Showing papers by "Arnold J. Levine published in 2011"

Topology based data analysis identifies a subgroup of breast cancers with a unique mutational profile and excellent survival.

Abstract: High-throughput biological data, whether generated as sequencing, transcriptional microarrays, proteomic, or other means, continues to require analytic methods that address its high dimensional aspects. Because the computational part of data analysis ultimately identifies shape characteristics in the organization of data sets, the mathematics of shape recognition in high dimensions continues to be a crucial part of data analysis. This article introduces a method that extracts information from high-throughput microarray data and, by using topology, provides greater depth of information than current analytic techniques. The method, termed Progression Analysis of Disease (PAD), first identifies robust aspects of cluster analysis, then goes deeper to find a multitude of biologically meaningful shape characteristics in these data. Additionally, because PAD incorporates a visualization tool, it provides a simple picture or graph that can be used to further explore these data. Although PAD can be applied to a wide range of high-throughput data types, it is used here as an example to analyze breast cancer transcriptional data. This identified a unique subgroup of Estrogen Receptor-positive (ER+) breast cancers that express high levels of c-MYB and low levels of innate inflammatory genes. These patients exhibit 100% survival and no metastasis. No supervised step beyond distinction between tumor and healthy patients was used to identify this subtype. The group has a clear and distinct, statistically significant molecular signature, it highlights coherent biology but is invisible to cluster methods, and does not fit into the accepted classification of Luminal A/B, Normal-like subtypes of ER+ breast cancers. We denote the group as c-MYB+ breast cancer.

Parkin, a p53 target gene, mediates the role of p53 in glucose metabolism and the Warburg effect

Abstract: Regulation of energy metabolism is a novel function of p53 in tumor suppression. Parkin (PARK2), a Parkinson disease-associated gene, is a potential tumor suppressor whose expression is frequently diminished in tumors. Here Parkin was identified as a p53 target gene that is an important mediator of p53's function in regulating energy metabolism. The human and mouse Parkin genes contain functional p53 responsive elements, and p53 increases the transcription of Parkin in both humans and mice. Parkin contributes to the function of p53 in glucose metabolism; Parkin deficiency activates glycolysis and reduces mitochondrial respiration, leading to the Warburg effect. Restoration of Parkin expression reverses the Warburg effect in cells. Thus, Parkin deficiency is a novel mechanism for the Warburg effect in tumors. Parkin also contributes to the function of p53 in antioxidant defense. Furthermore, Parkin deficiency sensitizes mice to γ-irradiation-induced tumorigenesis, which provides further direct evidence to support a role of Parkin in tumor suppression. Our results suggest that as a novel component in the p53 pathway, Parkin contributes to the functions of p53 in regulating energy metabolism, especially the Warburg effect, and antioxidant defense, and thus the function of p53 in tumor suppression.

The p53 family: guardians of maternal reproduction

Abstract: The p53 family of proteins consists of p53, p63 and p73, which are transcription factors that affect both cancer and development. It is now emerging that these proteins also regulate maternal reproduction. Whereas p63 is important for maturation of the egg, p73 ensures normal mitosis in the developing blastocyst. p53 subsequently regulates implantation of the embryo through transcriptional control of leukaemia inhibitory factor. Elucidating the cell biological basis of how these factors regulate female fertility may lead to new approaches to the control of human maternal reproduction.

Molecular classification of prostate cancer using curated expression signatures

Abstract: High Gleason score is currently the best prognostic indicator for poor prognosis in prostate cancer. However, a significant number of patients with low Gleason scores develop aggressive disease as well. In an effort to understand molecular signatures associated with poor outcome in prostate cancer, we analyzed a microarray dataset characterizing 281 prostate cancers from a Swedish watchful-waiting cohort. Patients were classified on the basis of their mRNA microarray signature profiles indicating embryonic stem cell expression patterns (stemness), inactivation of the tumor suppressors p53 and PTEN, activation of several oncogenic pathways, and the TMPRSS2–ERG fusion. Unsupervised clustering identified a subset of tumors manifesting stem-like signatures together with p53 and PTEN inactivation, which had very poor survival outcome, a second group with intermediate survival outcome, characterized by the TMPRSS2–ERG fusion, and three groups with benign outcome. The stratification was validated on a second independent dataset of 150 tumor and metastatic samples from a clinical cohort at Memorial Sloan–Kettering Cancer Center. This classification is independent of Gleason score and therefore provides useful unique molecular profiles for prostate cancer prognosis, helping to predict poor outcome in patients with low or average Gleason scores.

