Partially Ordered Statistics Demapping for Multi-Dimensional Modulation Formats

We propose a very low-complexity and high-performance algorithm for soft-demapping of multi-dimensional modulation formats. We assess its performance over the linear channel for four 8D formats, generated using binary arithmetics. This solution outperforms current algorithms in terms of complexity without loss in performances.Comment: Accepted in the Optical Fiber Communications Conference (OFC) 201

Inhibition of COP9-signalosome (CSN) deneddylating activity and tumor growth of diffuse large B-cell lymphomas by doxycycline

In searching for small-molecule compounds that inhibit proliferation and survival of diffuse large B-cell lymphoma (DLBCL) cells and may, therefore, be exploited as potential therapeutic agents for this disease, we identified the commonly used and well-tolerated antibiotic doxycycline as a strong candidate. Here, we demonstrate that doxycycline inhibits the growth of DLBCL cells both in vitro and in mouse xenograft models. In addition, we show that doxycycline accumulates in DLBCL cells to high concentrations and affects multiple signaling pathways that are crucial for lymphomagenesis. Our data reveal the deneddylating activity of COP-9 signalosome (CSN) as a novel target of doxycycline and suggest that doxycycline may exert its effects in DLBCL cells in part through a CSN5-HSP90 pathway. Consistently, knockdown of CSN5 exhibited similar effects as doxycycline treatment on DLBCL cell survival and HSP90 chaperone function. In addition to DLBCL cells, doxycycline inhibited growth of several other types of non-Hodgkin lymphoma cells in vitro. Together, our results suggest that doxycycline may represent a promising therapeutic agent for DLBCL and other non-Hodgkin lymphomas subtypes

Anticancer Activity of the Cholesterol Exporter ABCA1 Gene

The ABCA1 protein mediates the transfer of cellular cholesterol across the plasma membrane to apolipoprotein A-I. Loss-of-function mutations in the ABCA1 gene induce Tangier disease and familial hypoalphalipoproteinemia, both cardiovascular conditions characterized by abnormally low levels of serum cholesterol, increased cholesterol in macrophages, and subsequent formation of vascular plaque. Increased intracellular cholesterol levels are also frequently found in cancer cells. Here, we demonstrate anticancer activity of ABCA1 efflux function, which is compromised following inhibition of ABCA1 gene expression by oncogenic mutations or cancer-specific ABCA1 loss-of-function mutations. In concert with elevated cholesterol synthesis found in cancer cells, ABCA1 deficiency allows for increased mitochondrial cholesterol, inhibits release of mitochondrial cell death-promoting molecules, and thus facilitates cancer cell survival, suggesting that elevated mitochondrial cholesterol is essential to the cancer phenotype

Patterns in Dysregulated, Non-mutated Cancer Mediator Gene Expression

Thesis (Ph.D.)--University of Rochester. School of Medicine & Dentistry. Dept. of Biomedical Genetics, 2017.Genes dysregulated synergistically in response to oncogenic Ras and p53 mutations in young adult mouse colon (YAMC) cells are critical to the cancer phenotype at high frequency in transformed YAMC cells and a variety of human cancer cell lines. We found dysregulation of these genes, termed ‘cooperation response genes’ (CRGs), in 33 microarray gene expression datasets. Certain CRGs were frequently dysregulated with consistent directionality. Upon analysis of gene expression and somatic mutation data from The Cancer Genome Atlas and dbGAP, we discovered that despite widespread dysregulation, CRG expression was independent of the presence or absence of Ras or p53 mutations in cancer. However, a set of p53 response genes was highly differentially expressed in cancers with a p53 mutation. We investigated CRG dysregulation in precursor lesions in colon cancer and discovered that CRG dysregulation emerges at different points in the process of carcinogenesis. Our results suggest that CRG dysregulation is an essential and conserved element in the underlying regulatory architecture that brings about the malignant phenotype. Prostate cancer is the most common form of cancer among US men, with an increasing incidence due to the aging population. Patients diagnosed with clinically localized disease identified as intermediate or high-risk are typically treated by radical prostatectomy. Approximately 33% of these patients will suffer recurrence after surgery. Identifying patients likely to experience recurrence after radical prostatectomy would lead to improved clinical outcomes, as these patients could receive adjuvant radiotherapy. We developed a new tool for the prediction of prostate cancer recurrence based on the expression pattern of a small set of CRGs. We show that CRGs are systemically dysregulated in a new prostate cancer data set, including a 4-gene signature (HBEGF, HOXC13, IGFBP2, and SATB1) capable of differentiating recurrent from non-recurrent prostate cancer. To develop a suitable diagnostic tool to predict disease outcomes in individual patients, multiple algorithms and data handling strategies were evaluated on a training set using leave-one-out cross-validation (LOOCV). The best-performing algorithm, when used in combination with a predictive nomogram based on clinical staging, predicted recurrent and non-recurrent disease outcomes in a blinded validation set with 83% accuracy, outperforming previous methods. This test allows us to accurately identify prostate cancer patients likely to experience future recurrent disease, and demonstrates the potential for using CRG expression in predicting tumor phenotypic behavior

