Day 2 :
National Institutes of Health Bethesda, USA
Keynote: Altered UBIAD1 prenyltransferase function in schnyder cornea dystrophy affects cholesterol metabolism and mitochondrial function
Time : 09:30-10:15
Michael L Nickerson has obtained his PhD in Molecular Medicine from the George Washington University. He has made significant contributions to disease gene identification using positional cloning, including an altered Birt-Hogg-Dubé gene in chromophobe RCC, fumarate hydratase in papillary RCC, the dead-end gene in testicular cancer, and the UBIAD1 gene in Schnyder Corneal Dystrophy. More recently, he has sequenced urologic tumor genomes and identified alterations in TET2 in prostate cancer and the BRCA pathway in bladder and kidney cancer, which have been translated to a clinical trial starting in 2016. He is an active participant in Precision Medicine, ClinVar and the TCGA project.
Schnyder corneal dystrophy (SCD) is an autosomal dominant disease characterized by deposition of cholesterol in the cornea, progressive opacification, and loss of visual acuity. Germline UBIAD1 variants introduce missense mutations in over 50 SCD families, including four large families from Finland who share a likely founder mutation. UBIAD1 was recently shown to catalyze synthesis of two mitochondrial electron carriers, menaquinone-4 (MK-4) and coenzyme Q10/ubiquinone (CoQ10). MK-4 is the predominant active form of vitamin K and an important cofactor in bone metabolism and blood clotting. We show SCD-altered UBIAD1 results in reduced MK-4 synthesis and molecular models indicate mutations disrupt active site residues and transmembrane helices. Yeast two-hybrid screening, co-immunoprecipitation, and confocal microscopy show a physical interaction between UBIAD1 and the cholesterol synthesis and storage enzymes HMGCR and SOAT1. Molecular models indicate cholesterol and geranylgeranyl diphosphate, a substrate for MK-4 synthesis, binding the same substrate binding cleft and likely compete for occupancy of UBIAD1. Vitamin K was originally identified by depletion of dietary cholesterol in chickens, which co-depleted vitamin K resulting in hemorrhages and uncontrolled bleeding. Our data suggests a first physiologic role for endogenously produced vitamin K in maintaining cornea health and visual acuity, in addition to its role in blood clotting. The data indicates that the synthesis of vitamin K, CoQ10 and cholesterol may be tightly linked with implications for vision, mitochondria function, cardiovascular health and cancer.
- Nickerson M L, Bosley A, Weiss J S, Kostiha B N, Hirota Y, Brandt W, Esposito D, Kinoshita S, Wessjohann L, Morham S G, Andresson T, Kruth H S, Okano T, and Dean M (2013) The UBIAD1 prenyltransferase links menaquinone-4 synthesis to cholesterol metabolic enzymes. Hum Mutat 34: 317-329.
- Fredericks, W J, Mc Garvey, T Wang, H Zheng Y, Fredericks N J, Yin H, Wang, L P, Hsiao W, Lee R, Weiss J S, Nickerson, M L Kruth, H S Rauscher F J and Malkowicz S B (2013) The TERE1 protein interacts with mitochondrial TBL2: regulation of transmembrane potential, ROS/RNS and SXR target genes. J Cell Biochem 114 (9): 2170-87.
- Fredericks W J, Mc Garvey T, Wang H, Lal P, Puthiyaveettil R, Tomaszewski J, Sepulveda J, Labelle E, Weiss J S, Kruth H S, Brandt W, Wessjohann L A and Malkowicz S B (2011) The bladder tumor suppressor protein TERE1 (UBIAD1) modulates cell cholesterol: Implications for tumor progression. DNA Cell Biol 11: 851-64.
- Nickerson M L, Kostiha B N, Brandt W, Fredericks W, Xu K P, Yu F S, Gold B, Chodosh J, Goldberg M, Lu D W, Yamada M, Tervo T M, Grutzmacher D, Croasdale C, Hoeltzenbein M, Sutphin J, Malkowicz S B, Wessjohann L, Kruth H S, Dean M and Weiss J S (2010) UBIAD1 mutations alter a mitochondrial prenyltransferase to cause Schnyder Corneal Dystrophy. PLoS ONE 5 (5): e10760.
