Indiana University-Purdue University Indianapolis (IUPUI) / The marker strategy design (MSGD) has been proposed to assess and validate predictive markers for targeted therapies and immunotherapies. Under this design, patients are randomized into two strategies: the marker-based strategy, which treats patients based on their marker status, and the non-marker-based strategy, which randomizes patients into treatments independent of their marker status in the same way as in a standard randomized clinical trial. The strategy effect is then tested by comparing the response rate between the two strategies and this strategy effect is commonly used to evaluate the predictive capability of the markers. We show that this commonly used between-strategy test is flawed, which may cause investigators to miss the opportunity to discover important predictive markers or falsely claim an irrelevant marker as predictive. Then we propose new procedures to improve the power of the MSGD to detect the predictive marker effect. One is based on a binary response endpoint; the second is based on survival endpoints. We conduct simulation studies to compare the performance of the MSGD with the widely used marker stratified design (MSFD). Numerical studies show that the MSGD and MSFD has comparable performance. Hence, contrary to popular belief that the MSGD is an inferior design compared with the MSFD, we conclude that using the MSGD with the proposed tests is an efficient and ethical way to find predictive markers for targeted therapies.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第21637号 / 医博第4443号 / 新制||医||1034(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 河本 宏, 教授 松田 道行, 教授 小川 誠司 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第21686号 / 医博第4492号 / 新制||医||1036(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 妹尾 浩, 教授 小川 誠司, 教授 武田 俊一 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

NK cell based anti-tumour therapies demonstrate high efficacy in targeting hematological malignancies, however, treatments for advanced solid tumours face challenges. The immunosuppressive environment produced by tumours prevents NK cells from maintaining cytotoxic activity and reducing tumour burden. Enhancing NK cell activation is essential to improve their function against solid tumours. Genetic manipulation of primary NK cells with viral and non-viral methods has seen a drastic improvement in recent years. Lentiviral vectors are being used to generate CAR-NK cells ex vivo, while refinement of electroporation protocols has allowed for the generation of stable gene knockouts in primary NK cells. To establish and validate the generation of a stable knockout in primary human NK cells we focused on targeting the NCAM-1 (CD56) surface adhesion molecule. The high surface expression of CD56 in NK cells makes it a suitable target to establish the knockout protocol. Furthermore, despite its levels of expression being correlated to different functional phenotypes, the role of CD56 in NK cell function is not understood. Here we have shown that current lentiviral transduction protocols are not viable methods to deliver the sgRNA/Cas9 system into primary NK cells. However, we found that nucleofection of the sgRNA/Cas9 complex into NK cells is an efficient method to generate gene knockouts. Using newly generated CD56KO NK cells we have shown that the expression of CD56 has no effect on NK cell cytotoxicity, cytokine production, proliferation, and in vivo tissue trafficking. In parallel, we have also identified an intracellular pathway that is active in the tumour microenvironment and could inhibit NK cell function. Recent studies on the intracellular signaling of the E3 ubiquitin-protein ligase Cbl-b have highlighted its role in inhibiting NK cell tumour lytic and anti-metastatic activity. Immunosuppressive factors produced by tumours activate the Cbl-b pathway, leading to the targeted degradation of signaling proteins required for NK cell activation. We have shown that Cbl-b is upregulated in ex vivo expanded NK cells cultured with GAS6 or ovarian cancer ascites. Therefore, the generation of human primary Cbl-bKO NK cells could be a beneficial asset to enhance NK cell cancer immunotherapy. / Thesis / Master of Science (MSc)

