Recent Submissions

  • Georgia Cancer Center Integrated Genomics Resource & HPC Server

    Chang, Chang-Shen (Sam); Georgia Cancer Center
    Georgia Cancer Center at Augusta University is home to a High Performance Computing (HPC) Server. One goal of the HPC server is to host the new Biorepository software, LabVantage. This software is a web-based laboratory information management system, which tracks samples throughout their lifespan. All specimens that the Georgia Cancer Center Biorepository receives is entered into LabVantage, which generates a unique barcode number for each sample. Chain of custody is recorded throughout the sample’s lifespan, from inception to eventual withdrawal. LabVantage organizes data such as patient demographics, diagnosis, organ site, and linked pathology reports. 
LabVantage is compliant with all regulations relevant to patient privacy and satisfies all regulations set forth by The College of American Pathologists (CAP). All Biorepository personnel are trained to maintain confidentiality of patient information according to HIPAA regulations. The HPC Server is also used for the analysis of complex data including Next-Generation Sequencing data (NGS). It is currently used to perform data analysis on datasets such as those obtained from The Cancer Genome Atlas (TCGA). The analyses that used to take several weeks can now be performed in a matter of days. Georgia Cancer Center HPC Server is composed of 544 total compute cores and an aggregated memory of 2.9TB. The system is composed of (15) PowerEdge R430 1U systems (128 GB RAM each), (1) PowerEdge R830 (1024 GB RAM) and a high-speed 10GbE interconnect for intra-node communication. The HPCC also houses 633 TB RAW storage capacity. We will also be integrating existing Cancer Center servers including our Illumina Compute system that collects data directly from the Sequencer housed in the Georgia Cancer Center Integrated Genomics Shared Resource and the existing Bioinformatics HPC (see configuration diagram below). Access to the server is available to all Augusta University employees. There is a nominal fee associated with usage and users are required to undergo training.
  • T Cell Immune Response in Persistent Infection of Lymphocytic Choriomeningitis Virus (LCMV)

    Ou, Rong; Georgia Cancer Center (2004-07)
    The m urine LCMV system provides a ciassic model to study the mechanism of immunological tolerance, an efficient strategy used by virus to establish a persistent infection by selective down-regulation of virus-specific T lymphocytes. High viral burden in the onset o f infection drives responding cells into functional unresposiveness (anergy) that can, be followed by their physical elimination. In this study, the downregulation o f the virus-specific CD8^-T-ceil response was studied during a persistent infection o f adult mice, with particular emphasis on the contribution of the interferon response in promoting host defense, or perforin-, Fas/FasL-, or TN FR l-m ediated cytolysis in regulating T-cell homeostasis. Since LCMV infects a broad range o f host tissues, the functional properties o f virus-specific CD8'^ T cells in different tissues during LCMV infection were also evaluated. Infection of mice deficient in receptor for type I (IFN-a/p), type II (IFN-y), or both type I and II IFNs with LCMV isolates that vary in their capacity to induce T-celi exhaustion, revealed a critical role for IFN -a/p in restricting LCMV spread at the onset o f infection while IFN-y has impact on effector cells. The production o f IF N -a/p and/or IFN-y critically regulates the virus-host balance during the acute phase o f infection, such that a high viral burden drives responding cells into different programs o f exhaustion. Infection o f mice deficient in perferin, FasL or TNFRl with the Docile or Aggressive strains of LCMV revealed comparable kinetics of expansion and functional inactivation o f virusspecific C D ^ T cells in the early phase o f Infection in C57BL/6 controls. However, the data underscore a critical role for these molecules in the persistence o f the virus-specific CD8"‘-T-ceil population once it has become anergic. Study o f the functional properties of virus-specific CD8'^ T cells in different tissues during LCMV infections showed that a centra! role for the viral load in lymphoid tissue in the induction and maintenance of clonal exhaustion. The data strongly suggest that CD8^ T ceils may be differentially regulated in the environments o f lymphoid versus nonlymphoid tissues, and the pattern of T cell exhaustion observed with mice is likely a common feature o f the immune response during chronic infections in humans.
  • Regulation of T cell Immunity by Dendritic Cells Expressing Indoleamine 2,3- Dioxygenase (IDO)

