<p> A major goal of human genetics is to characterize the role of genetic variation on complex, polygenic phenotypes. With the discovery from genome-wide association studies (GWAS) that many associated variants have a small effect size and are located in non-coding regions of the genome, there has been a large effort to collect functional genomics data. The hope is that a better understanding of how the genome functions in diverse developmental states and environments will provide insight into the context-specific activity of associated non-coding variants. My research applies this paradigm to the complex phenotype of susceptibility to develop tuberculosis (TB). It has been estimated that 10% of individuals infected with <i>Mycobacterium tuberculosis </i> (MTB) progress to active disease. Despite being heritable, very few genetic variants have been associated with susceptibility to TB. For my studies, I use RNA sequencing (RNA-seq) to interrogate genome-wide transcript levels in <i>in vitro</i> cellular models. In Chapter 2, I use a joint Bayesian model to identify genes which are differentially expressed in macrophages only after infection with MTB and related mycobacteria, but not other bacterial pathogens. In Chapter 3, I build a support vector machine model to classify individuals as susceptible or resistant to TB based on the gene expression levels in their dendritic cells. In Chapter 4, I characterize the technical variation introduced by batch processing of single-cell RNA-seq (scRNA-seq) and propose an effective study design that accounts for technical variation while minimizing replication. In addition to providing insight into the genes important for the innate immune response to MTB infection, my work is informative for the design and analysis of future functional genomics experiments. (Note: Supplementary tables are provided in a .zip file available online. Captions for the tables are provided within the dissertation.)</p>

Diss. (sammanfattning) Uppsala : Univ., 2001. / Härtill 4 uppsatser.

Thesis (Ph. D.)--University of Toronto, 2008. / Includes bibliographical references.

