UC San Diego

Information technology continues to shape and transform biological research. Bioinformatic research and methods are as diverse and divergent as the biological issues aimed to solved, with RNA sequencing becoming a prominent tool to derive key breakthroughs. This dissertation capitalizes on the adoption of transcriptional platforms and various bioinformatics analysis to comprehend biological “memory” of cells expanded ex vivo for therapeutic approaches and evaluate spatial lung reprograming in a vaping-induced pulmonary injury inhalation model.Ex vivo expansion of cells is necessary in regenerative medicine to generate large populations for therapeutic use. Adaptation to culture conditions prompt an increase in transcriptome diversity and decreased population heterogeneity in cKit+ cardiac interstitial cells (cCICs). The “transcriptional memory” influenced by cellular origin remains unexplored and is likely to differ between neonatal versus senescent input cells undergoing culture expansion. The work presented in this dissertation demonstrates that age, pathology and the cellular stress associated to the in vivo tissue microenvironment persist after culture adaptation, influencing targets of 1) cell cycle, 2) senescence associated secretory phenotype (SASP), 3) RNA transport, and 4) ECM-receptor/fibrosis. Vaping continues to increase worldwide. Promoted as a “healthier” alternative to traditional smoking, emerging evidence indicates “healthier” should not be confused with “harmless”. Findings in this dissertation demonstrate pulmonary consequences of vaping after chronic direct inhalation exposure. Profound pathological changes to upper airway, lung tissue architecture, and cellular structure are evident within 9 week of exposure. Marked histologic changes include increased parenchyma tissue density, cellular infiltrates proximal to airway passages, alveolar rarefaction, increased collagen deposition, and bronchial thickening with elastin fiber disruption. Transcriptional reprogramming includes significant changes to gene families coding for xenobiotic response, glycerolipid metabolic processes, and oxidative stress. This vaping-induced pulmonary injury model demonstrates mechanistic underpinnings of vaping-related pathologic injury. Novel technologies are required to circumvent limitations associated with basic cardiopulmonary biology. Transcriptional profiling platforms continues to produce data essential for advancement of therapeutic approaches. Collectively, studies in this dissertation holds the potential to improve in vitro expansion protocols critical for adoptive transfer approaches, restore transcriptional phenotypes in vivo and ultimately to improve efficiency of therapeutic approaches after vaping or cardiac injury.