Bcl11b (B-cell lymphoma/leukemia 11b), also known as Ctip2 (Chicken ovalbumin upstream promoter transcription factor (COUP-TF)-interacting protein 2), is a C2H2 zinc finger transcriptional regulatory protein, which is an essential protein for post-natal life in the mouse and plays crucial roles in the development, and presumably function, of several organ systems, including the central nervous, immune, craniofacial formation and cutaneous/skin systems. Moreover, inactivation of Bcl11b has been implicated in the etiology of lymphoid malignancies, suggesting that Bcl11b may function as a tumor suppressor. Bcl11b was originally identified as a protein that interacted directly with the orphan nuclear receptor COUP-TF2. Later studies revealed that this C2H2 zinc finger protein can bind DNA directly in a COUP-independent manner, and it has been studied mostly as a transcription repressor. In T cells, gene repression mediated by Bcl11b involves the recruitment of class I HDACs, HDAC1 and HDAC2, within the context of the Nu It has become evident that post-translational modifications (PTMs) play essential roles in modulating activity of transcription regulators. By sensing extracellular signals, cells initiate a series of signaling cascades, which eventually transduce to transcription factors by PTMs, leading to changes of gene expression profile. cleosome Remodeling and Deacetylation (NuRD) complex. The hypothesis that Bcl11b functions as a transcriptional repressor has been supported by transcriptome analyses in mouse T cells and human neuroblastoma cells. However, approximately one-third of the genes that were dysregulated in the double positive (DP) cells of Bcl11b-null mice were down-regulated relative to control T cells, suggesting that Bcl11b may act as a transcriptional activator in some promoter and/or cell contexts. We have also found that Bcl11b functions as a transcriptional activator in a promoter context-dependent manner. However, how Bcl11b and its transcription regulatory activity is regulated still remain largely unknown. Here, we study the reversible, covalent modification of Bcl11b by phosphorylation and small ubiquitin-like modifier (SUMO). We have identifiedK679 and K877 as the two major Bcl11b SUMOylation sites by mutagenesis study. We have shown that phosphorylation and SUMOylation of Bcl11b are likely mutually exclusive processes, and phosphorylation of Bcl11b inhibits its SUMOylation by promoting the recruitment of SUMO specific protease SENP1. To study the function of Bcl11b SUMOylation, we fused SUMO1 to the amino terminus of Bcl11b. This generated a form of Bcl11b that was constitutively sumoylated without the complications of indirect effects associated with overexpression of SUMO1. Our data presented using the constitutive SUMO-Bcl11b demonstrated that SUMOylation compromises the transcription repression mediated by Bcl11b. Interestingly, when Bcl11b is fused to a cleavable form of SUMO, Bcl11b is targeted to ubiquitination pathway and it is degraded through proteasome machinery, suggesting that SUMOylation targets Bcl11b to the ubiquitination-proteasome machinery and deSUMOylation of SUMO conjugated Bcl11b is required for this process. These results described herein provide a framework for understanding the mechanisms underlying the transcription regulatory activities of Bcl11b, and how Bcl11b is regulated by post-translational modifications, including phosphorylation and SUMOylation. These studies may contribute to a better understanding of the molecular and cellular basis for Bcl11b function in vivo. / Graduation date: 2011 / Access restricted to the OSU Community at author's request from June 9, 2011 - June 9, 2012

The lymphoid tissues consist of distinct cell subpopulations of B and T cell lineages and possess complex signaling pathways that are controlled by a myriad of molecular interactions. During the fine-tuned developmental process of the lymphoid system, inappropriate activation of oncogenes and loss of tumor suppressor gene activity can push lymphocytes into uncontrolled clonal expansion, causing several lymphoid malignancies. V(D)J recombination is one such essential process, important for the proper development of the mammalian immune system. However, mistakes in normal V(D)J recombination can lead to deletion of tumor suppressor genes or activation of proto-oncogenes. In the first part of the study, the physiological and pathological roles of DNA binding domain of RAG1 have been characterized. RAG (Recombination Activating Gene) complex consisting of RAG1 and RAG2, is a site specific endonuclease responsible for the generation of antigen receptor diversity. It cleaves a specific DNA sequence termed as recombination signal sequence (RSS), comprising of a conserved heptamer and nonamer. Recent studies have shown that RAGs can also act as a structure-specific nuclease by cleaving flaps, heterologous loops, bubbles, hairpins etc. Nonamer binding domain (NBD) of RAG1 plays a central role in the