Day 1 :
Keynote Forum
Henry M Sobell
University of Rochester, USA
Keynote: The centers of premeltons signal the beginning and ends of genes
Time : 10:05-11:10
Biography:
Henry M Sobell has completed his studies at Brooklyn Technical High School (1948-1952), Columbia College (1952-1956) and the University of Virginia, School of Medicine (1956-1960) in Brooklyn New York. Instead of practicing Clinical Medicine, he then went to the Massachusetts Institute of Technology, Cambridge to join Professor Alexander Rich in the Department of Biology (1960-1965) as a Helen Hay Whitney Postdoctoral fellow; he learned the technique of single Crystal X- Ray Analysis. He then joined the Chemistry Department at the University of Rochester and was then jointly appointed to the Department of Biophysics School of Medicine and Dentistry becoming a full Professor in both departments (1965-1993). He is now retired and living in New York, USA.
Abstract:
Premeltons are examples of emergent-structures (i.e., structural-solitons) that arise spontaneously in DNA due to the presence of nonlinear-excitations in its structure. They are of two kinds: B-B (or A-A) premeltons form at specific DNA-regions to nucleate site-specific DNA melting. These are stationary and, being globally-nontopological, undergo breather-motions that allow drugs and dyes to intercalate into DNA. B-A (or A-B) premeltons, on the other hand, are mobile, and being globally-topological, act as phase-boundaries transforming B- into A- DNA during the structural phase-transition. They are not expected to undergo breather motions. A key feature of both types of premeltons is the presence of an intermediate structural-form in their central regions (proposed as being a transition-state intermediate in DNA-melting and in the B- to A- transition), which differs from either A- or B- DNA. Called beta-DNA, this is both metastable and hyperflexible – and contains an alternating sugar-puckering pattern along the polymer backbone combined with the partial unstacking (in its lower energy-forms) of every-other base-pair. Beta-DNA is connected to either B- or to A- DNA on either side by boundaries possessing a gradation of nonlinear structural-change, these being called the kink and the antikink regions. The presence of premeltons in DNA leads to a unifying theory to understand much of DNA physical chemistry and molecular biology. In particular, premeltons are predicted to define the 5’ and 3’ ends of genes in naked-DNA and DNA in active-chromatin, this having important implications for understanding physical aspects of the initiation, elongation and termination of RNA-synthesis during transcription. For these and other reasons, the model will be of broader interest to the general-audience working in these areas. The model explains a wide variety of data, and carries with it a number of experimental predictions – all readily testable – as will be described in this talk.
Keynote Forum
David L Perkins
University of Illinois at Chicago, USA
Keynote: Microbiome functions identified by the metatranscriptome
Time : 11:30-12:30
Biography:
David L Perkins is a MD, PhD who is currently a Professor of Medicine at University of Illinois at Chicago. He obtained his PhD in Immunology and is also a Practicing Kidney Transplant Nephrologist. His current research focuses on the role of the microbiome in immunosuppressed subjects. He has published more than 100 papers in reputed journals, serves on numerous editorial boards and has been a standing member of a NIH study section.
Abstract:
The human microbiome plays an important role in regulating human health and disease. Previous studies have relied on 16S rRNA amplicon and shotgun metagenome sequencing to investigate the bacterial composition of the microbiome. These approaches provide a taxonomic assignment that is used to predict microbial functions based on known genome sequences. Here we report an extremely deep shotgun sequencing and comparative analysis of the human fecal microbiome using metatranscriptomics and metagenomics. In our previous study, we analyzed the human fecal microbiome using a shotgun metagenomic approach, and in the present study we compiled a total of 139.6 million reads using multiple sequencing methods and platforms. Specifically, after establishing the reproducibility of our methods with extensive multiplexing, we compared the metagenome and metatranscriptome with following parameters: 1) the Illumina HiSeq versus MiSeq platforms, 2) the sequence reads versus de novo assembled contigs, and 3) the effect of shorter versus longer reads. Interestingly, our analysis identified differential expression of bacterial genes indicating over- and under-represented bacterial functions in the fecal microbiome.
