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Item Acquired STAT4 deficiency as a consequence of cancer chemotherapy(2011-08-16) Lupov, Ivan; Chang, Hua-Chen; Randall, Stephen Karl, 1953-; Robertson, Michael J.Signal Transducer and Activator of Transcription 4 (STAT4) is an important transcription factor activated by IL-12 signaling. Activated STAT4 is essential for Th1 cell differentiation, a process characterized by increased potential for interferon (IFN)-γ production. Defective IFN-γ production due to STAT4 deficiency occurs after autologous stem cell transplantation for lymphoma. We have investigated the mechanisms of post-transplant STAT4 deficiency. The tumor-bearing state is ruled out to be the cause because STAT4 levels were not significantly different in peripheral blood mononuclear cells (PBMCs) obtained from lymphoma patients prior to treatment and healthy control subjects. The magnitude of the decrease in STAT4 levels corresponded with increasing intensity of chemotherapeutic treatment in vivo. Furthermore, treatment of normal PBMC cultures or a natural killer (NK) cell line with chemotherapy drugs in vitro also resulted in reduced STAT4 protein and reduced IL-12-induced IFN-γ production. Chemotherapy drugs are shown to have no impact on the stability of STAT4 mRNA, while steady-state levels of STAT4 transcripts are decreased in lymphoma patients. Our findings demonstrated that chemotherapeutic drugs up-regulate the ubiquitination rates of the STAT4 protein, which in turn promotes its degradation via the proteasome-mediated pathway. Treatment with the proteasome inhibitor bortezomib largely reversed the chemotherapy-induced STAT4 deficiency. Thus, acquired STAT4 deficiency in lymphoma patients is a consequence of treatment with chemotherapy. These results have important implications for design of optimal immunotherapy for lymphoma.Item Amino acid divergence in the ligand-binding pocket of Vibrio LuxR/HapR proteins determines the efficacy of thiophenesulfonamide inhibitors(Wiley, 2021) Newman, Jane D.; Chopra, Jay; Shah, Priyanka; Shi, Eda; McFadden, Molly E.; Horness, Rachel E.; Brown, Laura C.; van Kessel, Julia C.; Medicine, School of MedicineThe quorum sensing signaling systems in Vibrio bacteria converge to control levels of the master transcription factors LuxR/HapR, a family of highly conserved proteins that regulate gene expression for bacterial behaviors. A compound library screen identified 2-thiophenesulfonamide compounds that specifically inhibit Vibrio campbellii LuxR but do not affect cell growth. We synthesized a panel of 50 thiophenesulfonamide compounds to examine the structure-activity relationship effects on Vibrio quorum sensing. The most potent molecule identified, PTSP (3-phenyl-1-(thiophen-2-ylsulfonyl)-1H-pyrazole), inhibits quorum sensing in multiple strains of Vibrio vulnificus, Vibrio parahaemolyticus, and V. campbellii at nanomolar concentrations. However, thiophenesulfonamide inhibition efficacy varies significantly among Vibrio species: PTSP is most inhibitory against V. vulnificus SmcR, but V. cholerae HapR is completely resistant to all thiophenesulfonamides tested. Reverse genetics experiments show that PTSP efficacy is dictated by amino acid sequence in the putative ligand binding pocket: F75Y and C170F SmcR substitutions are each sufficient to eliminate PTSP inhibition. Further, in silico modeling distinguished the most potent thiophenesulfonamides from less effective derivatives. Our results revealed the previously unknown differences in LuxR/HapR proteins that control quorum sensing in Vibrio species and underscore the potential for developing thiophenesulfonamides as specific quorum sensing-directed treatments for Vibrio infections.Item Analysis of Histone Lysine Methylation Using Mass Spectrometry(2012-12-11) True, Jason Donald; Goebl, Mark G.; Mosley, Amber L.; Witzmann, F. A. (Frank A.)Histones are highly basic proteins which when digested by trypsin are hard to analyze using mass spectrometry. Because histones are basic nuclear proteins, a nuclei prep followed by acid extraction is the best purification strategy to increase overall abundance of purified histones. Blocking the lysine residues and cleaving with trypsin is a useful technique to increase detection of histone peptides using MudPIT. In particular, carbamylation and propionylation are the best two methods to block lysine residues. Using both propionylation and carbamylation along with no treatment has been shown to increase the identification of unmodified and modified histone peptides when coupled with MudPIT analysis.Item An Animal Model of Combined Pituitary Hormone Deficiency Disease(2010-08) Colvin, Stephanie C.; Konieczny, Stephen F.; Rhodes, Simon J.; Walvoord, Emily C.; Belecky-Adams, Teri; Herring, B. Paul; Roper, RandallLHX3 is a LIM-homeodomain transcription factor that has essential roles in pituitary and nervous system development in mammals. Children who are homozygous for recessive mutations in the LHX3 gene present with combined pituitary hormone deficiency disease (CPHD) characterized by deficits of multiple anterior pituitary hormones. Most LHX3 patients also present with additional defects associated with the nervous system including a characteristic limited head rotation and sometimes deafness. However, of the 10 types of