Essential Role for a Link between the Tricarboxylic Acid (TCA) Cycle and Polyamine Metabolism in Malignant Cell Transformation

Thesis (Ph.D.)--University of Rochester. School of Medicine & Dentistry. Dept. of Genetics, 2014.Malignant transformation requires reprogramming of the molecular network that underlies cell metabolism in order to convert available nutrients to biomass and energy to respond to biological demands of proliferation and tumor microenvironment. In this context two apparently distinct metabolic pathways, glutamine-dependent anaplerosis and polyamine metabolism are commonly found up-regulated in cancer cells. Here we show that, increased glutamine-dependent anaplerosis in cancer cells is partly driven by increased polyamine metabolism. Dependency of anaplerosis on polyamine metabolism is observed when glutamine carbon is selected over arginine carbon to synthesize the polyamine precursor, ornithine. This unexpected relationship between polyamine and glutamine metabolism is shared by multiple cancer types and controlled by an ornithine aminotransferase (Oat)-driven transamination reaction. Oat uses L-glutamate-semialdehyde, a glutamate derived intermediate, as an amine group acceptor and glutamate as an amine group donor, producing ornithine and α-ketoglutarate (α-KG), with the latter fueling the TCA cycle. Genetic suppression of this metabolic link by targeting Oat leads to inhibition of tumor formation, down-regulation of glutamine-dependent anaplerosis and disruption of cellular redox homeostasis. Furthermore, down-regulation of polyamine metabolism by suppressing expression of spermine synthase (Sms), a polyamine biosynthetic enzyme that we find to be commonly up-regulated in multiple cancers compared to normal samples, also inhibits tumor growth. Metabolic analysis of cancer cells with Sms depletion shows that synthesis of ornithine and α-KG from glutamine is also decreased showing that increased polyamine metabolism is critical for glutamine-dependent anaplerosis of the TCA cycle in cancer cells. Overall, our findings demonstrate a direct link between polyamine metabolism and glutamine-dependent anaplerosis that is essential for the cancer phenotype. As this pathway is non-essential to normal cells, its aberrant up-regulation in cancer cells may provide novel opportunities for therapeutic intervention in cancer

Regulation of Autophagy and Lysosome Integrity by Plac8 in Cancer

Thesis (Ph.D.)--University of Rochester. School of Medicine & Dentistry. Dept. of Biomedical Genetics, 2015.The upregulation of stress control pathways such as autophagy is an emerging hallmark of cancer. Autophagy is a cellular recycling process whereby damaged organelles are degraded. This involves their sequestration into double-membraned vesicles, the autophagosomes, followed by fusion with lysosomes. The role of autophagy in cancer is complex and has been intensely debated. We previously identified a group of genes cooperatively regulated by activated Ras and mutant p53, termed the cooperation response genes (CRGs), which are critical to the cancer phenotype. Among the genes induced by cooperating oncogenic mutations, we identified Plac8, a gene of unknown function that encodes a protein localizing to lysosomes in cancer cells. Genetic experiments indicate a role for Plac8 in regulating autophagosome-lysosome fusion, an essential step for completion of autophagy. We demonstrate that Plac8 is synergistically induced by cooperating oncogenic mutations and is necessary for both induction of autophagy and progression to malignancy, thus providing a causal link between oncogenic drivers and autophagy. Further, we explore the function of Plac8 in the lysosomes of cancer cells. In contrast to inhibitors of autophagosome-lysosome fusion such as Chloroquine, Plac8 ablation does not alter the lysosomal pH or pH dependent endocytic degradation. Instead, Plac8 protects lysosomal integrity under stress in cancer cells and preserves the pool of lysosomes available for fusion with autophagosomes. Protection of lysosomal integrity by Plac8 cannot be detected in normal tissue. Similarly, mice with germ line deletion of Plac8 are viable, with minimal impact on normal tissue function. We therefore suggest that Plac8-mediated stabilization of lysosomal integrity may serve as a suitable target for intervention in cancer

Shared Role for Critical Mediator Genes in Ras-Dependent and Ras-Independent Malignant Cell Transformation

