Dr. Stephen Smale’s laboratory has broad interests in the molecular mechanisms of gene regulation in cells of the immune system. The two areas of interest are inflammation and innate immunity, and lymphocyte differentiation and gene regulation competence in embryonic stem cells.
Inflammation can be beneficial for a normal immune response to microbial pathogens. However, prolonged inflammation can promote tissue damage and has been linked to a diverse range of diseases, including cancer, atherosclerosis and several inflammatory autoimmune diseases. Although anti-inflammatory drugs are available, none of them is ideal for various reasons, including insufficient target specificity. Therefore, new strategies are needed for the development of selective modulators of pro-inflammatory genes or proteins. One major limitation in pursuing pharmaceuticals that inhibit the transcription of pro-inflammatory genes is that the understanding of the molecular mechanisms responsible for the selective regulation of genes within this large family remains rudimentary.
Toward the goal of understanding gene regulation selectivity mechanisms at a genome-wide level, Smale and his team recently found that genes induced by lipopolysaccharide (LPS) in murine macrophages can be divided into three classes on the basis of their regulatory properties. The first gene class, called the early primary response class, is activated rapidly in the absence of new protein synthesis and in the absence of SWI/SNF complexes, which are the main ATP-dependent nucleosome remodeling complexes in mammals. Late primary response genes are also activated in the absence of new protein synthesis, but genes in this class consistently require SWI/SNF complexes and are activated with delayed kinetics. Finally, secondary response genes require both new protein synthesis and SWI/SNF complexes for activation. A current goal of Smale’s laboratory is to elucidate the unique regulatory strategies employed by each of these classes to provide further insight into mechanisms underlying selective pro-inflammatory gene transcription.
A related area of interest is the molecular mechanisms responsible for selective gene regulation by members of the NF-kappaB family of transcription factors, which contribute to the activation of most pro-inflammatory genes. Although much has been learned about the signal transduction mechanisms that activate NF-kappaB dimers in response to various stimuli, the fundamental reasons different NF-kappaB dimers are capable of regulating distinct sets of genes remain largely unexplored. Because some genes that require a specific NF-kappaB family member for expression play critical roles in dictating the type of immune response elicited by a stimulus, an understanding of family member selectivity may lead to novel strategies for modulating immune responses with an unusually high degree of specificity. Smale’s laboratory has found that 46 residues within the DNA-binding domain of one NF-kappaB family member, c-Rel, are solely responsible for c-Rel’s ability to activate genes that cannot be activated by a closely related family member, RelA. The team’s current studies are providing further insight into c-Rel and RelA selectivity mechanisms, leading to hypotheses to explain the divergence of the c-Rel and RelA genes during vertebrate evolution.
Smale’s laboratory has also had a long-standing interest in the regulation of gene expression during lymphocyte differentiation. A primary focus has been on the Ikaros family of DNA-binding proteins, which are critical regulators of lymphocyte development and function as potent tumor suppressors. Because of its localization to foci of pericentromeric heterochromatin and its interaction with multiple transcriptional co-repressor complexes, Ikaros has been implicated in heritable gene silencing, although a role in gene activation has also been reported. Through biochemical purification and mass spectrometry analysis, Smale and his team recently found that both Ikaros and another member of the Ikaros family, Helios, are predominantly associated with a previously described co-repressor complex, NuRD, which contains an ATP-dependent nucleosome remodeling subunit and histone.
An additional focus has been the contributions of chromatin structure to the activation and silencing of specific model genes during lymphocyte differentiation. By focusing on primary thymocytes, which can be induced to differentiate efficiently and synchronously ex vivo, the team was able to document a temporal cascade of events that accompanies heritable gene silencing during thymocyte development. More recently, Smale’s laboratory has focused attention on embryonic stem cells after finding that enhancers for a number of typical tissue-specific genes studied in the lab, including genes expressed in mature hematopoietic and non-hematopoietic lineages, are marked by pioneer factor interactions and unmethylated CpG dinucleotides in pluripotent cells. The laboratory’s functional studies are consistent with a hypothesis in which pioneer factor interactions in embryonic stem cells promote the assembly of a chromatin structure that is permissive for subsequent activation, and in which differentiated tissues lack the machinery required for gene activation when these embryonic stem cell marks are absent.
Selected Cancer-Related Publications:
Smale ST. Selective transcription in response to an inflammatory stimulus. Cell. 2010 Mar 19;140(6):833-44.
Xu J, Watts JA, Pope SD, Gadue P, Kamps M, Plath K, Zaret KS, Smale ST. Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells. Genes Dev. 2009 Dec 15;23(24):2824-38.
Ramirez-Carrozzi VR, Braas D, Bhatt DM, Cheng CS, Hong C, Doty KR, Black JC, Hoffmann A, Carey M, Smale ST. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell. 2009 Jul 10;138(1):114-28.
Sridharan R, Smale ST. Predominant interaction of both Ikaros and Helios with the NuRD complex in immature thymocytes. J Biol Chem. 2007 Oct 12;282(41):30227-38. Epub 2007 Aug 6.
Sanjabi S, Williams KJ, Saccani S, Zhou L, Hoffmann A, Ghosh G, Gerondakis S, Natoli G, Smale ST. A c-Rel subdomain responsible for enhanced DNA-binding affinity and selective gene activation. Genes Dev. 2005; 19(18): 2138-51.