    Manlapat, Anna K; Georgia Cancer Center (2006-04)
    IDO-mediated tryptophan depletion inhibits T cell responses in vitro and in vivo. This work investigates the role of IDO-expressing dendritic cells (DCs) in regulating T cell responses. To determine the role of IDO-expressing DCs in the regulation o f T cell immunity, IDO-transfected DCs and IDO transgenic mice over-expressing IDO specifically in DCs were generated, and effects of IDO over-expression on T cell stimulatory functions of DCs were assessed. Results show that inhibition o f T cell proliferation in vivo requires induction of IDO expression in DCs by CTLA4-Ig rather than constitutive over-expression of IDO. In addition, we have recently shown that IDO induction leading to T cell suppression is mediated by CTLA4-Ig ligation of B7 molecules on a minor subset of DCs that express the surface marker CD 19. Interferon-a (IFNa) was rapidly produced by CD 19+ DCs after CTLA4-Ig treatment in vitro, and signaling via IFN a receptors (IFNAR) was essential for activation of the transcription factor STAT1, while IFNy signaling was not. To further understand the role of IDO expressing DCs, DCs from IDO-deficient mice were treated in vitro and in vivo with CTLA4-Ig. In addition, IDO wildtype mice were also treated in vitro with CTLA4-Ig in the presence of the pharmacological IDO inhibitor 1-methyl-tryptophan (1-MT). IFNa production in response to CTLA4-Ig was detected in IDO-WT but not in IDO-KO DCs or IDO-WT treated with 1-MT. These results show that IDO is both upstream and downstream of IFN a production following B7 ligation. This study provides a better understanding of the role of IDO in antigen-presenting cells and evaluates the tolerogenic activity of APCs.
  • Molecular Biology of Amino Acid and Peptide Transport Systems

    Li, Huiwu; Georgia Cancer Center (1999)
    (First Paragraph) Amino acids are essential components in cellular metabolism. Some of these amino acids can be synthesized within the cells from other biological molecules and these amino acids are termed ‘nonessential’. These ‘nonessential’ amino acids are alanine, aspartate, cysteine, glutamate, glycine, pro line, serine, tyrosine, glutamine and asparagine. In contrast, some amino acids cannot be synthesized endogenously and have to be supplied in the diet (1). These amino acids are termed ‘essential’. These ‘essential’ amino acids are histidine, arginine, leucine, isoleucine, lysine, methionine, threonine, phenylalanine, tryptophan, and valine. Mammalian cells require ‘essential’ as well as ‘nonessential’ amino acids for their metabolic activity. Even though the cells can synthesize the ‘nonessential’ amino acids to some extent, most of the amino acids have to be supplied to the cells via specific membrane transport mechanisms.
  • Regulation of T Cell Immunity by Cells Expressing Indoleamine 2,3-Dioxygenase

    Keskin, Derin B.; Georgia Cancer Center (2002-07)
    Indoleamine 2,3-dioxygenase (IDO) is an intracellular enzyme, that degrades the essential amino acid tryptophan along the kynurenine pathway. Historically, IDO enzyme function was implicated in antibacterial and antiviral innate immunity, inflammation and antioxidative functions. Recently our lab associated IDO enzyme function with regulation of T cell responses and maintenance of maternal immune tolerance during pregnancy. We hypothesize that cells expressing IDO inhibit T cell responses. We will generate IDO expressing cell lines and IDO transgenic mice to investigate regulation of T cell immune responses by IDO enzyme in this thesis project.
  • Indoleamine 2,3 -Dioxygenase Activity Suppresses T Ceil Responses

    Johnson, Theodore S.; Georgia Cancer Center (2002-06)
    Cells expressing indoleamine 2,3-dioxygenasc (IDO) inhibit proliferation of human T cells in vitro and protect murine fetuses from lethal attack by maternal T cells in vivo. This work investigates the hypothesis that IDO activity suppresses T cell responses. To test the prediction that pharmacological inhibition o f IDO enhances murine T cell responses in vivo, splenocytes from H-2Kb-specific T cell receptor transgenic (BM3) mice were injected into H-2Kb-expressing (CBK) recipients. As predicted, CD8+ T cell responses were augmented by 1-methyl-Dx-tryptophan (1-MeTrp) treatment o f recipient CBK mice, but only when BM3 donor T cells were derived from male mice. To further evaluate the prediction that IDO-expressing antigen presenting cells (APCs) inhibit antigen-specific T cell responses, we prepared IDO- and vectortransfected murine tumor cells expressing H-2Kb. BM3 T cell proliferation was diminished in co-cultures with IDO-transfected MCS7G cells, relative to vcctortransfected MCS7G cells. Furthermore, IDO-transfected MCS7G cells failed to prime H-2b-specific recall responses in allogeneic CBA mice unless co-administered with 1-MeTrp or endotoxin adjuvant. These results show that IDO-expressing APCs inhibit murine T cell responses in vitro and in vivo, and demonstrate the efficacy o f 1-MeTrp treatment in reversing the effects o f murine IDO-mediated T cell suppression in vivo.
  • Regulation and Function of the Major Stress-Induced HSP70 Molecular Chaperone in vivo: Analysis of Mice with Targeted Gene Disruption of the HSP70.1 or HSP70A1

