No description available.

Gene regulatory networks (GRNs) are central to every biological process from development to disease. GRNs are mediated through the activities of transcription factors (TFs), which interact in a sequence-specific manner with their target DNA elements to drive gene expression. In this thesis, two main aspects of GRNs are studied: (1) rewiring of GRNs by alternative TF isoforms, and (2) immune GRNs and strategies to modulate gene expression in immune diseases. TF isoforms resulting from alternative splicing, alternative transcription start sites, or alternative transcription termination sites, are prevalent and can have profound changes in GRNs. However, the extent to which differences in TF isoforms affect global GRNs and how such regulatory network rewiring leads to altered gene expression programs remain unclear. In this thesis, a large clone collection of ~800 human TF isoforms was generated, and then used in high-throughput systematic experimental strategies to investigate the extent to which TF isoforms differ at the level of molecular protein-DNA interactions (PDIs) and transcriptional regulatory activities. The findings show that at least half of alternative TF isoforms exhibit functional differences and tend to behave like distinct proteins with different molecular capabilities. In the context of global GRNs, these findings reveal a widespread expansion of PDI and transcriptional regulatory capabilities through alternative TF isoforms. Altogether, this work constitutes an important step towards the long-term goal of contextualizing and functionalizing large numbers of TF isoforms in rewiring GRNs. GRNs provide a wealth of information that can be leveraged in myriad ways including therapeutics. In particular, immune GRNs provide a framework for modulating cytokine gene expression, which are dysregulated in many human diseases. Proper cytokine gene expression is essential in development, homeostasis and immune responses. However, studies on the transcriptional control of cytokine genes over the last three decades have mostly focused on highly researched TFs and cytokines, resulting in an incomplete portrait of cytokine gene regulation. In this thesis, high-throughput assays were used to derive a comprehensive network that greatly expands the known repertoire of TF–cytokine gene PDIs and the set of TFs known to regulate cytokine genes. An enrichment of nuclear receptors was found and their role in cytokine regulation in primary macrophages was confirmed. Additionally, the network was used as a framework to identify TFs and synergistic TF pairs that can be targeted with FDA-approved drugs to modulate cytokine production. Finally, the PDI data was integrated with single cell RNA-seq datasets to identify druggable TF targets in cytokine-associated immune diseases (i.e., inflammatory bowel disease and COVID-19). Overall, this comprehensive cytokine GRN provides a rich resource to interrogate cytokine regulation in a variety of physiological and disease contexts. Altogether, the work in this thesis accomplishes the following: (1) identifies alternative TF isoforms as a major driver of GRN rewiring, (2) delineates a comprehensive cytokine GRN that greatly expands three decades of research, and (3) leverages the cytokine GRN to identify candidate therapeutic TF targets in diseases associated with dysregulated cytokine gene expression. These findings contribute a significant step in the effort to understand mechanisms of GRN rewiring and to generate comprehensive GRNs that provide a framework for modulating gene expression, particularly in diseases. / 2023-11-01T00:00:00Z

Systematic characterization of microbes in several tumors including colorectal cancer (CRC) and pancreatic ductal adenocarcinoma (PDAC) has revealed the presence of multiple species of intracellular bacteria within tumors. However, there is limited knowledge on how these bacteria colonize tumors, how they survive inside host cells, how they modulate host cell phenotypes, and if their elimination should complement cancer therapy. This is, in part, due to the lack of representative animal models, challenges in co-culture of host epithelial cells and bacteria, and limited resolution of available analytical techniques to study host-microbial interactions. I have addressed these challenges by harnessing multiple technologies from microbiology, genetic engineering, tissue engineering, and microfluidics, in order to investigate the role of an emerging oncomicrobe, Fusobacterium nucleatum, in the tumor microenvironment (TME). F. nucleatum is a Gram-negative, anaerobic bacterium that is normally found within the oral cavity. However, its selective enrichment in CRC and PDAC tumors is correlated with poor clinical outcomes. My work along with collaborators in the Verbridge, Slade, and Lu labs at Virginia Tech has revealed a multifactorial impact of F. nucleatum in influencing cancer progression. First, in CRC, we discovered that F. nucleatum infection of host cancer cells induced robust secretion of select cytokines that increased cancer cell migration, impacted cell seeding, and enhanced immune cell recruitment. In PDAC, we uncovered additional cytokines that were secreted from