- Track 1: Transcriptome analysis and Gene Expression
Track 2: Cancer Transcriptome
Track 3: Transcriptomics and Proteomics in Plants
Chair
Henry M Sobell
University of Rochester, USA
Co-Chair
Andrew Grimson
Cornell University, USA
Session Introduction
Andrew Grimson
Cornell University, USA
Title: Mining transcriptome data to identify consequential microRNAs and their targets
Time : 12:30 : 13:00
Biography:
Andrew Grimson has completed his PhD at the University of Wisconsin-Madison in 2004, investigating mRNA decay. He completed his Post-doctoral fellowship in 2009, mentored by Dr. David Bartel (Whitehead Institute/MIT), investigating microRNAs and their targets. Currently, he is an Assistant Professor of Molecular Biology and Genetics at Cornell University. His lab work is on post-transcriptional regulation, in particular the role of the 3′ untranslated region (3′UTR); research is focused upon the basic science of 3′UTRs, together with biological processes under post-transcriptional control. His research is supported by grants from the NIH, and by a Research Scholar Grant from the American Cancer Society.
Abstract:
Although microRNAs (miRNAs) contribute to essentially all mammalian gene regulatory pathways, the identification of consequential miRNAs active in a given cell-type remains challenging. To address this challenge, mRNA and miRNA transcriptome profiles can be used to infer the identities of miRNAs with regulatory impacts. We used such approaches to discover miRNAs that might underlie age-dependent differences in CD8+ T cells, which protect organisms from intracellular diseases. In early life, mice and other mammals are deficient at generating memory CD8+ T cells, which protect from re-infection; we hypothesized that age-specific activity of one or more miRNAs underlie these differences. We profiled mouse transcriptomes from CD8+ T cells at different stages of infection, comparing adult and neonatal profiles. Adult and neonatal miRNA profiles were surprisingly similar in effector cell populations created during infection; however, we observed large differences prior to infection; in particular, miR-29 and miR-130 exhibit significant differential expression between adult and neonatal naive cells. Importantly, we detected reciprocal changes in expression of mRNA targets for both miRNAs; moreover, targets include Eomes and Tbx21, key genes that regulate memory CD8+ T cell formation. In addition, the mRNA profiles of neonatal naive cells already resemble those of effector cells. Changes in miR-29 and miR-130 and their targets are conserved in human CD8+ T cells, and in other T cell lineages. Together, these results suggest that miR-29 and miR-130 are important regulators of memory CD8+ T cell formation, and that neonatal cells are committed to a short-lived effector cell fate prior to infection.
Michael Abend
Bundeswehr Institute of Radiobology, Germany
Title: Association of radiation-induced genes with non-cancer chronic diseases in Mayak workers occupationally exposed to prolonged radiation
Time : 13:00 : 13:30
Biography:
Michael Abend studied Human Medicine at the University Cologne and finished his medical examination for a Doctor degree (medicine) during the same time. He earned a Professorship for Radiobiology at the Technical University, Munich, Germany and a Master’s degree in Epidemiology from Institute for Biometry, Epidemiology and Informatics at the Clinics of the Gutenberg University, Mainz, Germany. He worked at different scientific institutions outside Germany (e.g. Radiation Epidemiology Branch, DCEG, Bethesda, USA). He is currently the Deputy Director of the Bundeswehr Institute of Radiobiology and published almost 100 papers in reputed journals.