Regulation of female reproduction by p53 and its family members

Abstract: Tumor suppressor p53 is crucial for embryonic implantation through transcriptional up-regulation of uterine leukemia inhibitory factor (LIF). This article reports that p53 and estrogen receptor α were activated in endometrial tissues during implantation to coordinately regulate LIF production. By using human p53 knockin (Hupki) mice carrying a single nucleotide polymorphism (SNP) at codon 72 (arginine/proline), the arginine allele was demonstrated to produce higher uterine LIF levels during implantation than the proline allele. In humans, the diversity of haplotypes of the p53 gene has decreased during evolution, because the arginine allele, existing in only a subset of haplotypes, is under positive selection. This observation is consistent with previous results showing that the proline allele is enriched in patients undergoing in vitro fertilization (IVF). Studies with p63- and p73-knockout mice have demonstrated the involvement of p63 and p73 in female reproduction and their roles in egg formation and apoptosis (p63) and spindle checkpoint (p73) in female mice. Here, the role of p63 and p73 in human reproduction was investigated. Selected alleles of SNPs in p63 and p73 genes were enriched in IVF patients. These findings demonstrate that the p53 family members are involved in several steps to regulate female reproduction in mice and humans.—Feng, Z., Zhang, C., Kang, H.-J., Sun, Y., Wang, H., Naqvi, A., Frank, A. K., Rosenwaks, Z., Murphy, M. E., Levine, A. J., Hu, W. Regulation of female reproduction by p53 and its family members.

Oligonucleotide Motifs That Disappear during the Evolution of Influenza Virus in Humans Increase Alpha Interferon Secretion by Plasmacytoid Dendritic Cells

Abstract: CpG motifs in an A/U context have been preferentially eliminated from classical H1N1 influenza virus genomes during virus evolution in humans. The hypothesis of the current work is that CpG motifs in a uracil context represent sequence patterns with the capacity to induce an immune response, and the avoidance of this immunostimulatory signal is the reason for the observed preferential decline. To analyze the immunogenicity of these domains, we used plasmacytoid dendritic cells (pDCs). pDCs express pattern recognition receptors, including Toll-like receptor 7 (TLR7), which recognizes guanosine- and uridine-rich viral single-stranded RNA (ssRNA), including influenza virus ssRNA. The signaling through TLR7 results in the induction of inflammatory cytokines and type I interferon (IFN-I), an essential process for the induction of specific adaptive immune responses and for mounting a robust antiviral response mediated by IFN-α. Secretion of IFN-α is also linked to the activation of other immune cells, potentially amplifying the effect of an initial IFN-α secretion. We therefore also examined the role of IFN-α-driven activation of NK cells as another source of selective pressure on the viral genome. We found direct evidence that CpG RNA motifs in a U-rich context control pDC activation and IFN-α-driven activation of NK cells, likely through TLR7. These data provide a potential explanation for the loss of CpG motifs from avian influenza viruses as they adapt to mammalian hosts. The selective decrease of CpG motifs surrounded by U/A may be a viral strategy to avoid immune recognition, a strategy likely shared by highly expressed human immune genes.

Polymorphic variants in TSC1 and TSC2 and their association with breast cancer phenotypes.

Abstract: TSC1 acts coordinately with TSC2 in a complex to inhibit mTOR, an emerging therapeutic target and known promoter of cell growth and cell cycle progression. Perturbation of the mTOR pathway, through abnormal expression or function of pathway genes, could lead to tumorigenesis. TSC1 and TSC2 expression is reduced in invasive breast cancer as compared with normal mammary epithelium. Because single nucleotide polymorphisms (SNPs) in regulatory genes have been implicated in risk and age at diagnosis of breast cancers, systematic SNP association studies were performed on TSC1 and TSC2 SNPs for their associations with clinical features of breast cancer. TSC1 and TSC2 haplotypes were constructed from genotyping of multiple loci in both genes in healthy volunteers. SNPs were selected for further study using a bioinformatics approach based on SNP associations with drug response in NCI-60 cell lines and evidence of selection bias based on haplotype frequencies. Genotyping for five TSC1 and one TSC2 loci were performed on genomic DNA from 1,137 women with breast cancer. This study found that for TSC1 rs7874234, TT variant carriers had a 9-year later age at diagnosis of estrogen receptor positive (ER+), but not ER−, ductal carcinomas (P = 0.0049). No other SNP locus showed an association with age at diagnosis, nor any other breast cancer phenotype. TSC1 rs7874234 is hypothesized to be functional in ER+ breast cancer because the T allele, but not the C allele, may create an estrogen receptor element (ERE) site, resulting in increased TSC1 transcription and subsequent inhibition of mTOR.