- Weiss J S, Kruth H S, Kuivaniemi H, Tromp G, White P S, Winters R S, Lisch W, Henn W, Denninger E, Krause M, Wasson P, Ebenezer N, Mahurkar S and Nickerson M L (2007) Mutations in the UBIAD1 gene on chromosome 1p36 cause schnyder crystalline corneal dystrophy. Invest Ophthalmol Vis Sci 48: 5007-5012.
Columbia University, USA
Keynote: Use of Carrier exome screening for prevention of childhood malignancies and other sever congenital abnormalities
Time : 10:15-11:00
Peter L Nagy is Board Certified in Anatomic and Molecular Genetic Pathology. He was a Principal Investigator on multiple NIH funded studies at University of Iowa and Columbia University and served as an Associate Director of Personalized Genomic Medicine Laboratory at Columbia University Medical Center. He has established an array of clinical next-generation sequencing tests including whole exome and transcriptome testing for constitutional and somatic (cancer) disorders. At Medical Neurogenetics Laboratories, he is continuing his groundbreaking work on developing computational tools to improve the clinical specificity and sensitivity of next generation sequencing data analysis.
Our work with the Columbia University Medical Center Precision Medicine for Kids with cancer (PIP-seq) project has shown that a significant percentage of pediatric malignancies arise because of genetic predisposition. We can consider cancer predisposition as a specialized case of the parents being carriers for a specific genetic disorder. MNG laboratories has developed a whole exome carrier test designed to fulfill the preconception genetic counseling needs of couples who suspect, based on shared ethnicity or family history, that they are potentially at risk of having children with debilitating health problems, including development of pediatric malignancies. In my presentation, I will discuss the technical, practical and ethical considerations to make such testing widely available for risk couples.
- Micro RNA | mRNA Analysis | Bioinformatics in Genomics | Comparative Genomics | Microbial Genomics | Plant Genomics | Future trends in Genomics | Genome Medicine | Genomics Market
Louisiana State University, USA
Title: Phenotypic and transcriptomic analyses of colonial phase variants of the cholera pathogen vibrio choleraeReveal a novel biofilm-defective form
Time : 11:15-11:45
Gregg S Pettis completed his PhD at University of Missouri and Post-doctoral fellowship in Department of Genetics at Stanford University School of Medicine. He is an Associate Professor in Department of Biological Sciences at Louisiana State University. He has published more than 30 papers in peer-reviewed journals, and his research has been supported by the National Science Foundation, United States Department of Agriculture, and the National Oceanic and Atmospheric Administration. He is an Editorial Board Member of Applied and Environmental Microbiology journal and is the Editor of the microbiology section of the Encyclopedia of Life Sciences.
In a process termed phase variation, the marine bacterium and cholera pathogen Vibrio cholerae alternately expresses smooth or rugose colony types, with the latter linked to sophisticated biofilm architecture and a greater resistance to environmental stress. To assess transcriptome changes in response to phase variation in V. cholerae O1 El Tor pandemic strain N16961, we compared the transcriptome obtained by RNA-seq among the smooth parent N16961, its rugose derivative (N16961R) and smooth isolates obtained directly from the rugose at high frequencies consistent with phase variation (N16961SD). Phenotypic characterization of these isolates, including the ability to form pellicles and produce biofilm, was also performed. Differentially regulated genes were revealed for various cellular functions, including acetate metabolism, gluconeogenesis, and anaerobic respiration, suggesting critical links between these processes and biofilm formation in this organism. Principal component analysis separated the transcriptome of the novel phase variant form N16961SD from the other phase variants entirely. Unexpectedly, although N16961SD produced no detectable biofilm, transcription of its biofilm genes was elevated similar to N16961R. Other transcriptome signatures involving two-component signal transduction, c-di-GMP synthesis, chemotaxis, and environmental persistence were also shared between N16961R and N16961SD. These share signatures may implicate a stress adaptation in the pathogen that facilitates transition of the N16961SD smooth form back to rugosity. We are currently exploring the genetic or epigenetic basis of this unusual biofilm-defective N16961SD isolates so that we may more fully understand their role in the ecology and potentially the pathogenesis of V. cholerae.
