Download INTERNSHIP OFFERS SUMMER 2014

INTERNSHIP OFFERS
SUMMER 2014
INTERNSHIP OFFERS
Internship #1: Structural and molecular determinants of the functional selectivity of G protein-coupled receptors ............. 3
Internship #2: Functional characterization of mutant forms of MC4R involved in genetic severe obesity ............................. 4
Internship #3: ERM regulation during cell division ................................................................................................................... 5
Internship #4: Generation of Drosophila mutants for candidate Rab11-GAP proteins ............................................................ 6
Internship #5: Cancer biomarkers development: An integrated approach .............................................................................. 7
Internship #6: SCL and LMO1 oncogenes disrupt thymocyte development............................................................................. 8
Internship #7: Evaluation of chemical inhibitors of motor proteins in vitro and in live cells ................................................... 9
Internship #8: Characterization of the mitotic motor protein kif14 that is linked to cancer progression ............................. 10
Internship #9: Understanding how adult stem cells divide in vivo ......................................................................................... 11
Internship #10: Complementary roles of BAF60A and BAF60B during the lymphoid vs myeloid differentiation .................. 12
Internship #11: Mechanisms of action of full antiestrogens in breast tumor cells ................................................................ 13
Internship #12: Prediction of lncRNA-protein interactions in synaptogenesis ....................................................................... 14
Internship #13: Deciphering the long non-coding RNA address code .................................................................................... 15
Internship #14: Functional genomics of thymic epithelial stem cells ..................................................................................... 16
Internship #15: Characterisation of the yeast Cas5 regulon................................................................................................... 17
Internship #16: Studying the impact of somatic mutations of RSK in cancer ......................................................................... 18
Internship #17: Generation of experimental leukemia cell lines from human cord blood stem cells .................................... 19
Internship #18: Characterization of new Ras/MAPK pathway components........................................................................... 20
Internship #19: Regulation of protein sumoylation in response to DNA damage. ................................................................. 21
Internship #20: Cell cycle and DNA damage regulation of the histone deacetylase Hst3 ...................................................... 22
Internship #21: Using model leukemias to study the genetic determinants of pediatric acute myeloid leukemia ............... 23
Internship #1:
Structural and molecular determinants of the functional selectivity of
G protein-coupled receptors
Research team:
Dr Michel Bouvier
Molecular Pharmacology Research Unit
Contact information:
 [email protected]
 http://www.iric.ca/en/research/principal-investigators/michel-bouvier/
Project description:
Based on the 3D crystal structure of the 2-adrenergic receptor, the Bouvier laboratory has identified receptor
domains and residues that play specific roles in activating distinct downstream effectors (ex: Gs, Gi, arrestins,
cAMP production, MAPK activation, endocytosis, etc..). This allows proposing a molecular/structural basis
explaining ligand-biased signalling (ie: different ligands can modulate distinct downstream effectors with
different efficacies) of G protein-coupled receptors. The project will aim at assessing the influence of the
diverse receptor domains and residues in the functionally selective response of a collection of adrenergic
ligands. The response profiles obtained for different ligands will then be translated in structural terms to
determine the receptor conformational states responsible for ligand-biased functional selectivity. This project
should provide new pharmacological and structural knowledge that could be used to rationally design new
classes of drugs with define signalling selectivity and thus, improved therapeutic potential.
Techniques used:
Site directed mutagenesis, cell culture, protein heterologous expression, Western blot analysis, ELISA, receptor
activity and second messenger generation using BRET-based biosensors.