LHX3 mutation described to date, one mutation type (W224ter) does not result in the limited head rotation, defining a new form of the disease. W224ter patients have CPHD but do not have nervous system symptoms. Whereas other mutations in LHX3 cause loss of the entire protein or its activity, the W224ter mutation causes specific loss of the carboxyl terminal of the LHX3 protein—a region that we have shown to contain critical regulatory domains for pituitary gene activation. To better understand the molecular and cellular etiology of CPHD associated with LHX3 gene mutations, I have generated knock-in mice that model the human LHX3 W224ter disease. The resulting mice display marked dwarfism, thyroid disease, female infertility, and reduced male fertility. Immunohistochemistry, real-time quantitative polymerase chain reaction (PCR), and enzyme-linked immunosorbant assays (ELISA) were used to measure hormones and regulatory factor protein and RNA levels, an approach which is not feasible with human patients. We have generated a novel mouse model of human pediatric CPHD. Our findings are consistent with the hypothesis that the actions of the LHX3 factor are molecularly separable in the nervous system and pituitary gland.Item ARID3A and ARID3B induce stem promoting pathways in ovarian cancer cells(Elsevier, 2020-05-15) Dausinas, Paige; Pulakanti, Kirthi; Rao, Sridhar; Cole, Jennifer M.; Dahl, Richard; Cowden Dahl, Karen D.; Biochemistry and Molecular Biology, School of MedicineARID3A and ARID3B are paralogs from the AT-Rich interactive Domain (ARID) family. ARID3A and ARID3B associate to regulate genes in B-cells and cancer. We were the first to demonstrate that ARID3B regulates stem cell genes and promotes the cancer stem cell phenotype. Importantly, different knockout phenotypes in mice and distinct patterns of expression in adult animals suggests that ARID3A and ARID3B may have unique functions. In addition, high levels of ARID3B but not ARID3A induce cell death. Our goal was to express ARID3A, ARID3B, or both genes at a moderate level (as can be observed in cancer) and then identify ARID3 regulated genes. We transduced ovarian cancer cells with ARID3A-GFP, ARID3B-RFP, or both. RNA-sequencing was conducted. ARID3A and ARID3B regulated nearly identical sets of genes. Few genes (<5%) were uniquely regulated by ARID3A or ARID3B. ARID3A/B induced genes involved in cancer and stem cell processes including: Twist, MYCN, MMP2, GLI2, TIMP3, and WNT5B. We found that ARID3A and ARID3B also induced expression of each other, providing evidence of the cooperativity. While ARID3A and ARID3B likely have unique functions in distinct contexts, they are largely capable of regulating the same stem cell genes in cancer cells. This study provides a comprehensive list of genes and pathways regulated by ARID3A and ARID3B in ovarian cancer cells.Item Author Correction: REST regulates the cell cycle for cardiac development and regeneration(Springer Nature, 2018-01-12) Zhang, Donghong; Wang, Yidong; Lu, Pengfei; Wang, Ping; Yuan, Xinchun; Yan, Jianyun; Cai, Chenleng; Chang, Ching-Pin; Zheng, Deyou; Wu, Bingruo; Zhou, Bin; Medicine, School of MedicineDespite the importance of cardiomyocyte proliferation in cardiac development and regeneration, the mechanisms that promote cardiomyocyte cell cycle remain incompletely understood. RE1 silencing transcription factor (REST) is a transcriptional repressor of neuronal genes. Here we show that REST also regulates the cardiomyocyte cell cycle. REST binds and represses the cell cycle inhibitor gene p21 and is required for mouse cardiac development and regeneration. Rest deletion de-represses p21 and inhibits the cardiomyocyte cell cycle and proliferation in embryonic or regenerating hearts. By contrast, REST overexpression in cultured cardiomyocytes represses p21 and increases proliferation. We further show that p21 knockout rescues cardiomyocyte cell cycle and proliferation defects resulting from Rest deletion. Our study reveals a REST-p21 regulatory axis as a mechanism for cell cycle progression in cardiomyocytes, which might be exploited therapeutically to enhance cardiac regeneration.Item Cell-specific actions of a human LHX3 gene enhancer during pituitary and spinal cord development(The Endocrine Society, 2013-12) Park, Soyoung; Mullen, Rachel D.; Rhodes, Simon J.; Department of Biology, School of ScienceThe LIM class of homeodomain protein 3 (LHX3) transcription factor is essential for pituitary gland and nervous system development in mammals. In humans, mutations in the LHX3 gene underlie complex pediatric syndromes featuring deficits in anterior pituitary hormones and defects in the nervous system. The mechanisms that control temporal and spatial expression of the LHX3 gene are poorly understood. The proximal promoters of the human LHX3 gene are insufficient to guide expression in vivo and downstream elements including a conserved enhancer region appear to play a role in tissue-specific expression in the pituitary and nervous system. Here we characterized the activity of this downstream enhancer region in regulating gene expression at the cellular level during development. Human LHX3 enhancer-driven Cre reporter transgenic mice were generated to facilitate studies of enhancer actions. The downstream LHX3 enhancer primarily guides gene transcription