Epidermal growth factor receptor (EGFR) is frequently overexpressed in the majority of triple negative breast cancer patients (TNBC). However, the molecular determinants behind their limited response to EGFR-targeted therapies are poorly understood. Here, both the acute and chronic responses of TNBC to the EGFR-targeted therapy, cetuximab (CTX), have been investigated. The expression of EGFR has been analyzed in a cohort of 2000 breast cancer tumours from the public dataset as well as in a panel of breast cancer cell lines. Furthermore, the response of TNBC cell lines to CTX has been investigated using conventional biochemical methods. Finally, a comprehensive transcriptomic profiling of an acquired CTX-resistant TNBC model by RNA sequencing has been performed to understand the molecular determinants of acquired CTX resistance. The results confirmed that EGFR is highly expressed in TNBC in comparison to non-TNBC breast cancer tumours and cell lines, which was associated with adverse clinical outcomes. Targeting EGFR in TNBC cell lines using CTX failed to completely inhibit the EGFR signalling pathway and was associated with an increase in ADAMs-mediated release of endogenous EGFR ligands, EGF and TGFα. Inhibition of ADAMs (ADAM10 and ADAM17) significantly enhanced the anti tumour efficacy of CTX both in vitro and in vivo. Furthermore, transcriptomic profiling of the acquired CTX-resistant TNBC cell line (MDA-MB-468CR) revealed an activation of several key oncogenic pathways and genes, including the TGFβ/BMP pathway. Blocking BMP receptors (BMPRs) restored the sensitivity of resistant cells to CTX treatment. Collectively, current findings offer alternative strategies that could enhance the CTX response in TNBC. We further reported that simultaneous targeting of both EGFR and BMPR pathways could overcome CTX resistance, which might have important implications for the treatment of TNBC.

<p>  </p> <p>Adoptive cell transfer of chimeric antigen receptors (CAR) T cells has successfully targeted hematological malignancies in human patients. However, unpredicted side effects experienced after injection of the CAR T cells suggests the need for an optimal predictive preclinical animal model. Dogs have intact immune systems and develop solid tumors spontaneously with similar morphology and genetics to humans. I hypothesize that generating CAR T cells for dogs will closely mimic human patients' outcomes, thus providing new understandings of the safety of this immunotherapy. In addition to the dog as a preclinical model, we propose using a universal CAR T cell to overcome various tumor-related immunosuppressive challenges and control the killing of the target cells. To achieve this, we established methods for activating and expanding canine T cells to a clinically relevant scale. Then, we expressed a second-generation anti-FITC-8-41BB-ζ CAR T cell via lentiviral transduction. In the presence of the correct low-molecular-weight bispecific adapter, we showed <em>in-vitro</em> CAR-mediated function. Our results proved that it is feasible to generate functional canine anti-FITC-8-BB-ζ CAR T cells for therapy.</p>

<p>Oncogenic mutations in KRAS are present in approximately 95% of patients diagnosed with pancreatic ductal adenocarcinoma (<b>PDAC</b>) and are considered the initiating event during the development of pancreatic intraepithelial neoplasia (<b>PanIN</b>) precursor lesions. While it is well established that KRAS mutations can drive the initiation of pancreatic oncogenesis, the effects of oncogenic KRAS signaling on regulation of phosphatases during this process is not fully appreciated. Protein Phosphatase 2A (<b>PP2A</b>) has been implicated in suppressing KRAS-driven cellular transformation. However, low PP2A activity is observed in PDAC cells compared to non-transformed cells, suggesting that suppression of PP2A activity is an important step in the overall development of PDAC. In the current study, we demonstrate that KRASG12D induces the expression of both Cancerous Inhibitor of PP2A (<b>CIP2A</b>), an endogenous inhibitor of PP2A activity, and the PP2A target, c-MYC. Consistent with these findings, KRASG12D sequestered the specific PP2A subunit responsible for c-MYC degradation, B56a, away from the active PP2A holoenzyme in a CIP2A-dependent manner. During PDAC initiation <i>in vivo</i>, knockout of B56a promoted KRASG12D tumorigenesis by accelerating acinar-to-ductal metaplasia (<b>ADM</b>) and the formation of PanIN lesions. The process of ADM was attenuated <i>ex vivo</i> in response to pharmacological re-activation of PP2A utilizing direct small molecule activators of PP2A (<b>SMAP</b>s). Together, the results of this study suggest that suppression of PP2A-B56a through KRAS signaling can promote Myc-driven initiation of pancreatic tumorigenesis.</p>

