The SOX (Sry-related HMG box) genes belong to a family of transcription factors containing a High-Mobility-Group box domain. In an initial screen, SOX7 was uniquely down-regulated in myeloid malignancies compared with most cases of precursor B-cell acute lymphoblastic leukemia (ALL) and normal bone marrow cell, leading us to examine the expression and function of SOX7 during normal hematopoietic differentiation and in acute lymphoblastic leukemia. By studying human umbilical cord blood (UCB), SOX7 expression in different hematopoietic lineages was evaluated by RT-PCR. SOX7 was preferentially expressed in CD34+CD38- compared with CD34+CD38+ population and in CD34-CD19+ compared with CD34-CD33+ cells. SOX7 expression was down-regulated in colonies in CFU assay and in engrafting myeloid cells in NOD/SCID mouse transplantation. Transfecting SOX7 siRNA into CD34+ cells reduced cell growth and the CD34+CD33+ population in 3-day culture; induced cell-cycle arrest at G1 phase; reduced clonogenic activities but had no effect on apoptosis. Overall engraftment into NOD/SCID mice were not affected but the engrafting myeloid populations were reduced. In acute lymphoblastic leukemia, SOX7 was robustly expressed, compared with that in normal UCB and acute myeloid leukemia (AML). In 5 ALL patients in whom the coding sequence of SOX7 was examined, 3 of them showed mutations (amino acid change) in the SOX C-terminal transactivation domain. No mutation was observed in the β-catenin binding site. Knockdown of SOX7 with specific siRNA significantly increased appoptosis and decreased cell proliferation. SOX7 knockdown by shRNA in a precursor B-cell ALL cell line Nalm20 significantly reduced its engraftment into NOD/SCID mice. In summary, SOX7 is preferentially expressed in early hematopoietic stem and progenitor cells and is important for the maintenance of myeloid progenitor. It is also expressed in the primitive population of ALL and is important for leukemia initiation in ALL. The present study has generated important information about the regulation of normal hematopoiesis and acute lymphoblastic leukemia / published_or_final_version / Medicine / Doctoral / Doctor of Philosophy

Acute Lymphoblastic Leukemia (ALL) is the most common cancer in children under the age of 15. At present, diagnosis, prognosis and treatment decisions are made based upon blood and bone marrow laboratory testing. With advances in microarray technology it is becoming more feasible to perform genetic assessment of individual patients as well. We used Singular Value Decomposition (SVD) on Illumina SNP, Affymetrix and cDNA gene-expression data and performed aggressive attribute se- lection using random forests to reduce the number of attributes to a manageable size. We then explored clustering and prediction of patient-specific properties such as disease sub-classification, and especially clinical outcome. We determined that integrating multiple types of data can provide more meaningful information than individual datasets, if combined properly. This method is able to capture the cor- relation between the attributes. The most striking result is an apparent connection between genetic background and patient mortality under existing treatment regimes. We find that we can cluster well using the mortality label of the patients. Also, using a Support Vector Machine (SVM) we can predict clinical outcome with high accu-racy. This thesis will discuss the data-mining methods used and their application to biomedical research, as well as our results and how this will affect the diagnosis and treatment of ALL in the future. / Thesis (Master, Computing) -- Queen's University, 2010-01-12 18:40:44.2

Thesis (Ph.D.)--Murdoch University, 2003. / Thesis submitted to the Division of Health Sciences. Bibliography: leaves 177-201.