A genetic variant in a PP2A regulatory subunit encoded by the PPP2R2B gene associates with altered breast cancer risk and recurrence.

Abstract: A recent candidate gene association study identified a single nucleotide polymorphism (SNP) in the PPP2R2B gene (rs319217, A/G) that manifests allelic differences in the cellular responses to treatment with chemotherapeutic agents (Vazquez et al., Nat Rev Drug Discov 2008;7:979-87). This gene encodes a regulatory subunit of protein phosphatase 2A (PP2A), one of the major Ser/Thr phosphatases implicated in the negative control of cell growth and division. Given the tumor suppressor activities of PP2A, here we evaluate whether this genetic variant associates with the age of diagnosis and recurrence of breast cancer in women. To investigate the linkage disequilibrium in the vicinity of this SNP, PPP2R2B haplotypes were analyzed using HapMap data for 90 Caucasians. It is found that the A variant of rs319217 tags a haplotype that appears to be under positive selection in the Caucasian population, implying that this SNP is functional. Subsequently, associations with cellular responses were investigated using data reported by the NCI anticancer drug screen and associations with breast cancer clinical variables were analyzed in a cohort of 819 Caucasian women. The A allele associates with a better response of tumor derived cell lines, lower risk of breast cancer recurrence, later time to recurrence, and later age of diagnosis of breast cancer in Caucasian women. Taken together these results indicate that the A variant of the rs319217 SNP is a marker of better prognosis in breast cancer.

Introduction: The Changing Directions of p53 Research:

Abstract: The p53 protein was first uncovered as a tumor antigen. Animals bearing tumors initiated by some viruses or transformed cells produced antibodies directed against a cellular protein of 53,000 Daltons.1,2 The p53 protein was also shown to form a complex with the viral oncogenic products from SV40,1,2 the adenoviruses,3 and subsequently the human papilloma viruses.4 The early c-DNA clones of the mouse or human p53 gene cooperated with other oncogenes to transform cells in culture,5,6 but these c-DNAs proved to encode a mutant p53 protein that acted as a dominant negative mutation and that had properties of a gain-of-function mutation.7 Later the wild-type p53 gene was shown to function as a tumor suppressor gene in cell culture8 and in human tumors.9 From attempts to understand the functions of the p53 protein it became apparent that it responded to a wide variety of cellular stresses, such as DNA damage, resulting in the modification of the p53 protein and increased concentrations of the p53 protein in a cell. This activated the p53 protein so it functioned as a transcription factor. The genes regulated by the p53 protein form the p53 pathway10 and can result in cell cycle arrest, apoptosis, and cell senescence. These observations helped to explain how the p53 protein functioned as a tumor suppressor by eliminating cells that make errors or mutations at a high rate in attempting to duplicate themselves under conditions of stress. In this way, p53 functions act to prevent cancers over a lifetime of exposures to stress. Just how important this process is to understanding cancer origins comes from the growing awareness that p53 gene mutations are the most common type of mutations observed in a wide variety of cancers. More than half of all cancers harbor p53 mutations, and in some cancers a p53 mutation can be found in 95% of the tumors produced in humans. In addition, a number of other mutations inactivate or dampen p53 functions in a cell. Gene amplifications in the MDM-2 and MDM-4 genes (the ubiquitin ligase complex that helps to degrade p53) and WIP-1 (a protein phosphatase) in cancers lower or eliminate p53 activities.11 Inherited mutations in the p53 gene increase the frequency of cancers in a family and lower the age of onset of those cancers.12

The paths to death and differentiation.

