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Discovered in 1980, HTLV-1 (Human T-cell Leukemia Virus-1), was the first identified human retrovirus and is shown to be associated with a variety of diseases including: adult T-cell leukemia lymphoma (ATLL), tropical spastic paraparesis/HTLV-1 associated myelopathy (TSP/HAM), chronic arthropathy, uveitis, infective dermatitis, and polymyositis. The mechanism by which the virus causes disease is still unknown. HTLV- 1 infection has been reported in many regions of the world but is most prevalent in Southern Japan, the Caribbean basin, Central and West Africa, the Southeastern United States, Melanesia, parts of South Africa, the Middle East and India. Approximately 30 million people are infected by HTLV-1 worldwide, although only 3-5% of the infected individuals evolve Adult T-cell Leukemia (ATL) during their life and the prognosis for those infected is still poor. The retroviral proteases (PRs) are essential for viral replication because they process viral Gag and Gag-(Pro)-Pol polyproteins during maturation, much like the PR from Human Immunodeficiency Virus-1 (HIV-1). Various antiviral inhibitors are in clinical use and one of the most significant classes is HIV-1 PR inhibitors, which have used for antiretroviral therapy in the treatment of AIDS. HTLV-1 PR and HIV-1 PR are homodimeric aspartic proteases with 125 and 99 residues, respectively. Even though substrate specificities of these two enzymes are different, HTLV-1 PR shares 28% similarity with HIV-1 PR overall and the substrate binding sites have 45% similarity. In addition to the 125-residue full length HTLV-1 PR, constructs with various C- terminal deletions (giving proteases with lengths of 116, 121, or 122 amino acids) were made in order to elucidate the effect of the residues in the C-terminal region. It was suggested that five amino acids in the C-terminal region are not necessary for the enzymatic activity in Hayakawa et al. 1992. In 2004 Herger et al. had suggested that 10 amino acids at the C-terminal region are not necessary for catalytic activity. A recent paper suggested that C-terminal residues are essential; and that catalytic activity lowers upon truncation, with even the last 5 amino acids necessary for full catalytic activity (1). The mutation L40I has been made to prevent autoproteolysis and the W98V mutation was made to make the active site of HTLV-1 PR similar to HIV-1 PR. We have characterized C-terminal amino acids of HTLV-1 PR as not being essential for full catalytic activity. We have discovered potential new inhibitors by in silico screening of 116-HTLV-1 PR. These small molecules were tested kinetically for various constructs including the 116, 121 and 122-amino acid forms of HTLV-1 PR. Inhibitors with the best inhibition constants were used in HTLV-1 infected cells and one of the inhibitors seems to inhibit gag processing.

Diss. (sammanfattning) Uppsala : Univ., 2004. / Härtill 5 uppsatser.

