Browsing by Author "Dahl, Richard"
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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 ARID3B increases ovarian tumor burden and is associated with a cancer stem cell gene signature(Impact Journals, 2014-09-30) Roy, Lynn; Samyesudhas, Serene J.; Carrasco, Martin; Joseph, Stancy; Dahl, Richard; Cowden Dahl, Karen D.; Biochemistry & Molecular Biology, School of MedicineOvarian cancer is the most deadly gynecological malignancy since most patients have metastatic disease at the time of diagnosis. Therefore, identification of critical pathways that contribute to ovarian cancer progression is necessary to yield novel therapeutic targets. Recently we reported that the DNA binding protein ARID3B is overexpressed in human ovarian tumors. To determine if ARID3B has oncogenic functions in vivo, ovarian cancer cell lines stably expressing ARID3B were injected intraperitoneally into nude mice. Overexpression of ARID3B increased tumor burden and decreased survival. To assess how ARID3B contributes to the increased tumor growth in vivo, we identified ARID3B induced genes in tumor ascites cells. ARID3B induced expression of genes associated with metastasis and cancer stem cells (CD44, LGR5, PROM1 (CD133), and Notch2). Moreover, ARID3B increased the number of CD133+ (a cancer stem cell marker) cells compared to control cells. The increase in CD133+ cells resulting from ARID3B expression was accompanied by enhanced paclitaxel resistance. Our data demonstrate that ARID3B boosts production CD133+ cells and increases ovarian cancer progression in vivo.Item Arid3b Is Critical for B Lymphocyte Development(Plos, 2016-08-18) Kurkewich, Jeffrey L.; Klopfenstein, Nathan; Hallas, William M.; Wood, Christian; Sattler, Rachel A.; Das, Chhaya; Tucker, Haley; Dahl, Richard; Dahl, Karen D. Cowden; Department of Biochemistry & Molecular Biology, IU School of MedicineArid3a and Arid3b belong to a subfamily of ARID (AT-rich interaction domain) transcription factors. The Arid family is involved in regulating chromatin accessibility, proliferation, and differentiation. Arid3a and Arid3b are closely related and share a unique REKLES domain that mediates their homo- and hetero-multimerization. Arid3a was originally isolated as a B cell transcription factor binding to the AT rich matrix attachment regions (MARS) of the immunoglobulin heavy chain intronic enhancer. Deletion of Arid3a results in a highly penetrant embryonic lethality with severe defects in erythropoiesis and hematopoietic stem cells (HSCs). The few surviving Arid3a-/- (<1%) animals have decreased HSCs and early progenitors in the bone marrow, but all mature lineages are normally represented in the bone marrow and periphery except for B cells. Arid3b-/- animals die around E7.5 precluding examination of hematopoietic development. So it is unclear whether the phenotype of Arid3a loss on hematopoiesis is dependent or independent of Arid3b. In this study we circumvented this limitation by also examining hematopoiesis in mice with a conditional allele of Arid3b. Bone marrow lacking Arid3b shows decreased common lymphoid progenitors (CLPs) and downstream B cell populations while the T cell and myeloid lineages are unchanged, reminiscent of the adult hematopoietic defect in Arid3a mice. Unlike Arid3a-/- mice, HSC populations are unperturbed in Arid3b-/- mice. This study demonstrates that HSC development is independent of Arid3b, whereas B cell development requires both Arid3a and Arid3b transcription factors.Item Brucella suppress STING expression via miR-24 to enhance infection(PloS, 2020-10-27) Khan, Mike; Harms, Jerome S.; Liu, Yiping; Eickhoff, Jens; Tan, Jin Wen; Hu, Tony; Cai, Fengwei; Guimaraes, Erika; Oliveira, Sergio Costa; Dahl, Richard; Cheng, Yong; Gutman, Delia; Barber, Glen N.; Splitter, Gary A.; Smith, Judith A.; Microbiology and Immunology, School of MedicineBrucellosis, caused by a number of Brucella species, remains the most prevalent zoonotic disease worldwide. Brucella establish chronic infections within host macrophages despite triggering cytosolic innate immune sensors, including Stimulator of Interferon Genes (STING), which potentially limit infection. In this study, STING was required for control of chronic Brucella infection in vivo. However, early