recognition of RSS during its sequence specific activity. To investigate its DNA binding properties, NBD of murine RAG1 was cloned, overexpressed and purified from E. coli. Electrophoretic mobility shift assays showed that NBD binds with high affinity to nonamer in the context of 12/23 RSS. However, it did not bind to heteroduplex DNA, irrespective of the sequence of the single-stranded region. Interestingly, when a nonamer was present next to a heteroduplex DNA, NBD exhibited robust binding. NBD binding was specific to thymines when single stranded DNA containing poly A, C, G and T were used. Biolayer interferometry studies showed that the observed poly T binding to NBD was robust with a binding constant of 0.45±0.16 µM. >23 nt was essential for NBD binding at homothymidine stretches. On a double-stranded DNA, NBD could bind to A:T stretches, but not G:C stretches or random sequences. Although NBD is indispensable for sequence-specific activity of RAGs, external supplementation of purified nonamer binding domain to NBD deleted cRAG1/cRAG2 did not restore the sequence specific activity, suggesting that the overall domain architecture of RAG1 is important for maintaining its properties. Therefore, we define the sequence requirements of NBD binding to double- and single-stranded DNA, which will have implications in generation of chromosomal rearrangement and genomic instability in lymphoid cells. Genetic alterations are one of the hallmarks of lymphoid malignancies. Many genes involved in chromosomal abnormalities are known to play central roles in the development of normal lymphocytes. In the second part of the study, molecular mechanism associated with fragility of the transcription factor, B cell leukemia 11B (BCL11B) that drives malignant transformation of T-cells has been studied. BCL11B is a zinc finger protein transcription factor with multiple functions. It plays a key role in both development and subsequent maintenance of T-cells. BCL11B gene alterations are implicated in a number of diseases including T-cell malignancies. It acts as a haplo-insufficient tumor suppressor and loss of BCL11B allele leads to susceptibility to mouse thymic lymphoma and human T-ALL. Recent studies reveal heterozygous BCL11B mutations and deletions across each of the major molecular subtypes of T-ALL (15% of patients). Most of the BCL11B missense mutations identified so far affected the residues within BCL11B zinc finger domains of the exon 4. However, mechanism of generation of such specific mutations leading to altered functions of BCL11B remains to be explored. In the present study, we address the potential mechanism of fragility of BCL11B gene during leukemia genesis. Firstly, we have evaluated different regions of BCL11B gene for presence of non-B DNA sequence motifs. Studies using non-B DB database reveal clustering of several non-B DNA forming motifs at the region spanning exon 4 of BCL11B gene. In order to biochemically evaluate the potential of non-B DNA structure formation, two different regions of exon 4 were PCR amplified and cloned. Using bisulfite modification assay we demonstrate that, single strandedness exists at both region I and II of BCL11B exon 4, when the region is present on a plasmid DNA. Bisulfite reactivity on chromosomal DNA confirmed existence of such altered DNA structures in the context of human genome. In vitro gel shift assays showed formation of both intra and intermolecular G-quadruplexes. Primer extension studies revealed that non-B DNA structures could block polymerization during replication on a plasmid, leading to DNA replication arrest. Extrachromosomal assays showed that non-B DNA structure motifs, in contrast to its mutants, blocked transcription leading to reduced expression of green fluorescent protein (GFP) within cells. Many non-B DNA-forming sequences have been mapped to regions of common chromosomal breakpoints in human tumors, known as “hotspots”, which are associated with leukemia, lymphomas and genomic disorders. Thus, alternative DNA conformations are believed to contribute to mutations, deletions and other genetic instability, leading to the deregulation of cancer-related genes in malignant diseases such as leukemia and lymphoma. Activation induced cytidine deaminase (AID), is an essential enzyme involved in antibody diversification of immunoglobulin genes. However, aberrant AID expression in B- cell and non-B cell background is reported in various cancers including leukemia and lymphoma. AID activity requires single stranded DNA (ssDNA) as a substrate. Since activation induced cytidine deaminase (AID) deaminates cytosines when present on a single stranded DNA and its expression is deregulated in many cancers, we investigated the role of AID in BCL11B gene mutagenesis. We observed substantial AID expression in many T-cell leukemic cell lines. Thus, we hypothesize that AID might be targeted to single stranded DNA present at BCL11B exon 4 due to formation of non-B DNA structures such as G-quadruplexes