<p>Adult prostate stem cells (PSC) are a rare epithelial progenitor population in the prostate. While essential for normal homeostasis, they have also been implicated in hyperplasia and cancer initiation. While studies have shown that inflammatory growth factors and cytokines can fuel stem cell expansion, the impact of inflammation on PSC is not well understood. To study the impact of inflammation on the prostate, the Ratliff laboratory developed the Prostate Ovalbumin Expressing Transgenic 3 (POET3), an inducible mouse model of abacterial T cell mediated prostate inflammation, which functions as a model for human autoimmune prostatitis. Previous studies using the POET3 demonstrated that inflammation increased proliferation and differentiation of PSC enrichments. Based on these findings, it was speculated that inflammation impacts prostate stem cells to enhance mechanisms of survival, possibly as a means of tissue protection.</p><p>Since androgen receptor (AR) signaling is the major driver of cellular differentiation and survival in the prostate, it was further hypothesized that inflammation promotes AR signaling in the PSC. To address this hypothesis, PSC and their resulting organoids from inflamed and non-inflamed (naïve) POET3 mice as well as human patient samples were assessed for AR and its signaling components.</p><p>These data were expanded by single cell mRNA sequencing using Fluidigm’s C1 platform, which revealed changes in stem cell populations, differential expression of interleukin 1 alpha (IL-1⍺) and its signaling components, and upregulation of various genes associated with immune regulation. Thus, experiments described herein probed the impacts of inflammation on AR, IL-1⍺, and T cell regulatory abilities in the PSC.</p>The results of these studies indicate that indeed, inflammation increases PSC survival. Inhibition of IL-1⍺ via inflammation-mediated up-regulation of IL-1 receptor antagonist (IL-1RA) promotes AR signaling, resulting in proliferation, differentiation, and AR target gene expression which can be modulated by Enzalutamide (a clinical AR inhibitor). Furthermore, PSC from inflamed mice are able to suppress cytotoxic T cell function in <i>ex vivo</i> assays. These studies set the foundation for new ways to treat proliferative diseases of the prostate by targeting IL-1⍺, AR, and immune regulation in the PSC.

<p>  </p> <p>Metastases are responsible for approximately 90% of all cancer-related deaths, with metastatic breast cancer (BC) holding a 5-year survival rate of only 27%. Recent research has highlighted a complex dynamic between cancer cells and the tumor microenvironment as essential for the formation of macrometastases. Within this field, tissue stiffening through matrix accumulation and altered matrix organization at the primary tumor site were recently linked with sustained proliferation and increased migration of tumor cells. Separately, elevated levels of the glycoprotein, fibronectin, were correlated to poor patient survival in BC and were linked to enhanced seeding of disseminated tumor cells at metastatic sites. Through my doctoral work, we have identified several mechanisms through which accumulated fibronectin impacts the metastatic potential of BC cells. First, we identified a transient increase in extracellular fibronectin in the lungs, which peaked before overt metastasis, coupled with a non-transient increase in total lung volume. To better recapitulate physiological conditions, we then developed a novel magnetically-actuated platform with the ability to apply tensile strain on cells at various amplitudes and frequencies in a high-throughput multi-well culture plate using suspended fibrillar fibronectin for 3D cell culture that is not reliant on a synthetic substrate. Using this as a biomimetic lung model, we found that cyclic mechanical force acted as a suppressor of cancer cell growth in a biomimetic lung model, implicating the accumulation and reorganization of extracellular matrix as an attempt by the cancer cells to alter the mechanical properties of the lung tissue and resist entering dormancy. However, our results showed that BC cells could not organize extracellular fibronectin independently. Instead, BC cells altered the accumulation and architecture of fibronectin by conditioning fibroblasts through soluble factors and extracellular vesicles. We observed that the fibronectin produced by conditioned fibroblasts varied as an effect of both the method of conditioning and the phenotype of the BC cell as the conditioning source. Taken together, these results have increased our knowledge of the relationship between disseminated breast cancer cells, fibroblasts, and fibronectin architecture in the early metastatic lung niche that paves the way for further investigation on targeting disseminated BC cells during early disease intervention in order to inhibit later overt metastatic outgrowth.</p>