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

Leung Kam Tong. / Thesis submitted in: September 2006. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 79-95). / Abstracts in English and Chinese. / Abstract --- p.i / Abstract (Chinese) --- p.iii / Acknowledgements --- p.v / Table of contents --- p.vi / List of figures --- p.ix / List of abbreviations --- p.xii / Chapter Chapter 1 --- General Introduction --- p.1 / Chapter 1.1 --- Acute lymphoblastic leukemia --- p.1 / Chapter 1.2 --- T-cell acute lymphoblastic leukemia --- p.2 / Chapter 1.2.1 --- Chemotherapy --- p.2 / Chapter 1.2.1.1 --- Induction therapy --- p.2 / Chapter 1.2.1.2 --- Intensification therapy --- p.3 / Chapter 1.2.1.3 --- Maintenance therapy --- p.3 / Chapter 1.2.2 --- Chemoresistance in T-ALL --- p.3 / Chapter 1.3 --- Apoptosis and chemoresistance --- p.5 / Chapter 1.3.1 --- "Initiation, execution and regulation of apoptosis" --- p.5 / Chapter 1.3.1.1 --- Initiation of apoptosis --- p.5 / Chapter 1.3.1.2 --- Execution of apoptosis --- p.7 / Chapter 1.3.1.3 --- Regulation of apoptosis --- p.7 / Chapter 1.3.2 --- Mechanisms of resistance to apoptosis --- p.9 / Chapter 1.3.2.1 --- Overexpression of pro-survival proteins --- p.9 / Chapter 1.3.2.2 --- Downregulation and mutation of pro-apoptotic proteins --- p.11 / Chapter 1.3.2.3 --- Other mechanisms --- p.13 / Chapter 1.4 --- Bcl-2 interating mediator of cell death --- p.14 / Chapter 1.4.1 --- Role of Bim in apoptosis --- p.16 / Chapter 1.4.2 --- Regulation of Bim --- p.17 / Chapter 1.4.2.1 --- Transcriptional regulation of Bim --- p.18 / Chapter 1.4.2.2 --- Post-transcriptional regulation of Bim --- p.18 / Chapter 1.5 --- c-Jun N-terminal kinase --- p.20 / Chapter 1.5.1 --- Pro-apoptotic role of JNK --- p.21 / Chapter 1.5.2 --- Anti-apoptotic role of JNK --- p.21 / Chapter 1.6 --- Hypotheses --- p.22 / Chapter Chapter 2 --- Materials and Methods --- p.23 / Chapter 2.1 --- Cell culture --- p.23 / Chapter 2.2 --- Induction of quantification of apoptosis --- p.24 / Chapter 2.3 --- Determination of caspase activities --- p.24 / Chapter 2.4 --- Western blotting --- p.25 / Chapter 2.4.1 --- Protein extraction and determination of protein concentration --- p.25 / Chapter 2.4.2 --- SDS-PAGE and immunodetection --- p.26 / Chapter 2.5 --- Cell-free apoptosis reactions --- p.27 / Chapter 2.6 --- Analysis of mitochondrial membrane potential --- p.27 / Chapter 2.7 --- Transient transfection of Sup-Tl cells --- p.28 / Chapter 2.8 --- Reverse transcription-polymerase chain reaction (RT-PCR) --- p.28 / Chapter 2.8.1 --- RNA isolation --- p.28 / Chapter 2.8.2 --- Synthesis of first-strand cDNA --- p.29 / Chapter 2.8.3 --- Polymerase chain reaction --- p.29 / Chapter 2.9 --- Alkaline phosphatase digestion of Bim --- p.30 / Chapter Chapter 3 --- Results --- p.31 / Chapter 3.1 --- The T-ALL cell line Sup-Tl is resistant to etoposide-induced apoptosis --- p.31 / Chapter 3.2 --- Sup-Tl cells are resistant to etoposide-induced caspase activation --- p.40 / Chapter 3.3 --- Sup-Tl cells are insusceptible to etoposide-induced mitochondrial alterations --- p.46 / Chapter 3.4 --- BimEL is required for etoposide-induced apoptosis in Sup-Tl cells --- p.51 / Chapter 3.5 --- The reduced level of BimEL in Sup-Tl cells is owing to the presence of constitutively active JNK --- p.58 / Chapter Chapter 4 --- Discussion --- p.67 / References --- p.79