Abstract: Ever since evolution began experimenting with the creation of invertebrate multicellular organisms, cell death and terminal differentiation have been employed as a central set of processes to permit these organisms to develop, survive and to reproduce Cell death and differentiation are employed in several related processes: (1) the development of the organism, (2) the asexual regeneration of the organism from stem cells after it is wounded or dissociated into its cellular parts, (3) the death and regeneration of cellular and tissue components over the normal lifespan of the organism (tissue turnover), (4) the sexual reproduction of an organism through its primordial germ cells and (5) cell death and differentiation are employed as processes to limit pathogenesis in an organism A terrific example of the cooperation of cell death and differentiation in the development of an organism comes from the study of C elegans where a fertilized egg gives rise to an organism with 959 cells in the hemaphrodite derived from many developmental lineages where 131 cells reproducibly die by the genetically programmed processes of apoptosis In the central nervous system of humans a programmed developmental production of neurons is further shaped by environmental experiences, which reinforce neuronal connections and neuronal cell death when such connections are not made The asexual regeneration of an organism or parts of an organism has been studied in worms, fish and amphibians and is regulated by the induction or reprogramming of stem cells that can regenerate parts or entire organisms How these latent stem cells are formed and regulated so as to not produce developmental abnormalities or cancers until an appropriate stress signal is given remains a mystery Starting with the vertebrates, (fish) tissue regeneration and turnover throughout the life span of the organism requires coordination between death and differentiation that permits the organism to function efficiently for longer periods of time extending its lifespan This in turn permits more complex organisms with longer gestation periods, longer times to develop to sexual maturity and enough time to have smaller numbers of offspring that are well taken care of for longer periods From hydra to humans, death and differentiation have important roles in the surveillance of fidelity of the germ line A cell death program in germ cells is activated by DNA damage, starvation conditions and many other stresses all across the invertebrate and vertebrate phyla The primordial germ cells harbor the ultimate information for immortality, the expression of which resides in a program of differentiation producing two (or more) sexes that enhance the exchange of combinations of information The passage of faithful information is insured by death in lineages that harbor too many mistakes Cell death and differentiation are employed effectively to limit pathogenesis This is observed in both the innate immune system of the invertebrates and vertebrates and in the adaptive immune system of vertebrates Programmed cell death in response to infection limits replication and spread of an organism Differentiation programs are commonly activated in response to infections or cytokines induced by infections The origins and propagation of cancers are responded to by programs for cell death, cell senescence and terminal differentiation Tumor necrosis factor, trail, fas and p53 respond to oncogene activation and abnormal developmental pathways triggered by oncogene and tumor suppressor gene mutations The p53 protein dramatically lowers the efficiency of producing induced pluripotent stem cells in culture Here p53 impacts upon dedifferentiation processes and epigenetic changes by limiting cell division or activating cell death In breast cancers there is a close association of a stem cell phenotype with p53 mutations in a tumor type Here the p53 protein, which can start the process of programmed cell death is also regulating the epigenetic changes in a cell and developmental fates of these cells A large number of disorders can arise by the failure of components of the death and differentiation pathways Neurodegenerative disorders are a tragic example of such processes Indeed the lifespan of an organism may be determined by the regulation of stem cell lineages over a lifetime Here decisions of renewal, differentiation and death may change the balance between long life and a brief existence The reviews that follow this introduction deal with many of these issues employing specific examples of programmed cell death1 or escape from death2, 3 and discussing the mechanisms that regulate them The regulation of the ubiquitin ligases4 and caspases5 are at the center of the death and differentiation pathways The p53 pathway can lead to apoptosis, senescence cellular repair processes and through its target gene, Wig-1, stem cell fates6 Similarly the PML tumor suppressor can regulate communication between the endoplasmic reticulum and mitochondria and in doing so control an apoptotic pathway7 The role of cell death in pathogenesis is nowhere more dramatic than in neurodegenerative disorders such as Parkinson's disease8 or ataxia-telangiectasia,9 which are reviewed in a new light in this issue These reviews employ specific examples to cover the broader landscape of how death and differentiation combine to control pathogenesis and just what happens when these processes fail For each of these failures we must learn the road to repair and treatment10 and we will only do that by understanding how the pathways to death function in many diverse cell types and organisms

Treatments for cellular proliferative disorders and identification thereof

Abstract: This invention concerns methods of identifying treatments for treating various disorders and related computer products and systems. Also disclosed are methods for treating cellular proliferative disorders and use of compounds identified for such treatment.

The Emergence of 2009 H1N1 Pandemic Influenza

Abstract: The emergence of a novel H1N1 virus in Mexico and the USA in spring 2009 and its rapid spread around the globe has led the World Health Organization to declare the first pandemic of the twenty-first century Employing almost real-time sequencing technologies and disseminating this information freely and widely has permitted the most intensive investigation of the origins and evolution of an influenza pandemic in the history of this disease The small levels of sequence diversity of the first isolates permitted a realistic estimate of when the 2009 H1N1 virus first entered the human population The rate of change in influenza RNA sequences permitted several groups to trace the origins of this virus to swine and a reassortment of North American and Eurasian swine influenza These virus strains in turn have been traced back to swine, avian, and human virus reassortments occurring years ago in swine, all the way back to the 1918–1930 H1N1 viruses The influenza virus sequence information spans the dimensions of time (90 years), space (locations all over the world), and hosts (birds, humans, swine, etc) The high evolutionary rate of this virus and the growing amount of information is allowing researchers to follow its changes in the search for possible factors that could contribute to an increase in its virulence