AN ABSTRACT OF THE THESIS OFChristopher T. Mandrell, for the Master of Science degree in Physics, presented on April 8, 2020, at Southern Illinois University Carbondale.TITLE: IMPROVING SPECTRAL ANALYSIS WITH THE APPLICATION OF MACHINE LEARNING: STUDY OF LASER-INDUCED BREAKDOWN SPECTROSCOPY (LIBS) AND RAMAN SPECTROSCOPY WITH CLASSIFICATION AND CLUSTERING TECHNIQUESMAJOR PROFESSOR: Dr. Poopalasingam SivakumarAtomic and molecular spectroscopy, in the form of LIBS emissions and Raman scattering, respectively, are tools that provide a vast amount of information with little to no sample preparation. For this reason, these techniques are finding their way into a wide range of fields. However, each spectrum is notoriously complicated to analyze, with many complex interactions at play. Machine learning is the result of work on artificial intelligence. It provides tools to train a computer to look for connections in complex data sets that would likely be missed, or not even looked for, by other analytical methods. The combination of highly informative yet complex data with an analysis that is specifically designed to probe highly complex data for meaningful information is a logical step in the analysis of these spectra. Here we apply statistical analysis and classification algorithms to Raman spectra of pancreatic cancer cells and clustering algorithms to LIBS spectra of Mars Curiosity Rover simulants and Raman spectra of Mars Perseverance Rover simulants. We report here high accuracy in the classification of different types of pancreatic cancer cells, and informative clustering of the two Mars rovers’ simulant data.

In 2011, Diabetes and prediabetes affected 9 million Canadians and 366 million people worldwide (Canadian Diabetes Website). The underlying pathophysiology of diabetes is beta cell dysfunction leading to loss of appropriate insulin secretion and resulting in hyperglycemia. I have focused on identifying critical molecular regulators of beta cell function and insulin secretion. The CRTC2-CREB pathway is required for maintaining beta cell mass and insulin secretion. I propose that identifying kinases that regulate CRTC-CREB activity will identify other important regulators of pancreatic beta cell survival and function. First, I have identified several AMP kinases as inhibitors of CRTC2-CREB that are activated by an upstream kinase, LKB1. I then went on to generate mice with a beta cell-specific deletion of LKB1 during adulthood. Loss of LKB1 increased insulin secretion and glucose clearance through enhanced beta cell mass and proliferation. The increased insulin secretion was largely the result of loss of AMPK activity and consequent constitutive mTor activity. AMPK is activated under starvation conditions and as such is thought to be a critical regulator of beta cell function. However, the decrease of AMPK activity in high glucose has been a strong argument against it being a critical effector of insulin secretion. I provide genetic evidence supporting the idea that AMPK activity attenuates insulin secretion. During periods of starvation where AMPK activity is high there is a chronic dampening effect on events that prepare beta cells for the next round of insulin secretion. Surprisingly, another downstream kinase of LKB1, SIK2, has opposing functions in the beta cell. I present evidence that the LKB1-AMPK axis attenuates beta cell functions and that targeting this pathway in beta cells may be of therapeutic benefit for T2D.

Pancreatic pseudocyst is a common complication of pancreatitis. Pseudocysts may require decompression when they become painful, infected, or start compressing surrounding organs. Decompression is achieved by endoscopic cystogastrostomy. Recently, the use of lumen-apposing metal stent (LAMS) for cystogastrostomy has gained popularity due to ease of use and high technical success. LAMS has a wider lumen, which allows for direct endoscopic necrosectomy in the cases of walled-off necrosis. Our patient is a 30-year-old male who presented with massive hematemesis and dizziness. He had a history of chronic alcohol-induced pancreatitis. Three weeks before the presentation, he underwent a cystogastrostomy with LAMS placement to treat a 10-cm walled-off necrosis. Urgent computed tomography (CT) scan did not reveal any acute finding suggestive of bleeding. Esophagogastroduodenoscopy showed blood protruding from the LAMS with a large clot formation. Attempts to stop bleeding were unsuccessful. He underwent CT angiography of the abdomen. CT angiography showed a bleeding pseudoaneurysm (PA) believed to be a complication of the LAMS. Subsequently, multiple coils were placed in the splenic artery near the PA. The patient continued to improve without a further drop in hemoglobin and was eventually discharged. PA formation and subsequent rupture is a rare delayed complication of LAMS. It may lead to massive gastrointestinal bleeding with a high mortality rate. Diagnostic delays have resulted in increased mortality by 60%. In this article, we present a case of massive gastrointestinal bleeding due to a ruptured splenic artery PA presenting as a delayed complication of LAMS.

