Michael Sikes
Publications
- Pharmacogenomic Analyses Implicate B Cell Developmental Status and MKL1 as Determinants of Sensitivity toward Anti-CD20 Monoclonal Antibody Therapy , CELLS (2023)
- Hands-on immunology: Engaging learners of all ages through tactile teaching tools , FRONTIERS IN MICROBIOLOGY (2022)
- Fur Negatively Regulates hns and Is Required for the Expression of HilA and Virulence in Salmonella enterica Serovar Typhimurium , JOURNAL OF BACTERIOLOGY (2011)
- The intestinal microbiota, gastrointestinal environment and colorectal cancer: a putative role for probiotics in prevention of colorectal cancer? , AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY (2011)
- Tetra-O-methyl nordihydroguaiaretic acid (Terameprocol) inhibits the NF-kappa B-dependent transcription of TNF-alpha and MCP-1/CCL2 genes by preventing RelA from binding its cognate sites on DNA , JOURNAL OF INFLAMMATION-LONDON (2010)
- The Center of Accessibility: D beta Control of V(D)J Recombination , ARCHIVUM IMMUNOLOGIAE ET THERAPIAE EXPERIMENTALIS (2010)
- A streamlined method for rapid and sensitive chromatin immunoprecipitation , JOURNAL OF IMMUNOLOGICAL METHODS (2009)
- Molybdenum and tungsten in Campylobacter jejuni: their physiological role and identification of separate transporters regulated by a single ModE-like protein , MOLECULAR MICROBIOLOGY (2009)
- Promoter activity 5 ' of D beta 2 is coordinated by E47, Runx1, and GATA-3 , MOLECULAR IMMUNOLOGY (2009)
- Differential activation of dual promoters alters D beta 2 germline transcription during thymocyte development , JOURNAL OF IMMUNOLOGY (2008)
Grants
Tetrachlorodibenzo-p-dioxin (TCDD) is a pervasive environmental contaminant that has been associated with a wide range of adverse health outcomes including liver damage, impaired immune function, and cancer of several organs. TCDD exposure induces a well-studied xenobiotic metabolism pathway that is downstream of the Aryl Hydrocarbon receptor, AhR. However, the molecular signatures of TCDD exposure last long after the acute response has subsided. We detected hundreds of differently expressed genes (DEGs) and differentially accessible chromatin regions (DARs) in mice several months after TCDD exposure had ceased, and these profiles had almost no overlap with the xenobiotic metabolism pathways. The goal of the proposed research is to understand how the global epigenome is remodeled during the period after the acute TCDD response subsides. We propose that the gene Tip30 is an essential part of the long-term response. Tip30 is upregulated during the acute response, but unlike most other genes remains upregulated for months afterwards. Likewise, accessible chromatin in a Tip30 intron was the most stable epigenetic modification that we associated with TCDD exposure, and it was found in exposed mice of both sexes throughout life up to 8 months after exposure. Separately, Tip30 has been identified as a tumor suppressor gene that has a protective role in human hepatocellular carcinomas. Our proposed research will elucidate the mechanisms of Tip30 upregulation and its effect on the global epigenome using molecular biology techniques, epigenomics, and a knockout mouse model.
The objective of this research project is to determine the role of Upstream Stimulatory Factor (or USF) in protecting cells from cancer after their DNA has been damaged. When a cell??????????????????s DNA is damaged, whether during normal cell function or after exposure to toxic chemicals, pathogens or radiation, the cell enters a program of DNA repair and recovery. During DNA repair, cells stop dividing since cell division can start a chain reaction that causes more DNA damage and cancerous transformation. An array of different transcriptional pathways orchestrate profound changes in the cell??????????????????s physiology that optimize the conditions for effective DNA repair, guide the repair process, and induce a permanent arrest or death when DNA cannot be repaired. A full DNA damage response simply cannot happen without transcription. Since these transcriptional DNA damage responses are critical safeguards against cancers that arise from DNA damage, they offer enormous potential for exploitation to develop new tools for diagnosing and treating cancer. Unfortunately, almost nothing is known about how these transcriptional programs are regulated or how they function. Our prior studies show that different forms of DNA damage alter the activity of a pair of related transcription proteins, Upstream Stimulatory Factor 1 (or USF1) and USF2. Critically, though USF1 and 2 are believed to suppress a number of cancers, their tumor suppressive activities are unknown. This gap in knowledge stems primarily from the ability of each USF protein to partially compensate for loss of the other, and the inability to generate mutant mouse models deficient for both proteins. Here, we propose a pilot study to investigate the tumor suppressive actions of the USF proteins, taking advantage of advances in RNA interference to deplete both USF1 and USF2 from cultured keratinocyte skin cells. Exposure of these USF-depleted cells to UV irradiation will allow us to define the role of USF in genome-wide response to DNA damage, and to dissect USF??????????????????s contributions to critical DNA damage response pathways like DNA repair, cell cycle control and cell death. Findings from our study of USF tumor suppression mechanisms will help to fill a critical gap in our understanding of how transcriptional programs protect cells from cancerous transformation when they lose the ability to prevent their own growth in the face of accumulating DNA damage. The long-term goal of this pilot study is to establish a foundation for larger mechanistic grant proposals aimed at defining the molecular mechanisms that ensure genome stability and suppress tumor formation in response to environmental DNA insult, to develop new prophylactic strategies to protect against cancer induced by DNA damage and new tools to detect and treat cancers that do arise.
