Congratulations Brandon Farmer, PhD

On Friday, May 15, 2020 Brandon Farmer successfully defended his dissertation and earned his PhD! Brandon is part of the MD/PhD Program and earned his PhD in Lance Johnson's Lab. He will now return to the MD portion of the program and continue his studies to become the next generation of physician-scientists. Congratulations Dr. Farmer!

Doctoral Committee Members

Dr. Lance Johnson
Department of Physiology, Mentor

Dr. Steven Estus
Department of Physiology

Dr. Donna Wilcock
Department of Physiology

Dr. Peter Nelson
Pathology, Division of Neuropathology

Outside Examiner, Dr. Erick Blalock
Pharmacology & Nutritional Sciences

Abstract

Altered metabolic pathways appear to play central roles in the pathophysiology of late-onset Alzheimer’s disease (AD). Carrier status of the E4 allele of the APOE gene is the strongest genetic risk factor for late-onset AD, and increasing evidence suggests that E4 carriers may be at an increased risk for neurodegeneration based on inherent metabolic impairments. A new appreciation is forming for the role of APOE in cerebral metabolism, and how nutritional factors may impact this role. In chapter 1, the literature on nutritional interventions in E4 carriers aimed at mitigating disease risk is reviewed. Studies investigating the mechanism by which E4 increases disease risk have focused primarily on the association of E4 with the neuropathological hallmarks. While these studies have aided in our understanding of the role of E4 in late-disease pathology, investigating metabolic signatures of E4 carriers who have not yet developed neuropathology gives insight into the potential earlier mechanisms of E4 as a risk factor for AD. For example, an early and consistent biological hallmark of AD is cerebral glucose hypometabolism as observed by fluorodeoxyglucose positron emission tomography (FDG-PET). Interestingly, E4 carriers also display an AD-like pattern of decreased glucose metabolism by FDG-PET far before clinical symptomology. Since glucose hypometabolism occurs early in AD and early in E4 carriers, it may represent a critical prodromal phase of AD. Beyond this brain imaging finding, it is unclear if APOE has any other discernable metabolic effects in cognitively unimpaired young people. In chapter 2 we answer this gap in the field. We utilized indirect calorimetry (IC) as a method for assessing metabolism in young and middle aged volunteers with and without the E4 allele. While IC is commonly used in clinical settings to assess nutritional status, it has never been used to assess risk for cognitive decline. Thus, repurposing IC to study the metabolic effects of an AD risk factor such as E4 represents a simple, cost-effective, and innovative new approach. We found that young female E4 carriers show a lower resting energy expenditure compared to non-carriers. We also tested how E4 carriage affects response to a glucose challenge by administering a glucose rich beverage in conjunction with IC measurements and plasma metabolomics. We found that female E4 carriers were unable to increase oxygen consumption relative to non-carriers, reflecting an impairment in glucose oxidation. Additionally, the plasma metabolome of E4 carriers showed increased lactate and an overall metabolic profile consistent with aerobic glycolysis. We translated these findings to mice expressing the human alleles of APOE. We found that E4 mice on a normal chow diet have lower energy expenditure than E3 mice, a difference further exacerbated by high carbohydrate diet feeding. Stable isotope tracing in mice whole brains and astrocytes implicate increased utilization of aerobic glycolysis as a mechanism for altered glucose handling in E4 carriers. A pathological feature of the Alzheimer’s brain is glial lipid accumulation. The mechanism for this is largely unknown. In chapter 3, the literature pertaining to lipid droplets (LD) in the brain is reviewed. We show that LDs are much more than simple fat depots, playing critical roles in metabolism, inflammation, and various neurodegenerative diseases. In chapter 4, the effect of the E4 allele on astrocyte LD accumulation and turnover is assessed. Using an in vitro model of APOE we probed the storage and oxidation capacity of fatty acids in E3 and E4 astrocytes. We observed that E4 astrocytes exhibit greater storage of fatty acids as LDs under control and lipid loaded conditions compared to E3 astrocytes. Furthermore, we found that E4 astrocytes rely on these LDs as a source of fuel for oxidation. Therefore, APOE appears to regulate whole body energy expenditure, cerebral glucose oxidation, astrocyte LD metabolism, and risk for a host of metabolic diseases. In chapter 5, the evolutionary history of APOE is presented to posit a hypothesis for why E4 may be disadvantageous in modern times compared to its prior advantages in the pre-historic era. These results point toward a larger role for APOE in the regulation of metabolism than previously understood and advocates for alternative nutritional approaches including calorie reduction and intermittent fasting as plausible interventions to mitigate disease risk in E4 carriers.

