The Taipale research group
Professor Jussi Taipale got his Ph.D. from the University of Helsinki in 1996, and continued with postdoctoral work at the University of Helsinki and at Johns Hopkins University (Baltimore, MD, USA). He has headed an independent research laboratory since 2003, focusing on systems biology of growth control and cancer. He started at the University of Helsinki, but in September of 2009, the move to Karolinska Institutet began. In February of 2010 the new robotic equipment was installed, consisting of an automated laboratory with 27 different instruments, two other robotic pipelines (for SELEX/ELISA and for PCR preparation/DNA barcoding), and two Illumina GAIIx massively parallel sequencers. (See also Karolinska High Throughput Centre)
The main expertise of the Taipale group is high-throughput screening using cDNA and RNA interference, computational and experimental methods to identify causative regulatory mutations in non-protein coding DNA and to analyze genetic networks. In addition, Taipale group has extensive expertise on mouse models of gene and regulatory region function.
Organ specific growth control remains one of the major, unresolved questions in developmental biology. It is not understood what determines organ size and shape, and it is not clear why tumors arising in different tissues harbor different oncogenic mutations. Much of what we do know about physiological mechanisms controlling cellular growth in mammals has been revealed by human cancer genetics. These studies have revealed that a large number of genes can contribute to aberrant cell growth. More than 350 genes have been linked to cancer and mutations found in cancer are often cell type specific, suggesting that different pathways in different cell lineages are coupled to the cell cycle machinery. Our hypothesis is that the problems of organ-specific growth control and specificity of oncogenes to particular tumors represent two sides of the same coin; that is, mutations in tumors are tissue specific, because tumors arise by the most economical mutagenic route, aberrantly activating the organ-specific growth mechanisms.
We are taking a systems-biology approach to understand how tissue-specific factors collaborate with oncogenic signals to drive cell proliferation. For this purpose, we have developed computational and experimental methods to identify direct target genes of oncogenic transcription factors that are commonly activated in major forms of human cancer. In addition, we have used high-throughput RNAi screening to identify genes required for cell cycle progression. Combining these two sets of data allows identification of specific transcription factors and gene regulatory elements which drive growth in particular tissues and tumor types.
The specific objectives of the research are the following:
1. To identify the genes and the mechanisms essential for cell cycle progression on a genome-wide level.
2. To understand the molecular basis of organ-specific growth control
1. Cell cycle
To determine which proteins are required for cell cycle progression, we have initiated a project that aims to systematically knock down all genes in the Drosophila genome by RNAi. We have screened ~ 14 000 genes, including all Drosophila genes that are conserved in human, identifying approximately 570 genes with cell cycle phenotypes. This screen resulted in the identification of a number of genes and pathways that have not previously been linked to regulation of the cell cycle. We cloned these Drosophila cell cycle components to GATEWAY-type recombination cloning vectors, which allow rapid transfer of the cDNA to different vector systems for analysis of gain-of-function phenotypes, protein-protein interactions and enzyme-substrate relationships between the identified genes.
2. Transcriptional regulation of cell growth
For analysis of transcriptional regulation of target genes controlling growth, we have set up a novel method for determination of transcription factor (TF) binding specificities. The method is based on next generation sequencing, and can generate accurate transcription factor binding profiles without any prior knowledge.
A second method, also developed by us, can be used to directly determine the relative affinities of a TF to different DNA sequences once one high-affinity site is known. We have applied this method for genome-wide prediction of mammalian enhancers, and identifying conserved target genes of the Hh/GLI and Wnt/Tcf4 developmental signaling pathways based on transcription factor affinity tables.
In collaboration with Drs. Kimmo Palin and Esko Ukkonen (UH Dept. of Computer Science), we have also previously established an in silico method, Enhancer Element Locator (EEL), for identification of mammalian enhancer elements.
Validation of regulatory elements
In selecting regulatory elements for analysis we prioritize elements within genomic areas known to be associated with increased cancer risk. Currently we are working with two interesting candidates in the vicinity of the c-Myc gene. One element was identified using EEL in a region associated with colorectal cancer. A Short Nucelotide Polymorphism (SNP) within this element increased binding of Tcf4, the transcription factor that is known to be activated in colorectal cancer (Figure 1). The other element is also located upstream of c-Myc, but in a region associated with prostate cancer. This element was identified in a genome-wide EEL analysis of target genes of the ETS-family of transcription factors.
Testing the tumor type and tissue specificity of the predicted enhancers will be performed using transgenic mice and a set of tumor cell lines harboring mutations activating the oncogenic TFs. The enhancers will be further analyzed by mutating the relevant TF binding sites. In addition, we will use RNAi targeting the oncogenic TF and other TFs whose sites are found in the enhancer element in cancer cell lines to test whether the activity of the factors is essential for cell growth. Finally, the enhancer element will be knocked out in mouse embryos to test whether it has a role in organ-specific growth control and tumorigenesis.
Figure 1. Outline of the project. The central hypothesis of the project is that multiple signaling pathways and oncogenes drive the cell cycle by targeting a limited set of downstream genes which function as master-regulators of growth. Regulatory elements (blue) controlled by oncogenic transcription factors (orange) will be identified using computational methods, by chromatin immunoprecipitation followed by sequencing (ChIP-seq) and from the literature. Genes which are required for cell-cycle progression are identified by RNAi screening followed by functional validation. The data is combined to identify genes which are both downstream of oncogenic TFs and required for cell growth. The identified regulatory elements will be validated using transgenic and knock-out mice.
DNA-binding specificities of human transcription factors
Cell. 2013 Jan 17;152(1-2):327-39. doi: 10.1016/j.cell.2012.12.009.
Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors
Science. 2012 Dec 7;338(6112):1360-3. Epub 2012 Nov 1.
Counting absolute numbers of molecules using unique molecular identifiers
Nature Methods. 9:72-4, 2011
Genome-Wide Analysis of ETS Family DNA-Binding in vitro and in vivo
EMBO J. 29:2147-2160, 2010
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities
Genome Res. 20:861-73, 2010
The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling
Nature Genetics 41:885-890, 2009
Application of active and kinase-deficient kinome collection for identification of kinases regulating Hedgehog signaling
Cell 133:537-548, 2008
(*corresponding author; # contributed equally, in reverse alphabetic order)
Identification of pathways regulating cell size and cell cycle progression by RNAi
Nature 439:1009-13, 2006
(*corresponding author; # contributed equally, in alphabetic order)
Genome-wide prediction of mammalian enhancers based on high-throughput analysis of transcription factor binding affinity
Cell 124:47-59, 2006
(*corresponding author; # contributed equally, in alphabetic order)
Hedgehog-mediated patterning of the mammalian embryo requires transporter-like function of dispatched
Cell 111:63-75, 2002