Oral squamous cell carcinoma (OSCC), or oral cancer, accounts for the majority of head and neck cancers. Resistance to therapy is a challenge, and 5-year survival rate remains at ~50 percent. Lysine-specific demethylase 1 (LSD1) plays a crucial role in controlling cell homeostasis in health and disease. LSD1 is elevated in oral cancer and promotes metastasis and correlates with poor prognosis. LSD1 is a nuclear histone demethylase that has been implicated in maintaining the undifferentiated state of cancer-initiating stem cells and promoting OSCC. Large dataset analysis showed that genetic alterations, including upregulation of LSD1, are seen in clinical cancers including OSCC. This study aims to evaluate the unknown mechanism of LSD1 and determine if pharmacologic inhibition of LSD1 has preventative and/or therapeutic applications for OSCC. This study used the 4NQO mouse model to induce OSCC in mice and split the mice into 8 treatment groups. Each group received a different immunotherapy treatment (SP2509, Verteporfin, anti PD-1 and anti PD-L1 alone and in combination). Our results have shown that LSD1 inhibition reduces the development of gross pathologic lesions. LSD1 inhibition has also shown to cause differences in gene expression in preneoplasia and OSCC, attenuating many genes that are part of the pro-oncogenic gene network (LSD1, YAP, EGFR), immune checkpoints (PD-1 and PD-L1), and Hippo signaling effectors (YAP, TAZ). Interestingly, LSD1 has shown a role in regulating the immune microenvironment and promoting antitumor immunity, which led us to investigate LSD1 in combination with immune checkpoint antibodies (anti PD-1 and anti PD-L1). Our results show that LSD1 sensitizes to anti-PD-1 and anti-PD-L1 antibodies to treat mouse tongue OSCC. Thus, we showed for the first time that blocking LSD1 inhibits preneoplasia and OSCC feed-forward loop, which could have implications in OSCC prevention, chemo- and immunotherapeutic combinations.

Tumors evade immune system tumor-controlling functions. T cells critical to antitumor immunity are tolerogenic in tumor-burdened animals, and fail to lyse neoplastic cells. Our goal was to investigate the kinetics of immune dysfunction related to tumor-burdened host (TBH) memory T cell responses (or the lack thereof). We demonstrate tumor growth impairs T cell activation by modulating CD4+ T cell infiltration and systemic CD44 and CD62L activation marker expression, and by downregulating TBH TH1 cytokine production by splenic CD4+ T cells. Since chemotherapeutic treatments have potent cytostatic effects, we posited they enhance T cell dysfunctionality; which leads to limited therapeutic efficacy. Paclitaxel is a potent chemotherapeutic agent currently being administered in Stage III clinical trials; however, it reduces T cell proliferative capacity and interferon-γ (IFN-γ) production. In contrast, our data suggest that administration of low dose paclitaxel prolongs adaptive immunity in a limited capacity. We show paclitaxel enhances CD4highCD62Llow cell populations that drive TH1 cytokine production and prolongs the production of interleukin-2 (IL-2) in TBHs. We hypothesize that the initiation and maintenance of activated TH1 cell populations in patients during therapy serves as a reliable prognostic indicator of a favorable therapeutic response. Paclitaxel's limited therapeutic effects are due, in part, to its suppression of T cell activities; but the administration of low dose chemotherapy in combination with immunotherapeutic agents temporally takes advantage of paclitaxel's immunostimulatory capabilities. Our work will enhance current understanding of immune dysregulation during cancer development, and promote advances in the monitoring and development of combinatorial cancer treatments. / Master of Science

<p dir="ltr">Influenza is a global public health concern, affecting approximately 1 billion people worldwide each year, resulting in 3-5 million severe cases and 300,000-500,000 reported fatalities, according to the World Health Organization (WHO). Despite the availability of influenza vaccines, their effectiveness has consistently been low over the past decade, with inadequate vaccine coverage, particularly in the United States, where influenza takes a heavy toll every season, impacting public health and economy. Currently available antivirals like oseltamivir and baloxavir are effective when administered very early in infection, reducing the sickness duration by a day or two. However, their efficacy diminishes with delayed administration, highlighting the need for improved influenza therapeutics, especially for severe and later-stage infections. This dissertation presents a platform technology for influenza treatment and demonstrates its versatility in treating other indications such as solid tumors. The proposed technology, a small-molecule based bispecific immune cell tether (miniBiT), can form molecular bridges between target cells and immune effector cells either via the recruitment of endogenous human antibodies or, direct interaction with the immune cell surface receptors in order to mediate killing of the target cells. This dissertation consists of five chapters. Chapter 1 outlines the global influenza burden, its economic impact, discusses influenza virology, and the limitations of currently available medical countermeasures, providing insight into the existing gaps and challenges in influenza treatment. Chapter 2 details the design, synthesis, and preclinical evaluation of a ligand-hapten miniBiT that forms immune complexes with virus particles and infected cells by recruiting endogenous human antibodies. Chapter 3 covers the design, synthesis, and evaluation of a ligand-mFc (monomeric Fc fragment of human IgG1) miniBiT, which forms immune complexes with virus particles and infected cells by directly engaging the immune cell surface receptors. Chapter 4 elaborates on the design, synthesis, and evaluation of a ligand-folate miniBiT that recruits activated macrophages to virus particles and infected cells. Finally, Chapter 5 delves into the extended application of the miniBiT platform in treating solid tumors.</p>