both normal and cancerous pancreatic cell lines upon infection with F. nucleatum that increased cancer cell proliferation and migration via paracrine and autocrine signaling, notably in the absence of immune cell participation. In order to examine the contribution of a hypoxic TME on infection dynamics, we used a multi-omics approach that combined RNA-seq and ChIP-seq of H3K27ac to determine epigenomic and transcriptomic alterations sustained within hypoxic CRC cells upon infection with F. nucleatum. Our findings revealed that F. nucleatum can subvert host cell recognition in hypoxia and can modulate the expression of multiple cancer-related genes to drive malignant transformation. Insights gained from this research will pave the way for future studies on the impact of the tumor microbiome in cancer and will identify novel targets for therapy and clinical intervention to control bacteria-induced exacerbation of cancer. / Doctor of Philosophy / Colorectal cancer (CRC) and pancreatic ductal adenocarcinoma (PDAC) are the second and third leading causes of cancer death in the United States, respectively. Recent systematic characterization of various tumor types revealed the presence of distinct bacteria within tumors. However, there is limited knowledge on how these bacteria colonize tumors, how they survive inside host cells, how they modulate host cell phenotypes, and if their elimination should complement cancer therapy. This is, in part, due to the lack of representative animal models, challenges in developing host cell-microbe co-culture models, and limited resolution of available analytical techniques to study host-microbial interactions. I have addressed these challenges by harnessing multiple technologies from microbiology, genetic engineering, tissue engineering, and microfluidics, in order to investigate the role of an emerging cancer-associated microbe, Fusobacterium nucleatum, in the tumor microenvironment (TME). F. nucleatum is a microbe commonly found within the oral cavity. However, clinical studies revealed that selective enrichment of F. nucleatum in CRC and PDAC tumors significantly correlated with poor prognosis. My work along with collaborators in the Verbridge, Slade, and Lu labs at Virginia Tech has revealed a multifactorial impact of F. nucleatum in influencing cancer progression. First, in CRC, we discovered that F. nucleatum invasion of host cancer cells induced the secretion of select proteins called cytokines that cells use to signal and communicate with each other. These cytokines directly stimulated the cell migration of host cancer cells which is usually associated with increased cancer aggressiveness. In PDAC, F. nucleatum infection induced the secretion of additional cytokines from both cancer cells and normal cells that, in addition to cell migration, impacted the proliferation of cancer cells, another feature of aggressive cancers. F. nucleatum usually thrives in a low oxygen environment that is prevalent in cancer tissue and hence, we examined how a low oxygen environment can influence infection dynamics using sequencing technologies that probe the genomic constitution within cells. Our findings revealed that F. nucleatum can escape recognition in low oxygen environments and can modulate the expression of multiple cancer-related programs within the cell to drive cancer progression. Insights gained from this research will pave the way for future studies on the impact of the tumor-associated microbes in cancer and will identify novel targets for therapy and clinical intervention to control bacteria-induced exacerbation of cancer.

京都大学 / 新制・課程博士 / 博士(人間健康科学) / 甲第24292号 / 人健博第107号 / 新制||人健||8(附属図書館) / 京都大学大学院医学研究科人間健康科学系専攻 / (主査)教授 藤井 康友, 教授 岡 昌吾, 教授 滝田 順子 / 学位規則第4条第1項該当 / Doctor of Human Health Sciences / Kyoto University / DFAM

京都大学 / 新制・課程博士 / 博士(医学) / 甲第24880号 / 医博第5014号 / 新制||医||1068(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 長船 健二, 教授 江木 盛時, 教授 妹尾 浩 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Macrophages (MΦ) as specialized immune cells are involved in rubella virus (RuV) pathogenesis and enable the study of its interaction with the innate immune system. A similar replication kinetics of RuV in the two human MΦ types, the pro-inflammatory M1-like (or GM-MΦ) and anti-inflammatory M2-like (M-MΦ), was especially in M-MΦ accompanied by a reduction in the expression of the innate immune receptor CD14. Similar to RuV infection, exogenous interferon (IFN) β induced a loss of glycolytic reserve in M-MΦ, but in contrast to RuV no noticeable influence on CD14 expression was detected. We next tested the contribution of CD14 to the generation of cytokines/chemokines during RuV infection of M-MΦ through the application of anti-CD14 blocking antibodies. Blockage of CD14 prior to RuV infection enhanced generation of virus progeny. In agreement with this observation, the expression of IFNs was significantly reduced in comparison to the isotype control. Additionally, the expression of TNF-α was slightly reduced, whereas the chemokine CXCL10 was not altered. In conclusion, the observed downmodulation of CD14 during RuV infection of M-MΦ appears to contribute to virus-host-adaptation through a reduction of the IFN response.