Abstract:
We examined the association of gene expression with non-cancer chronic disease outcomes in Mayak nuclear weapons plant workers who were exposed to radiation due to their occupation. We conducted a cross-sectional study with selection based on exposure status (either combined incorporated 239Pu or external gamma-ray [n=82], or external gamma-ray exposure only [n=18]) of Mayak plant workers living in Ozyorsk who were alive in 2011; and an unexposed comparison group (n=50) of Ozyorsk residents. Peripheral blood was taken and RNA was isolated, converted into cDNA and stored at -20°C. In a previous analysis, we screened the whole genome for radiation-associated candidate genes and validated 15 mRNAs and 15 microRNAs using qRT-PCR. Within the present analysis, we examined the association of these genes with 15 different chronic diseases on 92 samples (47 males, 45 females). We examined the radiation to gene and gene to disease associations in statistical models stratified by gender and separately for each disease and exposure. Unconditional logistic regression was used for genes that were significantly associated with radiation exposure and a specific disease outcome. Altogether 12 mRNAs and 9 microRNAs appeared to be significantly associated with 6 diseases, e.g. atherosclerotic diseases (4 genes, OR: 2.5-10, concordance: 70-75%), systolic blood pressure (6 genes, OR: 3.7-10.6, concordance: 81-88%) and body mass index (1 gene [miR-484], OR: 3.7, concordance: 81%). All associations were gender and exposure dependent. Hence, gene expression changes observed after occupational prolonged radiation exposures seem to increase the risk for certain non-cancer chronic diseases.
Arindam Basu
Penn State University, USA
Title: YY1 controls long range DNA interactions of Ig heavy chain locus during class-switch recombination
Time : 14:30: 15:00
Biography:
Arindam Basu has completed his PhD from Indian Institute of Science (IISc), Bangalore in India and continued his Post-doctoral research on gene expression and regulation in the laboratory of Dr. Michael L. Atchison at the University of Pennsylvania. He is currently an Assistant Professor at Penn State University, Brandywine campus where he teaches undergraduate courses. His primary research interests have been in the area of epigenetic regulation by Polycomb group of proteins and long-range DNA interactions. He has published several papers demonstrating the role of Polycomb proteins in chromatin organization.
Abstract:
B lymphocyte development involves a temporal order of long-range DNA recombination events that results in the assembly of variable (V), diversity (D) and joining (J) gene segments to produce functional Ig genes. In activated splenic B cells and germinal center cells, somatic hypermutation and class switch recombination (CSR) regulate IgH expression. The rearrangement of distal V genes requires locus contraction and DNA looping and studies showed that YY1-/- pro-B cells have greatly impaired distal VH gene rearrangement and IgH locus compaction. Studies have shown that YY1 is essential for B cell development and we have shown that numerous long range DNA loops are also required for CSR and loss of YY1 significantly reduces CSR. CSR involves DNA looping between the intronic enhancer (Eµ) and the 3’RR enhancer. This Eµ - 3’RR synapse is dependent on YY1 as measured by 3C and 3D-FISH assays, as well as by ChIP-seq. We performed ChIP-seq with splenic B cells to investigate whether YY1 colocalizes with condensins, cohesins and PcG proteins to understand the mechanism of YY1 mediated locus contraction. The raw sequences were analyzed using bowtie2. The Homer software package was used to analyze the aligned reads for regions of over representation of read depth (peaks) utilizing the find Peaks factor program and statistical significance was determined by using a FDR of 1%, 4-fold reads in peak over background, and requiring a cumulative poisson p-value of 0.0001. Our data indicated that SMC4, Rad21 and EZH2 bind at the 3’RR hs4 site along with YY1.
Alqaisi K M
University of Otago, New Zealand
Title: The application of transcriptome sequencing: New insights into the understanding of sex-steroid hormone synthesis in echinoderms
Time : 15:00: 15:30
Biography:
Alqaisi K M has completed his PhD in 2014 from the Department of Zoology at University of Otago, New Zealand. His PhD research was focused on understanding vitellogenesis and sex steroid hormone synthesis in Echinoderms using advance molecular and biochemical techniques. He also has research experience in the area of developmental neurotoxicity from his Master’s research. He has published several papers in peer-reviewed journals. Currently, he is interested in understanding the endogenous signals that control gametogenesis in Echinoderms. Also, he is interested in studying how brain signals control energy homeostasis and obesity in human.