Obesity is a recognized problem for children treated for acute lymphoblastic leukemia (ALL) and is present in roughly one fourth of children by the end of therapy. Obesity may lead to immediate health threats, such as an increased risk for cancer relapse, or may cause future heath issues such as diabetes, metabolic syndrome, hypertension, additional cancers, depression or cardiovascular disease. The purpose of this study was to determine if weight gain during two individual cycles of therapy (Induction or Delayed Intensification Cycle 1) were predictive of obesity (defined as body mass index ≥ 95th percentile for age and gender) at the end of treatment. This study retrospectively examined height and weight data from 1,017 childhood leukemia patients treated on Children's Oncology Group (COG) protocol number 1961. This study included patients that had fully completed therapy on protocol 1961 and who were between the ages of 2-20 years. Percentiles and z-scores for age and gender specific body mass index (BMI) were calculated using the height and weight measurements obtained at the beginning of each cycle of chemotherapy. Univariate and multivariate logistic regression analyses were performed. BMI z-score at the beginning of therapy and difference in BMI z-score during Induction were significant predictors (p<0.0001) of BMI ≥ 95th percentile at the end of maintenance in both males and females. A one unit increase in the difference of BMI z-score during Induction resulted in a 3.03 odds ratio (OR) for obesity at the end of therapy for males (95% CI, 1.90 to 4.84) and a 4.15 OR for females (95% CI, 2.32 to 7.43). The change in BMI z-score during Delayed Intensification I was not found to be significant in relationship to obesity at the end of therapy. Weight gain during Induction consisted of ≥ 20% increase in weight for 3.9% of the study participants. Weight gain during Induction therapy of childhood ALL treatment may be useful in predicting patients at increased risk for obesity development during therapy. Early identification of these at risk patients can assist with interventions aimed at normalizing weight gain during therapy.

Progress in understanding cancer progression has been hampered over the years by the different types of mutations present and irregular changes of gene regulation associated with any given cancer. In this work, molecular interactions between TALI, LMO1, and decorin were investigated. Numerous studies have shown that ectopic expression of decorin protein induced growth suppression in neoplastic cells of various histogenic origins. Furthermore, ectopic expression of TAL1 and LMOI oncoproteins has been shown to occur in approximately 50% of the cases of T-cell acute lymphoblastic leukemia (T-ALL). It was of interest then to determine the preventive or interactive role decorin played with the oncogenic activity of TAL I and LMO1. In this investigation, decorin was introduced into a murine T-cell line (AKR-DP-603) through the use of the mammalian expression vector pcDNA3.1 (-). This particular cell line was previously engineered to express TALI and LMO1. Protein expression patterns in all cell populations were analyzed using the Western blot technique and a proteoglycan with a molecular weight of 100 kDa before chondroitinase ABC treatment and a core protein of55 kDa after treatment with chondroitinase ABC was seen. This finding is significant since it implies that the pcDNA3. 1(-) vector containing decorin cDNA was present, and the corresponding decorin peptides were expressed in both cytoplasmic and nuclear extracts. Furthermore, Northern blot analysis was performed on total RNA extracts to determine the transcriptional state of endogenous decorin rRNA, as well as exogenously introduced decorin. Northern blot analysis revealed no decorin-specific mRNA transcripts from the various cell populations. This result did not imply a lack of possible regulatory effect on protein and mRNA levels of TALL and LMOI by decorin. Finally, cell growth assays were performed on all cell populations and cell counts were used to assess the growth pattern of each population after serum withdrawal. The results show possible growth suppressive effects of decorin on TAL1 and LMOI expressing cells. Results obtained from this study shed further light on the molecular interactions influencing T-ALL and may also help in the design of potentially beneficial cancer treatments using decorin. / Department of Biology

Thesis (Ph. D.)--University of Canterbury, 2008. / Typescript (photocopy). Includes bibliographical references (leaves 323-367). Also available via the World Wide Web.

Thesis (M.S.)--Ball State University, 2008. / Title from PDF t.p. (viewed on Sept. 09, 2009). Includes bibliographical references (p. [93]-101).