causing AID mediated deamination, further leading to nucleotide alterations and the mutational signature observed at BCL11B exon 4 resulting in T-ALL. Based on our findings, we propose that single strandedness resulted due to formation of non-B DNA structures such as G-quadruplex DNA, triplex DNA or cruciform DNA during physiological processes like DNA replication and transcription at exon 4 of BCL11B, can act as the target for AID. Thus, our findings uncover a new possible link between non-B DNA structure motifs and AID expression in causing mutations at BCL11B exon 4 which could lead to T cell leukemia genesis. BCL11B is a bifunctional transcriptional regulator that can act as a repressor and transactivator, and is known to differentially control the expression of specific genes in a context-dependent manner. In order to understand the transcriptional network involving BCL11B, it was cloned, overexpressed and purified from E. coli. To investigate the DNA binding properties of BCL11B protein, electrophoretic mobility shift assays were performed. Our results lead to identification of a specific sequence motif that is responsible for DNA binding. Competition experiments in presence of specific and nonspecific oligomers further confirmed the binding specificity. Thus, in the present study, we have characterized the binding properties of nonamer binding domain of RAG1, emphasizing its pathological relevance in causing genomic instability in lymphoid cells. The study may help in better understanding of RAG induced genomic instability in lymphoid tissues and role of aberrant AID expression in inducing mutations at BCL11B Zinc finger domain, leading to its deregulation and culminating into T-cell leukemia

Advancements of antiretroviral therapies (ART) have made significant strides in reducing human immunodeficiency virus (HIV) viral loads in patients to undetectable levels. Upon interruption of ART, viral load rebounds and AIDS symptoms return. Latent reservoirs of virus are responsible for this phenomenon because they contain integrated provirus, which is transcriptionally silent, thus unaffected by ART and hidden from host immune surveillance. A commonly proposed mechanism for HIV latency is the presence of host cell transcription factors that lead to transcriptional silencing. CD4+ T cells and other immune cells, whether due to their subset phenotype, activation state, or stage in development, will vary in their battery of transcription factors. Of particular interest is Bcl11b, a critical transcription factor involved in the commitment to a T-cell fate during thymocyte development that has recently been shown to play a role in silencing HIV-1 transcription. Bcl11b is required for inhibiting the development of natural killer cell-like traits during the early development of T cells. The repressive role of this zinc-finger transcription factor has recently been shown to inhibit HIV-1 transcription in the context of microglial cells via recruitment of chromatin remodeling factors. Also, Bcl11b has been shown to interact with other HIV-1 transcriptional silencing factors such as NuRD and NCoR. Preliminary mass spectrophotometry results have pointed to a physical interaction of Bcl11b with NELF, another proven repressive factor of HIV transcription. We hypothesize that Bcl11b represses HIV transcription and is recruited to the HIV-1 long terminal repeat (LTR) through a paused RNA polymerase II complex, contributing to the establishment and maintenance of latency. Our studies confirm Bcl11b's repressive role in T cells, and investigate the mechanism with NELF. Transfection of HEK293T cells with HIV-LUC shows nearly 50% reduction in HIV transcription in the presence of Bcl11b, and analysis of viral protein output by p24 ELISA confirms this result. Furthermore, when co-transfected with NELF-B, the two transcription factors lead to nearly 90% reduction in HIV transcription. Results suggest that these factors cooperate to repress HIV transcriptional elongation. Protein and chromatin immunoprecipitations (ChIP) were also performed to see a direct interaction between the two transcription factors and the HIV LTR. Physical interaction of the two factors was not witnessed, while ChIP analysis shows enrichment of RNA polymerase II at the transcriptional start site suggesting Bcl11b increasing RNA polymerase II pausing. We conclude that Bcl11b plays a repressive role in HIV transcription through promoter-proximal pausing with a synergistic effect with NELF, but a yet to be identified factor is responsible for the coordination of the two factors. As an important T-cell commitment factor, Bcl11b may play an important role in establishing and maintaining cellular latency through transcriptional repression via a complex with NELF. Confirming Bcl11b's role as a repressive transcription factor and providing further support for a synergistic role with NELF, could highlight a new target for therapeutic strategies against the elusive latent reservoir.