Abstract:
In invertebrates, the presence of sex steroid hormones such as progesterone (P4), testosterone (T) and estradiol-17β (E2) has been reported in Echinoderms and Molluscs and classified as vertebrate-like sex steroid hormones (VLSHs). In Echinoderms, VLSHs levels were found to change in relation to gametogenesis and suggested to be synthesized primarily in the ovary. However, the synthesis and functions of these VLSHs in Echinoderms are still poorly understood. Therefore, this study aimed to identify transcripts of enzymes that are crucial in the steroid biosynthetic pathway by selecting ovaries from the sea star Patiriella regularis in early and late stages of oogenesis for de novo transcriptome sequencing using Illumina HiSeq2000. The study also investigated the steroidogenic activity of P. regularis ovary and pyloric caeca during the reproductive cycle by incubating these tissues with pregnenolone (P5) or androstenedione (AD) and measuring P4, AD, T and E2 concentrations using liquid chromatography-atmospheric pressure chemical ionization tandem mass spectrometry. Surprisingly, the transcripts that encode key steroidogenic enzymes, such as P450scc, 3β-HSD and aromatase, were not found in the transcriptome from the ovary. The results also showed the ability of both pyloric caeca and ovary to convert P5 into P4 and AD into T, but the in vitro production of P4 or T was not significant during the reproductive cycle. Therefore, it seems probable that the synthesis of VLSHs in P. regularis stems from non-specific activity of hydroxysteroid dehydrogenases and P450 enzymes. More similar studies using advanced molecular techniques are needed to understand the synthesis and function of VLSHs in invertebrates.
Nina B Fedorova
Institute of Cytology and Genetics, Russia
Title: Transcriptomics: Genes and ontogenes in Drosophila
Time : 15:30: 16:00
Biography:
Nina B Fedorova has completed her graduation from Tomsk State University, The Biology Faculty. In 2002, she finished her Post-graduate studies at Institute of Cytology and Genetics in Novosibirsk. She received her PhD in Genetics in 2007. She is a Researcher in the Laboratory of Mechanisms of Cell Division of the Institute and has published more than 20 papers in reputed Russian and foreign journals. Her research interest is in the relationship between facts and concepts of classical genetics and modern investigations in epigenetics, molecular and cellular biology.
Abstract:
For the existence of genetic systems, independent hereditary factors are not sufficient, such as Mendelian genes. The search for the hereditary factors of a different type was held. A new class of mutations, called conditional, was isolated In D. melanogaster. In a restrictive genotype, mutant dies and permissive survives and reproduces. Besides their conditional nature, mutations in the permissive genotype display a set of specific features that drastically distinguish them from conventional mutations. They are: 1) dominant; 2) as a rule, lethal; 3) drastically decrease fertility; 4) interact with chromosome rearrangements; 5) switch the genome from a stable to an unstable state; 6) increase basal metabolism; 7) induce modifications and morphoses; and 8) their manifestation is inherited in a parental manner. Four properties of the mutations - conditional manifestation and 1), 4) and 8) allow asserting that the mutated genes are: (1) segments of DNA; (2) their products are duplexes of RNA (3) active in germ cells and (4) repeated in the genome. The formation of morphoses in mutants suggests that the genes control the ontogeny (called ontogenes). Thus the genetic system comprises the genes working on the script DNA-RNA-protein and ontogenes working on the script of DNA-RNA. First engaged in the production of the "building material" in the organism, the second controlled this process and maintained the functioning of the organism. Such different functions of the genes depend on the type of transcript formed by the DNA, time and place of its origin.
Juan Antonio Valdés
Universidad Andrés Bello, Chile
Title: RNA-seq analysis reveals significant transcriptome changes in the fine flounder (Paralichthys adspersus) and the red cusk-eel (Genypterus chilensis) under stress
Time : 16: 15: 16: 45
Biography:
Juan Antonio Valdés is working as an Associate Professor of the Faculty of Biological Sciences at the Andres Bello University, Chile and Associate Researcher of the Interdisciplinary Center for Aquaculture Research (INCAR), where he leads the Molecular Biotechnology laboratory. His research is focused on the understanding the molecular mechanisms regulating skeletal muscle growth in teleost. The application of this expertise has provided new insights in the field of stress response in marine fishes. Currently, he is focusing on the identification and characterization of cortisol-mediated non-genomic signaling in the stress response of salmonids, by using next-generation transcriptomic and proteomic tools.