in α-glycoprotein subunit -expressing cells secreting the TSHβ, LHβ, or FSHβ hormones and expressing the GATA2 and steroidogenic factor 1 transcription factors. In the developing nervous system, the enhancer serves as a targeting module active in V2a interneurons. These results demonstrate that the downstream LHX3 enhancer is important in specific endocrine and neural cell types but also indicate that additional regulatory elements are likely involved in LHX3 gene expression. Furthermore, these studies revealed significant gonadotrope cell heterogeneity during pituitary development, providing insights into the cellular physiology of this key reproductive regulatory cell. The human LHX3 enhancer-driven Cre reporter transgenic mice also provide a valuable tool for further developmental studies of cell determination and differentiation in the pituitary and nervous system.Item Characterization of the MDM2 binding regions of ribosomal protein L5(2010-07-20T16:29:38Z) Plummer, Kevin D.; Lu, Hua; Goebl, Mark, 1958-; Hurley, Thomas D., 1961-The MDM2-p53 feedback loop is a well-characterized pathway. p53 is a transcription factor and regulates the transcriptional expression of genes that encode proteins responsible for cellular senescence, cell cycle arrest, apoptosis, and DNA repair. Various cellular stresses can result in p53 activation, including hypoxia, DNA damage by agents such as UV or IR, oncogenic signaling, nucleotide depletion and nucleolar stress from perturbation of ribosomal biogenesis. Under normal conditions, MDM2’s role in the pathway is to inhibit p53 function by directly binding to this protein and facilitating its ubiquitylation and 26S proteasome-mediated degradation. Under stressful cellular conditions, certain proteins interact with and rescue MDM2’s inhibition of p53. For example, upon exposure to small amounts of Actinomycin D, rRNA transcript synthesis is stalled resulting in the release of various ribosomal proteins including RPL5, RPL11 and RPL23; each of which has been shown to bind MDM2 within its central acidic domain and inhibit its ability to destabilize p53. Although the RPL5 binding region of MDM2 have been mapped in prior investigations, the MDM2-binding region(s) of RPL5 have yet to be characterized. By employing RPL5 deletion mutagenesis and in vitro GST-fusion protein-protein association assays with purified proteins, this dissertation attempts to elucidate those regions of RPL5 that may interact with MDM2. Normalizing RPL5-WT to 1.00, our study reveals that the basic N and C-terminals of RPL5 appear to bind with MDM2 while RPL5’s central region displays negligible binding to the central acidic domain of MDM2. Also, the possible meanings of these RPL5 MDM2 binding domains are discussed along with their utilization in potential future applications.Item Chromatin Remodeling Subunit BRM and Valine Regulate Hematopoietic Stem/Progenitor Cell Function and Self-Renewal Via Intrinsic and Extrinsic Effects(Springer Nature, 2022) Naidu, Samisubbu R.; Capitano, Maegan; Ropa, James; Cooper, Scott; Huang, Xinxin; Broxmeyer, Hal E.; Microbiology and Immunology, School of MedicineLittle is known of hematopoietic stem (HSC) and progenitor (HPC) cell self-renewal. The role of Brahma (BRM), a chromatin remodeler, in HSC function is unknown. Bone marrow (BM) from Brm-/- mice manifested increased numbers of long- and short-term HSCs, GMPs, and increased numbers and cycling of functional HPCs. However, increased Brm-/- BM HSC numbers had decreased secondary and tertiary engraftment, suggesting BRM enhances HSC self-renewal. Valine was elevated in lineage negative Brm-/- BM cells, linking intracellular valine with Brm expression. Valine enhanced HPC colony formation, replating of human cord blood (CB) HPC-derived colonies, mouse BM and human CB HPC survival in vitro, and ex vivo expansion of normal mouse BM HSCs and HPCs. Valine increased oxygen consumption rates of WT cells. BRM through CD98 was linked to regulated import of branched chain amino acids, such as valine, in HPCs. Brm-/- LSK cells exhibited upregulated interferon response/cell cycle gene programs. Effects of BRM depletion are less apparent on isolated HSCs compared to HSCs in the presence of HPCs, suggesting cell extrinsic effects on HSCs. Thus, intracellular valine is regulated by BRM expression in HPCs, and the BRM/valine axis regulates HSC and HPC self-renewal, proliferation, and possibly differentiation fate decisions.Item The development and in vivo function of T helper 9 cells(SpringerNature, 2015-05) Kaplan, Mark H.; Hufford, Matthew M.; Olson, Matthew R.; Department of Pediatrics, IU School of MedicineThe specialized cytokine secretion profiles of T helper (TH) cells are the basis for a focused and efficient immune response. On the 20th anniversary of the first descriptions of cytokine signals that act to differentiate interleukin-9 (IL-9)-secreting T cells, this review focuses on the extracellular signals and transcription factors that promote the development of what we now term TH9 cells, which are characterized by the production of this cytokine. We summarize our current understanding of the contribution of TH9 cells to both effective immunity and immunopathological disease and propose that TH9 cells could be targeted for the treatment of allergic and autoimmune disease.