Stimuler le système immunitaire est un enjeu majeur dans le traitement des leucémies aigües. Nous avons centré notre étude sur la leucémie aigüe myéloïde (LAM) et la leucémie à cellules dendritiques plasmacytoïdes (LAPDC). Dans une première partie, nous avons étudié les médicaments immunomodulateurs (IMiDs) utilisés dans le traitement du myélome multiple et des syndromes myélodysplasiques à délétion 5q. Les IMiDs présentent des propriétés anti-angiogéniques, anti-prolifératives, pro-apoptotiques, et immunomodulatrices en particulier sur les cellules NK (Natural Killer). Nous avons évalué les effets anti-leucémiques des IMiDs (lenalidomide et pomalidomide) dans le but d’améliorer l’activité cytotoxique des NK dans la LAM. Nous avons mis en évidence une altération de la survie des blastes de LAM par les IMiDs in vitro, et dans un modèle in vivo de greffe dans les souris immunodéficientes NOD/SCID/IL2rg-/- (NSG). Nous avons également montré une sensibilisation par les IMiDs des blastes de LAM à la lyse par les NK allogéniques, indépendamment de la cible moléculaire connue, le cereblon. Le traitement des blastes de LAM par IMiDs stimule les fonctions NK. Enfin, nous avons décrit des modifications phénotypiques induites par les IMiDs sur les récepteurs NK, et une diminution d’expression de HLA-classe I sur les cellules de LAM. Ces résultats encouragent la poursuite du développement des IMiDs dans la LAM, en particulier les associations stimulant les fonctions NK. Dans une seconde partie, nous avons développé un modèle murin de LAPDC dans la souris NSG. Cet outil préclinique est indispensable dans l’élaboration de stratégies d’immunothérapie dans les leucémies aigües. / Boosting the Immune System is a major challenge in the treatment of acute leukemias. We focused our study on acute myeloid leukemia (AML) and plasmacytoid dendritic cell leukemia (BPDCN). In the first part, we studied immunomodulatory drugs (IMiDs) that are currently used in the treatment of patients with myeloma and myelodysplastic syndrome with 5q deletion. IMiDs exhibit anti-angiogenesis, anti-proliferative, pro-apoptotic, and immunomodulatory properties especially on NK cells and T lymphocytes. We investigated the anti-leukemic effects of two IMiDs (lenalidomide and pomalidomide) in order to improve NK cell cytotoxic activity in AML. We have shown that IMiDs impaired survival of AML blasts in vitro, and in vivo in NOD/SCID/IL2rg-/- (NSG) murine model. In addition, IMiDs treatment sensitized AML blasts to allogeneic NK cell mediated lysis, independently of Cereblon, the known molecular target of IMiDs. IMiDs treatment of AML blasts enhanced NK cell functions such as degranulation and cytokine production. Finally, we have described phenotypic changes induced by IMiDs on NK receptors, and a down-regulation of HLA-class I on AML blasts. These results encourage continuing investigation for the use of IMiDs in AML, especially in combination with immunotherapies based on NK cells. In a second part, we have developed a murine model of plasmacytoid dendritic cell leukemia (BPDCN) in NSG mice. Murine model of leukemia are essential preclinical tools in the development of new immunotherapies in acute leukemias.

<p>B cell lymphomas and leukemias are heterogeneous tumors with different cellular origins. Analysis of immunoglobulin (Ig) genes enables insight into the B cell progenitor, as Ig somatic hypermutation correlates with antigen-related B cell transit through the germinal center (GC). Also, restricted Ig variable heavy chain (V_H) gene repertoires in B cell malignancies could imply antigen selection during tumorigenesis. The length of telomeres has been shown to differ between GC B cells and pre/post-GC B cells, possibly representing an alternative angle to investigate B cell tumor origin. </p><p>Mantle cell lymphoma (MCL), previously postulated to derive from a naïve, pre-GC B cell, was shown to have an Ig-mutated subset (18/110 MCLs, 16%), suggestive of divergent cellular origin and GC exposure. Another subset of MCL (16/110, 15%), characterized by V_H3-21/V_λ3-19 gene usage, alludes to a role for antigen(s) in pathogenesis, also possible for hairy cell leukemia (HCL) in which the V_H3-30 gene (6/32, 19%) was overused. HCL consisted mainly of Ig-mutated cases (27/32, 84%) with low level intraclonal heterogeneity, contrasting with the proposed post-GC origin, for both Ig-mutated and Ig-unmutated HCLs. For MCL and HCL, derivation from naïve or memory marginal zone B cells which may acquire mutations without GC transit are tempting speculations, but currently little is known about this alternative immunological pathway. Heavily mutated Ig genes without intraclonal heterogeneity were demonstrated in lymphoplasmacytic lymphoma/Waldenström’s macroglobulinemia (13/14, 93%), confirming that the precursor cell was transformed after GC affinity maturation. Telomere length analysis within 304 B cell tumors revealed variable lengths; shortest in the Ig-unmutated subset of chronic lymphocytic leukemia, longest in the GC-like subtype of diffuse large B cell lymphoma, and homogeneous in MCL regardless of Ig mutation status. However, telomere length is complex with regard to GC-related origin.</p><p>In summary, this thesis has provided grounds for speculation that antigens play a role in MCL and HCL pathogenesis, although the potential antigens involved are currently unknown. It has also enabled a more informed postulation about the cellular origin of B cell tumors, which will ultimately enhance understanding of the biological background of the diseases. </p>