Abstract:
In the last years next generation sequencing technologies (NGS) and RNA-seq have revolutionized the fields of transcriptomics, providing the possibility to investigate gene expression and pathways involved in countless biological processes of non-model aquatic animals. In recent years, there is a trend towards diversifying breeding species to maintain the sustainability of the global aquaculture industry. Among the cultivated marine species are the red cusk-eel (Genypterus chilensis) and fine flounder (Paralichthys adspersus). These marine fishes are highly valued in national and international markets due to exceptional flesh quality and high nutritional value. However, these species in captivity are susceptible to stress, showing low growth and high mortality rates, which could be due to alteration in the compensatory response to stress. In this work, we studied the effect of handling stress (acute stress) and high density stress (chronic stress) on the metabolic and growth response of G. chilensis and P. adspersus. Using Illumina RNA-seq technology, skeletal muscle and liver transcriptomes were analyzed, revealing a significant up-regulation of genes associated with liver angiogenesis and skeletal muscle atrophy under stress. Conversely, the down-regulated genes were associated with liver steatosis and skeletal muscle contraction. This work will not only allow consolidating the red cusk-eel and fine flounder’s commercial cultivation but also lay the foundation of marine aquaculture industry having a significant impact on national economic development.
Rakesh Kumar
George Washington University, USA
Title: Breast cancer transcriptome: From triple negative breast cancer to HER2-overexpressing isogenic TNBC Cells
Time : 16:45: 17:15
Biography:
Rakesh Kumar is an internationally recognized Cancer Biologist with a particular focus on breast cancer. His research interests are focused on the mechanisms of cancer progression with special emphasis on chromatin and cytoskeleton remodeling, and targeted cancer therapeutics. He has received several awards and honors for his research work since 1995. He has authored over 220 original research papers, 67 reviews, 10 book chapters and edited 6 books/volumes in the area of cancer research. He has trained over 65 fellows and students, and shared his knowledge by delivering over 220 invited, keynote or plenary lectures at academic institutions, universities and scientific meetings
Abstract:
In recent years, Kumar’s lab used high-throughput whole genome sequencing to gain a deeper genomic insight of the triple-negative breast cancer (TNBC), estrogen receptor positive and HER2 positive breast cancers, and revealed new regulatory intricacies and pathways in breast cancer. These results re-validated an expected inter- and intra-tumor genomic heterogeneity due to differential expression of transcripts and splicing and promoter switching. To address the issue of clonal origin of breast cancer, the laboratory also generated isogenic TNBC breast cancer clones stably expressing HER2 as a part of a master dissertation project, and identified HER2-modulated genes through microarray analysis. The laboratory continued with this theme as a part of a doctoral dissertation project and subjected these isogenic clones to RNA-sequencing analysis in the context of HER2-transcriptome. This phase of the work was centered on identifying differential expressed genes and alternative spliced transcripts, transcription and splicing factors modulated by HER2 as an attempt to explain the basis of the noted differential expression in isogenic clones.
An Yuan Guo
Huazhong University of Science and Technology, China
Title: Regulatory network analysis reveals miR-146b-5p within BCR-ABL1–positive microvesicles promotes leukemic transformation of hematopoietic cells
Time : 17:15: 17:45
Biography:
An Yuan Guo has completed his PhD from Peking University and Post-doctoral studies from VCU and Vanderbilt University. His research focuses on the transcription factor and ncRNA regulatory network in complex diseases with NGS data and bioinformatics database construction. He is an expert in bioinformatics database and developed a serial of databases (AnimalTFDB, miRNASNP and lncRNASNP). He developed an approach to study the microRNA and TF co-regulatory network in complex diseases. He has published about 50 papers in Molecular Psychiatry, Cancer Research, NAR, Bioinformatics, Briefings in Bioinformatics, Human Mutation etc and served as an Editor of Scientific Reports.
