University of South Florida

Byrd Alzheimer’s Center: Basic research objectives and faculty recruitment strategy

June 3, 2019

Alzheimer’s disease (AD), also now used in conjunction with certain related dementias (known as Alzheimer’s disease and related dementias or ADRDs), affects more than 47 million people worldwide and more than 5 million people in the United States (U.S.). The ADRDs spectrum includes AD, frontotemporal dementia (FTD), Lewy body dementia (LBD), vascular dementia (VD), corticobasal degeneration (CBD), and progressive supranuclear palsy (PSP). The cost for caring for ADRD patients in the U.S. was $400 billion/year in 2012 and is expected to increase to $2.4 trillion/year in 2050 unadjusted for inflation. ADRDs will dominate and likely overwhelm the health care system in the U.S. if adequate treatment is not found soon. While the medical, social, caregiver/family, and overall financial burdens of ADRDs are astronomical, no treatment exists to prevent or halt the onset or progression of ADRDs, and even “symptomatic” treatment has only limited efficacy.

The mission: The mission of the Byrd Division of Basic Research is to address the growing challenge of ADRDs in 3 important ways: 1) to understand the root causes of the pathophysiology of disease onset and progression, 2) to identify molecular targets for therapeutic intervention based on the results of the basic science investigations, and 3) to translate the molecular targets to treatments to prevent or treat ADRDs. To meet this enormous challenge, the Byrd will need the best NIH-funded investigators with specific expertise to carry out internationally recognized research on ADRDs. A near-term goal for the Byrd is to rank among the top 20 Neuroscience Institutes dedicated to ADRD research in the U.S.

Organization of the Center: In 2018, the Byrd underwent significant reorganization together with birth of the USF Health Neuroscience Institute (NSI), an umbrella organization that includes the Byrd as its research epicenter. At the time (March 2018), Professor David Kang, PhD, was named the Director of the Division of Basic Research at Byrd. Since 2018, the Byrd has recruited 5 new NIH-funded investigators in joint efforts with the Vice Dean for Research, and the Departments of Molecular Medicine, and Molecular Pharmacology & Physiology: Gopal Thinakaran, Angele Parent, Alexa Woo, Lianchun Wang, and Krishna Bhat. Hence, since reorganization the Byrd has successfully reached an early critical mass of excellent investigators from which to attract additional outstanding ADRD research scientists to Byrd.

Among the 10 independent laboratories at Byrd, 17 NIH-R01 and 4 VA Merit funded studies are in progress, in addition to 10+ smaller funded studies.  These are supported by multiple sustainable Cores and the home academic Departmental Chairs, creating a performance-based, innovative and creative atmosphere. Byrd has enough laboratory space to recruit 3 to 4 additional investigators (particularly when Heart Institute labs are vacated), and with the proposed 4th and 6th floor laboratory expansion projects, the Center will be able to accommodate potentially  6 to 8 new faculty recruits into the building. As further delineated below, our intention is for new recruits to be a mixture of senior, mid-level, and junior investigators, each with NIH-funded research programs.

State of ADRD Research that Drives Byrd Recruitment: Two classes of drugs have been approved by the FDA for the treatment of AD patients (denoted 1st generation drugs) — the chlolinesterase inhibitors and noncompetitive NMDA receptor antagonists. Although some short-lived symptomatic relief is seen by these treatments in some patients, they do nothing to alter the course of disease. Based on the hypothesis that Ab protein accumulation in brain is the primary culprit in AD pathogenesis (amyloid cascade hypothesis), the 2nd generation of treatments targeting the Ab peptide have been developed and tested aggressively in multiple clinical trials over the last decade. Unfortunately, all these clinical trials have failed thus far, leading many investigators to doubt the amyloid cascade hypothesis as the magic bullet for targeting therapy.