Aortic stiffness underlies systolic hypertension, promotes heart failure and is associated with increased cardiovascular morbidity and mortality. It is regarded as a primary driver of left ventricular hypertrophy and aortic aneurysms and is linked to the pathogenesis of cognitive impairment, stroke and renal failure. Like most cardiovascular traits, aortic stiffness is a complex trait and is moderately heritable, yet the precise molecular mechanisms that underpin the stiffening process remain poorly defined. This study aimed to employ multiple approaches to further identify the genetic basis of aortic stiffness in a large repository of human donor aortas that had undergone ex vivo pulse wave velocity (PWV) phenotyping. The first part of this work sought to investigate the molecular basis of Loeys-Dietz type 4 syndrome in a pedigree with multiple cases of aortic aneurysms and dissections. A missense variant p.(Arg320Cys) was identified in a highly evolutionary conserved region of TGFB2. There was striking upregulation of TGFB1, TGFB2 and pSMAD2/3 on imunocytochemical straining and western blotting of the aortic tissue from the index case confirming the functional importance of the variant. This case highlighted the striking paradox of predicted loss-of-function mutations in TGFB2 causing enhanced TGFβ signalling in this emerging familial aortopathy and underscored the significance of TGFβ signalling in aortic extracellular matrix biology. The second part of this work attempted to characterise the biological basis for the susceptibility locus identified in the most recent genome wide analysis of carotid-femoral PWV. While the locus lies within the 14q32.2 gene desert, it contains regulatory elements, with the transcriptional regulator B-cell CLL/lymphoma 11B (BCL11B) and non-coding RNA DB129663 representing potential targets for these enhancers. The association of five lead SNPs from the genome-wide association studies (GWAS) meta-analysis was examined for ex vivo aortic stiffness and BCL11B and DB129663 aortic mRNA expression. Three of the five SNPs associated significantly with PWV and showed allele-specific differences in BCL11B mRNA. The risk alleles associated with lower BCL11B suggesting a protective role for BCL11B. Despite the strong association, BCL11B protein was not detected in the human aorta; however, qPCR for CD markers showed that BCL11B transcript correlated strongly with markers for activated lymphocytes. In contrast, DB129663 transcripts were detected in 55% of the samples, and of the five SNPs only one showed allele-specific differences in aortic DB129663 transcripts. No significant differences were observed in PWV between samples expressing or lack- ing DB129663, and therefore the implication of this lncRNA in aortic stiffness remains elusive. The BCL11B transcript detected in the human aorta may reflect lymphocyte infiltration, suggesting that immune mechanisms contribute to the observed association with PWV. For the final part of this work genetic associations with aortic stiffness were explored in a candidate gene-based study utilising tagging SNPs to effectively capture the genetic information from linkage disequilibrium blocks. Association analyses were performed in young, healthy ENIGMA study par- ticipants selected for high and low PWV values then validated in the remaining ENIGMA cohorts. The association of four lead SNPs was then examined for ex vivo aortic stiffness in human donor aortas. The tissue expression of these SNPs and their encoded proteins was also explored. Neither the aggrecan nor the fibulin-1 SNPs showed significant associations with ex vivo PWV in the donor aortas. The exonic aggrecan tagSNP rs2882676 displayed differential transcript abundance between homozygous allele carriers but this did not translate at the protein level. Both aggrecan and fibulin-1 were found in the aortic wall, but with marked differences in the distribution and glycosylation of aggrecan, reflecting loss of chondroitin-sulphate binding domains. These differences were age-dependent but the striking finding was the acceleration of this process in stiff versus elastic young aortas. These findings suggest that aggrecan and fibulin-1 have critical roles in determining the biomechanics of the aorta and their modification with age could underpin age-related aortic stiffening.