Key words:
G Protein-Coupled Receptors, Cell signalling, 3D structure, Modelling, Pharmacology, G proteins
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Internship #2:
Functional characterization of mutant forms of MC4R involved in genetic
severe obesity
Research team:
Dr Michel Bouvier
Molecular Pharmacology Research Unit
Contact information:
 [email protected]
 http://www.iric.ca/en/research/principal-investigators/michel-bouvier/
Project description:
Mutations in the gene encoding the melanocortin type-4 receptor (MC4R) represent the largest monogenetic
cause of early onset severe obesity; a disease increasing the probability of developing cardiopulmonary
diseases as well as divers cancers. The Bouvier laboratory discovered that the majority of the disease-causing
MC4R mutations (more than 75) lead to the intracellular retention of the receptor due to improper folding and
recognition by the endoplasmic reticulum quality control system of the cells. This miss-targeting of the
receptor is the cause for the loos of function phenotype and the development of the obesity phenotype
resulting from the loss of appetite regulation and energy expenditure under the control of MC4R. The Bouvier
laboratory has also identified small drug-like molecules, known as pharmacological chaperones, that can rescue
the cell-surface targeting of the function and restores the signalling activity of at least one of the signalling
cascades (Gs-mediated activation of the adenylyl cyclase and cAMP production) engaged by the MC4R. These
pharmacological chaperones therefore represent drug candidates for the development of novel therapies for
MC4R-caused obesity. However, the MC4R can also engage other signalling pathways. These include the
activation of MAP-kinases, recruitment of arrestin and most likely the stimulation of additional G proteins.
The present project therefore aims at determining if the MC4R pharmacological chaperones can restore the
ability of the mutant forms of the receptor toward these different pathways. For this purpose one of the most
frequent mutation R165WMC4R will be used as a test case. We also have generated a mouse model harbouring
this obesity-causing mutation, allowing to test the efficacy of the pharmacological chaperones in vivo.
Techniques used:
Site directed mutagenesis, cell culture, protein heterologous expression, Western blot analysis, ELISA, receptor
activity and second messenger generation using BRET-based biosensors.
Key words:
Genetic disease, Early onset severe obesity, Melanocortin type 4 receptor, protein folding, protein targeting,
Pharmacological chaperones, drug Discovery
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Internship #3:
ERM regulation during cell division
Research team:
Dr Sébastien Carréno
Cellular Biology of Mitotis Research Unit
Contact information:
 [email protected]
 http://www.iric.ca/en/research/principal-investigators/sebastien-carreno/
Project description:
Cell division involves a tight spatiotemporal control of cell shape transformations. Early in mitosis, the cortex
tightens, causing the cell to become round. During anaphase, the poles relax and the equator contracts,
allowing the cell to stretch and eventually split. Then the cellular cortex relaxes to allow cells to re-enter
interphase. Although this series of cell shape transformations were originally described more than 130 years
ago, the underlying mechanisms remain poorly understood. We have established that Ezrin, Radixin, Moesin
(ERM) proteins, control cell morphogenesis during mitosis. During mitosis Drosophila Moesin is activated by
phosphorylation and its localization dictates cell shape transformations. Until early anaphase, dMoe is spread
around the cortex, helping to keep the cell spherical. Subsequently dMoe begins to disappear from the poles
and build up at the equator. We have recently identified a regulatory network that provides a spatiotemporal
framework necessary for mitotic cell morphogenesis. We found that the increase in cortical rigidity that drives
cell shape remodelling at the interphase/mitosis transition involves a Pp1-87B_(phosphatase)/Slik_(kinase)
molecular switch that spatially and timely regulates dMoe phosphorylation and activation.
This research project aims to further understand how dMoe activating networks are controlled. This process
being critical for cancer metastasis, our research will help identify novel cellular targets to design new
therapeutics against cancer.
Techniques used:
Functional genomics, cloning, RNAi, 5D time-lapse microscopy, cell biology
Key words:
Cytokinesis, ERM proteins, actin, cancer
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Internship #4:
Generation of Drosophila mutants for candidate Rab11-GAP proteins
Research team:
Dr Gregory Emery
Vesicular Trafficking and Cell Signalling Research Unit
Contact information:
 [email protected]
 http://www.iric.ca/en/research/principal-investigators/gregory-emery/
Project description:
During this internship, the student will generate mutants for GAP proteins acting potentially on the small
GTPase Rab11. The student will then test for the effect of the loss-of-function of these proteins on asymmetric
cell division in the peripheral nervous system and during collective cell migration.
Techniques used:
Drosophila genetics, cell biology, molecular biology
Key words:
Small GTPase, Drosophila, cell migration, asymmetric cell division
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Internship #5:
Cancer biomarkers development: An integrated approach
Research team :
Dr Louis Gaboury
Histology and Molecular Pathology Research Unit
Contact information :
 [email protected]
 http://www.iric.ca/en/research/principal-investigators/louis-gaboury/
Project description:
Most cancers (lung, breast, colon etc.) are heterogeneous. At present, there is a great interest to segregate
each cancer into clinically relevant subtypes in terms of prognosis and response to treatment. To that end, we
propose an integrated approach using clinical-pathologic metrics (histological subtypes, tumor size, nodal
involvement, metastasis), immunohistochemistry on tissue microarrays constructed from paraffin embedded
fixed tumor tissues and mutational analysis on the most frequent genes altered in cancer as a means to identify
new biomarkers.