More recent studies, taking a non-biased, take-a-step-back approach, have indicated that the amyloid cascade hypothesis, though meritorious in cases of genetic AD, is far too simplistic for the heterogenous nature of late-onset sporadic AD, which accounts for  >95% of all cases. Hence, AD researchers have now been pushed to return to the bench to study the molecular basis of AD pathophysiology in fresh new ways, incorporating new insights gained from neuroscience research related to aging, neuronal molecular biology, memory and learning circuitry, microvascular physiology, and the spectrum of other ADRDs. Not unexpectedly, we now realize that while each ADRD is characterized by certain proteinopathies in the brain, most AD-diagnosed patients show clinical, molecular, and histological evidence of mixed pathologies of several types. For example, Lewy body pathology, which is characteristic of Parkinson’s disease (PD), is present in >50% of dementia patients. TAR DNA-binding protein 43 (TDP-43), a nuclear RNA-binding protein, when mislocalized to the cytoplasm forms insoluble inclusion bodies, which are characteristic of amyotrophic lateral sclerosis (ALS), but also present in >70% of dementia patients. Greater than 40% of dementia patients also have vascular components. This has led to the concept that AD cannot be studied in isolation but must incorporate the study of related diseases and the aging process of the central nervous system (CNS). As such in 2017, the NIH decided to aggregate the ADRDs together in multiple funding opportunities and to significantly increase funding for ADRD research. These actions further recognize the failure of AD research in the past to generate treatments and promote a more interdisciplinary approach to solving AD and ADRDs.

Current Basic and Translational ADRD Research at Byrd:  ADRDs, though heterogeneous in pathological and clinical phenotypes, nevertheless have several commonalities that point to some novel opportunities for focused research to redefine the molecular events in dementia leading to treatment: 1) proteinopathy (i.e. Ab, tau, a-synuclein, TDP-43, etc.), 2) oxidative stress & mitochondrial dysfunction, and 3) disruption of proteostasis pathways. During the aging process, misfolded proteins and dysfunctional mitochondria can accumulate in the brain, while proteostasis pathways attempt to remove such materials via multiple proteostatic mechanisms. Unfolded protein response (UPR) and chaperones play vital roles in folding, aggregation, and disaggregation of misfolded proteins, while the autophagy-lysosome and proteasome systems play major roles in the clearance of misfolded proteins and dysfunctional mitochondria.  Accumulation of either becomes toxic to neurons via multiple signaling pathways, compromising the cytoskeleton and synapse and ultimately leading to neuronal degeneration. A secondary response to initial and ongoing neuronal damage is neuroinflammation by immune cells of the brain (the microglia); when chronic and prolonged, neuroinflammation induces further damage to neurons thereby fueling the neurodegeneration cycle. Moreover, misfolded proteins that reach a critical state of aggregation acquire the ability to self-template and propagate from one neuron to another in a prion-like manner, thereby eventually spreading proteinopathy from one region of the brain to another via their synaptic connectivity. Inflammation, abnormal anatomy, hypoxia, and certain coagulation and cholesterol-related pathologies contribute to microvascular dysfunction and micro-ischemia, also feeding into the vicious cycle.  All these processes ultimately lead to degeneration of the brain and the resultant dementia with a heterogeneity of clinical manifestations.

At Byrd, basic science investigators now have expertise in several areas of interconnected research (see below) performed using multiple model systems such as cell lines, primary neurons, microglia, astrocytes, and endothelial cells, as well as animal models (drosophila, C. elegans, and mice). These research efforts are supported by 3 Byrd Cores: Electrophysiology Core, Microscopy Core, and Behavior Core. The current complement of researchers and their topics of investigation related to ADRDs follows:

Autophagy-mediated proteostasis (Kang, Woo, Liu)
Chaperone-mediated protein folding/misfolding (Blair, Kang, Woo)
Unfolded protein response & proteasome-mediated proteostasis (Blair, Kang, Thinakaran)
Mechanisms of proteotoxic protein generation (Thinakaran, Parent, Kang, Blair, Lee, Selenica)
Membrane trafficking (Thinakaran, Parent, Kang, Liu)
Neurotoxic signaling (Kang, Thinakaran, Parent, Woo, Bhat, Wang, Liu, Blair)
Mitochondrial dysfunction (Kang, Liu, Woo)
Axon guidance (Bhat)
Neurogenesis (Bhat)
Neuroinflammation (Thinakaran, Kang, Liu)
Circadian rhythm disruption (Gamsby, Gulick)
Neurovascular system disruption (Wang)
Synaptic plasticity changes (Kang, Woo, Liu, Blair, Lee, Thinakaran, Parent)
Cytoskeletal changes (Kang, Woo, Blair, Liu)
GPCR/Arrestin biology (Woo, Liggett)
Invertebrate models: Drosophila & C. elegans (Bhat, Kang)
Memory & behavior (Gulick, Gamsby, Blair, Kang, Woo, Thinakaran, Parent, Bhat)
Drug discovery (Kang, Woo, Blair, Liggett) 

