Second International
Epigenomics & Sequencing 2008
Meeting on ‘Chromatin Methylation to Disease Biology & Theranostics’
July 14-15, 2008

The Joseph B. Martin Conference Center at Harvard Medical School
77 Avenue Louis Pasteur, Boston, MA 02115, USA

“A Unique Theme to Combine Chromatin biology and Diseases with Sequencing Chemistry”

Click Here For Brochure

Click Here For Agenda

Scientific Organizing Committee:

Krishnarao Appasani, PhD., MBA (Chair)
Founder & CEO
GeneExpression Systems, Inc. Waltham, MA USA

Laurie Jackson-Grusby, Ph.D.
Assistant Professor of Pathology, Children's Hospital, Harvard Medical School, Boston, MA

Shuji Ogino, MD., PhD.
Assistant Professor & Associate Pathologist
Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA

Topics or Highlights of the Meeting:

Mechanisms of Chromatin in gene regulation
Nuclear dynamics and Methylation Assays
Parental imprinting and Histone Deacetylation inhibitors as drugs
Epigenetic re-programming in stem cells
Cutting-edge sequencing technology; Epigenome Sequencing
Epigenetic regulatory processes in diseases & environment
PharmacoEpigenomics

AGENDA/SPEAKERS

Monday, July 14, 2008

8:00 A.M: Registration Open
9.00 AM – 6.00 PM Scientific Sessions

Tuesday, July 15, 2008

7:30 A.M: Registration Open
8.00 AM – 5.00 PM Scientific Sessions
5:00 PM Meeting Concludes

Confirmed Speakers:

	Keynote Speaker on July 14 AM Stephen B. Baylin, MD. Professor of Oncology & Medicine Virginia & D.K. Ludwig Professor for Cancer Research The Johns Hopkins University School of Medicine Baltimore, MD, USA Title: TBA
	Industry Keynote Speaker Mathias Ehrich, M.D., Ph.D. Talk on July 15 AM Sequenom, Inc. San Diego, CA, USA

	Shuji Ogino, MD., PhD. Associate Pathologist Department of Pathology, Brigham and Women's Hospital Assistant Professor of Pathology, Harvard Medical School Boston, MA, 02115, USA Title: Significance of Epigenomic Alterations in Colorectal Cancer
	Laurie Jackson-Grusby, Ph.D. Assistant Professor of Pathology Harvard Medical School Children's Hospital Boston Boston, MA 02115, USA Title:TBA
	John F. Beeler, Ph.D. Director, Business Development OncoMethylome Sciences, Inc. Durham, NC, USA Title: PharmacoMethylomics: Use of Methylation-Specific PCR (MSP) for the identification of predictive biomarkers
	Andres Leschziner, PhD. Assistant Professor of Molecular and Cellular Biology Harvard University Cambridge, MA, USA Title: Structural studies of ATP-dependent chromatin remodeling
	Kornelia Polyak, M.D.,Ph.D. Associate Professor of Medicine Dana-Farber Cancer Institute & Harvard Medical School Boston, MA, USA Title: TBA
	Zhenghe John Wang, Ph. D. Assistant Professor of Genetics Case Western Reserve University Cleveland, OH, USA Title: TBA
	Michelle M. Hanna, PhD. CEO & Scientific Director Ribomed Biotechnologies, Inc. Carlsbad, CA, USA Title: Abscription Based Biomarker Detection – Application to CpG Methylation
	Bin Yang, MD., PhD. Staff Pathologist & Director of Cancer Epigenetics Core Facility The Cleveland Clinic Foundation Cleveland, OH 44195, USA Title: Combined Epigenetic and Genetic Tests Enhance the Sensitivity of Detection of Papillary Thyroid Carcinoma in Fine Needle Aspiration
	Gerald Schock, Ph.D. Global Product Manager Epigenetics QIAGEN GmbH, Hilden, Germany Title: Reliable Methylation Analysis for Epigenetic Research: Novel technologies offering a complete and standardized workflow
	Jeff Falk, PhD. Director of Technology & Business Applications Aviva Systems Biology San Diego, CA, USA Title: TBA
	Oliver J. Rando, Ph.D., M.D. Assistant Professor of Biochemistry University of Massachusetts Medical School Worcester, MA, USA Title: TBA
	Yuriko Mori, M.D., Ph.D. Assistant Professor of Medicine Johns Hopkins School of Medicine Baltimore MD 21287, USA Title: TBA
	John L. Rinn, PhD. Assistant Professor of Pathology Beth Israel Deaconess Medical Center & Harvard Medical School & Associate Member of the Broad Institute Boston, MA, USA Title: TBA
	Johnathan R. Whetstine, Ph.D. Assistant Professor of Medicine Massachusetts General Hospital Cancer Center, Charlestown, MA, USA Tilte: TBA
	Zdenko Herceg, PhD. Head, Epigenetics Group International Agency for Research on Cancer (IARC) Lyon, France Title: Epigenetic changes in cancer as a signature of exposure and tumorigenesis
	Jei Kim, MD. Professor of Neurology Chungnam National University Hospital Taejon, South Korea Title: Epigenetic alterations developing in atherosclerotic plaque
	Tim Roloff, PhD. Friedrich Miescher Inst. For Biomedical Research Basel, Switzerland
	Tal Raz, PhD. Senior Scientist, Methods development group Helicos Biosciences Corporation Cambridge, MA, USA Title: Transcript Counting by Single Molecule Sequencing
	Kam-Wing Jair Research Scientist BioNumerik Pharmaceuticals San Antonio, TX USA
	Gabor T. Marth, D.Sc. Assistant Professor of Biology Boston College, Chestnut Hill, MA, USA Title: TBA