Thesis (Ph.D.)--University of Rochester. School of Medicine & Dentistry. Dept. of Biomedical Genetics, 2015.Diverse types of cancer cells share a common set of critical properties that emerge in response to distinct oncogenic mutations. This suggests a role for common underlying mechanisms that mediate malignant cell transformation downstream of a variety of oncogenic drivers. Consistent with this idea, our lab has uncovered a set of genes responding synergistically to cooperating p53 and ras mutations that are critical to the cancer phenotype, and have an expression signature conserved among various types of cancers (Cooperation Response Genes, or CRGs). Using genetic models that permit modulation of oncogenic driver activities and/or identities in cancer cells, we show that the critical role of CRG expression is, at least in part, independent of the identity of given oncogenic drivers. In a conditional KrasG12D-driven model of pancreatic ductal adenocarcinoma (PDAC), the sustained loss of KrasG12D in vivo results in reductions in tumor volume commonly followed by c-Met pathway activation and tumor recurrence. In this model, CRG expression and functional relevance appear conserved together with key features of the metabolic phenotype established by Kras in the Met-driven recurrent cells. Oncogenic mutations play a continuous role in the maintenance of the cancer phenotype, and consistent with this notion expression of ~75% of CRGs tracks with ras attenuation after 3 days in vitro, in both the aforementioned PDAC model and a second independent model in which abrogation of the driving HrasG12V allele in transformed murine colon cells is achieved by cre/loxp-mediated recombination. Notably, expression of the other 25% of CRGs remains unaltered following attenuation of the primary oncogenic driver, providing evidence for hitherto unknown mechanisms which function to maintain the transformed state independently of the continuous presence of oncogenic mutations. Genetic perturbation of CRGs that are unresponsive to the alteration of oncogenic mutations resulted in tumor inhibition in secondary xenograft assays, suggesting that CRGs may represent an attractive new class of intervention targets, particularly in scenarios where molecular targeting of cancer mutations rapidly selects for treatment-resistant cancer cells that activate alternate oncogenic drivers

Autophagy Induced by Cooperating Oncogenic Mutations is Essential for the Cancer Phenotype and Requires the Expression of the Novel Cooperation Response Gene Plac8.

Thesis (Ph.D.)--University of Rochester. School of Medicine and Dentistry. Dept. of Biomedical Genetics, 2010.Cooperation of mutant p53 (mp53) and activated Ras (Ras) confers a malignant phenotype onto mouse colonic epithelial cells. Work in our laboratory has shown that conversion to malignancy is mediated, at least in part, via genes under synergistic oncogene regulation. We thus have identified such synergistically regulated genes at the genomic scale and have tested the contribution of these genes to the malignant state by genetic means. Perturbation of Plac8, one of the synergistically up-regulated genes at both the RNA and protein level, results in a complete loss of tumor formation capacity and is the largest negative affecter to tumor formation of the synergistic gene perturbations thus far in mp53/Ras transformed cells. Stable shRNA mediated knock-down of Plac8 in human colorectal and pancreatic adenocarcinoma cell lines also significantly inhibited tumor formation upon xenograft into immunocompromised mice. The biological significance of Plac8 to the cancer phenotype warranted further investigation of the function of Plac8 in malignant cells. We found Plac8 to be an internal lysosomal protein that is up-regulated in tumors around areas of necrosis in tumor tissue and under hypoxic and nutrient starvation conditions. These findings lead us to hypothesize that Plac8 had some functional role in the autophagy process, which is known to involve lysosomes, to be induced around areas of necrosis, and under hypoxic and nutrient starvation conditions. Autophagy or “self-eating” is a process in which cellular macromolecules and organelles are degraded in bulk to recycle the resulting metabolites for energy and anabolism. Plac8 perturbation resulted in an increase in autophagosomes, an accumulation of the autophagy markers p62, LC3-I, and LC3-II, and a decrease in autophagosome/lysosome fusion. These results could be phenocopied by the introduction of dominant negative Rab7, a gene known to be required for autophagosome/lysosome fusion, and the Plac8 knock-down phenotype could be rescued by over-expression of dominant active Rab7, however, over-expression of dominant active Rab7 was tumor inhibitory. The plac8 knock-down phenotype could also be rescued by expression of Atg12, a gene involved in autophagosome formation, however over-expression of Atg12 alone was tumor inhibitory. The cooperative up-regulation of Plac8 led us to investigate whether mp53 and Ras cooperatively regulated autophagy. Autophagosome number, loss of p62 and LC3-I to LC3-II conversion, and autophagosome/lysosomal fusion were all cooperatively up-regulated by mp53 and Ras. To investigate if autophagy is required for tumor formation we expressed shRNAs targeting Atg12 in malignant cells and found that tumor formation was inhibited upon xenograft into nude mice, which could be rescued by expressing an shRNA resistant form of Atg12. Once again over-expression of Atg12 was tumor inhibitory. These data suggest that Plac8 is required for tumor formation, involved in autophagosome/lysosome fusion, that both phases of autophagy are cooperatively up-regulated by mp53 and Ras, and the autophagy process, although cooperatively up-regulated, needs to be balanced for maintenance of the cancer phenotype