during infection, Brucella down-regulated STING mRNA and protein. Down-regulation occurred post-transcriptionally, required live bacteria, the Brucella type IV secretion system, and was independent of host IRE1-RNase activity. STING suppression occurred in MyD88-/- macrophages and was not induced by Toll-like receptor agonists or purified Brucella lipopolysaccharide (LPS). Rather, Brucella induced a STING-targeting microRNA, miR-24-2, in a type IV secretion system-dependent manner. Furthermore, STING downregulation was inhibited by miR-24 anti-miRs and in Mirn23a locus-deficient macrophages. Failure to suppress STING expression in Mirn23a-/- macrophages correlated with diminished Brucella replication, and was rescued by exogenous miR-24. Mirn23a-/- mice were also more resistant to splenic colonization one week post infection. Anti-miR-24 potently suppressed replication in wild type, but much less in STING-/- macrophages, suggesting most of the impact of miR-24 induction on replication occurred via STING suppression. In summary, Brucella sabotages cytosolic surveillance by miR-24-dependent suppression of STING expression; post-STING activation “damage control” via targeted STING destruction may enable establishment of chronic infection., Cytosolic pattern recognition receptors, such as the nucleotide-activated STING molecule, play a critical role in the innate immune system by detecting the presence of intracellular invaders. Brucella bacterial species establish chronic infections in macrophages despite initially activating STING. STING participates in the control of Brucella infection, as mice or cells lacking STING show a higher burden of Brucella infection. However, we have found that early following infection, Brucella upregulates a microRNA, miR-24, that targets the STING messenger RNA, resulting in lower STING levels. Dead bacteria or bacteria lacking a functional type IV secretion system were defective at upregulating miR-24 and STING suppression, suggesting an active bacteria-driven process. Failure to upregulate miR-24 and suppress STING greatly compromised the capacity of Brucella to replicate inside macrophages and in mice. Thus, although Brucella initially activate STING during infection, the ensuing STING downregulation serves as a “damage control” mechanism, enabling intracellular infection. Viruses have long been known to target immune sensors such as STING. Our results indicate that intracellular bacterial pathogens also directly target innate immune receptors to enhance their infectious success.Item Evaluation of the mirn23a Cluster through an iTRAQ-based Quantitative Proteomic Approach(ACS Publications, 2016-05-06) Ludwig, Katelyn R.; Dahl, Richard; Hummon, Amanda B.; Department of Microbiology and Immunology, School of MedicineMicroRNAs (miRNAs) are post-transcriptional regulators of gene expression that are implicated in a number of disease states. MiRNAs can exist as individual entities, or may be clustered and transcribed as a single polycistron. The mirn23a cluster consists of three miRNAs, miR-23a, miR-24-2, and miR-27a. While these miRNAs are transcribed together, they often exist at varying levels in the cell. Despite the fact that the mirn23a cluster is known to play a role in a number of diseases and developmental processes, few direct targets have been identified. In this study, we examined the effects of miR-23a, miR-24-2, miR-27a, or the mirn23a cluster overexpression on the proteome of 70Z/3 pre-B lymphoblast cells. Quantitative mass spectrometry using isobaric tags for relative and absolute quantification (iTRAQ) allowed for global profiling of cell lines after miRNA overexpression. We identified a number of targets of each miRNA that contained predicted miRNA seed sequences and are likely direct targets. In addition, we discovered a cohort of shared miRNA targets and cluster targets, demonstrating the importance of studying miRNA clusters in their entirety.Item MAPK Signaling Is Required for Generation of Tunneling Nanotube-Like Structures in Ovarian Cancer Cells(MDPI, 2021-01-13) Cole, Jennifer M.; Dahl, Richard; Cowden Dahl, Karen D.; Microbiology and Immunology, School of MedicineOvarian cancer (OC) cells survive in the peritoneal cavity in a complex microenvironment composed of diverse cell types. The interaction