4242: Metformin suppresses GRP78-dependent PI3-Kinase activity in clonogenic side population to enhance the anti-myeloma benefit of bortezomib

Multiple myeloma (MM) patients invariably relapse through mechanisms that remain elusive. Disease recurrence after treatment suggests that rare, tumor-initiating subpopulations with chemoresistant phenotypes persist or emerge to propagate and mediate tumor regrowth. Stem cell-like side population (SP) cells were isolated from myeloma cell lines and patient samples and exhibited resistance to proteasome inhibitors relative to the main population (MP). SP cell-based high-throughput screening detected pharmacologics that enhanced the anti-proliferative effect of bortezomib and revealed the anti-diabetic agent metformin. Bortezomib treatment increased levels of the molecular chaperone glucose-regulated protein GRP78 but metformin co-treatment suppressed bortezomib-induced GRP78 upregulation. Bortezomib treatment also promoted GRP78 co-localization with the signal transducer phosphatidylinositol-3-kinase (PI3K) that activates cell growth and survival pathways. SP cells displayed greater levels of the PI3K product phosphatidylinositol (3,4,5)-trisphosphate (PIP3) and enhanced PI3K-mediated phosphorylation of protein kinase B/AKT compared to MP cells. Metformin treatment or knockdown of GRP78-encoding HSPA5 enhanced sensitivity to bortezomib preferentially in SP cells. Tumor growth was significantly delayed and overall survival prolonged after metformin co-treatment with bortezomib in mice injected with parental or SP cells. Taken together, the results support the pharmacologic repositioning of metformin to inhibit GRP78 induction in therapy-resistant cells and enhance the anti-myeloma benefit of bortezomib.

Note: This abstract was not presented at the meeting.

Citation Format: James J. Driscoll, Sajjeev Jagannathan, Mohamed AY Abdel Malek, Nikhil Vad, Ehsan Malek. Metformin suppresses GRP78-dependent PI3-Kinase activity in clonogenic side population to enhance the anti-myeloma benefit of bortezomib. [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 4242. doi:10.1158/1538-7445.AM2015-4242

Abstract 1462: Tandem genome-wide and functional screening reveals that MiRNA-29 regulates the proteasome activator PSME4 to promote therapeutic resistance in myeloma

MicroRNAs (miRNAs) are newly recognized, master regulators of the human genome and hence play key roles in cellular pathways that govern proliferation, differentiation and apoptosis during both physiologic and pathologic states. Accordingly, alterations in miRNA levels contribute to myriad diseases including human cancers. MiRNAs have rapidly attracted significant attention as agents with significant potential as diagnostics and therapeutics to improve the outcome of cancer patients. While proteasome inhibitors (PIs) such as bortezomib (Velcade, Millennium-Takeda) have transformed management of the invariably fatal disease multiple myeloma, therapeutic resistance inevitably emerges through mechanisms that remain elusive. A goal of these studies was to investigate the role of individual miRNAs in regulating functional activity of the ubiquitin+proteasome system. Genome-wide expression profiling was performed to identify differentially expressed miRNAs in the PI-resistant cells relative to drug-naive parental cells. A live-cell functional screen that employed a recombinant fluorescent probe comprised of a short-lived reporter bearing a destabilizing modification to promote constitutive proteasomal degradation was used to quantitate the effect of individual miRNAs. MiRNAs-29a/b/c were significantly reduced in the PI-resistant cells and these miRNAs negatively regulated PSME4 which expresses the proteasome activator PA200. Transfection of synthetically-engineered miRNA-29 replacements reduced PSME4 levels, promoted myeloma cell death and overcame drug resistance. Deletion of a nuclear localization signal (NLS) enriched the cytoplasmic distribution and enhanced the functional effect of miRNA-29 replacements. Doxycycline-induced expression of miRNA-29b or miRNA-29 variants that lacked the NLS also dramatically reduced the in vivo growth of subcutaneously injected myeloma tumor cells in NOD/SCID mice. We demonstrate that the loss of a tumor suppressive miRNA activates not only inherently oncogenic pathways to promote the generation of a cancer phenotype but also to promote therapeutic resistance to PIs. We provide a platform to perform a genome-wide interrogation of miRNAs and other non-coding RNAs that regulate the ubiquitin+proteasome system. The significant cytotoxic effect of miRNA-29 replacements observed using MM cell lines and myeloma patient samples as well as ability to reduce tumor growth in vivo validate miRNA-29 replacements as highly effective anti-cancer tools to overcome therapeutic resistance, promote tumor cell death and eventually improve patient outcome.