University of Leicester, United Kingdom
Title: Identification of microRNAs signature and signalling pathway targets in an animal model of tinnitus
Time : 11:45-12:15
Martine Hamann is an Associate Professor of Neurosciences in Department of Neurosciences, Psychology and Behavior at University of Leicester, UK. She completed her Graduation and PhD in Neurosciences at University of Strasbourg (France) and Centre Medical Universitaire (Geneva, Switzerland). She has completed her Post-doctoral studies at University College London. Her research focuses on “Understanding cellular mechanisms associated to hearing loss and tinnitus in pre-clinical models, and aims at identifying markers to prevent and/or target those auditory deficits”.
Tinnitus, the pathological percept of phantom sound, is a highly prevalent disorder, affecting 10 to 15% of the population worldwide. Tinnitus can be triggered by prolonged exposure to loud noise damaging cochlear hair cells and introducing excitability changes in the auditory brainstem. There is no sensitive biomarker for diagnosis or early detection of tinnitus. MicroRNAs are approximately 22-nt RNA segments that are involved in the regulation of protein expression primarily by binding to one or more target sites on an mRNA transcript and inhibiting translation. MicroRNAs are highly stable and have been recently described as powerful biomarkers in a wide range of diseases. The study aims at identifying microRNAs present during tinnitus, assessed in CBA mice using the gap-prepulse inhibition of the acoustic startle reflex, a broadly applied paradigm to study changes in neural processing related to tinnitus. We demonstrate selective gap detection deficits in CBA mice 3-4 weeks following acoustic over-exposure and identify specific modulation of microRNA levels in the brainstem and blood in those tinnitus positive CBA mice. Using the database DIANA-TarBase v7.0 (1), we show that most regulated microRNAs (e.g. miR-128-3p, miR-140-5p, miR-151-5p and miR-204-5p) are involved in fatty acid metabolism and steroid signaling. The present results have important implications toward understanding tinnitus pathophysiology and designing novel pharmacotherapies targeting the function of those microRNAs.
Kuwait Institute for Scientific Research, Kuwait
Title: Diagnosis and genetic identification of tomato yellow leaf curl virus (TYLCV) infecting tomato crops in kuwait
Time : 12:15-12:45
Ebtesam Al-Ali completed her BSC in 1993 at Kuwait University and worked for Kuwait University as Research Assistant, then joined KISR on October 5, 1993 and led six projects. She has published more than 25 papers in reputed journals and international conferences. She has experience in Plant Virus Detection, Primer Design, Cloning and Sequencing, ELISA, DNA Extraction, PCR Amplification, RCA Rolling Circle Amplification and TYLCV detection on tomatoes. She was trained twice at University of Wisconsin Madison under the supervision of Professor Amy Charkowski as well as Washington State University under supervision of Professor Hanu Pappu.
In Kuwait, high economic losses induced by white fly-transmitted viruses necessitates a rapid action for identification and molecular characterization of the virus species present in Kuwait in order to develop and recommend appropriate control strategies. TYLCV was reported as a major pest of tomato but it was not fully characterized at the molecular level in addition to TYLCV. Tomato leaf samples were collected on monthly bases. Collections were made from greenhouses farms in south (Wafra) and north (Abdally) agricultural district areas in Kuwait. Gemini viral DNA was extracted from 100 collected infected tomato leaf samples using Dellaporta method. Then, PCR protocol was optimized and used on 50 collected infected leaf tomato samples by using two different primer pairs. Field observations carried out in this project for whole growing period of tomato grown under protection indicated that the symptoms such as leaf yellowing, leaf cupping, leaf curling and stunting of plants were common. Whitefly infestation was very common. Data from this activity showed that TY1(+) & TY2(-) primers were successful in detecting the TYLCV, and partially sequencing of the positive TYLCV done and the amplicon showed a new spp. of TYLCV was detected. These data indicate that the TYLCV present in Kuwait belongs to a separate species from those reported in other countries, and hence, has been named tomato yellow leaf curl Kuwait virus (TYLCKWV).
Ain Shams University, Egypt
Time : 12:45-13:15
Ahmed E M Azazy is a fourth year Medical Cadet at Armed Forces College of Medicine (AFCM), active member at International Genetic Engineering Machine (IGEM). He has published three papers in international journals.
Background: Long noncoding RNAs (lncRNAs) have emerged as key elements in modulating gene expression in different biological contexts. Accumulating evidence indicates that lncRNAs are strongly implicated in hepatocellular carcinoma (HCC) development and progression.