<p> <b><u>Lenalidomide (CC-5013; REVLIMID, Celgene Corp., NJ, USA) belongs to a new immunomodulatory class of drugs called IMiDs.</u></b> It is an oral thalidomide analogue drug that belongs to the second generation of IMiDs. Its parent compound thalidomide&rsquo;s initial descriptions of its teratogenicity are attributed to its anti-angiogenic properties. The drug has other mechanisms of action beyond just cytotoxicity and immune modulation. It includes effects on both the tumor and the tumor microenvironment. </p><p> Within <b><u>hematological malignancies</u></b>, lenalidomide is being used in a number of conditions. Lenalidomide is being used to treat myelodysplastic syndrome patients with 5q deletion resulting in improvement in their transfusion requirements. Lenalidomide in combination with steroids is used in patients with multiple myeloma. </p><p> Recently there has been increased interest to use lenalidomide to treat patients due to its immunomodulatory effect. According to the Surveillance, Epidemiology, and End Results Program (SEER), Non-Hodgkin Lymphoma (NHL) represents 4.3% of all new patients with cancer in United States, with an estimated 71,850 cases in 2015. Within NHL, diffuse large B-cell lymphoma (DLBCL) is most frequently seen constituting approximately 40% of these cases. </p><p> Therapies upfront (at the time of diagnosis) for DLBCL include chemotherapeutic options in combination with biologics/monoclonal antibodies (mAbs), which are curative in intent. In the <u>relapsed or refractory settings </u>, the intent treatment for patients with DLBCL is to achieve cure; however, these have to be consolidated with a stem cell transplant (autologous in most instances). The number of treatment options is increasing, and newer regimens and classes of drugs are being developed and tested for patients with DLBCL. These go beyond mAbs and traditional chemotherapeutic agents, and include novel targeted therapies, immunotherapies and immunomodulatory agents. Immune modulation, as noted, has been a focus of increasing interest particularly for patients with DBLCL. With lenalidomide, responses were seen in up to half of the patients treated with lenalidomide, with about a quarter achieving complete responses. Even as single agent, these responses appeared to be relatively durable (PFS 6.2 months), given the highly aggressive nature of disease. The side effect profile was noted to be manageable without any untoward adverse events. </p><p> This led to the development of clinical trials for patients incorporating lenalidomide. These were both in frontline as well as the relapsed/refractory setting. Lenalidomide (Revlimid) was added to the frontline regimen R-CHOP [referred to as R2CHOP] and showed significant activity and manageable safety profile. The focus of my thesis is the <b><u>development of the clinical trial of incorporating lenalidomide (Revlimid) in the relapsed/refractory setting</u></b> to one of the most commonly employed chemoimmunotherapy regimens called the R-ICE (rituximab-ifosfamide-carboplatin-etoposide) regimen. The regimen developed therefore, is called R2ICE. </p><p> The patients that we studied, who have refractory disease or relapse with lymphoma, constitute at least a quarter of all patients with DLBCL. The majority of these are patients who relapse within the first 1.5 years of upfront curative treatment. For patients with first-relapse/primary-refractory DLBCL, the response rate achieved prior to proceeding with a stem cell transplant (SCT) is a key variable. Usually this is an autologous stem cell transplant (ASCT). ASCT can be potentially curative for these patients who tend to show chemosensitivity by achieving either a complete response (CR) or partial response (PR) with their salvage chemotherapy prior to the transplant. Patients with CR tend to do better than patients who achieved PR after salvage chemotherapy. To achieve this, patients with relapsed/refractory disease are currently treated with a variety of treatment regimens prior to them going for a transplant. Currently the most commonly used regimen is the chemotherapy regimen of ICE (ifosfamide-carboplatin-etoposide). Historically, when rituximab was added to this regimen (R-ICE), the number of patients responding increased. This increase was clinically significant. However, this could further be increased, since at present, this is estimated to be around 40% for patients who receive 2 cycles of therapy prior to them getting a transplant. </p><p> The goals of my master&rsquo;s program and thesis were, therefore, to (a) <b><u>develop rationale</u></b> for a clinical trial incorporating the novel drug lenalidomide into regimens treating patients with lymphoma (Chapter 1); (b) <b><u>review literature on paradigm changes</u></b> on how to treat patients with DLBCL in a molecular era (Chapter 2); (c) <b><u>secure funding and develop a clinical trial protocol</u></b> of the addition of lenalidomide to treat patients with DLBCL to the standard R-ICE regimen [R2ICE](Chapter 3); (d) to <b><u>report the early results of the safety from the completed Phase-1 study and ongoing phase-2 study for our R2ICE regimen</u></b>, and for its potential to become a <b><u>new regimen</u></b> for patients with relapsed/refractory lymphoma (Chapter 4). </p><p>

Thesis (P.h.D.)--UCLA, 2006. / Vita. Includes bibliographical references (leaves 144-166).

Teladorsagia circumcincta is a common parasitic nematode of the sheep abomasum, causing reduced growth in young lambs. The widespread development of anthelmintic resistant parasites has driven the need for alternative control strategies. Resistant immunity is acquired through repeated exposure to the parasite. The immune response and clinical outcome vary greatly between animals, but resistance is heritable. The aims of this project were: 1) understand how sheep respond to nematode infection; 2) understand and identify genes associated with the response; 3) identify variation within those genes which may contribute to resistance. Using an artificially infected animal model, transcriptomic analysis in resistant and susceptible lambs identified genes involved in T helper cell polarization as integral to disease outcome. T helper cell (Th)1 and Th17 activation was associated with susceptibility (low antibody, high worm numbers) while a Th2 response was associated with resistance (high antibody levels and clearance of infection). The Th cell transcription factors (GATA3, TBX21, RORC2 and RORA) were sequenced with splice variants and SNPs identified. Analysis of gene expression in the abomasal lymph node identified RORAv2 as associated with susceptibility and RORAv5 as associated with resistance. In the abomasal mucosa, GATA3 expression was linked to resistance. Expression analysis of cytokine receptors expressed by Th cells identified IL17RB and IL17RBv2 as associated with resistance in the abomasal mucosa. Analysis of the SNPs within these genes in 3 naturally infected populations identified a significant association between SNPs in IL23R with weight and FEC. This project has provided an in-depth analysis of the ovine transcriptome and identified several genes associated with the development of resistance to nematodes.