Will be included more from academia, pharma and biotech.....

Exhibitors are welcome to reserve their booth space early!

Please contact if you are interested in speaking in the scientific or Technology workshops of this meeting.

GeneExpression Systems, Inc.
P.O. Box 540170
Waltham, MA 02454 USA
Tel: (781) 891-8181
Fax: (781) 891-8234
E-mail: Genexpsys@expressgenes.com
www.expressgenes.com

Poster Abstract Submission by July 5, 2008

ALL ABSTRACTS

Epigenetic signatures define progenitor and differentiated cells in normal and neoplastic human breast tissue
Kornelia Polyak, M.D.,Ph.D., Associate Professor of Medicine, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
Boston, MA, USA

Noga Bloushtain-Qimron, Michail Shipitsin, Jun Yao, Kornelia Polyak
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA 02115

Cellular identity and differentiation states are defined by epigenetic programs. To investigate this issue we characterized the comprehensive DNA methylation and gene expression profiles of differentiated and progenitor-like cells from normal human breast tissue. We identified discrete cell type and differentiation state-specific DNA methylation patterns that were maintained in breast carcinomas. The expression of FOXC1 a transcription factor hypomethylated and highly expressed in lin-/CD44+ cells, induced a progenitor-like phenotype in differentiated mammary epithelial cells. Our findings have implications for understanding epigenetic programs regulating breast epithelial cell differentiation and the relevance of this to breast tumorigenesis.

Structural studies of ATP-dependent chromatin remodeling
Andres Leschziner, PhD., Assistant Professor, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA

ATP-dependent chromatin remodeling complexes are large (often > 1 MDa), multi-subunit assemblies that utilize the energy from ATP hydrolysis to non-covalently alter the structure of nucleosomes, playing a role in the regulation of chromatin dynamics. Despite a significant body of biophysical, biochemical and genetic data on these large (often > 1 MDa) complexes we do not yet understand how they remodel chromatin.
We are taking a structural approach to elucidating the mechanism of ATP-dependent chromatin remodeling and use as our main techniques three-dimensional electron microscopy (3D EM) and image analysis. Our model system is RSC, a remodeling complex from the yeast S.cerevisiae.

Combined Epigenetic and Genetic Tests Enhance the Sensitivity of Detection of Papillary Thyroid Carcinoma in Fine Needle Aspiration
Bin Yang, MD., PhD. Staff Pathologist & Director of Cancer Epigenetics Core Facility, Pathology & Laboratory Medicine Institute,The Cleveland Clinic Foundation
Cleveland, OH, USA

Papillary thyroid carcinoma harbors both genetic mutations of Ras and BRAF genes and promoter hypermethylation of a set of candidate tumor suppressor genes. It has been suggested that these genetic and epigenetic alterations may be mutually exclusive in papillary thyroid carcinoma, thereby, potentially limiting the clinical utility of single gene analysis due to the low sensitivity. In an attempt to improve the sensitivity of molecular testing of thyroid neoplasms, using Pyro Q24 we studied the plausibility of testing most frequent genetic and epigenetic alterations, namely N-Ras mutation at codon 61, BRAF mutation at V600E and promoter methylation of RASSF1a, p16, E-cadherin and MGMT in 50 thyroid fine needle aspiration specimens. Our preliminary results indicate that simultaneous detection of both genetic and epigenetic alterations significantly increases the sensitivity and is potentially useful in facilitating detection of thyroid papillary carcinoma in clinical settings.

Genome-wide ChIP-DSL Profiling of promoter methylation patterns associated with cancer and stem cell differentiation.
Jeffrey D. Falk, PhD., Director of Technology & Business Applications, Aviva Systems Biology, San Diego, CA, USA

A novel promoter array technology, ChIP-DSL (Chromatin Immunoprecipitation – DNA Selection and Ligation), was used for global promoter mapping of epigenetic modifications. Studies will be presented correlating global ChIP-DSL DNA Methylation with gene expression profiling data resulting in the elucidation of biomarkers associated with liver, brain, lung, breast and prostate cancer detection. Additional studies will be described using ChIP-DSL to identify unique promoter methylation patterns associated with various stages of human stem cell differentiation. We will also describe ongoing efforts to define the methylome of normal CD34+ cells, as well as promoter methylation changes associated with stem cells from AML leukemia patients.