    Huang, Lei; Georgia Cancer Center (6/3/2002)
    (First Paragraph) The cellular response to stress, including exposure to environmental (UV radiation, heat shock, heavy metals), pathological (infection, fever, inflammation, malignancy, ischemia) or physiological (growth factor, hormonal stimulation, tissue development) stimuli is represented at the molecular level by synthesis of groups of protein named heat shock proteins [hsp(s)] (Benjamin 1998; Feder and others 1992; Jolly and Morimoto 2000; Li and Mivechi 1986; Lindquist 1986; Smith 1998). The presence of hsp(s) protect host cells from the damage caused by thermal stress, and after induction of hsp expression, cells are protected well from higher temperatures than they can normally tolerate. This phenomenon is defined as themiotoleranee (Gemer 1975; Li and Mivechi 1986). The protective role of hsp(s) is attributed to several functional properties, including active participation in maintaining proteins in their native correctly folded states, promoting degradation and refolding of misfolded proteins, and minimizing aggregation and incorrect interactions between proteins (Agashe and Hartl 2000; Gething and Sambrook 1992). In addition, hsp(s) can function in cellular protection by modulating the engagement and progression of apoptosis induced by a variety of stress stimuli (Beere and Green 2001). Besides the recognition of the cytoprotective function of hsp(s) under stress conditions, widespread clinical interests exist in their chaperone function during a range of human pathologies, including neurodegenerative conditions, such as amyloidosis, prion disease, and Alzheimer's disease, and cardiovascular diseases, such as myocardial ischemia, cardiac hypertrophy, stroke, and blood vessel injury (Benjamin 1998; Planas and others 1997; Smith 1998).
  • Protection Against Colonic Inflammation and Colon Cancer by Commensal Bacterial Metabolites: An Obligatory Role for the Short- Chain Fatty Acid Transporter Slc5a8

    Gurav, Ashish; Georgia Cancer Center (2014-11)
    Dietary fiber consumption has long been known to protect against inflammatory bowel diseases and colorectal carcinogenesis. In mammals, large intestinal microorganisms ferment dietary fiber to generate energy, while releasing short-chain fatty acids (SCFAs), such as acetate, propionate and butyrate. Interestingly, SCFAs are also known to protect against intestinal inflammation and colorectal carcinogenesis, although the molecular mechanisms behind these actions are still being investigated. For most of their biological effects, SCFAs must be transported from lumen into the intestinal tissue, where they activate multiple biological processes. We and others have reported Slc5a8 as a high affinity transport mechanism for SCFAs, which would remain fully functional, even when SCFA concentration drops to sub-millimolar range, whereas other transport mechanisms are rendered inefficient. The aim of the current study was to test protective role of Slc5a8 against intestinal inflammation and colorectal carcinogenesis during suboptimal intake of dietary fiber. We observed that Slc5a8 is obligatory for HDAC-inhibition in colonic epithelium and intestinal barrier function, only when the animals were fed a dietary fiber-free diet (FF diet), and not when the animals were fed diet containing optimal amounts of fibers (FC Diet). Compared to WT, Slc5a8-/- animals demonstrated higher susceptibility to AOMDSS- mediated intestinal inflammation and colorectal carcinogenesis under FF dietary conditions, but not under FC dietary conditions. At molecular level, we found that butyrate and propionate could induce potent immunosuppressive enzymes Indoleamine 2,3-dioxygenase and Aldehyde Dehydrogenase 1A2 in dendritic cells obtained from WT animals, but not from Slc5a8-/- animals. Butyrate, transported via Slc5a8 enabled DCs to suppress conversion of naïve T cells to interferon-γ secreting pro-inflammatory T cells and Slc5a8-/- animals harbored higher proportion of interferon-γ+ CD4+ T cells in vivo. Taken together, our data provide crucial evidence for critical role of Slc5a8 mediating protective effects of dietary fiber metabolites, SCFAs in protecting against intestinal inflammation and colorectal carcinogenesis.
  • The Role of RYBP in the Regulation of Apoptosis