Techniques used:
Automated Immunohistochemistry, in situ hybridization, Tissue microarrays, Mutational analysis using Next
Generation Sequencing
Key words:
Breast Cancer, Colon Cancer, Functional Genomics, Pathology, Personalized Medicine
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Internship #6:
SCL and LMO1 oncogenes disrupt thymocyte development
Research team:
Dr Trang Hoang
Hematopoiesis and Leukemia Research Unit
Contact information:
 [email protected]
 http://www.iric.ca/en/research/principal-investigators/trang-hoang/
Project description:
SCL and LMO oncogenes are frequently activated by chromosomal translocations in T-lineage acute
lymphoblastic leukemia (T-ALL) in children. We have a transgenic mouse model in which the SCL and LMO1
oncogene induce leukemia. Our results indicate that the oncogenic background inhibit differentiation in the
thymus by inhibiting the activity of the transcription factors HEB and E2A, two factors essential to the
development of T lymphocytes. The goal of this project is to determine the molecular basis by which SCL and
LMO1 oncogenes induce leukemia.
Techniques used:
Flow cytometry, cell cycle analysis, quantitative RT-PCR, western-blot, immunofluorescence
Key words:
Oncogene, leukemia, T lymphocyte, transcription factors
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Internship #7:
Evaluation of chemical inhibitors of motor proteins in vitro and in live cells
Research team:
Dr Benjamin Kwok
Chemical Biology of Cell Division Research Unit
Contact information:
 [email protected]
 http://www.iric.ca/en/research/principal-investigators/benjamin-kwok/
Project description:
The formation of the mitotic spindle, a microtubule-based machine, is required for chromosome segregation
during cell division. Inhibition of spindle assembly blocks cell division and is a viable mean to treat cancer.
Paclitaxel, one of the most successful chemotherapeutics, targets tubulin, which is the building block of
microtubules, and inhibits its polymerization dynamics. However, its success has been limited by the
development of drug resistance in patients. Therefore, alternative strategies are needed to overcome this
hurdle.
Kinesin motor proteins which have the ability to control microtubule organization and polymerization dynamics
provide attractive targets for chemical inhibition. Recently, we have completed two high-throughput screens
to identify small molecule chemical inhibitors for kinesins. From 110,000 compounds that we have screened,
we obtained about more than one hundred candidate hits with different level of selectivity against different
kinesin families. We have now completed the initial phase of characterizing the candidate hit compounds in
vitro using biochemical assays and in cells using high-resolution microscopy. This internship project is to help
determine the precise mechanisms of action of these kinesin inhibitors on enzymatic activity of the motor
proteins and their impact on mitotic processes such as spindle assembly and chromosome segregation. Our
ultimate goal is to understand how we can use these small molecules to suppress cell proliferation as a way to
treat cancer.
Techniques used:
Biochemistry, cell culture, microscopy
Key words:
Chemical biology, cancer, microscopy, cell biology, motor proteins
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Internship #8:
Characterization of the mitotic motor protein kif14 that is linked to
cancer progression
Research team:
Dr Benjamin Kwok
Chemical Biology of Cell Division Research Unit
Contact information:
 [email protected]
 http://www.iric.ca/en/research/principal-investigators/benjamin-kwok/
Project description:
The mitotic kinesin kif14 has been shown to be overexpressed in multiple cancers. Its overexpression correlates
positively with disease progression and poor prognosis. In addition, kif14 is a prime candidate oncogene on
chromosome 1q32, a hot spot of genomic gain found in many of these cancers. Depletion of kif14 in cultured
human cancer cells lead to chromosome segregation defects, cytokinesis failure, and apoptosis. Despite its
importance, kif14 is one of the most understudied kinesins. There are less than 40 articles on kif14 published
to date. The molecular basis of kif14’s role in tumorigenesis and in mitosis remains largely unknown. We have
successfully purified active recombinant kif14 constructs and solved the crystal structure of Kif14 motor
domain. Our recent data revealed many properties of Kif14 that are distinctly different from conventional
microtubule-based motors. The goal of the internship project is to understand how these characteristics link to
kif14 functions and to validate our findings in living cells. Results obtained from this study will be crucial to
understand kif14’s role in cell division and tumorigenesis.