Citation Format: James J. Driscoll, Sajjeev Jagannathan. Tandem genome-wide and functional screening reveals that MiRNA-29 regulates the proteasome activator PSME4 to promote therapeutic resistance in myeloma. [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 1462. doi:10.1158/1538-7445.AM2014-1462

Abstract LB-140: The Hsp90 inhibitor ganetespib overcomes EGFR-based intratumoral heterogeneity to block glioma proliferation

Intratumoral heterogeneity is evident as distinct subpopulations of cancer cells within and between tumor lesions that profoundly impact therapeutic response and patient outcome. While the advent of targeted therapies to exploit a tumor's dependence on critical proliferative or survival pathways has significantly improved patient outcomes in a range of solid tumor types, it is also apparent that targeted therapeutics do not help all molecularly selected patients and even when clinical benefit is observed, it is often of limited duration. To address this question, we have explored the invariably fatal adult brain tumor glioblastoma multiforme (GBM). Heterogeneous forms of the epidermal growth factor receptor (EGFR) arise through amplification or mutation as signature pathogenetic events in this highly aggressive disease. While EGFR deregulation promotes tumor cell proliferation, drug resistance and tumor survival, functional blockade of the EGFR kinase activity alone does not achieve maximal therapeutic benefit. Since intratumoral heterogeneity represents a major impediment to the development of effective therapeutics in GBM, we sought to identify small molecules cytotoxic to glioma cells engineered to overexpress either wildtype (WT), constitutively active mutant EGFR-vIII, kinase-dead (KD) form or a basal level of EGFR-WT using a live cell-based, high-throughput screen (HTS) of ∼2,000 FDA-approved or bioactive compounds. Our screen revealed that the Hsp90 inhibitor ganetespib (STA-9090, Synta Pharmaceuticals, Lexington, MA) was highly cytotoxic (IC50 ∼20nM) to glioma cells that overexpressed each of the EGFR forms. Real-time measurements were then performed to demonstrate that ganetespib at nM concentrations reduced the proliferation of brain tumor cells expressing EGFR-WT, -vIII or KD forms, induced apoptosis and inhibited glioma migration. Ganetespib also potently reduced the proliferation of human GBM patient-derived tumor-initiating stem cells but not that of untransformed glial cells. Ganetespib effectively impaired the growth of subcutaneously implanted human brain tumor xenotransplants that expressed either EGFR-WT, -vIII or both EGFR forms placed in immunocompromised mice. In addition, ganetespib provided a survival benefit compared to untreated mice. The Hsp90 inhibitor ganetespib is a highly potent agent that impairs the growth-promoting functional kinase-dependent and independent activities of EGFR to overcome context-dependent intratumoral heterogeneity with potential benefits for GBM patients.

Citation Format: James J. Driscoll, Nitin S. Narayanan, Sajjeev Jagannathan. The Hsp90 inhibitor ganetespib overcomes EGFR-based intratumoral heterogeneity to block glioma proliferation. [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-140. doi:10.1158/1538-7445.AM2014-LB-140

Correlation of long non-coding RNA expression with metastasis, drug resistance and clinical outcome in cancer

The therapeutic response and clinical outcome of patients diagnosed with the same cancer type and that receive identical treatment is highly variable to reflect the genetic heterogeneity within tumor cells. Non-coding RNAs (ncRNAs) are recently discovered molecules that regulate eukaryotic gene expression and represent a significant advance towards a better understanding of the mechanisms that govern cellular growth. NcRNAs are essential for the proper regulation of cell proliferation and survival under physiologic conditions and are deregulated in many pathologies, e.g., human cancers. NcRNAs have been associated with cancer diagnosis, staging, treatment response, metastasis and survival and include distinct subtypes, e.g., long ncRNAs (lncRNAs) and microRNAs (miRNAs). LncRNAs have been linked to essential growth-promoting activities and their deregulation contributes to tumor cell survival. A prominent example is the Hox transcript antisense intergenic lncRNA, HOTAIR, that cooperates with the polycomb repressive complex to reprogram chromatin organization. HOTAIR expression is deregulated in a spectrum of cancers and HOTAIR expression correlates with patient survival. Here, we highlight emerging evidence that supports a role for lncRNAs in cancer with implications for the development of novel diagnostics and therapeutics.