Chung, Po Yin. / Thesis submitted in: December 2006. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 128-155). / Abstracts in English and Chinese. / Thesis Abstract --- p.i / 論文摘要 --- p.iv / Acknowledgements --- p.vi / Abbreviations --- p.vii / Thesis Content --- p.xi / List of Figures --- p.xv / List of Tables --- p.xvii / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1. --- Normal Hematopoiesis --- p.1 / Chapter 1.2. --- Hematological Malignancy and the Aberrant Development of Blood Cells --- p.2 / Chapter 1.3. --- Leukemia and Its Classification --- p.3 / Chapter 1.4. --- Childhood Acute Lymphoblastic Leukemia (ALL) --- p.5 / Chapter 1.4.1. --- Epidem iology --- p.5 / Chapter 1.4.2. --- Causes and Risk Factors --- p.6 / Chapter 1.4.3. --- Molecular Pathophysiology --- p.7 / Chapter 1.4.4. --- Clinical Presentation --- p.9 / Chapter 1.4.5. --- Classification --- p.10 / Chapter 1.4.5.1. --- Immunophenotyping --- p.10 / Chapter 1.4.5.2. --- French-American-British (FAB) Classification --- p.12 / Chapter 1.4.6. --- Diagnosis and Prognosis --- p.14 / Chapter 1.4.6.1. --- Morphological and Cytochemical Analysis --- p.15 / Chapter 1.4.6.2. --- Cytogenetic and Molecular Genetic Characterizations --- p.16 / Chapter 1.4.7. --- Treatment --- p.19 / Chapter 1.5. --- Overview of Epigenetics --- p.21 / Chapter 1.6. --- Concepts ofDNA Methylation --- p.23 / Chapter 1.6.1. --- CpG Islands --- p.23 / Chapter 1.6.2 --- Mechanisms of DNA Methylation --- p.24 / Chapter 1.6.3 --- Physiological Roles of DNA Methylation --- p.28 / Chapter 1.6.4 --- Initiation of Aberrant DNA Methylation --- p.30 / Chapter 1.7. --- DNA Methylation in Tumorigenesis --- p.31 / Chapter 1.7.1. --- Regional Hypermethylation --- p.33 / Chapter 1.7.2 --- Global and Regional Hypomethylation --- p.34 / Chapter 1.7.3 --- Microatellite Instability and Oncogeneic Mutation --- p.35 / Chapter Chapter 2 --- Literature Review --- p.37 / Chapter 2.1. --- Aberrant DNA Methylation in Childhood ALL --- p.37 / Chapter 2.1.1. --- Cell Cycle --- p.39 / Chapter 2.1.2. --- Apoptosis --- p.41 / Chapter 2.1.3. --- Tissue Invasion and Metastasis --- p.42 / Chapter 2.1.4. --- Transcription Factors and Metabolic Enzymes --- p.44 / Chapter 2.1.5. --- Putative Tumor Suppressor Genes --- p.44 / Chapter 2.1.6. --- Chromosome Instability --- p.46 / Chapter 2.2. --- Methodologies in DNA Methylation Analysis --- p.50 / Chapter 2.2.1. --- Principle of Methylation-sensitive Arbitrarily Primed PCR (MS-AP PCR) --- p.50 / Chapter 2.2.2. --- Combined Bisulfite Restriction Analysis (COBRA) --- p.53 / Chapter 2.2.3. --- Cloned Bisulfite Sequencing --- p.55 / Chapter 2.2.4. --- Experimental Use of Demethylating Agents --- p.55 / Chapter Chapter 3 --- Background of Research --- p.58 / Chapter 3.1. --- Current Methylation Studies in Childhood ALL --- p.58 / Chapter 3.2. --- Objectives of Research --- p.60 / Chapter 3.3. --- Study Approach and Experimental Design --- p.61 / Chapter Chapter 4 --- Materials and Methods --- p.63 / Chapter 4.1. --- Clinical Samples and ALL Cell Lines --- p.63 / Chapter 4.1.1. --- Clinical Samples from Pediatric Patients with ALL and Normal Healthy Donors --- p.63 / Chapter 4.1.2. --- ALL Cell Lines --- p.63 / Chapter 4.2. --- Genomic DNA Isolation from Clinical Samples and Cell Lines --- p.64 / Chapter 4.2.1. --- Ficoll Gradient Centrifugation --- p.64 / Chapter 4.2.2. --- DNA Extraction --- p.64 / Chapter 4.3. --- MS-AP PCR --- p.65 / Chapter 4.3.1. --- Methylation-sensitive Restriction Enzyme Digestion of Genomic DNA --- p.65 / Chapter 4.3.2. --- Arbitrarily Primed Polymerase Chain Reaction --- p.66 / Chapter 4.3.3. --- Isolation of Differentially Methylated DNA Fragments --- p.69 / Chapter 4.4. --- Cloning of Differentially Methylated DNA Fragments --- p.70 / Chapter 4.4.1. --- TA Cloning --- p.70 / Chapter 4.4.2. --- Screening of Positive Clones --- p.71 / Chapter 4.4.3. --- Preparation of Plasmid DNA by Alkaline Lysis Method --- p.72 / Chapter 4.5. --- DNA Sequence Analysis of Differentially Methylated DNA Fragments --- p.72 / Chapter 4.5.1. --- Dye-terminator Cycle Sequencing --- p.72 / Chapter 4.5.2. --- CpG islands Analysis of Differentially Methylated Sequences --- p.73 / Chapter 4.6. --- DNA Methylation Analysis --- p.74 / Chapter 4.6.1. --- Sodium Bisulfite Modification --- p.74 / Chapter 4.6.2. --- Combined Bisulfite Restriction Analysis --- p.75 / Chapter 4.6.3. --- Cloned Bisulfite Genomic Sequencing --- p.76 / Chapter 4.7 --- Gene Expression Study --- p.76 / Chapter 4.7.1. --- RNA Extraction from Clinical Samples and ALL Cell Lines --- p.76 / Chapter 4.1.2. --- Reverse Transcription PCR --- p.77 / Chapter 4.7.3. --- Semi-quantitative RT-PCR --- p.78 / Chapter 4.7.4. --- 5-aza-2 '-deoxycytidine Demethylation Treatment --- p.79 / Chapter Chapter 5 --- Results --- p.80 / Chapter 5.1. --- Generation of DNA Methylation Pattern by MS-AP PCR --- p.80 / Chapter 5.1.1. --- Differential Methylation Patterns of Childhood ALL --- p.84 / Chapter 5.1.2. --- Methylation Patterns of B and T lineages Childhood ALL --- p.86 / Chapter 5.2. --- UCSC BLAT Analysis of Differential Methylated DNA Sequences / Chapter 5.3. --- Identification of Candidate Gene --- p.89 / Chapter 5.4. --- Fibrillin 2 --- p.90 / Chapter 5.4.1. --- FBN2 CpG Islands: UCSC BLAT Search Analysis --- p.90 / Chapter 5.4.2. --- Verification ofFBN2 by ALL Cell Lines --- p.91 / Chapter 5.4.2.1. --- Semi-quantitative RT-PCR --- p.91 / Chapter 5.4.2.2. --- COBRA --- p.92 / Chapter 5.4.2.3. --- Cloned Bisulfite Sequencing --- p.94 / Chapter 5.4.2.4. --- Demethylation Treatment Resorted FBN2 mRNA Expression in ALL Cell Lines --- p.98 / Chapter 5.4.3. --- Studies ofFBN2 in Childhood ALL --- p.99 / Chapter 5.4.3.1. --- Methylation Analysis --- p.99 / Chapter 5.4.3.2. --- Semi-quantitative RT-PCR --- p.105 / Chapter Chapter 6 --- Discussion --- p.107 / Chapter 6.1. --- Genome-wide Screening Approach: MS-AP PCR --- p.107 / Chapter 6.2. --- Sample Selection in this Study --- p.109 / Chapter 6.2.1. --- MS-AP PCR --- p.109 / Chapter 6.2.2. --- Methylation Studies --- p.109 / Chapter 6.2.3. --- Studies in ALL Cell Lines --- p.110 / Chapter 6.3. --- Methylation Patterns in Childhood ALL --- p.111 / Chapter 6.4. --- Candidate Genes Selection Strategies in MS-AP PCR --- p.112 / Chapter 6.5. --- Fibrillin 2: mRNA Expression and Methylation Studies --- p.113 / Chapter 6.5.1 --- ALL Cell Lines --- p.113 / Chapter 6.5.2 --- Childhood ALL --- p.113 / Chapter 6.5.2.1 --- mRNA Expression and Methylation Studies --- p.113 / Chapter 6.5.2.2 --- Statistical Analysis --- p.115 / Chapter 6.5.3. --- Possible Roles of FBN2 in Leukemogenesis --- p.116 / Chapter 6.6. --- Clinical Application of FBN2 Aberrant Methylation --- p.119 / Chapter 6.6.1. --- Tumor Markers --- p.119 / Chapter 6.6.2. --- Use of Demethylating Drugs in Chemotherapy --- p.121 / Chapter 6.7. --- Limitations of Methylation Studies --- p.122 / Chapter 6.7.1. --- MS-AP PCR --- p.122 / Chapter 6.7.2. --- Techniques Used in Methylation Study --- p.122 / Chapter 6.7.3. --- Problems in Methylation Study --- p.123 / Chapter 6.8. --- Future Studies --- p.125 / Chapter Chapter 7 --- Conclusion --- p.127 / References --- p.128 / Appendix --- p.155