Stem cells may revolutionize medicine, but they are also providing critical insights on cancer development and progression. Recent studies have underscored the similarities between transcription networks in embryonic stem cells (ESCs) and cancer cells. ES pluripotency critically depends on a panel of factors including the core pluripotency factors Nanog, Oct4 and Sox2, and the early embryonic microRNA cluster (EEmiRC). Each of these genes is bound by CTCF, a multifunctional genome regulator that can block the spread of repressive DNA methylation. While knockdown studies have implicated CTCF in controlling some of these factors, we find that loss of CTCF alters both expression and DNA methylation. We hypothesize that CTCF coordinates pluripotency factor expression in ES cells by maintaining a permissive epigenetic environment at their promoters. Alternatively, given the strong degree of cross-regulation of these genes, maintenance of the pluripotency network may require methylation protection of one or two master genes. To fill this critical gap in our understanding of pluripotency control, we will dissect how CTCF regulates expression of the pluripotency factors and microRNAs. These studies will lay the foundation for more mechanistic investigations into the critical contributions of CTCF to stem cell and cancer development.
Human development requires the stable and heritable activation of discrete genome regions in developing tissue without altering DNA sequence integrity. The developmental mechanisms by which this epigenetic regulation is imposed are only just coming to light. One startling example of epigenetic regulation occurs in developing lymphocytes which assemble antigen receptor genes from pools of related gene segments via a series of somatic rearrangements termed V(D)J recombination. Rearrangement of each antigen receptor gene is restricted to a discrete lineage and stage of lymphopoiesis. For example, developing T cells assemble genes for the T cell receptor (TCR) by first rearranging the beta chain gene in a two-step process involving D-to-J, then V-to-DJ recombination. TCRbeta recombination occurs early in T cell development, and is necessary for developmental progression and initiation of TCRalpha assembly. Such tight control is central to production of mature lymphocytes and safeguards the integrity of the genome. Indeed, mistargeting of recombination has been linked to a variety of leukemias. Gene segment targeting requires modulations in their chromatin accessibility by associated transcriptional enhancers and promoters. However, it remains unclear how these elements coordinate differential accessibility of gene segments within a single locus. This proposal tests the hypothesis that developmental variations in the activation and strength of individual promoters direct differential accessibility of associated gene segments. Using TCRbeta as a model, we propose to examine the roles of promoters in epigenetic regulation of recombinational accessibility by (1) dissecting promoter contributions to differential recombination of Dbeta1 and Dbeta2; (2) defining promoter contributions to activating V recombination; and (3) defining the roles of V and D positioning within the locus in limiting inappropriate recombination. Results promise insight into the general mechanisms by which cis-acting elements direct epigenetic control of gene activation. V(D)J recombination allows us to generate a robust immune system. But altering DNA can be dangerous, leading to cancer formation. By understanding the mechanisms that target recombination at specific DNA sites, we will gain insight into to pathways that lead to inappropriate, cancer-causing rearrangements. Such insights will be important for identifying potential cancers before they develop.
Despite intensive research, massive aid programs, and a breathtaking advance in knowledge and treatments, AIDS remains a disease of staggering global proportions. As of 2008, 1 in every 100 adults aged 15 to 49 worldwide was HIV-infected. HIV infection cannot yet be ?cured.? Once infected, the individual will likely always carry the viral genome as part of their own genome in progeny of the originally infected cells. The effectiveness of current state of the art therapeutics is dependent on patient adherence to the treatment regimen, as HIV rapidly acquires resistance via mutation. GlaxoSmithKline has developed a new panel of therapeutics that target a protein HIV uses to integrate its proviral genome into the host cell?s genome. Because of its central role in the HIV lifecycle, HIV integrase is more subject to selective pressures that limit its mutation, making it an ideal drug target. However, early integrase inhibitors were found to impair the ability of RAG1 and RAG2 to direct assembly of antigen receptors in developing lymphocytes. Because such unintended off-target effects would dramatically compromise a patient?s immune system, integrase inhibitors have been slow to reach the market. We propose to use our novel B and T cell-based recombination systems to directly test the potential impact of the developmental GSK compound, GSK1349572, and related molecules on RAG expression, DNA binding, and subsequent recombination of endogenous antigen receptor genes. Such testing is now expected prior to drug approval. Consequently, this work has the highest impact on HIV drug development and AIDS treatment.
Many childhood leukemias including some T cell acute lymphoblastic leukemias and Burkitt?s lymphoma are triggered by a unique and potentially dangerous program of DNA rearrangement, termed V(D)J recombination, that occurs during lymphocyte development. These cancers derive from translocations of antigen receptor genes that result in activating unrelated oncogenes. To better predict these transforming events, our research is primarily focused on understanding the regulatory programs that target segments of the antigen receptor genes during normal V(D)J recombination. Transcriptional enhancers within each antigen receptor gene are predicted to direct recombination by modulating the chromatin structure of large DNA domains. However, such globally acting elements could not impose the strict order that recombination of each antigen receptor gene follows. For example, developing T lymphocytes assemble the alpha and beta genes for the T cell receptor (TCR) by first rearranging the ? gene in a two-step process involving recombination of D and J gene segments, and then V-to-DJ recombination. Only when TCR? recombination is complete does the cell initiate recombination of the TCR? gene. If the TCR? enhancer plays an early role in opening the ? chromatin to recombination, how is the order of TCR? recombination regulated? A growing body of evidence suggests that additional, as yet unidentified elements may take over for the enhancer once D-to-J recombination has occurred. We propose a novel series of genetic and molecular experiments to identify and characterize enhancer-independent regulatory elements in the TCR? gene. These pilot studies are expected to lay a firm foundation for future mechanistic studies regarding the differential control of TCR? recombinational access. Such an understanding will be essential to identifying and predicting the metastatic transformations that derive from failures in the recombination process.