B cell lymphomas and leukemias are heterogeneous tumors with different cellular origins. Analysis of immunoglobulin (Ig) genes enables insight into the B cell progenitor, as Ig somatic hypermutation correlates with antigen-related B cell transit through the germinal center (GC). Also, restricted Ig variable heavy chain (VH) gene repertoires in B cell malignancies could imply antigen selection during tumorigenesis. The length of telomeres has been shown to differ between GC B cells and pre/post-GC B cells, possibly representing an alternative angle to investigate B cell tumor origin. Mantle cell lymphoma (MCL), previously postulated to derive from a naïve, pre-GC B cell, was shown to have an Ig-mutated subset (18/110 MCLs, 16%), suggestive of divergent cellular origin and GC exposure. Another subset of MCL (16/110, 15%), characterized by VH3-21/Vλ3-19 gene usage, alludes to a role for antigen(s) in pathogenesis, also possible for hairy cell leukemia (HCL) in which the VH3-30 gene (6/32, 19%) was overused. HCL consisted mainly of Ig-mutated cases (27/32, 84%) with low level intraclonal heterogeneity, contrasting with the proposed post-GC origin, for both Ig-mutated and Ig-unmutated HCLs. For MCL and HCL, derivation from naïve or memory marginal zone B cells which may acquire mutations without GC transit are tempting speculations, but currently little is known about this alternative immunological pathway. Heavily mutated Ig genes without intraclonal heterogeneity were demonstrated in lymphoplasmacytic lymphoma/Waldenström’s macroglobulinemia (13/14, 93%), confirming that the precursor cell was transformed after GC affinity maturation. Telomere length analysis within 304 B cell tumors revealed variable lengths; shortest in the Ig-unmutated subset of chronic lymphocytic leukemia, longest in the GC-like subtype of diffuse large B cell lymphoma, and homogeneous in MCL regardless of Ig mutation status. However, telomere length is complex with regard to GC-related origin. In summary, this thesis has provided grounds for speculation that antigens play a role in MCL and HCL pathogenesis, although the potential antigens involved are currently unknown. It has also enabled a more informed postulation about the cellular origin of B cell tumors, which will ultimately enhance understanding of the biological background of the diseases.

Multiple myeloma and its aggressive variant, plasma cell leukemia, are still considered to be incurable diseases despite the progressive treatment approaches comprising novel drugs. This can be attributed to the presence of the bone marrow microenvironment which plays an important role in drug resistance of myeloma cells. Hematopoietic cell lines derived from hematologic malignancies are suitable models for the study of etiopathogenesis of these malignant diseases and for testing new potential drugs. Establishment of these cell lines is still considered to be coincidental and rare event. The first part of the thesis is focused on establishment and characterization of the cell line UHKT-944 derived from a patient with primary plasma cell leukemia, and on completion of characterization of the cell line UHKT-893 derived from a patient with multiple myeloma. Additional analysis of UHKT-893 cell line were performed including sequence analysis of IgVH gene rearrangements and cytogenetic analysis which contributed to more detailed characterization of this cell line. During cultivation of UHKT-944 cells, we monitored the cell growth and confirmed dependence on interleukin-6 (IL-6). Immunophenotype analysis revealed the presence of surface markers characteristic of malignant plasma cells. UHKT-944 cells...