<p> Crohn&rsquo;s Disease (CD) is a type of Inflammatory Bowel Disease (IBD) with increasing incidence worldwide. In the US alone, prevalence of CD is shown to be 214 per 100,000. CD is not fatal, but deeply impacts the quality of life of an individual. While existing therapies alleviate the symptoms of the disease, there is no cure yet. Even with proper treatment, as many as two-thirds to three-quarters of people with CD will require surgery, which involves high risk of compromised bowel function and malnutrition. Therefore, there is a great need for the development of novel therapies for treatment and prevention of the disease. A better understanding of how CD-associated genetic mutations impact biological pathways involved in disease pathogenesis could offer insights into the development of new therapeutic strategies. </p><p> An autophagy gene associated with CD is Leucine-rich repeat kinase 2 (<i>LRRK2</i>). LRRK2 is a multidomain protein with numerous suggested biological functions including vesicular traffic, immune response regulation and autophagy. While <i>LRRK2</i>&rsquo;s involvement in Parkinson&rsquo;s disease (PD) development has been investigated for over a decade, only recently have studies detected associations between <i>LRRK2</i> mutations and susceptibility to CD. Recently, our group identified novel association signals at <i>LRRK2</i> conferring CD risk, N2081D; or protection, N551K, tagging the R1398H-associated haplotype. Interestingly, the <i> LRRK2</i> N2081D CD risk allele is located in the same kinase domain as G2019S, a mutation that is the major genetic cause of familial and sporadic PD. </p><p> The main goal of my thesis was to elucidate the functional consequences of these novel CD-associated <i>LRRK2</i> mutations, N2081D and N551K+R1398H, on the autophagy process. To study autophagy and its role in regulating inflammation, the major component of CD, we utilized macrophages, white blood cells, important in the process of phagocytosis that highly express <i> LRRK2</i>. Through our study of human-derived macrophages, we found that carriers of the <i>LRRK2</i> N2081D mutation exhibited impaired autophagy when compared to N551K+R1398H carriers and non-carriers. We also found that impaired autophagy in N2081D carriers was associated with increased total LRRK2 protein levels and defective lysosomal pH and tubulin acetylation regulation. Additionally, we studied autophagy in macrophages from wildtype (WT) and <i>Lrrk2</i> knockout (KO) mice and found that the regulation of lysosomal pH in KO macrophages was significantly affected, further suggesting that <i>LRRK2</i> may play a role in autophagy through regulation of lysosomal pH. Another experimental goal was to determine if knocking out <i>Lrrk2</i> would result in changes to the microbiota in a mouse model with induced colitis and without. Specifically, we explored <i> Lrrk2</i>&rsquo;s role in association with the microbiota and found that <i> Lrrk2</i> participates in regulating microbial taxa under inflammatory circumstances. </p><p> In summary, our findings suggest that CD&ndash;associated mutations in the <i>LRRK2</i> gene conferring risk (N2081D) or protection (N551K+R1398H) affect gene expression, lysosomal acidity and tubulin acetylation in monocyte-derived macrophages (MDM) implicating them in the process of autophagy. We also propose <i> Lrrk2</i> as a modulator of microbiota changes under inflammation. These results should warrant future studies to explore <i>LRRK2</i> as a potential target for new therapies to treat CD.</p><p>