Mediastinal pancreatic pseudocyst (MPP) is a rare, but known, complication of both acute and chronic pancreatitis. Most pseudocysts are associated with alcoholic pancreatitis. Recent advances in endoscopic techniques have shown promising results, with reduced chances of infection and recurrence than with percutaneous drainage, but limited availability restricts widespread use. Left gastric artery pseudoaneurysm with mediastinal pseudocyst has not been described in the literature to date. We report a successful resolution of hemorrhagic MPP with embolization of pseudoaneurysm and percutaneous trans-hepatic pseudocyst drainage.

The development of a drug able to distinguish between tumor and host cells has been long sought, but the solid tumor microenvironment (TME) confounds many current therapeutics. Solid tumors present several challenges for oncotherapeutics, primarily, (1) aberrant vascularization, resulting in hypoxia, necrosis, abnormally high pH, and (2) tumor immune suppression. Oncolytic microbes are drawn to this microenvironment by an innate ability to selectively penetrate, colonize, and eradicate solid tumors as well as reactivate tumor associated immune components. To consider oncolytic bacteria deployment into this microenvironment, Chapter 1 dives into the background of oncolytic microbes. A discussion of the oncolytic bacterial field state, identifying Clostridium novyi? as a promising species, and details genetic engineering techniques to develop customized bacteria. Despite the promise of C.novyi in preclinical/clinical trials when administered intratumorally, the genetic and biochemical uniqueness of C.novyi necessitated the development of new methodologies to facilitate more widespread acceptance. Chapter 2 reports the development of methods that facilitate experimental work and therapeutic translation of C.novyi, including the ability to work with this obligate micro-anaerobe aerobically on the benchtop. While methods development is a necessary step in the clinical translation of C.novyi so too is choosing the correct model of the TME within which to test a potential anti-cancer therapy. While the typical solid TME includes both phenotypic and genotypic heterogeneity, the methods used to model this disease state often do not reflect this complexity. This simplistic approach may have contributed to stagnant five-year survival rates over the past four decades. Nevertheless, simplistic models are a necessary first step in clinical translation. Chapter 3 explores the impact of cancer cell lines co-cultured with C. novyi to establish the efficacy of this oncolytic bacteria in a monolayer culture. Chapter 4 extends this analysis adding not only a level of complexity by using an in vivo model, but also using CRISPR/Cas9 to modify the genome of C.novyi to encode a tumor targeting peptide, RGD, for expression within the spore coat. The combination of these studies indicates that C. novyi is uniquely poised to accomplish the long sought after selective tumor localization via intravenous delivery.

Tocotrienols are members of the vitamin E family but, unlike tocopherols, possess an unsaturated isoprenoid side chain that confers superior anti-cancer properties. The ability of tocotrienols to selectively inhibit the HMG-CoA reductase pathway through posttranslational degradation and to suppress the activity of transcription factor NF-κB could be the basis for some of these properties. Our studies indicate that γ- and δ-tocotrienols have potent antiproliferative activity in pancreatic cancer cells (Panc-28, MIA PaCa-2, Panc-1, and BxPC-3). Indeed both tocotrienols induced cell death (> 50%) by the MTT cell viability assay in all four pancreatic cancer cell lines. We also examined the effects of the tocotrienols on the AKT and the Ras/Raf/MEK/ERK signaling pathways by Western blotting analysis. γ- and δ-tocotrienol treatment of cells reduced the activation of ERK MAP kinase and that of its downstream mediator RSK (ribosomal protein S6 kinase) in addition to suppressing the activation of protein kinase AKT. Suppression of activation of AKT by γ-tocotrienol led to downregulation of p-GSK-3β and upregulation accompanied by nuclear translocation of Foxo3. These effects were mediated by the downregulation of Her2/ErbB2 at the messenger level. Tocotrienols but not tocopherols were able to induce the observed effects. Our results suggest that the tocotrienol isoforms of vitamin E can induce apoptosis in pancreatic cancer cells through the suppression of vital cell survival and proliferative signaling pathways such as those mediated by the PI3-kinase/AKT and ERK/MAP kinases via downregulation of Her2/ErbB2 expression. The molecular components for this mechanism are not completely elucidated and need further investigation.