<p>Polycomb repressive complex 1 (PRC1) is critical for mediating gene expression during development. Five chromobox (CBX) homolog proteins, CBX2,4,6,7,8, are incorporated into PRC1 complexes, where they mediate targeting to trimethylated lysine 27 of histone H3 (H3K27me3) via the N-terminal chromodomain (ChD). Individual CBX paralogs have been implicated as drug targets in cancer; however, high similarity in sequence and structure among the CBX ChDs provide a major obstacle in developing selective CBX ChD inhibitors. Here a selection of small, focused, DNA-encoded libraries (DELs) against multiple homologous ChDs was reported to identify modifications to a parental ligand that confer both selectivity and potency for the ChD of CBX8. This on-DNA, medicinal chemistry approach enabled the development of SW2_110A, a selective, cell-permeable inhibitor of the CBX8 ChD. SW2_110A binds CBX8 ChD with a Kd of 800 nM, with minimal 5-fold selectivity for CBX8 ChD over all other CBX paralogs in vitro. SW2_110A specifically inhibits the association of CBX8 with chromatin in cells and inhibits the proliferation of THP1 leukemia cells driven by the MLL-AF9 translocation. In THP1 cells, SW2_110A treatment significantly decreases expression of MLL-AF9 target genes, including HOXA9, validating the previously established role for CBX8 in MLL-AF9 transcriptional activation, and defining the ChD as necessary for this function. The success of SW2_110A provides great promise for the development of highly selective and cell permeable probes for the full CBX family. In addition, the approach taken provides a proof-of-principle demonstration of how DELs can be used iteratively for optimization of both ligand potency and selectivity.</p> <p>CBX2 is upregulated in a variety of cancers, particularly in advanced prostate cancers. Using CBX2 inhibitors to understand and target CBX2 in prostate cancer is highly desirable. Here, selections of focused DNA encoded libraries (DELs) were performed for the discovery of a selective CBX2 chromodomain probe, SW2_152F. SW2_152F binds to CBX2 ChD with a Kd of 80 nM and displays 24-1000-fold selectivity for CBX2 ChD over other CBX paralogs <em>in vitro</em>. SW2_152F is cell permeable, selectively inhibits CBX2 chromatin binding in cells, and blocks neuroendocrine differentiation of prostate cancer cell lines in response to androgen deprivation.</p> <p>Targeted covalent inhibitors (TCIs) are rationally designed inhibitors that bind to a target protein and specifically label a non-conserved amino acid on proteins by means of reactive moieties (warheads). TCIs typically function by two steps, in which inhibitors first non-covalently bind to the target protein and then covalent bond formation occurs between the inhibitor- warhead and a proximal nucleophile on protein. Covalent inhibitors or drugs have prolonged target engagement and enhanced pharmacokinetic potency in vivo, compared to non-covalent molecules. Strategies to develop effective warheads of TCIs have been reported for labeling different nucleophilic amino acid residues, of which cysteine and lysine are the most established for covalent labeling. Tyrosine is recently becoming an attractive nucleophile for TCIs as an alternative choice, yet currently developed warheads that label tyrosine do so with modest specificity over other side chains. Here, I report the development of novel Mannich electrophiles and use those electrophiles as covalent warheads on an inhibitor to specifically target tyrosine in protein labeling. To my knowledge, this is first demonstration of the use of Mannich electrophiles in covalent inhibitors. Specifically, I leveraged a previously developed CBX8 chromodomain inhibitor to specifically label a non-conserved tyrosine within CBX8 using cyclic imine derivatives as warheads. This ligand-directed, specific tyrosine conjugation on CBX8 but not on CBX2, significantly improves both the potency and selectivity of inhibition. Biochemical, proteomic, and cellular validation further showed the cyclic imine covalent inhibitors can increase both potency and selectivity to the target protein CBX8 in cells, serving as a robust chemical probe for target function evaluation and modulation. This new type of tyrosine labeling warhead is a useful addition to the toolbox of medicinal chemists for covalent inhibitor development.</p> <p>The following chapters are modified from following publications, with permissions from Sijie Wang, Emily C.Dykhuizen, and Casey J. Krusemark. </p> <p>Wang, S., Denton, K. E., Hobbs, K. F., Weaver, T., McFarlane, J. M., Connelly, K. E., Gignac, M.C., Milosevich, N., Hof, F., Paci, I., Musselman, C. A., Dykhuizen, E.C., Krusemark, C. J. Optimization of Ligands Using Focused DNA-Encoded Libraries To Develop a Selective, Cell-Permeable CBX8 Chromodomain Inhibitor. <em>ACS Chem Biol. </em>2020, 15, 112-131</p> <p>Wang, S., Alpsoy, A., Sood, S., Ordonez-Rubiano, S. C., Dhiman, A., Sun, Y., Krusemark, C. J., Dykhuizen, E. C. A Potent, Selective CBX2 Chromodomain Ligand and its Cellular Activity During Prostate Cancer Neuroendocrine Differentiation. <em>ChemBioChem.</em> 2021, 22, 2335-2344</p> <p>Wang, S., Ordonez-Rubiano, S. C., Dhiman, A., Jiao G., Strohmier B. P., Krusemark, C. J., Dykhuizen, E. C. Polycomb Group proteins in cancer: multifaceted functions and strategies for modulation Modulators. <em>NAR Cancer</em>. 2021, 3, zcab039</p>