Acknowledgements

MD/PhD training brings with it unique challenges that I do not possess the constitution to weather independently. These individuals formed my support structure and are due as much credit as I for this dissertation. Lance, I approached you as an orphaned graduate student looking for a lab. I attempted to bribe you with pseudo-knowledge of your past publications, a promise of strong work ethic, and donuts. The bribery worked and you took a chance on me resulting in three years, three fellowships, five (six?) papers, countless lab/data/mentor meetings, poster and paper revisions, conferences, and oral presentations. But these “research products” do not compare with the training and mentorship that I have been privileged to receive as your first graduate student. The knowledge you have imparted with regards to leadership, grantsmanship, ethics, work-life balance, conflict resolution, and so many more invaluable lessons has truly shaped my scientific outlook. Your example as a PI will serve as my construct for how I manage my own laboratory one day, and if I approach any semblance of your management style I will be golden. I could not have asked for a better mentor who is so receptive to my ideas, who constructively redirects me when I need it, who supports me missing lab to go see a patient, who believes in my potential and is willing to work at 3am to ensure that I am successful. I was incredibly fortunate to stumble into your office in October 2017 and will forever be grateful for your mentorship and friendship. To members of the Johnson Lab past and present, you created an environment that is rare in academia, one which is collaborative and socially pleasant. To DJ and Logan, the OGs, thank you for enduring my ramblings as a first year grad student who thought he had it all figured out. To Holden, thanks for being a co-graduate student that I can trust, bounce ideas off of, and academically develop with. Your humor and stories helped me to get through some tough times in grad school. To Grant, your assistance and organization of the clinical trial was pivotal to its success. To Jude, you were a workhorse for the projects in this dissertation. Your long days at the microscope, on the cryostat, reformatting of tables for the fiftieth time have paid off with dividends. I was a lucky grad student to have such a motivated and intelligent “minion” as you. Your can-do attitude will continue to serve you well, as well as your future patients. To Addie, Maggie, and Rebika you each contributed key comments, edits, or suggestions to shape this work and I am thankful for you all and excited to see what you do in the future. I would also like to thank my committee members who helped guide me as I tackled this project. Dr. Estus, I recall finding you in your office one day as I anguished over a grant submission decision. Your calm and wise scientific input at that point, and throughout my PhD, was more valuable than you know. To Dr. Wilcock, thank you for teaching to refine ideas and ask good scientific questions. To Dr. Nelson, thank you for emphasizing the need for an appreciation of the human relevance of my work. Your example as a physician-scientist that takes time to mentor me at the microscope or in your office has impacted me and I’m grateful for that. To my graduate student crew including Ben Shaw, Brooke Ahern, Beth Oates, Ryan Cloyd, and Laura Brown. Each of you played critical roles in the maintenance of my sanity during grad school. Through wallyball, “late-lunches” at KSR Bar, costume parties, bonfires, memes, Zoom happy hours, and Euchre games your companionship was the social outlet I needed. I am particularly thankful for Ben who taught me many fundamental research techniques in my brief stent in the Taylor Lab which I continue to rely on today. There are not sufficient words to describe my gratitude for my parents Lisa and Charles Farmer. You enabled me to believe that I have the potential to accomplish anything, and through all of this I have only tried to do my best to make you proud of what I have done. I have felt nothing but love and support from you both as I have reached higher and gone further. I am the person, scientist, and doctor I am today because of my parents. Mara, you likely did not know the full scope of my career when you agreed to marry me. But through your sincere commitment and love you have stuck with me despite my late nights in the office studying, my inability to think about anything but that upcoming paper, my rantings about astrocyte fatty acid metabolism, and my disgusting pictures of mice brains. You were the calming voice of reason in the darker moments of this journey where I questioned myself and my career path. You were the first person to celebrate the news of a publication or grant with me whether at two in the morning or in a Camaro on Mulholland Drive. Your constancy and your faith in me and my work has been so uplifting when I was most needed it. And though the training seems endless, and pandemics come, and experiments fail, I will always have you. And that’s what keeps me going.