The major obstacle in using pancreatic islet transplantation to cure type I and some type II diabetes is the shortage of the donors. One of ways to overcome such obstacle is to isolate and clone pancreatic stem cells as "seed cells" and induce their differentiation into functional islets as an abundant transplantation source. In this study, a monoclonal human pancreatic stem cell (mhPSC) line was obtained from abortive fetal pancreatic tissues. Pancreatic tissues were taken from abortive fetus by sterile procedures, and digested into single cells and cell clusters with 0.1% type IV collagenase. Cultured in modified glucose-low DMEM with 10% fetal bovine serum (FBS), these single cells and cell clusters adhered to culture dishes, and then primary epidermal-like pancreatic stem cells started to clone. After digesting with 0.25% trypsin and 0.04% EDTA, fibroblasts and other cells were gradually eliminated and epithelioid pancreatic stem cells were gradually purified during generations. Using clone-ring selection, the mhPSCs were obtained. After addition of 10 ng/mL epidermal growth factor (EGF) in cell culture medium, the mhPSCs quickly grew and formed a gravelstone-like monolayer. Continuously proliferated, a mhPSC line, which was derived from a male abortive fetus of 4 months old, has been passed through 50 generations. More than 1×10 9 mhPSCs were cryo-preserved in liquid nitrogen. Karyotype analysis showed that the chromosome set of the mhPSC line was normal diploid. Immunocytochemistry results demonstrated that the mhPSC line was positive for the pdx1, glucagon, nestin and CK19, and negative for the insulin, CD34, CD44 and CD45 protein expression. RT-PCR revealed further that the mhPSCs expressed transcription factors of the pdx1, glucagon, nestin and CK19. Also, in vitro induced with β-mercaptoethanol, the mhPSCs differentiated into nerve cells that expressed the NF protein. Induced with nicotinamide, the mhPSCs differentiated into functional islet-like clusters, as identified by dithizone staining, which expressed the transcription factor of the insulin and secreted the insulin and C-peptide. Furthermore, the transplantation of mhPSCs-induced pancreatic islets into the subcapsular region of the kidney in streptozotocin-induced diabetic rats could reduce blood glucose levels and prolong the life time.

Pancreatic carcinoma or pancreatic cancer (PaCa) is an insidious disease with a prognosis of 6- to 12-month survival time for a late stage diagnosis. This problem has become crucial given that no study to date had been able to establish a definitive association between independent factors (other than a few diseases) and the survival rate of pancreatic cancer. The purpose of this quantitative, cross-sectional study was to determine whether an association exists between the independent, sociodemographic variables (marital status, age, education, income, and employment) and the outcome variable of survival rate. The social cognitive theory was the framework that provided the blueprint throughout the development of this study and helped guide the analysis of the secondary data, which was procured from the surveillance, epidemiology, and end results program. The sample of 56,166 participants was collected from 2009 to 2013 and Cox proportional hazard was used to analyze the data and arrive at the answers to the research hypotheses. A Cox proportional hazard model was used to analyze whether an association existed between each of the independent variables and the outcome variable. The analysis showed significant association between age, education, income, and employment and survival rate. It was not the same for marital status. These findings could stimulate social change by allowing stakeholders and other policy makers to become aware of the role that sociodemographic factors can play in health care. In addition, a need exists for effective research to be undertaken in the prevention and intervention of this disease. This could then lead to private and public health innovations and procedures to benefit patients with PaCa.