BACKGROUND: Arterial stiffness (AS), or loss of elastic compliance of large arteries, is an independent risk factor for cardiovascular events1. A recent study demonstrated that single nucleotide polymorphisms (SNPs) in a genetic locus downstream of the gene Bcl11b are associated with AS2. However, how this genetic locus and Bcl11b regulate AS is unknown. OBJECTIVES: To determine the molecular mechanisms by which Bcl11b effects the aortic wall and AS. METHODS: Vascular smooth muscle (VSM) cells were isolated from aortas of wildtype (WT) mice and mice with VSM-specific Bcl11b deletion (BKO). mRNA levels of Bcl11b, vascular contractile markers (myosin heavy chain 11 (MYH11), smooth muscle -actin (ACTA2), and myocardin (MYOCD)) and a cell proliferation marker (Ki67) were measured in WT and BKO VSM cells isolated from murine aortas. VSM cell contractility in response to angiotensin II (angII), a contractile stimulus, was measured in WT and BKO VSM cells using an optimized collagen gel contractility assay. RESULTS: BKO VSM cells had decreased expression of contractile markers compared to WT cells, which resulted in impaired collagen gel contraction in response to angII. CONCLUSIONS: Bc111b is expressed in aortic smooth muscle cells and it regulates the expression of VSM contractile proteins. Our data strongly supports the hypothesis that Bcl11b regulates AS by regulating the contractile function of VSM cells in the aortic wall. / 2019-07-11T00:00:00Z

Cell proliferation is a process that is strictly regulated by a large number of proteins. An alteration in one of the encoding genes inserts an error into the regulative protein, which may result in uncontrolled cell growth and eventually tumor formation. Lymphoma is a cancer type originating in the lymphocytes, which are part of the body’s immune defence. In the present thesis, Znfn1a1, Notch1 and Bcl11b were studied; all involved in the differentiation of T lymphocytes. The three genes are located in chromosomal regions that have previously shown frequent loss of heterozygosity in tumor DNA. Ikaros is a protein involved in the early differentiation of T lymphocytes. In this thesis, mutation analysis of the Znfn1a1 gene in chemically induced murine lymphomas revealed point mutations and homozygous deletions in 13 % of the tumors. All of the detected deletions lead to amino acid substitutions or abrogation of the functional domains in the Ikaros protein. Our results support the role of Ikaros as a potential tumor suppressor in a subset of tumors. Notch1 is a protein involved in many differentiation processes in the body. In lymphocytes, Notch1 drives the differentiation towards a T-cell fate and activating alterations in the Notch1 gene have been suggested to be involved in T-cell lymphoma. We identified activating mutations in Notch1 in 39 % of the chemically induced murine lymphomas, supporting the involvement of activating Notch1 mutations in the development of T-cell lymphoma. Bcl11b has been suggested to be involved in the early T-cell specification, and mutations in the Bcl11b gene has been identified in T-cell lymphoma. In this thesis, point mutations and deletions were detected in the DNA-binding zinc finger regions of Bcl11b in 15 % of the chemically induced lymphomas in C57Bl/6×C3H/HeJ F1 mice. A mutational hotspot was identified, where four of the tumors carried the same mutation. Three of the identified alterations, including the hotspot mutation in Bcl11b, increased cell proliferation when introduced in a cell without endogenous Bcl11b, whereas cell proliferation was suppressed by wild-type Bcl11b in the same cell line. Mutations in Bcl11b may therefore be an important contributing factor to lymphomagenesis in a subset of tumors. A germ line point mutation was identified in BCL11B in one of 33 human B-cell lymphoma patients. Expression of BCL11B in infiltrating T cells was significantly lower in aggressive compared to indolent lymphomas, suggesting that the infiltrating T cells may affect the B-cell lymphomas.

