Program and Abstracts

Program

7:30 - 8:15   Registration
 
Session I
8:15 - 8:20   Opening Remarks & Keynote Introduction
8:20 - 9:05   Keynote: Ed Scolnick - Broad Institute of MIT and Harvard
9:05 - 9:35   Ed Holson - Broad Institute of MIT and Harvard
9:35 - 10:05
 
  Susan Lindquist - Whitehead Institute for Biomedical Research and HHMI, Dept. of Biology, MIT
10:05 - 10:25   Networking/refreshment break
10:30 - 11:00   Ana Rodriguez - New York University
11:00 - 11:30   Matt Boxer - NIH Chemical Genomics Center
11:30 - 12:00
 
  Lee Rubin - Harvard Stem Cell Institute, Harvard University
     
12:00 - 1:00   Lunch break (boxed lunch provided)
   
Session II
1:00 - 1:05   Opening Remarks & Keynote Introduction
1:05 - 1:50
 
  Keynote: Stuart Schreiber - Broad Institute of MIT and Harvard
1:50 - 2:20   Stuart Orkin - Dana-Farber Cancer Institute
2:20 - 2:50   Barbara Imperiali - Massachusetts Institute of Technology
2:50 - 3:15   Networking/refreshment break
3:15 - 3:45   Stephen Haggarty - Massachusetts General Hospital
3:45 - 4:15   Channing Yu - Dana-Farber Cancer Institute
4:15 - 4:45   Kiran Musunuru - Harvard University
4:45 - 5:00   Closing Remarks, followed by reception

 

Abstracts

Session I
Chair: Mike Foley, Broad Institute of MIT and Harvard

Keynote
Unraveling the genetic mysteries of psychotic illnesses.
Edward Scolnick, M.D.
The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard

Large whole genome association studies have identified loci associated with risk for schizophrenia and bipolar illness, exome sequencing studies have also been carried out. Results will be presented with implications for new approaches for drug discovery and diagnosis. Over the next two years whole exome sequencing data will be available on at least 5000 cases of schizophrenia and 5000 controls, 600 trios, and additional genome and exome scans on several thousand samples. The rational is to find the genetic causes of this illness and thus help to define new pathways and targets for drug discovery.

 

Presentations
HDACs in memory and cognition: Development of isoform selective inhibitors with improved CNS drug properties
Ed Holson
Broad Institute of MIT and Harvard

Deficits in cognition and memory are associated with many disease states including Alzheimer’s disease, Rubinstein Taybi Syndrome and Schizophrenia. Altered acetylation states and the effects on specific gene expression and protein regulation underlie components of CNS disorders. Hypoacetylation states are found in neurological contexts and HDACs offer an attractive target to remedy these altered acetylation states. We describe our efforts to optimize HDAC inhibitors with greater isoform selectivity, improved CNS drug properties and efficacy in mouse models of learning and memory.

 

Diverse phenotypic screens for problems in protein homeostasis: cancer, neurodegeneration, antifungals, and malaria
Susan Lindquist, Ph.D.
Whitehead Institute for Biomedical Research and HHMI, Dept. of Biology, MIT

In living cells, proteins are packed together in a crowded and constantly fluctuating environment, which increases their efficiency but also creates many problems in protein homeostasis. The heat-shock response and its component chaperone proteins protect cells from the protein-folding problems that arise with a wide variety of stresses. We use yeast cells as “living test tubes” to investigate these problems and to discover potential new therapies for the diseases that can result. While there are many important differences between yeast and mammalian cells, much of the basic protein-folding and chaperone machinery is similar. Importantly, yeast is inexpensive and easy to grow and manipulate, even in high-throughput screens. We have modeled the phenotypes associated with a diverse array of diseases by inserting exogenous proteins into yeast. In the case of neurodegenerative diseases, we have inserted disease-associated human proteins to recapitulate the toxicity seen in neurons. And, we have modeled the unique protein-folding process of the malarial parasite by inserting malarial heat-shock proteins into yeast. We have also employed reporter constructs in yeast that measure inhibition or activation of the heat-shock response. We have taken advantage of these models to conduct high-throughput screens and discovered both genes and compounds that rescue the phenotypes caused by these misfolded proteins. Hits from these screens have been validated in higher order disease models, demonstrating the utility of the yeast system as a discovery platform.

 

In vivo activity of anti-Trypanosoma cruzi compounds selected from a high throughput screen
Ana Rodriguez
New York University

Novel technologies that include recombinant pathogens and rapid detection methods are contributing to the development of drugs for neglected diseases. Based on the results from the first high throughput screening (HTS) to test compounds for activity against Trypanosoma cruzi trypomastigote infection of host cells, we selected 23 compounds, which were reported to have high anti-trypanosomal activity and low toxicity to host cells. These compounds were highly purified and their structures confirmed by HPLC/mass spectrometry. The compounds were tested in vitro, where about half of them confirmed the anti-T. cruzi activity reported in the HTS. We have also developed a rapid assay to test anti-T. cruzi compounds In vivo using mice infected with transgenic T. cruzi expressing luciferase as a model for acute infection. The compounds that were active in vitro were also tested In vivo using this new assay, where we found two related compounds that present strong anti-T. cruzi activity in the mouse model.