Acute lymphoblastic leukemia (ALL) encompasses a spectrum of lymphoid progenitors that have undergone malignant transformation and clonal proliferation at various stages of differentiation. Some cases of ALL have been documented to have prenatal origins and in particular neonatal exposure to various environmental pollutants is associated with increased disease risk, including childhood lymphoma and leukemia. Dibenzo[def,p]chrysene (DBC) is a polycyclic aromatic hydrocarbon (PAH) and in our laboratory has been established as a transplacental carcinogen in mice, producing aggressive T-cell lymphoblastic lymphomas, lung, liver, uterine, ovarian, and testicular lesions, depending on timing and dose of exposure. Investigation of the transplacental and translactational transfer of DBC was warranted following a cross-foster experiment demonstrating the greatest tumorigenic response occurred in offspring both gestating in and nursed by an exposed female. [¹⁴C]-DBC (GD17) dosing was utilized to examine time-dependent alterations of [¹⁴C] in maternal and fetal tissues, excreta, and residual levels at weaning. Fetal tissue levels of [¹⁴C]-DBC equivalents were 10-fold lower than maternal tissue, and after weaning the residual body burden was roughly equivalent in offspring exposed only in utero or only via lactation. Certain bioactive food components, including indole-3-carbinol (I3C), 3,3'-diindolylmethane (DIM), and sulforaphane (SFN) from cruciferous vegetables have been shown to target cellular pathways regulating carcinogenesis. In the above mentioned DBC initiated model of carcinogenesis, I3C is an effective transplacental chemopreventive agent. We sought to extend our chemoprevention studies in mice to a human neoplasm in cell culture, analogous to the observed murine T-cell lymphomas. Treatment of the human T-ALL cell line CCRF-CEM (CEM) with I3C reduced cell proliferation and viability only at supraphysiologic concentrations whereas DIM, the primary acid condensation product of I3C, had a marked effect at low micromolar concentrations in vitro and reduced growth of CEM xenografts in vivo. Additional T-ALL lines, selected to represent the heterogeneity of the disease, (CCRF-HSB2, Jurkat, and SUP-T1) responded similarly in vitro, demonstrating a potential therapeutic value of DIM in T-ALL. Given that epigenetic reprograming is especially active during fetal development and that DNA hypermethylation contributes to the etiology of T-ALL we examined genome-wide DNA methylation in CEM. Differential methylation analysis revealed that DIM and I3C alter CpG methylation in unique, yet overlapping, gene targets. DIM treated cells exhibited a dose-dependent decrease in hypermethylation, an observation consistent with an epigenetic mechanism of cancer suppression. Pyroseqencing and RTPCR technologies were utilized to validate changes in DNA methylation and to compare these patterns with a transcriptional response in both novel targets and candidate genes selected from the literature. Collectively, these studies merited returning to the murine transplacental model for further