between tumor cells and non-malignant cells is crucial to the success of the metastatic process. Macrophages activate pro-metastatic signaling pathways in ovarian cancer cells (OCCs), induce tumor angiogenesis, and orchestrate a tumor suppressive immune response by releasing anti-inflammatory cytokines. Understanding the interaction between immune cells and tumor cells will enhance our ability to combat tumor growth and dissemination. When co-cultured with OCCs, macrophages induce projections consistent with tunneling nanotubes (TnTs) to form between OCCs. TnTs mediate transfer of material between cells, thus promoting invasiveness, angiogenesis, proliferation, and/or therapy resistance. Macrophage induction of OCC TnTs occurs through a soluble mediator as macrophage-conditioned media potently induced TnT formation in OCCs. Additionally, EGFR-induced TnT formation in OCCs through MAPK signaling may occur. In particular, inhibition of ERK and RSK prevented EGFR-induced TnTs. TnT formation in response to macrophage-conditioned media or EGFR signaling required MAPK signaling. Collectively, these studies suggest that inhibition of ERK/RSK activity may dampen macrophage-OCC communication and be a promising therapeutic strategy.Item The miR-23a∼27a∼24-2 microRNA Cluster Promotes Inflammatory Polarization of Macrophages(The American Association of Immunologists, 2021) Boucher, Austin; Klopfenstein, Nathan; Hallas, William Morgan; Skibbe, Jennifer; Appert, Andrew; Jang, Seok Hee; Pulakanti, Kirthi; Rao, Sridhar; Cowden Dahl, Karen D.; Dahl, Richard; Microbiology and Immunology, School of MedicineMacrophages are critical for regulating inflammatory responses. Environmental signals polarize macrophages to either a pro-inflammatory (M1) state or an anti-inflammatory (M2) state. We observed that the microRNA cluster mirn23a, coding for miRs-23a~27a~24–2, regulates mouse macrophage polarization. Gene expression analysis of mirn23a deficient myeloid progenitors revealed a decrease in Toll like receptor and interferon signaling. Mirn23a−/− bone marrow derived macrophages (BMDMs) have an attenuated response to lipopolysaccharide (LPS) demonstrating an anti-inflammatory phenotype in mature cells. In vitro, mirn23a−/− BMDMs have decreased M1 responses and an enhanced M2 responses. Overexpression of mirn23a has the opposite effect enhancing M1 and inhibiting M2 gene expression. Interestingly expression of mirn23a miRNAs goes down with inflammatory stimulation and up with anti-inflammatory stimulation suggesting that its regulation prevents locking macrophages into polarized states. M2 polarization of tumor associated macrophages (TAMs) correlates with poor outcome for many tumors, so to determine if there was a functional consequence of mirn23a loss modulating immune cell polarization we assayed syngeneic tumor growth in wildtype and mirn23a−/− mice. Consistent with the increased anti-inflammatory/ immunosuppressive phenotype in vitro, mirn23a−/− mice inoculated with syngeneic tumor cells had worse outcomes compared to wildtype mice. Co-injecting tumor cells with mirn23a−/− BMDMs into wildtype mice phenocopied tumor growth in mirn23a−/− mice supporting a critical role for mirn23a miRNAs in macrophage mediated tumor immunity. Our data demonstrates that mirn23a regulates M1/M2 polarization and suggests that manipulation of mirn23a miRNA can be used to direct macrophage polarization to drive a desired immune response.Item MiR-24 is required for hematopoietic differentiation of mouse embryonic stem cells(PLoS, 2015-01-29) Roy, Lynn; Bikorimana, Emmanuel; Lapid, Danica; Choi, Hyewon; Nguyen, Tan; Dahl, Richard; Department of Microbiology and Immunology, IU School of MedicineOverexpression of miRNA, miR-24, in mouse hematopoietic progenitors increases monocytic/ granulocytic differentiation and inhibits B cell development. To determine if endogenous miR-24 is required for hematopoiesis, we antagonized miR-24 in mouse embryonic stem cells (ESCs) and performed in vitro differentiations. Suppression of miR-24 resulted in an inability to produce blood and hematopoietic progenitors (HPCs) from ESCs. The phenotype is not a general defect in mesoderm production since we observe production of nascent mesoderm as well as mesoderm derived cardiac muscle and endothelial cells. Results