    Novak, Rachel Lynn; Georgia Cancer Center (6/5/2014)
    The tumor suppressor Tp53 is the most frequently mutated gene in human cancer. Tp53 encodes a sequence specific transcription factor termed p53 that activates a number of biological programs contributing to tumor suppression, most notably, the promotion of cell cycle arrest and apoptosis. To identify new regulators of p53’s transcriptional activity, we performed a yeast 2-hyrbid screen and have identified Ring 1 YY1 Binding Protein (Rybp) as a novel p53-interacting partner. Consistent with its role as a transcriptional repressor, we have demonstrated that Rybp inhibits p53-mediated transcription. In addition, Rybp forms a trimeric complex with the critical negative regulator of p53, Mdm2. Mdm2 is an E3 ligase that ubiquitinates p53, targeting it for degradation, and expression of Rybp enhances the Mdm2-mediated ubiquitination. To further investigate the role of Rybp in the regulation of endogenous p53 stability we constructed a recombinant adenovirus expressing Rybp (Ad-Rybp). Ad-Rybp infection inhibited the accumulation of p53 and the induction of p53 target genes in response to genotoxic stress. However, interpretation of the results was confounded by Ad-Rybp infection reducing global mRNA levels. Despite inhibition of p53, Ad-Rybp was a powerful inducer of apoptosis, and we investigated this in more detail. Analysis of a panel of tumor cell and untransformed cell types revealed that Ad-Rybp infection specifically induces apoptosis in tumor cells but not in normal diploid cells. Furthermore, at a low multiplicity of infection, Ad-Rybp sensitizes tumor cells to apoptosis in the presence of the death receptor ligands, Tumor Necrosis Factor alpha (TNFα) and TNF related apoptosis inducing ligand (TRAIL). These results suggest that the tumor-specific killing properties of Rybp may be exploited for therapeutic advantage.
  • De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system

    Peterson, Mark P; Whittaker, Danielle J; Ambreth, Shruthi; Sureshchandra, Suhas; Buechlein, Aaron; Podicheti, Ram; Choi, Jeong-Hyeon; Lai, Zhao; Mockatis, Keithanne; Colbourne, John K.; et al. (2012-07-9)
    Background: Though genomic-level data are becoming widely available, many of the metazoan species sequenced are laboratory systems whose natural history is not well documented. In contrast, the wide array of species with very well-characterized natural history have, until recently, lacked genomics tools. It is now possible to address significant evolutionary genomics questions by applying high-throughput sequencing to discover the majority of genes for ecologically tractable species, and by subsequently developing microarray platforms from which to investigate gene regulatory networks that function in natural systems. We used GS-FLX Titanium Sequencing (Roche/454-Sequencing) of two normalized libraries of pooled RNA samples to characterize a transcriptome of the dark-eyed junco (Junco hyemalis), a North American sparrow that is a classically studied species in the fields of photoperiodism, speciation, and hormone-mediated behavior.
  • Novel Somatic Mutations to PI3K Pathway Genes in Metastatic Melanoma

    Shull, Austin Y.; Latham-Schwark, Alicia; Ramasamy, Poornema; Leskoske, Kristin; Oroian, Dora; Birtwistle, Marc R.; Buckhaults, Phillip J.; GHSU Cancer Center (2012-08-17)
    Background: BRAFV600 inhibitors have offered a new gateway for better treatment of metastatic melanoma. However, the overall efficacy of BRAFV600 inhibitors has been lower than expected in clinical trials, and many patients have shown resistance to the drugâ s effect. We hypothesized that somatic mutations in the Phosphoinositide 3-Kinase (PI3K) pathway, which promotes proliferation and survival, may coincide with BRAFV600 mutations and contribute to chemotherapeutic resistance.
  • Towards Curative Cancer Immunotherapy: Overcoming Posttherapy Tumor Escape