Our findings evidence the benefits of chemical HTS, for the drug discovery pathway of neglected diseases, but also caution about the need to confirm the results in vitro. Also, rapid methods of In vivo screening based in luciferase-expressing parasites can be very useful to prioritize compounds early in the chain of development.

 

Identification of Galactokinase Inhibitors: Tools to study galactose metabolism and Classic Galactosemia
Matt Boxer
NIH Chemical Genomics Center

Classic Galactosemia (CG) is a rare genetic metabolic disorder (1/60,000 births) that is characterized by decreased production of galactose-1-phosphate uridyltransferase (GALT), an enzyme responsible for the conversion of galactose-1-phosphate (gal-1-p) to glucose-1-phosphate. The resulting elevated intracellular concentration of gal-1-p is believed to be the major pathogenic mechanism in classic galactosemia that leads to a myriad of secondary symptoms and, if untreated, death of the patient. Galactokinase (GALK) is an upstream enzyme in the Leloir pathway that is responsible for conversion of galactose to gal-1-p. Therefore, it was hypothesized that the identification of a small-molecule inhibitor of GALK would act to decrease levels of gal-1-p and enable studies on the role of gal-1-p in CG. At the NIH Chemical Genomics Center (NCGC), in collaboration with Professor Kent Lai of the University of Utah, a quantitative high-throughput screening (qHTS) assay was run and identified a lead compound bearing a 1,4-dihydropyrimidine core. Subsequent rounds of medicinal chemistry have provided interesting structural-activity-relationship data for this chemical series and have resulted in the first small molecule to show clear inhibition of GALK in primary patient fibroblast cells.

 

Finding Therapeutics for Motor Neuron Diseases
Lee L. Rubin
Harvard Stem Cell Institute, Harvard University

Several aspects of neurodegenerative disease have made them especially challenging to study: First, they tend to involve specific sets of neurons. Second, they are mostly late-onset. Third, most of the diseases are predominantly sporadic, with only a minor genetic component. Finally, neurons, especially individual types or neurons, have traditionally been very difficult to isolate in large numbers and high degrees of purity. I will discuss how new advances in stem cell biology may provide solutions for some of these problems and permit new insights into the causes of particular neural disorders and the discovery of transformative therapeutics.

 

Session II
Chair: Michelle Palmer, Broad Institute of MIT and Harvard

Keynote
Linking genetic features of human cancers to cancer therapeutics.
Stuart Schreiber
Broad Institute of MIT and Harvard

The ability to understand cancer genomes and the advances in small-molecule science provide a radically new foundation for creating the medicines we’ve only imagined since declaring the war on cancer decades earlier – the ones needed to take out this disease. We’ve learned the power of linking genetic features of cancers to drug efficacies – and that the extraordinary consequences of exemplars like imatinib are not restricted to this drug and its genetically matched leukemia, CML. Recent studies show, for example, high response rates with genetically matched drugs targeting extremely challenging cancers such as melanoma. These advances are encouraging, but they still only affect < 1% of patients suffering today from cancer. And the most dramatic cases are ones rationalized during or even after the discovery of the actual small-molecule therapeutic (e.g., the compound later named imatinib).

In my ECASS Lecture, I will discuss a project that aims to understand the relationship of the genetic features of human cancers to small-molecule sensitivities (as a surrogate for drug efficacies) as comprehensively as possible. The project also aims to discover small-molecule probes to test the novel hypotheses that are emerging in physiologically relevant contexts.

 

Presentations
Targeting BCL11A for reactivation of fetal hemoglobin (HbF)
Stuart Orkin
Dana-Farber Cancer Institute

The major hemoglobin disorders are due to mutations affecting either the structure (sickle cell anemia) or expression (thalassemia) of the β-chain of adult hemoglobin (HbA, α2β2)). During development γ-globin-containing fetal hemoglobin (HbF, α2γ2) predominates and is replaced by HbA around birth. In the adult HbF persists to the level of ~ 1-2% and subject to genetic control. Increased HbF greatly ameliorates the severity of sickle cell anemia and thalassemia. GWAS studies identified the BCL11A locus on human chromosome 2p as a site of genetic variation that correlates with HbF levels in populations. Through a series of ex vivo and in vivo (mouse) experiments we demonstrated that BCL11A is a major regulator of the γ-β globin switch in development and silencer of γ-globin expression in adult erythroid cells. Molecular studies reveal that BCL11A (with associated proteins) occupies critical elements in erythroid chromatin. Biochemical studies show that BCL11A interacts and funcitons with multiple corepressor/epigenetic regulators. Taken together, these findings validate BCL11A as a target for downregulation (or inhibition) to reactivate HbF for treatment of hemoglobin disorders. Various screens have been initiated to discover novel small molecule inducers of HbF that are dependent on BCL11A. The goal of these efforts is the development of leads for new therapeutics.