MiR-29b replacement inhibits proteasomes and disrupts aggresome+autophagosome formation to enhance the antimyeloma benefit of bortezomib

Evading apoptosis is a cancer hallmark that remains a serious obstacle in current treatment approaches. Although proteasome inhibitors (PIs) have transformed management of multiple myeloma (MM), drug resistance emerges through induction of the aggresome+autophagy pathway as a compensatory protein clearance mechanism. Genome-wide profiling identified microRNAs (miRs) differentially expressed in bortezomib-resistant myeloma cells compared with drug-naive cells. The effect of individual miRs on proteasomal degradation of short-lived fluorescent reporter proteins was then determined in live cells. MiR-29b was significantly reduced in bortezomib-resistant cells as well as in cells resistant to second-generation PIs carfilzomib and ixazomib. Luciferase reporter assays demonstrated that miR-29b targeted PSME4 that encodes the proteasome activator PA200. Synthetically engineered miR-29b replacements impaired the growth of myeloma cells, patient tumor cells and xenotransplants. MiR-29b replacements also decreased PA200 association with proteasomes, reduced the proteasome's peptidase activity and inhibited ornithine decarboxylase turnover, a proteasome substrate degraded through ubiquitin-independent mechanisms. Immunofluorescence studies revealed that miR-29b replacements enhanced the bortezomib-induced accumulation of ubiquitinated proteins but did not reveal aggresome or autophagosome formation. Taken together, our study identifies miR-29b replacements as the first-in-class miR-based PIs that also disrupt the autophagy pathway and highlight their potential to synergistically enhance the antimyeloma effect of bortezomib.

Zero-sum two-player game theoretic formulation of affine nonlinear discrete-time systems using neural networks

In this paper, the nearly optimal solution for discrete-time (DT) affine nonlinear control systems in the presence of partially unknown internal system dynamics and disturbances is considered. The approach is based on successive approximate solution of the Hamilton-Jacobi-Isaacs (HJI) equation, which appears in optimal control. Successive approximation approach for updating control and disturbance inputs for DT nonlinear affine systems are proposed. Moreover, sufficient conditions for the convergence of the approximate HJI solution to the saddle point are derived, and an iterative approach to approximate the HJI equation using a neural network (NN) is presented. Then, the requirement of full knowledge of the internal dynamics of the nonlinear DT system is relaxed by using a second NN online approximator. The result is a closed-loop optimal NN controller via offline learning. A numerical example is provided illustrating the effectiveness of the approach.

MicroRNA theragnostics for the clinical management of multiple myeloma

Theragnostics represent cutting-edge, multi-disciplinary strategies that combine diagnostics with therapeutics in order to generate personalized therapies that improve patient outcome. In oncology, the approach is aimed at more accurate diagnosis of cancer, optimization of patient selection to identify those most likely to benefit from a specific therapy and to generate effective therapeutics that enhance patient survival. MicroRNAs (miRNAs) are master regulators of the human genome that orchestrate myriad cellular pathways to control growth during physiologic and pathologic conditions. Compelling evidence shows that miRNA deregulation promotes events linked to tumor initiation, metastasis and drug resistance as seen in multiple myeloma (MM), an invariably fatal hematologic malignancy. miRNAs are readily detected in body fluids, for example, serum, plasma, urine, as well as circulating tumor cells to demonstrate their potential as readily accessible, non-invasive diagnostic and prognostic biomarkers and potential therapeutics. Specific miRNAs are aberrantly expressed early in myelomagenesis and may more readily detect high-risk disease than current methods. Although only recently discovered miRNAs have rapidly advanced from preclinical studies to evaluation in human clinical trials. The development of miRNA theragnostics should provide widely applicable tools for the targeted delivery of personalized medicines to improve the outcome of patients with MM.