DNA methylation microarray analysis of human colonic tissues
Yuriko Mori, M.D., Ph.D., Assistant Professor, Division of Gastroenterology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD
 
Recent technological advances enabled us to perform direct analysis of the genomic DNA methylation status in a genome-wide and locus specific manner. One of these emerging approaches is Methylated CpG island amplification-coupled with DNA microarray (MCAM). We have employed the Agilent human 244K CpG island microarray platform for our MCAM method, which enabled us a robust analysis of more than 100,000 CpG islands including over 7,000 gene promoter regions. This talk will discuss the characteristics of MCAM analysis in general and the outcome of our study on human colonic epithelial tissues utilizing this method.

Epitope tagging of endogenous proteins for genome-wide ChIP-chip studies
Zhenghe John Wang, Ph. D., Assistant Professor of Genetics, Case Western Reserve University Cleveland, OH, USA

Zhenghe Wang, Xiaodong Zhang and Peter Scacheri
Department of Genetics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106

Studying the function of proteins often relies on antibodies with high affinity and specificity, yet such antibodies are not available for most proteins. In principle, this problem can be circumvented by utilizing ectopically expressed epitope-tagged proteins recognizable by well-characterized antibodies, but such expression is no longer endogenous. To surmount this problem, we developed a strategy whereby recombinant adeno-associated virus (rAAV) is used to epitope tag endogenous loci by homologous recombination-mediated "knock-in". The tagging approach is easy, can be applied to numerous loci and multiple somatic cell lines, and facilitates western, immunofluorescence, and immunoprecipitation analyses of targeted proteins. Of particular interest, we show that an endogenously tagged transcription factor, STAT3, can be successfully utilized for chromatin immunoprecipitation coupled with DNA microarray (ChIP-chip) analysis. The knock-in approach provides a general solution for the study of proteins for which antibodies are substandard or not available.

Epigenetic alterations developing in atherosclerotic plaque
Jei Kim, MD., Professor of Neurology, Chungnam National University Hospital, Joong-ku, Taejon, South Korea

Epigenetic alterations have been well-known as a pathological mechanism developing in age-related disease, particularly cancer. Although atherosclerosis is a typical age-related disease, epigenetic alteration has not been well known so far. In recent studies, estrogen receptor alpha and beta showed promoter methylation changes in anthersclerotic tissues and vascular aging. VEGF and VEGFR also showed evidences of promoter methylation changes in atherosclerotic plaque. In this presentation, I will discuss evidences of gene-specific methylation developing in atherosclerotic tissues.

Epigenetic changes in cancer as a signature of exposure and tumorigenesis
Zdenko Herceg, PhD. Epigenetics Group Leader, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, F-69008, Lyon, France

Almost spectacular progress in the field of epigenetics and epigenomics is now recognized as critical for understanding the causes of complex diseases such as cancer. The potential utility of epigenetics in cancer research is highlighted by the fact that many funding agencies put cancer epigenetics on the priority list. Epigenetic events play key roles in the control of key cellular process and their deregulation has been associated with many stages of cancer development and progression. A number of critical processes found in cancer cells, such as silencing of tumour suppressor genes, activation of oncogenes, aberrant cell cycle, and defects in DNA repair, can be caused by aberrant epigenetic states. Although the role of epigenetic events is supported by both epidemiological and experimental studies, the precise contribution of epigenetic mechanisms and cellular targets epigenetic alterations to human cancers are largely unknown. Remarkable technological advances in epigenetics and epigenomics now allow powerful screening of large series of samples with unprecedented resolution. These approaches are beginning to reveal a number of genes (tumor suppressors and other cancer-associated genes) susceptible to inactivation through epigenetic mechanism. Epigenetic profiling using both genome-wide and candidate-gene approaches in normal tissues and different tumor types will help to elucidate the mechanism underlying tumourigenesis. Technological advances in epigenetics and epigenomics have now been exploited to identify specific epigenetic targets, environmental factors, and the critical windows of vulnerability to environmentally induced epigenetic changes in cancer. A list of genes and gene networks that are targets of epigenetic alterations are likely to grow with the progress of major programmes in the field. New emerging concepts involving epigenetic mechanisms and technological advances in epigenomics and well as their implication for mechanistic understanding of carcinogenesis and the development of preventive strategies will be discussed.