Techniques used:
Molecular biology, protein biochemistry, high-resolution microscopy, cell culture
Key words:
Cell division, protein biochemistry, microscopy, cancer, molecular motors
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Internship #9:
Understanding how adult stem cells divide in vivo
Research team:
Dr Jean-Claude Labbé
Cell Division and Differentiation Research Unit
Contact information:
 [email protected]
 http://www.iric.ca/en/research/principal-investigators/jean-claude-labbe/
Project description:
How do adult stem cells divide in vivo, in response to niche signaling? Answering this question has been
challenging, mainly due to the lack of appropriate models to visualize stem cells in vivo. We have developed a
novel method to image the division of adult stem cells in vivo, using the nematode Caenorhabditis elegans
(C. elegans) as model organism. Genetic analysis has revealed specific pathways and regulators that are
essential to coordinate stem cell division during development and aging of the animal. We are seeking
motivated individuals to pursue the characterization of some of these regulators, to better understand how
they contribute to the regulation of stem cell division, using genetic analysis and high-resolution time-lapse
imaging approaches.
Techniques used:
Genetic analysis; RNAi; in vivo time-lapse imaging; quantitative image analysis
Key words:
Stem cells, mitosis, C. elegans
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Internship #10:
Complementary roles of BAF60A and BAF60B during the lymphoid vs
myeloid differentiation
Research team:
Dr Julie Lessard
Chromatin Structure and Stem Cell Biology Research Unit
Contact information:
 [email protected]
 http://www.iric.ca/en/research/principal-investigators/julie-lessard/
Project description:
In mammals, BAF chromatin remodelling complexes (Brg/Brm associated factor) are composed of a dozen
subunits assembled around two alternative ATPases, Brg and Brm. The variety of complexes resulting from the
combinatorial assembly of BAF subunits seems to confer functional specificity that allows recognition of
distinct gene targets during cell differentiation. To study the role of the BAF60a BAF60b subunits in adult
hematopoiesis, our lab generated knockout mice for these genes. The deletion of BAF60a in neonatal mice
induces a lack of B- and T-cell precursors in the bone marrow and severe atrophy of the thymus, suggesting an
essential role for BAF60a in lymphopoiesis. Although BAF60b seems dispensable for lymphopoiesis, it is
essential for granulocyte differentiation: the deletion of BAF60b induced severe neutropenia characterized by
an accumulation of granulocyte-macrophage progenitors (GMPs) in the bone marrow and a diminution of the
differentiation to granulocytes. The generation of hematopoietic chimeras showed that this phenotype is cellintrinsic and independent of the microenvironment.
Quantitative PCR (Q-PCR) assays helped us identify several potential targets for BAF60b and BAF60a that could
mediate their function in lymphoid and granulocytic differentiation, respectively. Interestingly, mutations in
several of these genes are associated with lymphopenia and neutropenia syndromes in humans. In the coming
months, we want to assess their importance for BAF60a and BAF60b functions by conducting transcomplementation assays in BAF60a- and BAF60b-deficient cells. In summary, this project should help us to
better understand the complementary role of BAF60a and BAF60b subunits in lymphoid and myeloid
differentiation and potentially develop new treatments for various hematological diseases.
Techniques used:
Flow cytometry, cell culture, retroviral infection, bone marrow transplant
Key words:
Hematopoietic stem cells, BAF complex chromatin
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Internship #11:
Mechanisms of action of full antiestrogens in breast tumor cells
Research team:
Dr Sylvie Mader
Molecular Targeting for Breast Cancer Treatment Research Unit
Contact information:
 [email protected]
 http://www.iric.ca/en/research/principal-investigators/sylvie-mader/
Project description:
About 2/3 of breast tumors express or overexpress the estrogen receptor and its growth is stimulated by
estrogen. Anti-estrogens are competitive inhibitors of estrogen receptors. There are two classes of antiestrogens, which act by different mechanisms. The goal of this project is to characterize the mechanisms of
action of anti-estrogen such as fulvestrant, a drug used as a second-line therapy for tumors that are resistant to
tamoxifen. Our results indicate that anti-estrogens induce SUMOylation of the receptor and its interaction with
a chromatin remodeling complex. The goal of the project is to characterize the importance of these effects in
the anti-estrogenicity of fulvestrant.