investigation of genetic and epigenetic changes upon maternal dietary intervention with I3C. More importantly we incorporated whole cruciferous vegetable diets (10% broccoli sprouts or 10% Brussels sprouts), SFN diet, or the combination of SFN and I3C, in order to examine matrix and mixture effects. Preliminary analysis suggests a worse prognosis for those animals exposed in utero to SFN or the whole foods, especially males. As this is the first study to administer SFN or whole cruciferous vegetables in a transplacental model of carcinogenesis, our results warrant further study on the concentration dependent influence of these potent phytochemicals during the perinatal window. / Graduation date: 2012

The t(1;19) chromosomal translocation is present in 5% of acute lymphoblastic leukemia (ALL) cases and leads to expression of the oncogenic transcription factor, E2A-PBX1. Although t(1;19) is exclusively associated with pre-B ALL in clinical cases, murine models produce myeloid or T-lymphoid leukemias, which are not representative of the clinical disease. In this work, we have advanced progress towards the development an E2A-PBX1-driven experimental leukemia model. We initially determined that lineage-negative (lin-) hematopoietic progenitors expressing E2A-PBX1 expression fail to repopulate the B-lymphoid lineage when transplanted into irradiated recipient mice. Furthermore, E2A-PBX1 expressing, lin- fetal liver progenitors (FLPs) fail to differentiate into B-lymphocytes ex vivo. The majority of E2A-PBX1-expressing FLPs manifested an immature phenotype and displayed stem cell factor (SCF)-dependency and enhanced self-renewal. Additionally, these cells retained myeloid potential upon transplantation or stimulation with granulocyte macrophage colony-stimulating factor (GM-CSF). DNA binding was required for the differentiation block, suggesting that E2A-PBX1 target genes are incompatible with B-lineage specification. E2A-PBX1 FLPs had a stem cell like gene expression profile, including up-regulation of the leukemic transcription factors, Hoxa9 and Meis1. These findings explain why E2A-PBX1-driven bone marrow transplant models fail to generate B-lymphoid disease and suggest that future efforts in developing a model of E2A-PBX1-driven pre-B ALL leukemia should focus on expressing E2A-PBX1 subsequent to B-lymphoid commitment. In an attempt to override the B-lymphoid differentiation block, we next expressed E2A-PBX1 in primary pre-B cells. E2A-PBX1 induced an apoptotic response in pre-B cells, which was consistent with previous observations. Since pre-B ALL induction requires secondary genetic events, we attempted to abrogate these E2A-PBX1-mediated effects by modulating expression of the Cdkn2a locus. Loss of Cdkn2a through deletion or Bmi1 overexpression failed to ameliorate the apoptotic response, suggesting that E2A-PBX1 mediated apoptosis occurs independently of Cdkn2a in murine pre-B cells. However, in the absence of Cdkn2a, co-expression of constitutively active MerTK or Ras attenuated the E2A-PBX1 mediated apoptosis. Cumulatively, these results support the notion that t(1;19) occurs subsequent to B-lymphoid commitment and requires multiple secondary genetic lesions. Data presented in this thesis represents crucial initiating steps towards the development of a pre-B ALL model mediated by E2A-PBX1. / Thesis (Ph.D, Pathology & Molecular Medicine) -- Queen's University, 2013-09-03 00:09:29.299