Thesis (Ph. D.)--University of Nevada, Reno, 2007. / "December 2007." Includes bibliographical references (leaves 137-164). Online version available on the World Wide Web.

Thesis (Ph. D.)--University of Washington, 1998. / Vita. Includes bibliographical references (leaves [78]-93).

Thesis (M. Phil.)--University of Hong Kong, 2002. / Includes bibliographical references (leaves 92-103).

Thesis (Ph. D.)--University of Washington, 2005. / Vita. Includes bibliographical references (leaves 162-177).

The eukaryotic cell nucleus is a highly organised organelle, with distinct specialised sub- compartments responsible for specific nuclear functions. Within the context of this functional framework, the genome is organised, allowing contact between specific genomic regions and sub-compartments. Previous work has shown that genes in both cis and trans can make specific contacts with each other. I hypothesise that such a preferred juxtaposition may impact the propensity for specific cancerinitiating chromosomal translocations to occur. In this thesis, I describe how I have extended and developed a ligation based proximity assay known as enriched 4C. I have coupled this technique with high throughput sequencing to determine genomic regions that spatially co-associate with the proto-oncogenes MLL, ABL1 and BCR. In addition to further developing the laboratory protocol, I have created bioinformatics tools used in the analysis of the sequencing data. I find that the association profiles of the three genes show strong correlation to the binding profile of RNA polymerase II and other active marks, suggesting that transcribed genes have a propensity to associate with other transcribed regions of the genome. Each gene also exhibits a unique repertoire of preferred associations with specific regions of the genome. Significantly, I find that the most frequent trans association of BCR is telomeric chromosome 9, encompassing its recurrent translocation partner gene ABL1. Interestingly, ABL1 is not at the maximum point of interaction. I use DNA-fluorescence in-situ hybridisation to validate the e4C association. My data supports a hypothesis that gene transcription has a direct role on genome organisation. I suggest that preferred co-associations of genes at transcription factories may promote the occurrence of specific chromosomal translocations.

Although the key role played by stem cells in maintaining hemopoiesis is well recognized, mechanisms that determine stem cell behaviour (e.g. self-renewal) have remained poorly defined. Historical precedent has illustrated the usefulness of in viitro colony assays in facilitating the investigation of various primitive hemopoietic progenitor classes with restricted differentiation and proliferative potential. In particular, such assays have made possible the definition of the sequential nature of a series of events that early erythropoietic cells undergo and suggested properties that might be anticipated to characterize colonies derived from stem cells proliferating and differentiating in vitro. The present studies were undertaken to test the hypothesis that very large, late maturing erythroid colonies previously noted on occasion in routine erythroid colony assays were, in fact, derived from progenitors with the self-renewal and multiple myeloid differentiation properties associated with stem cells. Initial experiments showed that cells capable of yielding macroscopic sized erythroid colonies were present at low frequency in normal marrow but became the predominant erythropoietic cell type after 2 to 3 weeks in flask culture. Macroscopic erythroid colony formation in assays of cells from either source were shown to have: 1) identical very late maturation kinetics (onset of hemoglobinization after 1 week of initial colony growth), 2) the same high erythropoietin requirements, and 3) similar responsiveness to factors present in media conditioned by mitogen stimulated spleen cells. Optimization of these 2 classes of stimulant yielded an assay that was linear down to very low cell concentrations (less than 5 x 103 cells/ml). This made possible the cytological analysis of macroscopic erythroid colonies under conditions where overlap with other colony types was minimal. Such studies revealed that macroscopic colonies contained, in addition to erythroid cells, megakaryocytes ( > 90% of colonies) and granulocyte cells (30% of colonies) including cells of the eosinophil lineage. Such colonies were also found to contain cells capable of macroscopic spleen colony formation in irradiated mice, the conventional assay for mouse hemopoietic stem cells (on average 1 CFU-S per colony of flask culture origin, and 0.3 CFU-S per colony in assays of fresh marrow). Direct evidence for self-renewal was obtained from replating experiments using irradiated feeders to optimize plating efficiency. Mixed colonies of macroscopic size were regularly demonstrable in replating assays after 1, and even 2, generations of mixed colony formation indicating up to 6 self-renewal divisions during colony formation. By comparison to flask culture cells, the extent of self-renewal exhibited by cells in fresh marrow yielding macroscopic erythroid colonies was found to be 5-fold lower. Finally, the in vitro expression of stem cell self-renewal behaviour was investigated in individual colonies. The number of stem cells generated, when assessed either by CFU-S or replating assays was found to vary markedly. This variation was not accounted for by errors of detection or by variations in colony size. Such findings are similar to previous data on the CFU-S content of individual spleen colonies and provide the first evidence that the type of variation in stem cell self-renewal observed in vivo also occurs in vitro where microenvironmental factors are unlikely to be contributing factors. These results are consistent with a model of stem cell self-renewal in which intrinsic cellular factors play the key role in influencing the decision of individual cells to self-renew. / Medicine, Faculty of / Medical Genetics, Department of / Graduate