    Zhou, Gang; Levitsky, Hyam; GHSU Cancer Center; Department of Medicine (2012-05-31)
    The past decade has witnessed the evolvement of cancer immunotherapy as an increasingly effective therapeutic modality, evidenced by the approval of two immune-based products by the FDA, that is, the cancer vaccine Provenge (sipuleucel-T) for prostate cancer and the antagonist antibody against cytotoxic T-lymphocyte antigen-4 (CTLA-4) ipilimumab for advanced melanoma. In addition, the clinical evaluations of a variety of promising immunotherapy drugs are well under way. Benefiting from more efficacious immunotherapeutic agents and treatment strategies, a number of recent clinical studies have achieved unprecedented therapeutic outcomes in some patients with certain types of cancers. Despite these advances, however, the efficacy of most cancer immunotherapies currently under clinical development has been modest. A recurring scenario is that therapeutic maneuvers initially led to measurable antitumor immune responses in cancer patients but ultimately failed to improve patient outcomes. It is increasingly recognized that tumor cells can antagonize therapy-induced immune attacks through a variety of counterregulation mechanisms, which represent a fundamental barrier to the success of cancer immunotherapy. Herein we summarize the findings from some recent preclinical and clinical studies, focusing on how tumor cells advance their survival and expansion by hijacking therapy-induced immune effector mechanisms that would otherwise mediate their destruction.
  • Acute Progression of BCR-FGFR1 Induced Murine B-Lympho/Myeloproliferative Disorder Suggests Involvement of Lineages at the Pro-B Cell Stage

    Ren, MingQiang; Tidwell, Josephine A.; Sharma, Suash; Cowell, John K.; GHSU Cancer Center; Department of Pathology (2012-06-6)
    Constitutive activation of FGFR1, through rearrangement with various dimerization domains, leads to atypical myeloproliferative disorders where, although T cell lymphoma are common, the BCR-FGFR1 chimeric kinase results in CML-like leukemia. As with the human disease, mouse bone marrow transduction/transplantation with BCR-FGFR1 leads to CML-like myeloproliferation as well as B-cell leukemia/lymphoma. The murine disease described in this report is virtually identical to the human disease in that both showed bi-lineage involvement of myeloid and B-cells, splenomegaly, leukocytosis and bone marrow hypercellularity. A CD19+ IgMâ CD43+ immunophenotype was seen both in primary tumors and two cell lines derived from these tumors. In all primary tumors, subpopulations of these CD19+ IgMâ CD43+ were also either B220+ or B220â , suggesting a block in differentiation at the pro-B cell stage. The B220â phenotype was retained in one of the cell lines while the other was B220+. When the two cell lines were transplanted into syngeneic mice, all animals developed the same B-lymphoblastic leukemia within 2-weeks. Thus, the murine model described here closely mimics the human disease with bilineage myeloid and B-cell leukemia/lymphoma which provides a representative model to investigate therapeutic intervention and a better understanding of the etiology of the disease.
  • Toward integrative cancer immunotherapy: targeting the tumor microenvironment

    Emens, Leisha A; Silverstein, Samuel C; Khleif, Samir; Marincola, Francesco M; Galon, Jérôme; GHSU Cancer Center (2012-04-10)
    The development of cancer has historically been attributed to genomic alterations of normal host cells. Accordingly, the aim of most traditional cancer therapies has been to destroy the transformed cells themselves. There is now widespread appreciation that the progressive growth and metastatic spread of cancer cells requires the cooperation of normal host cells (endothelial cells, fibroblasts, other mesenchymal cells, and immune cells), both local to, and at sites distant from, the site at which malignant transformation occurs. It is the balance of these cellular interactions that both determines the natural history of the cancer, and influences its response to therapy. This active tumor-host dynamic has stimulated interest in the tumor microenvironment as a key target for both cancer diagnosis and therapy. Recent data has demonstrated both that the presence of CD8+ T cells within a tumor is associated with a good prognosis, and that the eradication of all malignantly transformed cells within a tumor requires that the intra-tumoral concentration of cytolytically active CD8+ effector T cells remain above a critical concentration until every tumor cell has been killed. These findings have stimulated two initiatives in the field of cancer immunotherapy that focus on the tumor microenvironment. The first is the development of the immune score as part of the routine diagnostic and prognostic evaluation of human cancers, and the second is the development of combinatorial immune-based therapies that reduce tumor-associated immune suppression to unleash pre-existing or therapeutically-induced tumor immunity. In support of these efforts, the Society for the Immunotherapy of Cancer (SITC) is sponsoring a workshop entitled "Focus on the Target: The Tumor Microenvironment" to be held October 24-25, 2012 in Bethesda, Maryland. This meeting should support development of the immune score, and result in a position paper highlighting opportunities for the development of integrative cancer immunotherapies that sculpt the tumor microenvironment to promote definitive tumor rejection.
  • Cytotoxic Chemotherapy and CD4+ Effector T Cells: An Emerging Alliance for Durable Antitumor Effects