Brain microenvironment-induced reduction in microRNAs to promote metastatic tumor growth, drug resistance, and survival

e22030

Background: Brain metastases remain a serious obstacle that negatively impacts cancer patient survival. Most deaths due to cancer result from the progressive growth of metastatic, drug-resistant lesions. Moreover, the incidence of brain metastases is rising as a result of an aging population, superior imaging modalities, earlier cancer detection and more effective treatment of systemic disease. Methods: To investigate the role of the brain microenvironment in metastasis, tumor cells were co-cultured with astrocytes - the most abundant normal cell type in the metastatic brain tumor niche. This led to increased tumor cell viability, proliferation and chemoresistance. Microarray-based profiling was then performed to address the effect of the brain microenvironment on miRNA expression levels in tumor cells. Results: Profiling revealed that astrocyte co-culture reduced miRNAs-768-3p, 886-5p and 200c in tumor cells. Inhibition of miRNA-768-3p increased KRas expression, and a specific binding site was identified in the KRas 3’UTR and validated using a luciferase construct. miRNA-768-3p levels were reduced in patient-derived brain metastases relative to normal adult brain. Additionally, miRNA-768-3p was also lower in brain metastases compared to the primary tumors in matched paired samples. Our data demonstrates that the brain microenvironment modulates miRNA-768-3p in metastatic lesions to enhance KRas-mediated tumor survival and promote metastasis. Conclusions: The brain microenvironment regulates the expression of individual miRNAs in tumor cells to promote growth, survival and drug resistance. The brain microenvironment down-regulates the level of certain miRNAs to promote oncogenic signaling and tumor growth while our studies indicate that chemically-engineered miRNA mimics can restore the loss-of-function to reduce the viability of cancer cells. miRNA replacement therapy is a promising and novel therapeutic concept that could save thousands of patients from ineffective treatment, improve patient quality-of-life, overall survival and reduce the devastating impact of brain metastases on the healthcare system.

Abstract LB-277: Microenvironment-induced changes in miRNA levels promote brain metastasis, drug resistance and KRA expression

Brain metastases remain a serious obstacle that negatively impacts cancer patient survival. Nearly 180,000 patients in the U.S. are diagnosed annually with metastatic brain lesions, more than ten times the incidence of primary brain tumors such as glioblastoma. Brain metastases remain a challenging complication despite advances in surgical, chemo-radiation and targeted therapies. Most deaths due to cancer result from the progressive growth of metastatic, drug-resistant lesions. Moreover, the incidence of brain metastases is rising as a result of superior imaging modalities, earlier cancer detection and more effective treatment of systemic disease. To investigate the role of the brain microenvironment in metastasis, lung and breast tumor cells were co-cultured with astrocytes, the most abundant normal cell type in the metastatic brain tumor niche. Astrocyte co-culture led to increased tumor cell viability, proliferation and chemoresistance. After co-culture with astreocytes, tumor cells were then removed and total RNA was isolated. A panel of individual microRNAs (miRNAs) were identified that were reduced in tumor cells after co-culture. The rationale for developing miRNA therapeutic replacements is based upon the premise that aberrantly expressed miRNAs play a key role in controlling tumorigenesis, drug resistance and metastasis. Correcting these miRNA deficiencies through antagonisitc or replacement of miRNA function may provide a therapeutic benefit. Microarray-based profiling revealed that astrocyte co-culture reduced miRNAs-768-3p, 886-5p and 200c in the lung tumor cells. Vector-based forced expression of sequence complementary to miRNA768-3p or transfection of inhibitory miRNA-768-3p oligonucleotide inhibitors into tumor cells led to increased cell growth. Also, inhibition of miRNA-768-3p increased KRas expression, and a specific binding site was identified in the KRas 3′UTR was validated using a luciferase construct. Moreover, shRNA-mediated KRas knockdown reduced growth-promotion by the miRNA-768-3p inhibitor. MiRNA-768-3p levels were lower in tissue samples obtained from patients diagnosed with brain metastases relative to normal human adult brain tissue. In addition, the level of miRNA-768-3p was lower in tissue from patients diagnosed with brain metastases compared to the primary tumors in matched paired samples obtained from the same patient. The results demonstrate that the brain microenvironment modulates numerous miRNA, sush as miRNA-768-3p, in metastatic lesions to enhance KRas-mediated tumor growth and drug resistance and ultimately to promote brain metastasis. The therapeutic application of miRNA may allow for the rapid and coordinated manipulation of proteins that regualte multiple key intracellular pathways that promote tumorigenesis and metastasis.