Background: Histotripsy is a non-thermal, non-invasive high-intensity focused ultrasound (HIFU) ablative technique that causes mechanical fragmentation of tissue, resulting in liquefied acellular debris with histologically clear demarcated boundaries between treated and non-treated tissues. The acellular debris may include tumor antigens with preserved immunogenicity and the potential to generate systemic immune response against tumor cells. Soft tissue sarcomas (STS) are a common form of cancer in dogs with biological behavior similar to STS in humans. Long-term tumor control requires complete removal with extensive surgical resection, which in many cases is not feasible. As a result, there is need for alternative therapies. Objectives: The primary objective of this study was to demonstrate safety and feasibility of histotripsy in a small animal model of spontaneous STS. The secondary objective was to characterize the impact of histotripsy on the immunologic response. Materials and methods: Pet dogs diagnosed with spontaneous STS were recruited. CT scan of the chest, abdomen, and the tumor was performed for staging and treatment planning. Pretreatment biopsies were obtained. Safety was monitored with physical examinations, owner reports, and CBC/serum biochemistry. Partial tumor ablation was performed using a 500 kHz prototype histotripsy system. A spherical treatment zone of up to 3 cm diameter in each tumor was treated with histotripsy according to the patient-specific treatment plan using 1-2 cycle pulses applied at a pulse repetition frequency (PRF) of 500 Hz. Anatomical ablation zones were evaluated with contrast CT at 1- and 4-days post-treatment, with tumor resection at 4-6 days post-treatment. Tumor microenvironment (TME) gene expression was evaluated with the Nanostring Canine IO panel, and the systemic immune response was evaluated using multiplex serum cytokine levels. Results: Ten dogs were recruited and treated. Tumor histologies included 3 grade III STS, 4 grade II STS, 2 grade I STS, and 1 malignant mesenchymoma. Six dogs were alive, three dogs were euthanized due to disease progression, and one dog was lost to follow up. Histotripsy-related complications were generally self-limiting, with only one patient having increased cutaneous injury score from 1 to 2 (scale 1-5) post-treatment, likely due to prefocal cavitation at the skin. No significant adverse events impacting patient outcome were noted in any of the patients. Visible histotripsy cavitation bubble clouds were seen on real-time ultrasound imaging in nine of ten treatments. Post-treatment histopathology indicated sharply defined regions of ablation that were clearly identifiable grossly and histologically in all samples. Treatment zones were characterized by loss of cell viability, hyalinization, and acute hemorrhage. Post-treatment contrast-enhanced CT images revealed clear, demarcated regions of histotripsy ablated tissue in seven of ten patients. Differential gene expression analysis identified 79 genes with at least 2-fold change following treatment. Genes associated with inflammation, immune cell migration, and immune cell interactions were the highest upregulated. Amongst the gene set analyses, the myeloid compartment gene sets obtained the highest significance score. There were no statistically significant differences between pre- and post-treatment cytokine concentrations for any of the analytes. Conclusions: Histotripsy can achieve safe and effective tumor ablation in dogs diagnosed with STS. Histotripsy induced pro-inflammatory changes within the tumor microenvironment. Histotripsy as an immunotherapeutic treatment option needs to be further investigated. Histotripsy has a potential to be a precise, non-invasive treatment for canine STS. / Master of Science / Histotripsy is a non-thermal high-intensity focused ultrasound (HIFU) ablative technique that uses controlled acoustic cavitation to cause mechanical fragmentation of tissue. To date, there are no reports investigating histotripsy for the treatment of soft tissue sarcoma (STS). This study aimed to investigate the in vivo feasibility of ablating STS with histotripsy and to characterize the impact of partial histotripsy ablation on the acute immunologic response in canine patients with spontaneous STS. CT of the chest, abdomen, and the tumor was performed for staging and treatment-planning. Pretreatment biopsies were obtained. Safety was monitored with physical examinations, through owner reports, and CBC/serum biochemistry. A custom 500 kHz histotripsy system was used to treat ten dogs with naturally occurring STS. Anatomical ablation zones were evaluated with contrast CT at 1- and 4-days post-treatment, with tumor resection at 4-days post-treatment. Safety was determined by monitoring vital signs during treatment and post-treatment physical examinations, routine lab work, and owners' reports. Ablation was characterized using radiologic and histopathologic analyses. Systemic immunological impact was evaluated by measuring changes in cytokine concentrations, and tumor microenvironment changes were evaluated by characterizing changes in infiltration with tumor-associated macrophages (TAMs) and tumor-infiltrating lymphocytes (TILs) using multiplex immunohistochemistry and differential gene expression. Results showed histotripsy ablation can achieve safe and effective tumor ablation in all ten dogs. Immunological results showed histotripsy induced pro-inflammatory changes in the tumor microenvironment. Histotripsy as an immunotherapeutic treatment option needs to be further investigated. Overall, this study demonstrates histotripsy's potential as a precise, non-invasive treatment for STS.

