Kidney cancer or renal cell carcinoma (RCC) is the 6th most common type of cancer in men and the 9th common cancer in women in the United States and claims nearly 15,000 lives annually. 75% of total RCC cases are clear-cell renal cell carcinoma (ccRCC) which is refractory to the conventional chemotherapy and there is currently no effective cure against ccRCC except for surgical removal. While Fuhrman nuclear grading has been widely used as a prognostic tool for ccRCC, its subjective nature hinders precise and reliable patient-specific prognosis. The overarching aim of this dissertation is to characterize the molecular components of Fuhrman nuclear grades to understand the molecular underpinning of ccRCC chemoresistance and to identify proteomic and metabolomic signatures of ccRCC that can be harnessed to establish novel diagnostic tools complimentary to the Fuhrman nuclear grading and to identify potential novel grade-defined pharmacological targets. This dissertation first aims to characterize the molecular mechanisms behind the ccRCC chemoresistance using Roscovitine (Seliciclib) as an example of conventional chemotherapy via cyclin dependent kinase (CDK) inhibition. Second, Fuhrman nuclear grade-defined proteomes are characterised to identify a set of proteins that can be used as diagnostic biomarkers and grade-specific pharmacological ccRCC targets. Third, the potential role of Argininosuccinate Synthetase (ASS1), whose expression was suppressed across all Fuhrman grades, in ccRCC pathogenesis is investigated. Additionally, in order to establish novel diagnostic criteria, this study aims to characterize the grade-dependent subcellular localization of novel ccRCC biomarker proteins that are found to behave as moonlighting proteins.

This dissertation focuses on discussing how metabolic reprogramming shapes pulmonary fibrosis, particularly idiopathic pulmonary fibrosis (IPF). IPF is a detrimental interstitial lung disease with an unfavorable outcome. Although the etiology remains unknown, cigarette smoking has been considered as a risk factor for IPF. Previous findings have found that smoking can alter metabolic regulation in inflammatory lung diseases, including COPD, asthma and IPF. Metabolomics has been a powerful tool to identify putative biomarkers and novel signaling mechanisms in disease research. Untargeted metabolomics approach was used in our study to profile cellular metabolic changes in primary lung fibroblasts derived from normal and IPF patients. IPF lung fibroblasts displayed a different metabolic landscape as compared to normal lung fibroblasts, in which arginine-related metabolic pathways were significantly altered due to the absence of argininosuccinate synthase (ASS1) expression in IPF lung fibroblasts. Removing arginine from cell culture and media was specific to IPF lung fibroblast and pulmonary fibrosis. Because of the critical function of arginine metabolism in lung fibroblasts, ASS1 expression was knocked down in normal lung fibroblasts to examine the changes in metabolic pathways. Myo-inositol metabolism was found to be significantly disturbed in ASS1-deficient lung fibroblasts. Myo-inositol treatment demonstrated in vivo and in vitro antifibrotic effects. Overall, our studies have demonstrated the pivotal role of amino acid metabolism in IPF lung fibroblasts.

Overall, this review aims to outline IPF regarding macrophage and fibroblast interactions, in addition to the therapeutic roles that macrophages may play in becoming an inhibitory target for IPF. Idiopathic pulmonary fibrosis (IPF) is a chronic inflammatory disease in which the tissue surrounding the alveoli within the lungs undergoes fibrosis or permanent scarring. IPF and the consequent disruption to lung blood flow, in addition to the change in immune landscape, will cause severe impact to lung function to the point of fatalities. The estimated number of patients in the United States affected by IPF is between 35,000 and 55,000 cases, with cases expected to rise as older generations continue to grow proportional to the total size of the population.2,53,141,142 Due to a lack of effective therapies, this disease exhibits a median survival time of 3 to 5 years from the time of diagnosis53,140, much worse than many cancer types. In recent years, there has been a renewed appreciation for the role of immune cells in mediating the fibrotic process with an increased interest in the role of macrophages, a type of innate immune cell which responds to environmental stimuli by secreting a wide range of biochemical signaling compounds. Macrophages help to break down the ECM using matrix metalloproteinases (MMPs). Macrophages also produce tissue inhibitors of metalloproteinases (TIMPs) to inhibit the process of ECM breakdown. Macrophages have been shown to be increased in IPF lung tissue and have a significant and poorly appreciated role in mediating fibrosis. In general, fibrotic diseases are characterized by excessive M2-associated and Th2-driven responses. Therefore, macrophages are an attractive target for inhibiting progressive pulmonary fibrosis. Recent literature has further shown that macrophages and fibroblasts directly interact with each other to influence the tissue microenvironment to affect disease outcomes26,28. In other words, both cell types interact to maintain tissue homeostasis. Together, these cells may interact during IPF and the overall fibrotic lung process to affect pulmonary homeostasis and IPF disease progression.