INTRODUCTION: Multiple myeloma (MM) is a disease that results in the production of ineffective immunoglobulins and monoclonal proteins in the blood and urine, leading to insufficient organ function or death. Currently, there is a 5-year survival rate of 47% for patients diagnosed with MM, with a proportion of patients ultimately succumbing to the disease. The current standard of care for MM includes toxic combinations of chemotherapy. The evolution of chimeric antigen receptor (CAR) T-cell therapy for hematologic cancers such as lymphoma, leukemia, and now myeloma has provided another effective treatment option for patients who have relapsed after standard treatments for MM. Idecabtagene Vicleucel (ide-cel), was approved in March 2021 for patients with relapsed and refractory MM. While CAR T-cell treatment appears to be far less toxic than standard chemotherapy, this therapy comes with its own associated toxicities, mainly cytokine release syndrome (CRS) and neurotoxicity (NT). In clinical trials, ide-cel demonstrated to be an effective treatment in some patients, leading to the FDA approval for patients who have exhausted multiple other lines of therapy. Currently, it is unclear why patients respond differently to CAR T-cell treatment and why some patients present with more severe toxicity than others. Therefore, this study aims to examine patient factors such as demographics, age, and treatment history to determine if such characteristics may influence the CAR T-cell response; also, we assess the efficacy of ide-cel in a real-world experience outside of a clinical trial. METHODS: In this study, 14 patients’ medical records were reviewed after receiving commercial CAR T-cell therapy between August 2021 and January 2022. Eligible patients for the therapy were determined by strict inclusion criteria, including having a confirmed diagnosis of MM and exhausting at least four prior lines of therapy, as well as exclusion criteria, such as excluding individuals who have received CAR T-cells prior in a clinical trial setting. Approximately one month before preparation lymphodepletion chemotherapy, eligible patients underwent leukapheresis and had their blood sent to a laboratory to extract T-cells and genetically modify them to express the CAR for reinfusion. On 3 and 5 days prior to CAR T-cell infusion, patients underwent lymphodepletion using fludarabine and cyclophosphamide. Patients remained in the hospital for approximately one week following infusion, pending adverse reactions. After discharge, patients returned to the hospital for routine follow-ups. Data analysis was then performed on collected clinical readouts such as: prior treatments, bone marrow biopsies, response rates, laboratory values from blood samples, and pre- and post-infusion scans of various tissues within the body. RESULTS: At a median follow-up time of 15 weeks, six patients (43%) achieved a complete response (CR), three patients demonstrated a partial response (PR, 21%), and four patients showed disease progression (PD, 28%). Post-infusion scans were not available for one subject (7%) as they were still in the hospital. These results are similar to the phase I and phase II trials in which 45% and 33% of patients demonstrated a CR post-infusion, respectively. As for associated toxicities, 10 patients (71%) experienced CRS and one patient (7%) presented with ICANS. All patients that achieved a CR experienced ide-cel related toxicities, compared with only 38% of those with less favorable or unknown outcomes, which indicates that systemic immune system activation which causes CRS may be required to achieve a CR but CRS is not always linked with a CR outcome. There were 28 different chemotherapy regimens used as the standard of care treatment prior to ide-cel therapy. We assessed the most recent chemotherapeutic regimen in each patient to assess whether there is an association with most recent treatment and response. Of the six patients that achieved a CR to ide-cel, all were previously treated with RVD or CyBorD regimens, compared to the four patients who had disease progression who were mainly treated with salvage DCEP chemotherapy. Four patients (29%) received DCEP as their final chemotherapy regimen, and 3 of these 4 (75%) demonstrated progressive disease after ide-cel. Two patients received Belantamab-Mafodotin prior to ide-cel treatment, with one patient presenting with disease progression and the other patient achieving CR. 71% of patients experienced CRS following ide-cel infusion, which is resembles the phase II trial of ide-cel in which 84% of patients demonstrated CRS. In this study, only 7% of patients experienced neurological toxicity, which is comparable to the 18% of patients that demonstrated to have ICANS in the phase II study. CONCLUSIONS: We found similar performance of the ide-cel CAR-T therapy in the real world setting as in the clinical trial. Also, the complete responses were achieved by subjects with an array of characteristics, including varying recent chemotherapeutic treatments, IgG, IgA, and light-chain only subtypes of MM, and diverse demographics and other characteristics. The characteristic that demonstrated the most predictability and somewhat unique to subjects with CR was the associated toxicities from ide-cel. Development of these associated toxicities may attest that substantial immune activation, of CAR T-cells and other immune cells, leads to the efficacy of the product in eliminating cancer cells. Further analysis will need to be completed as more individuals enroll in this study to be able to determine if there are significant associations between demographics and prior lines of treatment with response to ide-cel CAR-T therapy. Lastly, future studies should assess the immune cell effector functions that are generated in CR patients that will help to specify the association between ide-cel activation, experienced associated toxicities, and its efficacy.