This document only includes an excerpt of the corresponding thesis or dissertation. To request a digital scan of the full text, please contact the Ruth Lilly Medical Library's Interlibrary Loan Department (rlmlill@iu.edu).

For over 50 years, bone marrow transplants have used CD34 to select stem cells. Recent research suggests that the most primitive hematopoietic stem cells (HSCs), long-term HSCs (LT-HSCs), are found in the CD34-negative portion of murine and human bone marrow cells. LT-HSCs are rare and cannot be isolated directly, making them difficult to study. During a bone marrow transplant, these stem cells must find their way to the bone marrow niche and engraft to become blood cells. Several cell adhesion molecules on the stem cell engage with their ligands on the endothelial cells lining the bone marrow vasculature to control this migration. Human LT-HSCs cells do not migrate and engraft well when infused in vivo, which may be due to a lack of adhesion molecules. Thus, the goal of this study was to determine whether this population of HSCs lacked adhesion systems (proteins and carbohydrate modifications) and, if so, to improve their migration and engraft ability by modifying key mechanistic steps in the adhesion cascade. Therefore, we investigated how distinct hematopoietic stem cell populations migrate to the bone marrow using adhesion mechanisms. This study represents the first direct analysis of adhesion molecules expression in LT-HSC and will potentially shed light on methods to optimally use these very valuable cells in the clinical bone marrow and cord blood transplants worldwide.

"Human umbilical cord blood (CB) hematopoietic stem cells (HSCs) have well established applications for cellular therapy. Current protocols for isolating HSCs from bone marrow or cord select for CD34 + cells, however some CD34 - populations have recently been shown to also contain strong HSC activity. Thus the positive selection of HSCs based on cell surface markers remains controversial. However, it is clear from the literature that differentiated hematopoietic cells (lineage positive, Lin + ), representing the vast majority (>90%) of most blood populations, contain no long-term reconstitution potential. Thus Viacell Inc. (Worcester, MA) expands and enriches its populations of cells containing HSCs by removing only those Lin + cells known not to contain HSCs. This is accomplished on two separation columns (post-sep-1, and post-sep-2) (separated by 7 days of cell growth) that contain a variety of antibodies to known differentiation surface markers. Although this process strongly enriches functional HCSs, these primitive cell populations remain biochemically uncharacterized. Because HSC populations containing long chromosomal telomeres and high telomerase activity (which helps maintain telomeres) have been shown to display the strongest long-term reconstitution potential, the purpose of this thesis was to investigate these two parameters in selected samples of Viacell’s ex vivo amplification procedure. Two specific hypotheses were tested: 1. the removal of Lin + cells will appear to increase the telomerase activity and telomere lengths in the remaining cell population, and 2. these two parameters will decrease upon hematopoietic cell differentiation and proliferation. Telomerase activity was assayed using a telomeric repeat amplication protocol (TRAP), and normalized relative to a cancer cell line positive control. Relative to fresh cord blood, telomerase activity was found to increase significantly in post-sep-1 (from 8.5 ± 1.5% to 76.2 ± 4.9%, p = 0.0001, n = 5) and post-sep-2 (8.5 ± 1.5% to 111.3 ± 4.9%, p = 0.0001, n = 5) fractions following the removal of Lin + cells. This increase was found to be highly reproducible, showing very low intra-cord and inter-cord variability. Telomere lengths were assayed using a telomere length assay (TLA). Relative to fresh cord blood, telomere lengths increased significantly in post-sep-1 (from 10 to 12 kb, n = 2) and post-sep- 2 (from 10 to 14 kb, p = 0.001, n = 2) fractions. These apparent increases likely result from the direct removal of cells low in telomerase activity with short telomeres since the Lin + cells from the post-sep-1 column were found to contain relatively low telomerase activity (32.1 ± 15%, p = 0.001, n = 2) and short telomeres (7.5 kb, p = 0.001), which supports our first hypothesis. Finally, we show that telomerase activity and telomere lengths decreased in Day-14 cells (expanded and differentiated 14 days) relative to post-sep-2 (from 111.8 ± 19.6% to 54 ± 21.2%, p = 0.001, n = 3 for the TRAP, and from 14 kb to 9 kb, p = 0.0001, n = 2 for the TLA). Those two parameters also decreased in pre-sep-3 cells (terminally differentiated by treatment with All Trans Retinoic Acid for 14 days) relative to post-sep-2 (from 111.3 ± 4.9% to 14.8 ± 1.7%, p = 0.0001, n = 6 for the TRAP, and from 14 kb to 7.5 kb, p = 0.001 for the TLA), supporting our second hypothesis. Telomerase activity was found to not directly correlate with CD34 + CD38 - content, supporting recent observations that a significant portion of HSCs reside outside this population."