<p>  </p> <p>Epstein-Barr virus (EBV) is a complex oncogenic symbiont. The molecular mechanisms governing EBV carcinogenesis remain elusive and the functional interactions between virus and host cells are incompletely defined. Some of the known mechanisms include viral integration into the host genome, expression and mutation(s) of viral genes and the host response to the virus. Despite decades of research there is a lack of effective treatment options for EBV-positive cancer patients underscoring an urgent need to further investigate the mechanisms underlying tumorigenesis as well as explore and develop personalized treatment strategies for patients with EBV-positive cancers. In Chapter 1, I introduce Epstein-Barr Virus (EBV), the two phases of EBV lifecycle and an overview of certain EBV-associated carcinomas. I will also discuss the underlying mechanisms and few current therapeutic strategies against EBV infection. Next, I will discuss some of the preclinical model systems and high-throughput computation techniques that are commonly used by researchers in the field of EBV.  </p> <p>In chapter 2, we have systematically analyzed RNA-sequencing from >1000 patients with 15 different cancer types, comparing virus and host factors of EBV+ to EBV- tissues to reveal novel insights into EBV-positive tumors. First, we observed that EBV preferentially integrates at highly accessible regions of the cancer genome with significant enrichment in super-enhancer architecture. Second, we determined that the expression of twelve EBV transcripts, including LMP1 and LMP2, correlated inversely with EBV reactivation signature. Over-expression of these genes significantly suppressed viral reactivation, consistent with a ‘Virostatic’ function. Third, we identified hundreds of novel frequent missense and nonsense variations in Virostatic genes in cancer samples, and that the variant genes failed to regulate their viral and cellular targets in cancer. Lastly, we were able to dichotomously classify EBV-positive tumors based on patterns of host interferon signature genes and immune checkpoint markers, such as PD-L1 and IDO1. </p> <p>In chapter 3, we probed the lifecycle of EBV on a cell-by-cell basis using single cell RNA sequencing (scRNA-seq) data from six EBV-immortalized lymphoblastoid cell lines (LCL). While the majority of LCLs comprised cells containing EBV in the latent phase of its life cycle, we identified two additional clusters that had distinct expression of both host and viral genes. Both clusters were high expressors of EBV Latent Membrane Protein-1 (LMP1) but differed in their expression of other EBV lytic genes, including glycoprotein gene GP350. We further probed into the transcriptional landscape of these clusters to identify potential regulators which will be discussed in further detail in the chapter. Importantly, I was able to demonstrate enhancing HIF1-a signaling by using Pevonedistat, a compound that stabilized HIF1-a can preferentially induce the transcriptional program specific to one of the three identified clusters. </p> <p>In Chapter 4, I describe some of my recent work. In this project, we have used an intuitive <em>in-silico </em>drug prediction approach to rapidly screen and identify FDA-approved or clinically available compounds that can be repurposed to induce lytic cycle in different EBV+ tumors. Using this strategy, we identified Ciclopirox, an antifungal drug, as a potent inducer of lytic cycle in EBV+ epithelial cancers. We used EBV+ GC cells to determine the effect of Ciclopirox on EBV reactivation as well as identify the underlying mechanisms. In summary, we discovered that reactivation of EBV lytic cycle by Ciclopirox is mediated by multiple pathways, two of the major ones being the HIF1-a and NF-kB pathways. Although, Ciclopirox treatment enhanced the killing effect of antiviral, further investigation is needed to effectively deliver this drug <em>in vivo.</em> Throughout this chapter, I have discussed findings that needs further investigation and proposed necessary experiments. Finally, in Chapter 5 I have summarized my work and described how our work can provide novel insights that can help delineate some of the complexities of host-pathogen interactions in EBV-associated malignancies. </p>

No description available.