Abstract:
Evidence is accumulating that extracellular microvesicles (MV) facilitate progression and relapse in cancer. Using a model in which MVs derived from K562 chronic myelogenous leukemia (CML) cells transform normal hematopoietic transplants into leukemia-like cells, we defined the underlying mechanisms of this process through gene-expression studies and network analyses of transcription factors (TF) and miRNAs. We found that antitumor miRNAs were increased and several defense pathways were initiated during the early phases of oncogenic transformation. Later, oncomiRs and genes involved in cell cycle, DNA repair and energy metabolism pathways were upregulated. Regulatory network analyses revealed that a number of TFs and miRNAs were responsible for the pathway dysregulation and the oncogenic transformation. In particular, we found that miR-146b-5p, which was highly expressed in MVs, coordinated the regulation of cancer-related genes to promote cell-transforming processes. Notably, treatment of recipient cells with MV derived from K562 cells expressing mimics of miR-146b-5p revealed that it accelerated the transformation process in large part by silencing the tumor-suppressor NUMB. High levels of miR-146b-5p also enhanced reactive oxygen species levels and genome instability of recipient cells. Taken together, our findings showed how upregulation of oncogenic miRNAs in MVs promote hematopoetic cells to a leukemic state, as well as a demonstration for TF and miRNA coregulatory analysis in exploring the dysregulation of cancers and discovering key factors.
Byung Wook Yun
Kyungpook National University, South Korea
Title: Drought stress-mediated transcriptome profile reveals NCED as a key player modulating drought tolerance in different cultivars of P. davidiana (Korean Aspen)
Time : 17:45: 18:15
Biography:
Byung-Wook Yun has completed his PhD jointly at Kyungpook National University (KNU) and Korea Research Institute of Bioscience & Biotechnology (KRIBB) in 1998, investigating the function of plant peroxidases. He completed his Post-doctoral and senior research fellowship at the University of Edinburgh (UK), studying Nitric Oxide (NO) signaling in plant immune system, mentored by Professor Gary Loake. Currently he is working as an Associate Professor of the School of Applied Biosciences at KNU. His Plant Functional Genomics Lab is focusing on NO-mediated plant defense system toward both biotic and abiotic stresses using transcriptomics approaches.
Abstract:
Forest trees, including poplar, have evolved to overcome harsh environmental conditions including drought stress. Populus trichocarpa has been studied as a model poplar species through biomolecular approaches and is the first tree species to be genome sequenced. In contrast, the genome of P. davidiana, the Korean aspen, has not been sequenced and is considered highly tolerant to drought stress. In this study, we used high throughput RNA-Seq mediated leaf transcriptome analysis to investigate the response of 4 different P. davidiana cultivars to drought stress. Based upon preliminary studies including H2O2 measurements and histological staining, the cultivars were divided into two major groups “drought-tolerant (Seogwang9, Palgong2)” and “drought-susceptible (Palgong1, Junguk6-2)”. P. davidiana plants grown on MS (Murashige and Skoog) media for 8 weeks were air-dried for 10 minutes and leaves were harvested for transcriptome analysis along with untreated control samples. Following RNA-Seq, we compared the transcriptome profiles between the two groups for DEGs (Differentially Expressed Gene), GO (Gene Ontology) enrichment analysis, and identified common drought stress marker genes. Further analysis identified two distinct DEGs with contrasting expression patterns in the drought-sensitive and tolerant groups i.e. up-regulated in the drought-tolerant group while down-regulated in the sensitive group. BLAST analysis showed that both these genes encode 9-cis-epoxycarotenoid dioxygenase (NCED), a key enzyme required for ABA biosynthesis. This suggests a significant role of these two genes in conferring drought tolerance to P. davidiana cultivars in the drought-tolerant group. This study presents the first evidence of a significant role of NCED genes in regulating ABA-dependent drought stress responses in P. davidiana as it has already been shown that NCED regulate ABA-dependent drought adaptation via mRNA de-capping machinery in certain varieties of some plant species. We therefore, suggest the utility of these genes as genetic markers for differentiating drought tolerant and sensitive poplar cultivars.