Allogeneic haematopoietic stem cell transplantation (HSCT) has been used successfully to treat children and adults with high-risk or relapsed hematopoietic malignancies, marrow failure syndromes, and hereditary immunodeficiency disorders. When initially developed, allogeneic HSCT was conceived as a method of rescuing patients from the toxic side effects of dose-intensive chemoradiotherapy. Due to transplant-related toxicities, the application of myeloablative allogeneic HSCT has been limited to younger patients without organ dysfunctions. Since the early 1990s many groups of investigators have explored strategies using less intensive preparative regimens that would allow engraftment of hematopoietic progenitor cells from either identical or non-identical donors. These reduced-intensity conditioning (RIC) regimens result in less tissue damage, less inflammatory cytokine secretion, and possibly lower rates of graft-versus-host disease (GVHD) and non-relapse mortality (NRM). Such non-myeloablative approach, or "mini-transplant", has been suggested to benefit older patients as well as in conditions in which traditional myeloablative conditioning regimens are associated with high rates of non-relapse mortality. / Allogeneic HSCT is the only curative therapy for many patients with myeloid malignancies or myelodysplastic syndrome (MDS). The development of reduced-intensity preparative regimens may allow the extension of this form of treatment to older and patients with coexisting medical illness. On the other hand, relapse after transplantation remains the most important cause of treatment failure in patients with refractory acute myeloid leukemia (AML) or MDS, and is associated with poor survival. Evaluation of prognostic factors may help to improve the results of myeloablative and RIC allogeneic HSCT in this group of patients. Furthermore, the impact of comorbidities on outcomes of RIC allogeneic HSCT in this group of patients with refractory AML or MDS needs to be defined. / The application of embryonic and adult stem cells in regenerative and reparative therapies of non-hematopoietic diseases is emerging rapidly. Human umbilical cord blood (UCB) is a rich source of hematopoietic stem cells and mesenchymal progenitor cells. Although clinical experience to date with UCB has focused on hematological application, early preclinical studies support the hypothesis that multipotential stem cells derived from UCB exhibit functional characteristics similar to that observed in adult marrow-derived stem cells in mediating vascular and organ regenerative capabilities. However, the application of these preclinical findings in clinical setting needs to be further studied. Mini-transplant of human UCB may be an effective approach to repair organ damage in patients with non-hematological diseases. / Wong Siu Ming Raymond. / Adviser: Joseph J.Y. Sung. / Source: Dissertation Abstracts International, Volume: 73-01, Section: B, page: . / Thesis (M.D.)--Chinese University of Hong Kong, 2006. / Includes bibliographical references (leaves 187-223). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [201-] System requirements: Adobe Acrobat Reader. Available via World Wide Web.