Indiana University-Purdue University Indianapolis (IUPUI) / Pancreatic ductal adenocarcinoma (PDAC) and colorectal cancer (CRC) are among the most commonly diagnosed forms of cancer in the United States. Due to their widespread prevalence and high mortality rate, it is vital to develop effective therapeutic drugs to combat these deadly diseases. In both PDAC and CRC, the multifunctional factor nuclear factor kappa B (NF-kB), a central coordinator of cellular immune responses, is activated abnormally, leading to tumorigenesis and cancer progression. Therefore, controlling NF-kB activity is critical in the treatment of these cancers. In a previous study, we identified a new mechanism by which NF-kB activity is regulated by an epigenetic enzyme known as protein arginine methyltransferase 5 (PRMT5). We showed that overexpression of PRMT5 not only activated NF-kB, but also significantly promoted several characteristics associated with cancer, including increased cell proliferation, migration, and anchorage-independent growth in both PDAC and CRC cells. Moreover, in order to examine the therapeutic potential of PRMT5 in these cancers, we adapted the state-of-the-art AlphaLISA technique into a high throughput screen (HTS) platform to screen for PRMT5 inhibitors. As a result, we successfully identified the small molecule PR5-LL-CM01 as our lead hit. Further validation experiments confirmed that PR5-LL-CM01 is a potent and specific PRMT5 inhibitor that exhibits significant anti-tumor efficacy in both in vitro and in vivo models of PDAC and CRC. Additionally, in a second screen, we discovered two natural compounds, P1608K04 and P1618J22, that can also function as the PRMT5 inhibitors. These findings further highlight the robustness of the PRMT5- specific AlphaLISA HTS technique. To conclude, we describe here for the first time a novel role of PRMT5 as a tumor-promoting factor in PDAC and CRC through NF-kB activation. By successfully developing and applying an innovative AlphaLISA HTS technique, we discovered PR5-LL-CM01, P1608K04, and P1618J22 as novel PRMT5 inhibitors, with PR5-LL-CM01 showing the strongest potency in both PDAC and CRC models. Therefore, we demonstrated that PRMT5 is a promising therapeutic target in PDAC and CRC, and the novel PRMT5 inhibitor PR5-LL-CM01 could serve as a promising basis for new drug development in PDAC and CRC.

Indiana University-Purdue University Indianapolis (IUPUI) / Pancreatic ductal adenocarcinoma (PDAC) is currently the fourth leading cause of cancer-related death in the United States, and is characterized by key driver mutations (e.g. KRAS, TP53, CDKN2A, and SMAD4), elevated expression of growth factors such as TGF-βs and the EGF receptor (EGFR), a markedly desmoplastic stroma, and a propensity to develop multi-organ metastases and chemoresistance. Consistent with its aggressive nature, the 5-year survival rate for PDAC is 8-9%, which demonstrates an urgent need to develop novel therapies. High expression levels of microRNA-10b (miR-10b) in PDAC tissues are associated with decreased patient survival and earlier appearance of metastatic disease following neoadjuvant chemoradiotherapy. miR-10b downregulates the expression of transcription coactivator Tat-Interacting Protein 30 (TIP30) by targeting its 3’UTR. TIP30 has multiple reported functions. TIP30 suppresses tumor formation and metastasis, forms a complex that regulates EGFR trafficking and degradation, and transcriptionally upregulates pro-apoptotic genes. Alterations in TIP30 have been reported in multiple human cancers, including pancreatic cancer. We hypothesized that Tip30-deficiency accelerates PDAC progression and metastasis in a murine model of PDAC. To test this hypothesis, we crossed mice with oncogenic Kras (KC) localized to the pancreas epithelium, with Tip30-deficient mice (K30C). We compared PDAC histopathology between Tip30-heterozygous (K30+/-C) and Tip30-null (K30-/-C) mice. Tip30-heterozygosity accelerated PDAC-lesion-associated pancreatic cancer cell (PCC) pulmonary seeding. By contrast, total loss of Tip30 enhanced PCC micrometastatic seeding to the liver and hepatic metastasis. K30+/-C mice also presented with an early, increased penetrance of lung lesions and lung adenocarcinoma; and PCCs isolated from K30+/-C pancreata exhibited increased EGFR protein levels. These findings suggest that TIP30 deficiency can have a dose-dependent effect on organotropic metastasis and EGFR levels in PCCs. Future studies will delineate the molecular consequences of TIP30 loss in PDAC and contribute to a broader understanding of pancreatic cancer metastasis. / 2020-08-05