Skin is the largest organ in the body that protects the organism from environmental, chemical and physical traumas of each passing day. The protective skin epidermal permeability barrier (EPB) is formed within the exterior layers of the epidermis, which are regularly sloughed off and repopulated by movement of inner cells. The epidermal permeability barrier is established during in utero development and maintained through lifetime. Impaired epidermal barrier formation is one of the major features of several dermatoses such as psoriasis and atopic dermatitis. Chicken ovalbumin upstream promoter transcription factor (COUP-TF)-interacting protein 2 (Ctip2), also known as Bcl11b, is a C���H��� zinc finger protein expressed in many organs and tissues. It has been shown to regulate the development of thymocyte, tooth and corticospinal motor neurons. Ctip2 is highly expressed in mouse epidermis during skin organogenesis and in adulthood. It is crucial for epidermal homeostasis and protective barrier formation in developing mouse embryos. Germline (Ctip2- null mice) and selective ablation of Ctip2 in mouse epidermis (Ctip2[superscript ep-/-] mice) leads to increased transepidermal water loss (TEWL), impaired epidermal proliferation and terminal differentiation as well as altered lipid distribution during embryogenesis. Sphingolipids account for ~50% of total skin lipids by weight and are crucial components of epidermal barrier. We have recently identified Ctip2 as a key regulator of skin lipid metabolism. Germline deletion of Ctip2 in mouse embryos leads to altered lipid composition in the developing mouse epidermis by modulating the expression levels of key enzymes involved in lipid metabolism (bio-synthesis and catabolism). We also demonstrated that Ctip2 is recruited to the promoter regions of several genes involved in the ceramide and sphingomyelin biosynthesis pathways and could directly regulate their expression. Thus, we have identified Ctip2 as a key regulator of several lipid metabolizing genes and hence epidermal sphingolipid biosynthesis during skin development. To study the role of Ctip2 in adult skin homeostasis, we have utilized Ctip2[superscript ep-/-] mouse model in which Ctip2 is selectively deleted in epidermal keratinocytes. We showed that keratinocytic ablation of Ctip2 leads to atopic dermatitis (AD)-like skin inflammation, characterized by alopecia, pruritus and scaling, as well as high infiltration of T lymphocytes and immune cells. We have also observed increased expression of Th2-type cytokines and chemokines in the mutant skin, as well as systemic immune responses that share similarity with human AD patients. Furthermore, we discovered that thymic stromal lymphopoietin (TSLP) expression is significantly upregulated in the mutant epidermis as early as postnatal day 1 and Ctip2 was recruited to the promoter region of the TSLP gene in mouse epidermal keratinocytes. The results suggest that upregulation of TSLP expression in the Ctip2[superscript ep-/-] epidermis could be due to a derepression of gene transcription in absence of Ctip2. Thus, our data demonstrated a cell-autonomous role of Ctip2 in barrier maintenance and epidermal homeostasis in adult skin, as well as a non-cell autonomous role of keratinocytic Ctip2 in suppressing skin inflammatory responses by regulating the expression of Th2-type cytokines in adult mouse skin. Present results establish an initiating role of epidermal TSLP in AD pathogenesis via a novel repressive regulatory mechanism mediated by Ctip2 in mouse epidermal keratinocytes. Altogether, our study indicates that Ctip2 could be involved in a diverse range of biological events in skin including barrier formation, maintenance and epidermal homeostasis. Ctip2 appears to be a master regulator in skin barrier functions by directly regulating the transcription of a subset of genes involved in lipid metabolism and inflammatory responses. / Graduation date: 2013