Citation Format: James J. Driscoll, Arasakumar Subramani, Samer Alsidawi, Sajjeev Jagannathan, Kazutaka Sumita, Atsuo Sasaki, Ronald E. Warnick, Sean Lawler. Microenvironment-induced changes in miRNA levels promote brain metastasis, drug resistance and KRA expression. [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 LB-277. doi:10.1158/1538-7445.AM2013-LB-277

Abstract 1708: Metabolic regulation of the ubiquitin+proteasome system

The ubiquitin+proteasome system (UPS) is a highly complex network that maintains protein homeostasis and cell viability through the highly regulated and selective turnover of targeted proteins. The proteasome is the major intracellular protease in eukaryotes and serves as the catalytic core of the UPS. The cytotoxic effect of proteasome inhibition has been translated therapeutically to dramatically improve the overall survival of patients diagnosed with the plasma cell malignancy multiple myeloma (MM). Bortezomib has emerged as the standard-of-care therapy for MM to catapult the UPS into a position of prominence in cancer biology and drug development but significant obstacles remain since many patients do not respond to bortezomib, clinical responses are not sustained and drug resistance inevitably emerges through unknown mechanisms. Gene profiling was performed as an unbiased approach to address the precise molecular events that promote bortezomib-resistance. Results indicated that effectors of energy metabolism were differentially expressed in cells resistant to bortezomib. Subunits of the cellular energy sensor AMP-activated protein kinase (AMPK) were expressed at lower levels in resistant cells relative to the parental cells. Real-time, cell-based metabolic measurements demonstrated that bortezomib rapidly and dramatically reduced tumor cell oxygen-consumption while bortezomib-resistant cells were less sensitive to metabolic deregulation. Genetic ablation of the AMPKα1/α2 encoding-genes also reduced the effect of bortezomib to promote autophagosome formation as well as bortezomib-induced cytotoxicity. Similarly, knockout of the AMPK-substrate and autophagy-initiating kinase ULK1 also reduced bortezomib-induced autophagosome formation and cell death. Proteasome inhibition promoted ULK-1 association with the autophagosome initiators ATG13, FIP200 and beclin-1. The AMPK activator AICAR further enhanced bortezomib-induced cytotoxicity in myeloma, lymphoma, leukemic and solid tumor cells. Proteasome inhibitors induce AMPK+ULK-mediated autophagosome formation that is coupled to apoptosis and can be exploited as a novel anti-cancer therapeutic strategy.

Citation Format: James J. Driscoll, Sajjeev Jagannathan. Metabolic regulation of the ubiquitin+proteasome system. [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 1708. doi:10.1158/1538-7445.AM2013-1708

Standardization and assessment of cell culture media quantities in roller poly ethylene terephthalate bottles employed in the industrial rabies viral vaccine production

Vero cells are utilized for production of rabies vaccine. This study deals with the optimize quantity media require for the rabies vaccine production in the smooth roller surface. The rabies virus (Pasteur vaccine strain) is infected to monolayer of the various experimented bottles. To analyze the optimal quantity of media for the production of rabies viral harvest during the process of Vero cell derived rabies vaccine. The trials are started from 200 to 400 mL (PTARV-1, PTARV-2, PTARV-3, PTARV-4 and PTARV-5). The samples are taken in an appropriate time intervals for analysis of In Process Quality Control (IPQC) tests. The collected viral harvests are further processed to rabies vaccine in a pilot level and in addition to scale up an industrial level. Based on the evaluation the PTARV-2 (250 mL) show highly encouraging results for the Vero cell derived rabies vaccine production.

Predictive models of hepatotoxicity using gene expression data from primary rat hepatocytes

With the aim of evaluating the usefulness of an in vitro system for assessing the potential hepatotoxicity of compounds, the paper describes several methods of obtaining mathematical models for the prediction of compound-induced toxicity in vivo. These models are based on data derived from treating rat primary hepatocytes with various compounds, and thereafter using microarrays to obtain gene expression 'profiles' for each compound. Predictive models were constructed so as to reduce the number of 'probesets' (genes) required, and subjected to rigorous cross-validation. Since there are a number of possible approaches to derive predictive models, several distinct modelling strategies were applied to the same data set, and the outcomes were compared and contrasted. While all the strategies tested showed significant predictive capability, it was interesting to note that the different approaches generated models based on widely disparate probesets. This implies that while these models may be useful in ascribing relative potential toxicity to compounds, they are unlikely to provide significant information on underlying toxicity mechanisms. Improved predictivity will be obtained through the generation of more comprehensive gene expression databases, covering more 'toxicity space', and by the development of models that maximize the observation, and combination, of individual differences between compounds.