Techniques used:
Cell culture, western-blot, chromatin immunoprecipitation, luciferase assay
Key words:
Breast cancer, antiestrogens, fulvestrant, SUMOylation
13
Internship #12:
Prediction of lncRNA-protein interactions in synaptogenesis
Research team:
Dr François Major
RNA Engineering Research Unit
Contact information:
 [email protected]
 http://www.iric.ca/en/research/principal-investigators/francois-major/
Project description:
Long non-coding RNAs (lncRNAs) play a direct role in the regulation of genes involved in neuronal
differentiation and in the synaptic plasticity of neurons. A precise knowledge of the structure and the
interactions between long non-coding RNAs and proteins is an excellent starting point for understanding and
studying their mechanisms. This project aims at describing and predicting the molecular docking between a
lncRNA and a protein. To achieve this goal, the binding between lncRNA Evf2 and protein Dlx2 in mice will be
modeled.
Techniques used:
MC-Fold and MC-Sym pipeline (3D modeling), Genbank and the protein DataBank (databases), molecular
docking.
Key words:
Neuron, synapse, long non-coding RNA, modeling
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Internship #13:
Deciphering the long non-coding RNA address code
Research team:
Dr François Major
RNA Engineering Research Unit
Contact information:
 [email protected]
 http://www.iric.ca/en/research/principal-investigators/francois-major/
Project description:
The objective of this project is to determine SHAPE and cisplatin (Pt) binding sites in long non-coding RNAs
(lncRNAs) in vivo. These experiments will provide structural information that will be compared with
computational predictions that will be made in my lab, helping with their interpretation and validation. We will
map SHAPE chemicals and Pt on human lncRNAs in vivo by primer extension. We will use next-generation
sequencing in collaboration with the genomics core facility at IRIC. These data will be particularly invaluable in
and outside the field of lncRNAs.
Techniques used:
SHAPE chemistry, cisplatin probing, primer extension, Next generation sequencing (HiSeq2000)
Key words:
Long non-coding RNA, in vivo probing, SHAPE, cisplatin, structure
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Internship #14:
Functional genomics of thymic epithelial stem cells
Research team:
Dr Claude Perreault
Immunobiology Research Unit
Contact information:
 [email protected]
 http://www.iric.ca/en/research/principal-investigators/claude-perreault/
Project description:
In the animal kingdom, the thymus is the sole organ that can produce T lymphocytes. The thymus is therefore
essential to life in vertebrates. However, thymic aging precedes that of other organs and leads to a progressive
decline in thymic function with age. By the age of 45 years, approximately 75% of thymic epithelial cells (TECs)
have been replaced by fibroblasts and adipocytes in the human thymus. The precocious loss of TECs is
intriguing considering that TECs are not postmitotic cells such as mature neurons or differentiated
cardiomyocytes. Indeed, TECs proliferate actively in vivo (but not in vitro). We have recently identified putative
TEC stem/progenitor cells in the mouse thymus. The goal of the present projet is to perform functional
genomic analyses on TEC progenitor/stem cells in order to understand what their mitotic behavior is, why they
age prematurely and how we might rejuvenate the thymus of adult vertebrates
Techniques used:
Transcriptome sequencing, cell culture and transplantation, flow cytometry and microscopy, bioinformatics
Key words:
Thymus, stem cells, next-generation sequencing
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Internship #15:
Characterisation of the yeast Cas5 regulon
Research team :
Dr Martine Raymond
Yeast Molecular Biology Research Unit
Contact information :
 [email protected]
 http://www.iric.ca/en/research/principal-investigators/martine-raymond/
Project description:
Candida albicans (C. albicans) is a diploid yeast that is a human commensal but can cause severe infections in
immunosuppressed cancer patients. Its genome has been sequenced and found to include approximately 250
genes encoding transcription factors, many still uncharacterized. One of these, Cas5, has been shown to
regulate important cellular processes such as morphogenesis, virulence, susceptibility to antifungal drugs, and
quorum sensing. However, the molecular mechanisms underlying Cas5 functions are still largely unknown. The
goal of this project is to identify the Cas5 transcriptional targets at the whole genome level to address this
question. Such knowledge will improve our understanding of transcriptional networks regulating C. albicans
biology and may provide conceptual and molecular tools to better treat Candida infections.