DNA methylation is an epigenetic mechanism that usually occurs at CpG sites in the genome. Both sequencing and array-based techniques are available to detect methylation patterns. Whole-genome bisulfite sequencing is the most comprehensive but cost-prohibitive approach, and microarrays represent an affordable alternative approach. Array-based methods are generally cheaper but assess a specific number of genomic loci, such as Illumina methylation arrays. Differentially methylated regions (DMRs) are genomic regions with specific methylation patterns across multiple CpG sites that associate with a phenotype. Methylation at nearby sites tends to be correlated, therefore it may be more powerful to study sets of sites to detect methylation differences as well as reduce the multiple testing burden, compared to utilizing individual sites. Several statistical approaches exist for identifying DMRs, and a few prior publications compared the performance of several commonly used DMR methods. However, as far as we know, no comprehensive comparisons have been made based on genome-wide simulation studies. This dissertation provides some comprehensive suggestions for DMR analysis based on genome-wide evaluations of existing DMR tools and presents the development of a novel approach to increase the power to identify DMRs with clinical value in genomic research. The second chapter presents genome-wide null simulations to compare five commonly used array-based DMR methods (Bumphunter, comb-p, DMRcate, mCSEA and coMethDMR) and identifies coMethDMR as the only approach that consistently yields appropriate Type I error control. We suggest that a genome-wide evaluation of false positive (FP) rates is critical for DMR methods. The third chapter develops a novel Principal Component Analysis based DMR method (denoted as DMRPC), which demonstrates its ability to identify DMRs using genome-wide methylation arrays with well-controlled FP rates at the level of 0.05. Compared to coMethDMR, DMRPC is a robust and powerful novel DMR tool that can examine more genomic regions and extract signals from low-correlation regions. The fourth chapter applies the new DMR approach DMRPC in two “real-world” datasets and identifies novel DMRs that are associated with several inflammatory markers.

Serum half-life elongation as well as the immobilization of small proteins like cytokines is still one of the key challenges for biologics. This accounts also for cytokines, which often have a molecular weight between 5 and 40 kDa and are therefore prone to elimination by renal filtration and sinusoidal lining cells. To solve this problem biologics are often conjugated to poly(ethylene glycol) (PEG), which is the gold standard for the so called PEGylation. PEG is a synthetic, non-biodegradable polymer for increasing the hydrodynamic radius of the conjugated protein to modulate their pharmacokinetic performance and prolong their therapeutic outcome. Though the benefits of PEGylation are significant, they also come with a prize, which is a loss in bioactivity due to steric hindrance and most often the usage of heterogeneous bioconjugation chemistries. While PEG is a safe excipient in most cases, an increasing number of PEG related side-effects, such as immunological responses like hypersensitivity and accelerated blood clearance upon repetitive exposure occur, which highlights the need for PEG alternative polymers, that can replace PEG in such cases. Another promising method to significantly prolong the residence time of biologics is to immobilize them at a desired location. To achieve this, the transglutaminase (TG) Factor XIIIa (FXIIIa), which is an important human enzyme during blood coagulation can be used. FXIIIa can recognize specific peptide sequences that contain a lysine as substrates and link them covalently to another peptide sequence, that contains a glutamine, forming an isopeptide bond. This mechanism can be used to link modified proteins, which have a N- or C-terminal incorporated signal peptide by mutation, to the extracellular matrix (ECM) of tissues. Additionally, both above-described methods can be combined. By artificially introducing a TG recognition sequence, it is possible to attach an azide group containing peptide site-specifically to the TG, recognition sequence. This allows the creation of a site-selective reactive site at the proteins N- or C-terminus, which can then be targeted