    Ding, Zhi-Chun; Zhou, Gang; GHSU Cancer Center; Department of Medicine (2012-02-6)
    Standard cytotoxic chemotherapy can initially achieve high response rates, but relapses often occur in patients and represent a severe clinical problem. As increasing numbers of chemotherapeutic agents are found to have immunostimulatory effects, there is a growing interest to combine chemotherapy and immunotherapy for synergistic antitumor effects and improved clinical benefits. Findings from recent studies suggest that highly activated, polyfunctional CD4+ effector T cells have tremendous potential in strengthening and sustaining the overall host antitumor immunity in the postchemotherapy window. This review focuses on the latest progresses regarding the impact of chemotherapy on CD4+ T-cell phenotype and function and discusses the prospect of exploiting CD4+ T cells to control tumor progression and prevent relapse after chemotherapy.
  • Loss of Zebrafish lgi1b Leads to Hydrocephalus and Sensitization to Pentylenetetrazol Induced Seizure-Like Behavior

    Teng, Yong; Xie, Xiayang; Walker, Steven L.; Saxena, Meera T.; Kozlowski, David J.; Mumm, Jeff S.; Cowell, John K.; GHSU Cancer Center; Department of Cellular Biology and Anatomy; Vision Discovery Institute; et al. (2011-09-16)
    Mutations in the LGI1 gene predispose to a hereditary epilepsy syndrome and is the first gene associated with this disease which does not encode an ion channel protein. In zebrafish, there are two paralogs of the LGI1 gene, lgi1a and lgi1b. Knockdown of lgi1a results in a seizure-like hyperactivity phenotype with associated developmental abnormalities characterized by cellular loss in the eyes and brain. We have now generated knockdown morphants for the lgi1b gene which also show developmental abnormalities but do not show a seizure-like behavior. Instead, the most striking phenotype involves significant enlargement of the ventricles (hydrocephalus). As shown for the lgi1a morphants, however, lgi1b morphants are also sensitized to PTZ-induced hyperactivity. The different phenotypes between the two lgi1 morphants support a subfunctionalization model for the two paralogs.
  • Linear Approaches to Intramolecular Forster Resonance Energy Transfer Probe Measurements for Quantitative Modeling

    Birtwistle, Marc R.; von Kriegsheim, Alexander; Kida, Katarzyna; Schwarz, Juliane P.; Anderson, Kurt I.; Kolch, Walter; GHSU Cancer Center (2011-11-16)
    Numerous unimolecular, genetically-encoded Forster Resonance Energy Transfer (FRET) probes for monitoring biochemical activities in live cells have been developed over the past decade. As these probes allow for collection of high frequency, spatially resolved data on signaling events in live cells and tissues, they are an attractive technology for obtaining data to develop quantitative, mathematical models of spatiotemporal signaling dynamics. However, to be useful for such purposes the observed FRET from such probes should be related to a biological quantity of interest through a defined mathematical relationship, which is straightforward when this relationship is linear, and can be difficult otherwise. First, we show that only in rare circumstances is the observed FRET linearly proportional to a biochemical activity. Therefore in most cases FRET measurements should only be compared either to explicitly modeled probes or to concentrations of products of the biochemical activity, but not to activities themselves. Importantly, we find that FRET measured by standard intensity-based, ratiometric methods is inherently non-linear with respect to the fraction of probes undergoing FRET. Alternatively, we find that quantifying FRET either via (1) fluorescence lifetime imaging (FLIM) or (2) ratiometric methods where the donor emission intensity is divided by the directly-excited acceptor emission intensity (denoted Ralt) is linear with respect to the fraction of probes undergoing FRET. This linearity property allows one to calculate the fraction of active probes based on the FRET measurement. Thus, our results suggest that either FLIM or ratiometric methods based on Ralt are the preferred techniques for obtaining quantitative data from FRET probe experiments for mathematical modeling purposes.
  • Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing

    Lee, Eun-Joon; Pei, Lirong; Srivastava, Gyan; Joshi, Trupti; Kushwaha, Garima; Choi, Jeong-Hyeon; Robertson, Keith D.; Wang, Xinguo; Colbourne, John K.; Zhang, Lu; et al. (2011-10-23)
    We applied a solution hybrid selection approach to the enrichment of CpG islands (CGIs) and promoter sequences from the human genome for targeted high-throughput bisulfite sequencing. A single lane of Illumina sequences allowed accurate and quantitative analysis of ~1 million CpGs in more than 21â 408 CGIs and more than 15â 946 transcriptional regulatory regions. Of the CpGs analyzed, 77â 84% fell on or near capture probe sequences; 69â 75% fell within CGIs. More than 85% of capture probes successfully yielded quantitative DNA methylation information of targeted regions. Differentially methylated regions (DMRs) were identified in the 5â ²-end regulatory regions, as well as the intra- and intergenic regions, particularly in the X-chromosome among the three breast cancer cell lines analyzed. We chose 46 candidate loci (762 CpGs) for confirmation with PCR-based bisulfite sequencing and demonstrated excellent correlation between two data sets. Targeted bisulfite sequencing of three DNA methyltransferase (DNMT) knockout cell lines and the wild-type HCT116 colon cancer cell line revealed a significant decrease in CpG methylation for the DNMT1 knockout and DNMT1, 3B double knockout cell lines, but not in DNMT3B knockout cell line. We demonstrated the targeted bisulfite sequencing approach to be a powerful method to uncover novel aberrant methylation in the cancer epigenome. Since all targets were captured and sequenced as a pool through a series of single-tube reactions, this method can be easily scaled up to deal with a large number of samples.
  • The temporal and spatial expression pattern of the LGI1 epilepsy predisposition gene during mouse embryonic cranial development

    Silva, Jeane; Wang, Guanghu; Cowell, John K.; GHSU Cancer Center; Department of Neurology; Institute of Molecular Medicine and Genetics (2011-05-13)
    Background: Mutations in the LGI1 gene predispose to a rare, hereditary form of temporal epilepsy. Currently, little is known about the temporal and spatial expression pattern of Lgi1 during normal embryogenesis and so to define this more clearly we used a transgenic mouse line that expresses GFP under the control of Lgi1 cis-regulatory elements.
  • Functional Dissection of HOXD Cluster Genes in Regulation of Neuroblastoma Cell Proliferation and Differentiation

    Zha, Yunhong; Ding, Emily; Yang, Liqun; Mao, Ling; Wang, Xiangwei; McCarthy, Brian A.; Huang, Shuang; Ding, Han-Fei; GHSU Cancer Center; Department of Pathology; et al. (2012-08-7)
    Retinoic acid (RA) can induce growth arrest and neuronal differentiation of neuroblastoma cells and has been used in clinic for treatment of neuroblastoma. It has been reported that RA induces the expression of several HOXD genes in human neuroblastoma cell lines, but their roles in RA action are largely unknown. The HOXD cluster contains nine genes (HOXD1, HOXD3, HOXD4, and HOXD8-13) that are positioned sequentially from 3â ² to 5â ², with HOXD1 at the 3â ² end and HOXD13 the 5â ² end. Here we show that all HOXD genes are induced by RA in the human neuroblastoma BE(2)-C cells, with the genes located at the 3â ² end being activated generally earlier than those positioned more 5â ² within the cluster. Individual induction of HOXD8, HOXD9, HOXD10 or HOXD12 is sufficient to induce both growth arrest and neuronal differentiation, which is associated with downregulation of cell cycle-promoting genes and upregulation of neuronal differentiation genes. However, induction of other HOXD genes either has no effect (HOXD1) or has partial effects (HOXD3, HOXD4, HOXD11 and HOXD13) on BE(2)-C cell proliferation or differentiation. We further show that knockdown of HOXD8 expression, but not that of HOXD9 expression, significantly inhibits the differentiation-inducing activity of RA. HOXD8 directly activates the transcription of HOXC9, a key effector of RA action in neuroblastoma cells. These findings highlight the distinct functions of HOXD genes in RA induction of neuroblastoma cell differentiation.

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