Techniques used :
Gene deletion by homologous recombination, DNA and RNA purification, Southern and Northern blots,
expression profiling (DNA microarrays), location profiling (ChIP-on-chip).
Key words :
Genomics, yeast, transcription
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Internship #16:
Studying the impact of somatic mutations of RSK in cancer
Research team:
Dr Philippe P. Roux
Cellular Signalling and Proteomics Research Unit
Contact information:
 [email protected]
 http://www.iric.ca/en/research/principal-investigators/philippe-roux/
Project description:
Proteins from the RSK kinase family (p90 ribosomal S6 kinase) are involved in cell proliferation, cell survival and
cell motility. These kinases are normally activated by the Ras/MAPK signaling pathway, which is itself
frequently overactive in cancers, including melanoma, lung and intestine cancer. With the help of highthroughput sequencing of human tumors, several studies have identified somatic mutations in the genes
encoding RSK isoforms (Rsk1-4). The purpose of this project is to generate these mutations experimentally and
to verify their impact on the catalytic activity. With the help of a doctoral student, the student will have to
generate point mutations by site-directed mutagenesis and to verify the integrity of the mutated proteins.
These proteins will then be expressed in human cells and catalytic activity will be measured in vitro and in cells.
This project will help determine whether the somatic mutations that are found in the genes encoding the RSK
family contribute to cancer progression.
Techniques used:
Western blot, transfection, cell culture, mutagenesis, subcloning, kinase assay
Key words:
Kinase, phosphorylation, cancer, somatic mutations
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Internship #17:
Generation of experimental leukemia cell lines from human cord blood
stem cells
Research team:
Dr Guy Sauvageau
Molecular Genetics of Stem Cells Research Unit
Contact information:
 [email protected]
 http://www.iric.ca/en/research/principal-investigators/guy-sauvageau/
Project description:
The aim of this project is to generate an experimental AML cell line from hematopoietic stem cells that are
purified from human cord blood. The cell line will be generated to express both the MLL-AF9 leukemia
oncogene and a doxycycline-responsive transcriptional activator. This will allow the doxycycline-inducible
expression of shRNA constructs knocking-down essential regulators of AML progression and thereby study
their molecular functions
Techniques used:
Purification and culture of human hematopoietic stem cells obtained from cord blood, genetic manipulation of
these cells by two alternative methods (transfection, viral transduction), initial characterization of the obtained
cells by biochemical and molecular biology methods (PCR, Southern blot, Western analysis), functional
validation in tissue-culture and in vivo based experiments.
Key words:
Hematopoietic stem cells, AML
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Internship #18:
Characterization of new Ras/MAPK pathway components
Research team:
Dr Marc Therrien
Intracellular Signalling Research Unit
Contact information:
 [email protected]
 http://www.iric.ca/en/research/principal-investigators/marc-therrien/
Project description:
The Ras/MAPK pathway plays a central role in the control of cell proliferation and its aberrant up-regulation
often leads to cancer. Signaling through the Ras/MAPK pathway depends on a number of core pathway
components that include a module a three kinases known as RAF, MEK and MAPK. We have recently
completed a genome-wide functional (RNAi-based) screen to identify additional factors modulating Ras/MAPK
signaling. Interestingly, this led to the identification of several proteins that appear to control the levels of core
pathway components. In particular, we identified two putative transcription factors that specifically control the
level of mek mRNAs. A position for a summer student is available in the laboratory for validating these findings
and then initiating a characterization of the role these two factors play in controlling MEK levels.
Techniques used:
Molecular biology, biochemistry
Key words:
Ras/MAPK, kinases, transcription factors
20
Internship #19:
Regulation of protein sumoylation in response to DNA damage.