Natural Killer (NK) cell based immunotherapies have demonstrated success against malignancies and hematological cancers. However, tumors have developed mechanisms to evade detection by and suppress the immune system, commonly through altering the expression of cell-surface proteins. Overexpression of human leukocyte antigen-E (HLA-E), which binds to the inhibitory NKG2A on NK cells, protects malignant cells from lysis. Downregulating the NKG2A receptor on NK cells should release NK cell inhibition, but proves challenging as NK cells are difficult to transfect and no good methods currently exist. This project is designed to investigate the use of exosomes – small vesicles and natural carriers of regulatory microRNAs (miRNAs) and proteins that are shed from cells – as delivery vehicles for small RNAs (sRNAs) to immune cells. Exosomes are biologically compatible, immunologically inert, and interact with target cells through receptor-ligand interactions, allowing for targeted delivery of cargo. Exosomes loaded with shRNA against NKG2A were cultured in vitro with NK cells. Delivery success was assessed by monitoring NKG2A receptor expression on NK cells through flow cytometry. This research will provide valuable information that will likely impact the delivery of RNA therapeutics and unlock the full cytotoxic potential of NK immunotherapy.

In the field of cancer immunotherapy, NK cells are recognized for their ability to provide a form of innate immunity against tumor cells. However, the average abundance of NK cells in the blood can be as low as 5% of the total lymphocyte population. As a result, it has been a focus to find novel therapies to expand NK cells in vitro while subsequently enhancing the cytotoxicity of these cells. Previously-defined methods include the minimal expansion of NK cells with high levels of cytokines such as IL-2 and IL-15, as well as co-culturing NK cells with feeder cell populations that are genetically modified to express NK-stimulating factors. Another method involves the use of artificially-derived plasma membrane nanoparticles (PM21) that express membrane-bound IL-21 (mb21) to successfully expand NK cells by a factor of 103 in 14 days. Exosomes, which are cell-derived vesicles naturally secreted by cancer cells, may reveal a novel way to expand NK cells and enhance their cytotoxicity by taking advantage of the exchange of genetic information within the tumor microenvironment. To test this hypothesis, NK cells have been cultured with varying concentrations of exosomes derived from modified K562-mb21-41BBl (a chronic myelogenous leukemia cell line) and shown to achieve 200-fold expansion of NK cells from other PBMCs in 14 days, a growth comparable to that of PM-21 particles. In vitro assays as well as co-culturing with various tumor cell lines will determine the cytotoxicity of these expanded cells. Potentially, exosomes may be applied as an in vivo therapy for NK cell expansion.