Objectives: Long non coding RNA-urothelial cancer associated 1 (lncRNA-UCA1) and cellular jun proto-oncogene (c-JUN) have been scheduled in this study to discuss their possible association in HCC patients based on bioinformatics tools and clinical validation.
Patient & Methods: We used quantitative real-time PCR (QPCR) to evaluate the expression of lncRNA-UCA1 and C-JUN in serum of 70 patients with HCC, 32 patients chronic hepatitis C (CHC) and 38 healthy subjects and their correlation with different clinicopathological factors. The prognostic significance of lncRNA-UCA1 and c-JUN were tested by Kaplan-Meier survival analysis.
Results: The expression of lncRNA-UCA1 and C-JUN was positive in 91.4% HCC patients with strong discriminating power between HCC and healthy subjects and CHC patients as well. The median follow up period was 29 months. The survival analysis showed that both lncRNA-UCA1 and C-JUN were independent prognostic factors. Of note, we identified C-JUN expression changes consistent with the lncRNA-UCA1 target regulation.
Conclusion: Our study sheds light on the possible role of lncRNA-UCA1 and C-JUN mRNA as promising diagnostic and prognostic markers as well as potential therapeutic targets in HCC.
Tel-Aviv University, Israel
Ruth Navon is currently working in the 1Tel Aviv University, Israel. Ruth Navon international experience includes various programs, contributions and participation in different countries for diverse fields of study. Ruth Navon research interests reflect wide range of publications in various national and international journals.
Late onset Tay-Sachs disease (LOTS) is a rare neurodegenerative lysosomal storage disease which results from mutations in the gene encoding the a-subunit (HEXA) of beta-hexosaminidase enzyme (HexA). At present, no effective treatment exists for LOTS. Pyrimethamine (PMT) was previously shown to act as a HexA chaperone in human fibroblasts in vitro carrying some (e.g., aG269S), but not all LOTS-related mutations. The present study assessed the effect of cyclic, low dose and long term pyrimethamine treatment on HexA in subjects with LOTS. In an open label trial in 4 LOTS patients, PMT was initiated at an average daily dose of similar to 2.7 mg and administered cyclically guided blood lymphocyte HexA activity for a mean duration of 82.8 (+/- 22.5; SD) weeks. HexA activity rose in all subjects, with a mean peak increase of 2.24 folds (+/- 0.52; SD) over baseline activity was observed. The mean treatment time required to attain this peak was of 15.7 (+/- 4.8; SD) weeks. Following increase in activity, HexA gradually declined with the continued use of PMT, which was then stopped, resulting in the return of HexA activity to baseline. A second cycle of PMT treatment was then initiated, resulting again in an increase in HexA activity. Three of the patients experienced a measurable neuropsychiatric deterioration whereas one subject remained entirely stable. We conclude that cyclic low dose of PMT can increase HexA activity in LOTS patients. However, the observed increase is repeatedly transient and not associated with discernible beneficial neurological or psychiatric effects.
National Institute of Animal Science, Korea
Haesu Ko has completed her Bachelor’s degree in 2016 at Chonbuk National University, South Korea and presently, she is pursuing her Master's degree from the same university. She is a Junior Researcher of Animal Genomics & Bioinformatics Division, National Institute of Animal Science, South Korea.
CD (cluster of differentiation) markers are cell surface molecules on immune-related cells such as leucocytes, which have various physiological functions, especially immune responses. CD markers presently range from CD1 to CD371 in human. CD molecules are mostly cell surface proteins encoded by genes. In the case of swine CD genes, it remains less well known by comparison with human CD genes. We defined the structures of the swine CD genes by assembly of transcriptome sequencing data and comparing with multi-species CD genes. Transcriptomic data were produced by RNA sequencing in 15 tissues of pigs in NIAS and obtained from public database such as Ensembl and NCBI. All swine CD genes were annotated on the Korean native pig genome map constructed by de novo assembly. We classified the all annotated swine CD genes by comparing the genomic sequences and finding common motif conserved between them. After annotating swine CD genes, genomic variations were investigated using mapping with paired-end sequencing data of a total of 59 pigs of five breeds. In the study, furthermore, we predicted variant effects on the swine CD genes based on their protein structure-functional relationships. We hope to provide new insights and extend information for understanding of swine immune system based on the genomic variations of the swine CD genes.