Research team:
Dr Pierre Thibault
Proteomics and Bioanalytical Mass Spectrometry Research Unit
Contact information:
 [email protected]
 http://www.iric.ca/en/research/principal-investigators/pierre-thibault/
Project description:
DNA damage is very common in mammalian cells ( > 60 000 times a day) and gives rise to
modifications ( oxidative damage , single or double strand break ) following metabolic and enzymatic
reactions. The maintenance of genomic integrity is essential to cell survival and protein sumoylation
was found to regulate various pathways of DNA damage recognition, signaling, and repair. This
project aims at a better understanding of the role of protein sumoylation and the identification of the
different molecular players involved in DNA repair . To this end, we will use hydroxyurea (HU) , and
methyl methanesulphonate (MMS) as a chemical agents to investigate protein sumoylation and the
molecular mechanisms of DNA repair. Metabolic labeling of human cells with stable isotopes will be
used to determine changes in protein sumoylation following different treatments. This will be
achieved using quantitative proteomics on a high performance LTQ-Orbitrap mass spectrometer.
These large-scale proteomics analyses will provide valuable insights on the regulation of protein
SUMOylation in response DNA damage agents. Through this internship, the trainee will be exposed to
cutting-edge approaches in biochemistry, protein chemistry, separation sciences, proteomics, and
microscopy.
Techniques used:
Cell culture, microscopy, affinity chromatography, proteomics, mass spectrometry
Key words:
SUMOylation, cell signaling, proteomics
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Internship #20:
Cell cycle and DNA damage regulation of the histone deacetylase Hst3
Research team:
Dr Alain Verreault
Chromosome Biogenesis Research Unit
Contact information:
 [email protected]
 http://www.iric.ca/en/research/principal-investigators/alain-verreault/
Project description:
Our laboratory discovered a novel and fascinating feature of chromosome physiology. During DNA replication,
chromatin structure needs to be duplicated and this is achieved through the incorporation of newly
synthesized histones into nascent chromatin. We showed that new histone H3 molecules deposited throughout
the genome are acetylated at lysine 56 (H3K56ac). Both H3K56ac and deacetylation play important roles in the
response to a broad spectrum of DNA damaging agents that are frequently used in cancer chemotherapy
(Nature (2005) 436: 294; Curr Biol (2006) 16: 1280; Cell (2008) 134: 244; Mol. Cell. Biol. (2012) 32: 154).
Notably, we found that the enzyme that deacetylates H3K56, known as Hst3, is conserved in many human
pathogens such as Candida and Aspergillus species. Remarkably, inhibition of Hst3 using nicotinamide, a form
of vitamin B3, leads to catastrophic chromosome damage and fungal cell death (Nature Medicine (2010) 16:
775). Thus, inhibitors of Hst3 represent a novel therapeutic approach to treat fungal infections that can be lifethreatening in patients that are immunosuppressed (e.g. patients undergoing cancer chemotherapy or organ
transplant). For these reasons, we are actively studying the mechanism of action and the regulation of the
deacetylase Hst3.
The aim of this project will be to decipher the mechanisms that regulate the activity and the stability of the
Hst3 enzyme during the cell cycle and in response to DNA damaging agents.
Techniques used:
Cell synchronization, immunoblotting, DNA damage sensitivity assays, immunoaffinity purification
Key words:
Histone, Chromatin, Acetylation, Cell Cycle, DNA Damage
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Internship #21:
Using model leukemias to study the genetic determinants of pediatric
acute myeloid leukemia
Research team:
Dr Brian Wilhelm
High-Throughput Genomics Research Unit
Contact information:
 [email protected]
 http://www.iric.ca/en/research/principal-investigators/brian-wilhelm/
Project description:
One of our principle interests is in studying the role of the impact of epigenetic changes in pediatric acute
myeloid leukemia (AML). In particular we study leukemias with MLL-MLLT3 (AF9) translocations using both
patient samples as well as a single donor model leukemia system developed in collaboration with Dr Frederic
Barabé. Through comparison of these models with sequencing data from pediatric AML patients, we hope to
derive a better understanding of the genetic determinants of the disease. The candidate genes we have now
identified are being characterized in terms of the role in leukemia in maintaining growth, preventing death and
differentiation. To do this, we work with cells in culture to alter candidate gene expression levels and validate
the phenotype through western blots, RNA-seq or FACS
Techniques used:
High throughput DNA sequencing, cell culture, shRNA knock downs, bioinformatics, FACS, Western blot
Key words:
High throughput DNA sequencing, cell culture, shRNA knock downs, bioinformatics, leukemia, cancer, NGS
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