 

Targeting Prokaryote-Specific Saccharide Biosynthesis in Microbial Pathogens
Barbara Imperiali
Massachusetts Institute of Technology

Cell surface glycoconjugates, including the lipopolysaccharide component of the outer cell wall and cell surface N- and O-linked glycoproteins of numerous medically relevant Gram-negative bacterial pathogens, have been characterized in molecular detail and found to be essential for virulence and pathogenicity. These glycoconjugates commonly include highly modified carbohydrate building blocks such as di-N-acetyl bacillosamin, legionaminic acid and pseudaminic acid that are prokaryote specific and not found in the glycoconjugates of eukaryotic cells. Current research in the Imperiali group focuses on the development and in vitro and in vivo validation of inhibitors to enzymes involved in the conversion of UDP-GlcNAc into UDP-di-N-acetyl-bacillosamine (UDP-diNAcBac) in the N- and O-linked protein glycosylation pathways of C. jejuni and N. gonorrhoeae. Since UDP-diNAcBac is a critical intermediate in the pathways that result in the biosynthesis of the bacterial glycoconjugates, these inhibitors will be valuable as selective chemical tools to elucidate the fundamental roles of highly modified saccharides in microbial pathogenesis.

 

Targeting Neuropsychiatric Disease Mechanism Using Patient-Specific Stem Cell Models
Stephen Haggarty
Massachusetts General Hospital

Major challenges for the field of neuropsychiatry are the limited knowledge of disease pathogenesis and the fundamental paucity of disease-modifying targets whose molecular mechanisms are firmly rooted in knowledge of the underlying etiology. To begin to address these limitations, here we will describe recent progress toward developing human induced pluripotent stem cell (iPSC) models and to subsequently derive neural progenitors that can expanded and differentiated in vitro into functional neurons under HTS compatible conditions. The ability to routinely create iPSC-derived human neurons with defined genotypes on a large scale opens up new avenues for investigating disease pathogenesis in physiologically relevant model systems and for novel target identification/validation using small-molecule probes and RNAi. Given emerging evidence suggesting that neuroplasticity, the ability of the nervous system to undergo adaptive changes in structure and function during development and in response to neural activity, plays a fundamentally important role in mental health and may be compromised in the context of neuropsychiatric disease, we have developed a panel of assays that measure key mechanisms of neuroplasticity using these iPSC-derived human neurons. To illustrate these advances and future opportunities, examples of generating and characterizing iPSC models of Fragile X syndrome, a monogenetic disorder that is the leading inherited cause of intellectual disability, and bipolar disorder, a genetically complex disorder will be described.

 

Decoding cancer vulnerabilities simultaneously in mixtures of barcoded tumor cell lines with PRISM
Channing Yu
Dana-Farber Cancer Institute

Patients with the same type of cancer may have alterations in distinctly different genetic pathways, and these differences may determine the success of treatment with a given chemotherapeutic agent. Those patients with tumors containing genetic alterations not found in current drug development models are less likely to benefit from novel targeted therapies. Unfortunately, evaluation of potential novel treatments across a range of genetic dependencies is currently limited largely by cost and labor. To address this, we have created a novel technology, PRISM (Profiling Relative Inhibition Simultaneously in Mixture), to effectively analyze functional responses of multiplexed cancer cells across a broad range of genotypes in a high-throughput manner. Introduction of unique DNA “barcodes” into cancer cell lines allows different lines to be mixed together for concurrent treatment with the same agent; detection of barcodes of surviving lines using microbead hybridization reflects relative numbers of surviving cells. We have created a panel of 100 barcoded cancer cell lines which together represent 18 different tumor types. Performing PRISM analysis using 28 active chemotherapeutic agents against these 100 cell lines in mixture effectively and efficiently recapitulates results from more laborious assays of cell viability. This functional assay will facilitate rapid identification of lead compounds which demonstrate specific activity against predefined subclasses of tumors and enhance discovery of those genetic alterations which are linked most strongly to drug response.

 

From genotype to phenotype at the chromosome 1p13 cholesterol and heart attack locus: implications for drug development
Kiran Musunuru
Harvard University

Recent genome-wide association studies (GWASs) have identified a locus on chromosome 1p13 as strongly associated with both serum low-density lipoprotein cholesterol (LDL-C) and myocardial infarction (MI) in humans. We have shown through a series of studies in human cohorts and human-derived hepatocytes that the minor allele of a common noncoding polymorphism at the 1p13 locus, rs12740374, creates a C/EBP transcription factor binding site, increases the hepatic expression of the SORT1 gene, and reduces plasma LDL-C and very low-density lipoprotein (VLDL) particle levels by modulating hepatic VLDL secretion. Thus, we have obtained functional evidence for a novel regulatory pathway for lipoprotein metabolism and suggest that modulation of this pathway may alter risk for MI in humans. We have undertaken small molecule screens to identify probes that increase SORT1 expression in cultured human hepatoma cells and thereby replicate the effects of the minor allele of rs12740374.