Transcript Counting by Single Molecule Sequencing
Tal Raz, PhD., Senior Scientist, Methods development group, Helicos Biosciences Corporation, Cambridge, MA, USA

Tal Raz, Doron Lipson, Alix Kieu and Marie Causey
Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA, USA

Accurate and sensitive full transcriptome profiling is pertinent to the understanding of cellular mechanisms. We have developed a transcript counting method using single molecule sequencing to generate efficient, unbiased, and accurate quantification for the complete transcriptional dynamic range of typical cells. Our method is not subject to the typical biases inherent to most digital gene expression profiling. We demonstrate the application of single molecule transcript counting requiring no ratiometric comparison between samples for accurate inventorying of the complete transcriptome of a Saccharomyces cerevisiae mRNA, and a human placenta mRNA. We compare our results to microarray and qPCR measurements and demonstrate the ability to quantify low-abundance transcripts.
Epigenetic Therapy: a New Era for Cancer Treatment
Kam-Wing Jair, PhD. Research Scientist, BioNumerik Pharmaceuticals, Inc., San Antonio, USA

The field of epigenetics has made significant progress over the last twenty years and epigenetics is increasingly being recognized as one of the important players in the development of human diseases such as cancer. DNA methylation, histone modification and nucleosome remodeling are critical biological processes that regulate the epigenomic composition in both normal and cancer cells. Epigenetic therapy using inhibitors of chromatin modifying enzymes including histone deacetylase (HDAC) inhibitors and DNA methyltransferase (DNMT) inhibitors have been used in clinical trials with remarkable results. I will discuss how the next generation of epigenetic drugs may be developed and approaches for studying the mechanisms of action for these drugs.

PharmacoMethylomics: Use of Methylation-Specific PCR (MSP) for the identification of predictive biomarkers
John F. Beeler, Ph.D.,Director, Business Development, Pharmacogenomics, North America, OncoMethylome Sciences, Inc., Durham, NC, USA

OncoMethylome Sciences is utilizing its patented Methylation-Specific-PCR (MSP) technology to measure the methylation status of genes that could be used to personalize cancer therapy. Methylation of the DNA-repair gene, MGMT, has been shown to have predictive value in brain cancer patients undergoing alkylating agent-based therapy. Currently integrated into over thirty clinical trials, evaluation of the MGMT methylation status in tumor tissue can optimize patient selection and trial design while providing insight into therapy response. OncoMethylome is partnering with numerous pharmaceutical companies to identify additional predictive methylation biomarkers using a highly versatile and integrated high throughput methylation profiling platform.

Significance of Epigenomic Alterations in Colorectal Cancer
Shuji Ogino, MD., PhD., Associate Pathologist, Department of Pathology, Brigham and Women's Hospital & Assistant Professor of Pathology, Harvard Medical School
Boston, MA, USA

Epigenomic aberrations are important mechanisms in carcinogenesis. In colorectal neoplasia pathways, promoter CpG island methylation and genome-wide DNA hypomethylation play significant roles. In particular, the CpG island methylator phenotype (CIMP) has been established as a distinct phenomenon in colorectal cancer. Utilizing large prospective cohort studies, we have been examining the relations between epigenomic aberrations, germline genotypes, somatic genetic events, and patient survival. We have found that epigenomic alterations can be biomarkers for the elucidation of carcinogenic process as well as for patient prognostication.

Reliable Methylation Analysis for Epigenetic Research: Novel technologies offering a complete and standardized workflow
Gerald Schock, PhD., Global Product Manager Epigenetics, QIAGEN GmbH, Germany

The analysis of changes in DNA methylation is challenging due to the lack of standardized methods for providing reproducible data. This presentation will highlight steps of critical importance — such as the complete conversion of unmethylated cytosine and the importance of a DNA protection mechanism to avoid excessive DNA degradation.

We will describe a new method for the reliable amplification of the entire bisulfite converted genomic DNA — the bisulfitome — to overcome limitations in methylation analysis derived by limited DNA amounts. We also present a newly developed DNA Polymerase which enables single base discrimination in Methylation Specific PCR (MSP) reactions. In addition, we will provide information on the improvement of highly sensitive TaqMan probe based real-time PCR (MethyLight Assays) and discuss control experiments that can increase the success of DNA methylation assays.

Abscription Based Biomarker Detection – Application to CpG Methylation
Michelle M. Hanna, PhD., CEO & Scientific Director, Ribomed Biotechnologies, Inc., Carlsbad, CA, USA

Abscription is a robust, linear, isothermal molecular detection process that is resistant to blood, saliva and most environmental substances that inhibit the Polymerase Chain Reaction (PCR). Abscription can be used for detection of DNA, RNA, protein, or CpG methylation with a common set of reagents, allows detection of multiple targets in a single sample and can be formatted for several detection methods. Ribomed is developing abscription-based assays for determining the methylation levels of one or more CpG sites or islands in a sample. Assays can be applied to native DNA or deaminated and amplified DNA when limited sample is available.