by cyclooctyne functionalized polymers, just like amber codon functionalized proteins. This thesis has focused on the two cytokines human Interferon-α2a (IFN-α2a) and human, as well as murine Interleukin-4 (IL-4) as model proteins to investigate the above-described challenges. IFN-α2a has been chosen as a model protein because it is an approved drug since 1986 in systemic applications against some viral infections, as well as several types of cancer. Furthermore, IFN-α2 is also approved in three PEGylated forms, which have different molecular weights and use different conjugation techniques for polymer attachment. This turns it into an ideal candidate to compare new polymers against the gold standard PEG. Interleukin-4 (IL-4) has been chosen as the second model protein due to its similar size and biopotency. This allows to compare found trends from IFN-α2a with another bioconjugate platform and distinguish between IFN-α2a specific, or general trends. Furthermore, IL-4 is a promising candidate for clinical applications as it is a potent anti-inflammatory protein, which polarizes macrophages from the pro-inflammatory M1 state into the anti-inflammatory M2 state. / Die Verlängerung der Serum-Halbwertszeit sowie die Immobilisierung kleiner Proteine wie Zytokine ist nach wie vor eine der größten Herausforderungen für Biologika. Dies gilt auch für Zytokine, die häufig ein Molekulargewicht zwischen 5 und 40 kDa haben und daher leicht durch die Nierenfiltration und sinusoidale Endothelzellen eliminiert werden können. Um dieses Problem zu lösen, werden Biologika häufig an Poly(ethylenglykol) (PEG) konjugiert, das den Goldstandard für die so genannte PEGylierung darstellt. PEG ist ein synthetisches, biologisch nicht abbaubares Polymer, das den hydrodynamischen Radius des konjugierten Proteins vergrößert, um die pharmakokinetische Leistung zu modulieren und die therapeutische Wirkung zu verlängern. Obwohl die Vorteile der PEGylierung beträchtlich sind, haben sie auch ihren Preis, nämlich einen Verlust an Bioaktivität aufgrund sterischer Hindernisse und meist die Verwendung heterogener Biokonjugationstechniken. Obwohl PEG in den meisten Fällen ein sicherer Hilfsstoff ist, treten immer mehr PEG-bedingte Nebenwirkungen auf, wie z. B. immunologische Reaktionen wie Überempfindlichkeit und beschleunigter Abbau bei wiederholter Exposition, was den Bedarf an alternativen PEG-Polymeren unterstreicht, die PEG in solchen Fällen ersetzen können. Eine weitere vielversprechende Methode, um die Verweildauer von Biologika deutlich zu verlängern, besteht darin, sie an einem gewünschten Ort zu immobilisieren. Dazu kann die Transglutaminase (TG) Faktor XIIIa (FXIIIa) verwendet werden, die ein wichtiges menschliches Enzym bei der Blutgerinnung ist. FXIIIa kann bestimmte Peptidsequenzen, die ein Lysin enthalten, als Substrate erkennen und sie kovalent an eine andere Peptidsequenz, die ein Glutamin enthält, binden, wobei eine Isopeptidbindung entsteht. Dieser Mechanismus kann benutzt werden um modifizierte Proteine, welche durch Mutation ein N- oder C-terminal eingebautes Signalpeptid besitzen, mit der extrazellularen Gewebematrix (ECM) zu verknüpfen. Diese Arbeit konzentriert sich auf die beiden Zytokine humanes Interferon-α2a (IFN-α2a) und humanes sowie murines Interleukin-4 (IL-4) als Modellproteine, um die oben beschriebenen Herausforderungen zu untersuchen. IFN-α2a wurde als Modellprotein ausgewählt, weil es seit 1986 ein zugelassenes Medikament für die systemische Anwendung gegen einige Virusinfektionen und verschiedene Krebsarten ist. Darüber hinaus ist IFN-α2 auch in drei PEGylierten Formen zugelassen, die unterschiedliche Molekulargewichte haben und verschiedene Konjugationstechniken für die Polymeranbindung verwenden. Dies macht es zu einem idealen Kandidaten für den Vergleich neuer Polymere mit dem Goldstandard PEG. Interleukin-4 (IL-4) wurde als zweites Modellprotein gewählt, da es eine ähnliche Größe und Biopotenz aufweist. Dies ermöglicht es, die von IFN-α2a gefundenen Trends mit einer anderen Biokonjugat-Plattform zu vergleichen und zwischen IFN-α2a-spezifischen und allgemeinen Trends zu unterscheiden. Darüber hinaus ist IL-4 ein vielversprechender Kandidat für klinische Anwendungen, da es ein starkes entzündungshemmendes Protein ist, das Makrophagen vom entzündungsfördernden M1-Zustand in den entzündungshemmenden M2-Zustand polarisiert.

No description available.