<p dir="ltr">Pancreatic ductal adenocarcinoma (PDAC) remains one of the most deadliest cancer and despite advancements in cancer therapy, remain highly refractory to treatment, largely due to its desmoplastic tumor microenvironment (TME) characterized by complex interactions among cancer cells and stromal components. Particularly, the PDAC associated coagulation system due to leaky tumor vasculatures plays a pivotal role in reshaping the PDAC stroma and its pathogenesis. Understanding the intricate interplay between tumor cells, stromal cells, and the elevated coagulation pathway elements, including tissue factor, thrombin, and fibrin, is essential for developing effective therapeutic strategies. To address these challenges, this research proposes the engineering of a novel PDAC-associated coagulation system using a microfluidic technology, known as coagulation-on-tumor-microenvironment-on-chip (cT-MOC). The study aims to integrate key coagulation pathways in cT-MOC to investigate pivotal interactions in the PDAC stroma: <i>i)</i> thrombin-protease-activated receptors (PARs) mediated promotion of PDAC fibrosis via activation of cancer-fibroblast cross-talk; <i>ii)</i> in-depth analysis of transport and mechanical properties of collagen-fibrin microstructure; <i>iii)</i> inhibited drug delivery in reprogrammed PDAC stroma due to pronounced fibrin deposition on collagen. By leveraging innovative microfluidic technologies and comprehensive experimental approaches, the research endeavors to provide a novel platform that bridges traditional <i>in vitro</i> and <i>in vivo</i> models to overcome the challenges posed by the desmoplastic TME and enhance therapeutic strategies for treatment by targeting the coagulation at the PDAC TME.</p>

<div>Cancer is responsible for the second highest cause of death in the United States, and lung cancer accounts for 13% of new cancer diagnoses, with the highest rate of cancer death at 24%. Almost 85% of these cases represent non-small cell lung cancer (NSCLC), which includes lung adenocarcinoma, the most common NSCLC subtype. Traditional cancer treatments often only temporarily stop the spread of the disease, but immunotherapies, which are becoming a standard of care, are much more promising. Natural killer (NK) cells are powerful effectors of innate immunity, and genetically engineered NK cells as immunotherapies have had encouraging clinical responses in the treatment of various cancers. However, more progress is needed for solid tumor treatment, especially for lung adenocarcinoma. The activation of cancer-associated ectoenzymes, CD39 and CD73 catalyze the phosphorylation of ATP to AMP to produce extracellular adenosine (ADO), which is a highly immunosuppressive mechanism contributing to the pathogenesis of solid tumors. Understanding adenosine effects on NK cells will help develop more robust immunotherapeutic treatments to improve cytotoxicity against solid tumors. Here, we established that tumor microenvironment ADO results in impaired metabolic and anti-tumor functions of cytokine-primed NK cells. Specifically, peripheral blood-derived NK cells stimulated with IL-2, IL-15, or a combination of IL-12 and IL-15 showed suppressed anti-tumor immunity due to ADO. This was observed by the downregulation of activation receptor expression, cytotoxicity inhibition, impairment of metabolic activity, and alterations in gene expression. To target ADO-producing CD73 on cancer cells, we redirected NK cells by fusing CD73 ScFv with intracellular and transmembrane regions of NK cell specific signaling components derived from FCyRIIIa (CD16). Engineered NK cells were shown to be cytotoxic against lung adenocarcinoma <i>in vitro</i> and impede tumor growth in a lung adenocarcinoma mouse model <i>in vivo</i>. Engineered cells also had higher levels of degranulation and cytokine release, as well as more infiltration into tumors and longer survival time in mice. In summary, the microenvironment of solid tumors is highly immunosupressive, and redirecting NK cell function using a NK-specific anti-CD73 targeting construct will help to promote anti-tumor immunity and</div><div>inhibit cancer growth for a potentially powerful new immunotherapy against solid tumors.</div>