Welcome to the home page of the Paddison Laboratory.

We use functional genetics to probe the underlying biology of mammalian stem/progenitor cells. We identify and characterize gene products affecting stem cell self-renewal, differentiation, proliferation, or survival through the use of RNAi knockdown technologies. We currently use four in vitro stem cell culture systems: embryonic stem cells, hematopoietic stem cells, neural progenitor cells, and brain tumor initiating cells (i.e., brain tumor stem cells). One goal of our research is to define the biological modules of self-renewal, lineage commitment, proliferation, and survival in each of these model systems. Another is to identify molecular vulnerabilities of cancer initiating cells derived directly from patients to create more effective therapeutic strategies. A description of several current projects can be found below, starting with our work with brain tumor initiating cells.

If you are interested in joining the Paddison Lab as an undergraduate, graduate student, postdoctoral fellow, or visiting scientist, please contact Patrick Paddison with a statement of your research interests and CV. We welcome applications from motivated individuals with an interest in bringing creative and interdisciplinary approaches to the study of stem cell and cancer biology.
Lab Projects

Glioblastoma multiforme (GBM) as a model cancer system. In cancer biology it has become evident that requirements for specific gene activities can vary widely across cancer types. These differences presumably arise from context-specific molecular constraints intrinsic to the tissue or cell type of origin and to the process of cancer development itself. Our current lack of knowledge of cancer-specific gene requirements and the processes driving their requirement has hampered development of targeted therapeutic strategies for cancer. However, in the past five years significant progress has been made in the development of culture systems for patient cancers that allow unprecedented access to cancer-evolved molecular pathways and cellular phenotypes.

At the forefront of cancer patient-derived experimental systems is Glioblastoma multiforme (GBM), the most aggressive and common form of brain cancer in adults. Tumor-initiating GBM stem cells (GSCs) can now be routinely isolated, with the development potential and specific genetic alterations found in the patient’s tumor. GSCs express neural progenitor cell markers and exhibit, to varying degrees, the capacity for multi-lineage differentiation. Direct access to and experimentation with patient cancer cells may hold the key to understanding phenotypic variation among different cancers and matching phenotypic behavior with genetic alterations.

Over the past three years Dr. Paddison’s group has adopted the GSC model using a new method for isolating and growing GSCs in defined monolayer culture. By this method, GSCs can be isolated and grown in defined monolayer culture while uniformly retaining tumor-initiating potential and tumor-specific genetic and epigenetic signatures. In proof of concept studies, we have performed kinome and genome-scale RNAi screens in GSCs and also in human non-transformed neural stem cells (NSCs).  As a result, we have demonstrated the existence of GBM-lethal genes, a subset of which, when inhibited render patient GBM tumor cells sensitive to cellular stresses that arise as a consequence of cellular transformation.

Project publication: Ding et al. Cancer-specific requirement for BUB1B/BUBR1 in human brain tumor isolates and genetically transformed cells. Cancer Discovery Nov 15 Online, 2012.

Science Spolight for this paper.

Human hematopoietic stem cell expansion and differentiation.
The mammalian hematopoietic system is hierarchically organized such that the potential to produce different lineages and to proliferate is progressively restricted. Our understanding of the process of hematopoietic lineage formation is continually being redefined through the discovery of new intermediate developmental stages (e.g., through prospective isolation via cell surface markers), the molecular profiling of progenitors (e.g., gene expression analysis) and genetic studies demonstrating involvement of genes and pathways in hematopoiesis (e.g., knockout or knock-in mice). Such pursuits have revealed a key concept regarding epigenetics and lineage formation: that changes in chromatin structures during lineage formation can confer heritable, but often reversible, changes in gene expression that restrict developmental potential and promote lineage-specific cell characteristics. Epigenetic gene regulation is often driven by specific histone modifications that can facilitate transient and long-term changes in gene transcription during organismal development. We have recently discovered novel roles for histone H3K9me2 during lineage formation in human hematopoietic stem and progenitor cells (HSPCs). In addition, we have also performed RNAi screens to identify genes responsible for maintenance of HSPCs developmental potential.

Project publication: Chen et al. G9a/GLP-dependent histone H3K9me2 patterning during human hematopoietic stem cell lineage commitment. Genes and Dev. 26: 2499-511, 2012.

Science Spolight for this paper.

Embryonic stem cell expansion and differentiation.
Embryonic stem cells (ESCs) are cell lines derived from the inner cell mass (ICM) of blastocyst stage mammalian embryos. They can grow indefinitely in culture and give rise to cells of all three embryonic germ layers as well as germ cells (Keller, 2005). For these reasons ES cells hold great promise for regenerative medicine. While some molecular details of the ESC self-renewal network have emerged, more in depth knowledge will be required to facilitate future ESC-based clinical applications. We have now identified several novel activators and repressors of ESC self-renewal gene expression through performing multiple RNAi screens. We are now characterizing several genes with roles in facilitating ESC fate and integrating distinct modes of epigenetic regulation.

Project publication: Schaniel et al. Smarcc1/Baf155 couples self-renewal gene repression with changes in chromatin structure in mouse embryonic stem cells. Stem Cells 27: 2979-91, 2009.

Project Odysseus: Can we outwit cancer?
In this project, we seek to re-define paradigms for identifying single and combination agent therapies for cancer. This effort brings together multiple groups across different biomedical disciplines (including: systems biology, functional genetics, chemico-genetics, developmental biology, and clinical practice) to define clinically relevant therapeutic networks in patient-specific cancers. We begin with Glioblastoma multiforme, the most aggressive and lethal brain cancer and will move to other cancers. Project Odysseus includes collaborations with groups from institutions around the world including US, S. Korea, and UK.

Other selected publications:

Paddison et al. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes and Dev 16: 948-958, 2002.

Paddison PJ, Hannon GJ. RNA interference: The New Somatic Cell Genetics? Cancer Cell 2:17-23, 2002

Paddison et al. A resource for large-scale RNAi based screens in mammals. Nature 428: 427-431, 2004.

Paddison PJ. RNA interference in mammalian cell systems. In: RNA interference. Current Topics in Microbiology and Immunology. Paddison PJ, Vogt PK (eds.). Springer Press 2008.

 

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