from blast colony forming cell (BL-CFC) assays demonstrate that miR-24 is not required for generation of the hemangioblast, the mesoderm progenitor that gives rise to blood and endothelial cells. However, expression of the transcription factors Runx1 and Scl is greatly reduced, suggesting an impaired ability of the hemangioblast to differentiate. Lastly, we observed that known miR-24 target, Trib3, is upregulated in the miR-24 antagonized embryoid bodies (EBs). Overexpression of Trib3 alone in ESCs was able to decrease HPC production, though not as great as seen with miR-24 knockdown. These results demonstrate an essential role for miR-24 in the hematopoietic differentiation of ESCs. Although many miRNAs have been implicated in regulation of hematopoiesis, this is the first miRNA observed to be required for the specification of mammalian blood progenitors from early mesoderm.Item Mirc11 Disrupts Inflammatory but Not Cytotoxic Responses of NK Cells(AACR, 2019-10) Nanbakhsh, Arash; Srinivasamani, Anupallavi; Holzhauer, Sandra; Riese, Matthew J.; Zheng, Yongwei; Wang, Demin; Burns, Robert; Reimer, Michael H.; Rao, Sridhar; Lemke, Angela; Tsaih, Shirng-Wern; Flister, Michael J.; Lao, Shunhua; Dahl, Richard; Thakar, Monica S.; Malarkannan, Subramaniam; Microbiology and Immunology, School of MedicineNatural killer (NK) cells generate proinflammatory cytokines that are required to contain infections and tumor growth. However, the posttranscriptional mechanisms that regulate NK cell functions are not fully understood. Here, we define the role of the microRNA cluster known as Mirc11 (which includes miRNA-23a, miRNA-24a, and miRNA-27a) in NK cell–mediated proinflammatory responses. Absence of Mirc11 did not alter the development or the antitumor cytotoxicity of NK cells. However, loss of Mirc11 reduced generation of proinflammatory factors in vitro and interferon-γ–dependent clearance of Listeria monocytogenes or B16F10 melanoma in vivo by NK cells. These functional changes resulted from Mirc11 silencing ubiquitin modifiers A20, Cbl-b, and Itch, allowing TRAF6-dependent activation of NF-κB and AP-1. Lack of Mirc11 caused increased translation of A20, Cbl-b, and Itch proteins, resulting in deubiquitylation of scaffolding K63 and addition of degradative K48 moieties on TRAF6. Collectively, our results describe a function of Mirc11 that regulates generation of proinflammatory cytokines from effector lymphocytes.Item The mirn23a and mirn23b microrna clusters are necessary for proper hematopoietic progenitor cell production and differentiation(Elsevier, 2018) Kurkewich, Jeffrey L.; Boucher, Austin; Klopfenstein, Nathan; Baskar, Ramdas; Kapur, Reuben; Dahl, Richard; Microbiology and Immunology, School of MedicineMice deficient for microRNA (miRNA) cluster mirn23a exhibit increased B lymphopoiesis at the expense of myelopoiesis, whereas hematopoietic stem and progenitor cell (HSPC) populations are unchanged. Mammals possess a paralogous mirn23b gene that can give rise to three mature miRNAs (miR-23b, miR-24-1, and miR-27b) that have identical seed/mRNA-targeting sequences to their mirn23a counterparts. To assess whether compound deletion of mirn23a and mirn23b exacerbates the hematopoietic phenotype observed in mirn23a−/− mice, we generated a compound mirn23a−/−mirn23bfl/fl:Mx1-Cre conditional knockout mouse and assayed hematopoietic development after excision of mirn23b. Loss of both genes in adult bone marrow further skewed HSPC differentiation toward B cells at the expense of myeloid cells, demonstrating a dosage-dependent effect on regulating cell differentiation. Strikingly, double-knockout (DKO) mice had decreased bone marrow cellularity with significantly decreased hematopoietic stem cell and HSPC populations, a phenotype not observed in mice deficient for mirn23a alone. Competitive transplantation assays showed decreased contribution of mirn23a−/−mirn23b−/− HSPCs to hematopoietic lineages at 6 and 12 weeks after transplantation. Defects in the proliferation of mirn23a−/−b−/− HSPCs was not observed; however, DKO cells were more apoptotic compared with both wild-type and mirn23a−/− cells. Together, our data show that complete loss of mirn23a/mirn23b miRNAs results in decreased blood production and affects lineage output in a concentration-dependent manner.