Asset map of Current Byrd Basic Science Research:

Current NIH grant expenditures per year for all faculty: $8,111,800

Total portfolio of NIH-funding of Byrd investigators (over the life of current grants): $38,522,518
Gopal Thinakaran: 3 R01
Angele Parent: 1 R01
David Kang: 2 R01 + 1 R21
Krishna Bhat: 2 R01
Lianchun Wang: 2 R01 + 1 U01
Alexa Woo: 1 R01
Laura Blair: 2 R01
Stephen Liggett: 1 R01 + 1 P01 project
Dan Lee: 1 R01 + 1 R21

Total portfolio of foundation, VA, and other funding of Byrd Investigators (over the life of the current grants): $4,536,923
Gopal Thinakaran: 1 Alz Assoc
Angele Parent: 1 Foundation
David Kang: 2 Florida grants + 3 VA merit
Krishna Bhat: N/A
Lianchun Wang: N/A
Alexa Woo: 1 Florida grant (co-PI with Kang)
Laura Blair: 1 Florida grant + 1 Alz Assoc + 1 VA merit
Dan Lee: 1 Florida grant + 1 Alz Assoc
Joshua Gamsby: 2 Florida grants

Total Neuroscience endowments and yearly interest:
Principal: $10,524,156
Annual Interest Earnings: $389,002

Indirect cost funds provided to USF from agencies funding the current grants (federal and other) per year: $2,750,835

Total space allotted for wet-lab research at Byrd (including new expansion projects): 18,186 sq. ft. (3rd, 4th & 5th floors), 4th floor expansion (2650 sq. ft.), and 6th floor expansion (2583 sq. ft.)

Expansion into the Next Phase of Byrd ADRD Research: The 5 new recruits in 2018-2019 have certainly improved the interdisciplinary nature and quality of the scientific output at Byrd and added several important dimensions to ADRD research for USF Health. Together with existing investigators, the Byrd/NSI is well poised for the next phase of expansion.  Necessarily, there are some areas of research that need to be strengthened and other key areas in which the Byrd and NSI have yet to participate (and may never due to resource limitations).

We are thus taking a focused approach to ADRD research recruitment at Byrd that is feasible, synergizes with current strengths, and fills the gaps in the science of these devastating diseases. New recruits in the areas of research outlined below will add the necessary building blocks to facilitate the funding of competitive multi-PI NIH program projects. These areas will be key to the success of the Byrd and NSI, which will define both the depth and direction of ADRD research into the next decade.

Epigenetics: Epigenetics refers to the study of DNA and chromatin modification typically by methylation or acetylation. Epigenetic modification occurs as a function of aging, disease and environment, resulting in changes in the accessibility to genomic DNA and/or the ability to turn on/off specific sets of genes by transcription factors. Multiple studies have shown that the pattern of epigenetic marks in AD patients is completely different from age-matched healthy controls, indicating that the pathogenic process in AD changes the way genes responds to the same stimuli. Because the accumulation of Ab and tau begins 10-20 years prior to the onset of clinical symptoms, some researchers believe that reversing amyloid burden or even tauopathy will be insufficient to reverse the epigenetic changes that have occurred over many years. At present, no investigator at Byrd or NSI has significant expertise in this important and growing field of epigenetics. An expert investigator in epigenetics will take advantage of genomic and informatics resources at USF Health and Moffitt, as well as the Byrd patient population, and will add tremendous depth to ADRD research at Byrd and NSI. This person would also be instrumental in organizing and aggregating genomics and transcriptomics resources for Byrd and NSI (i.e. the Genomics Core)

Modeling neuronal diseases by human iPSCs and direct reprogramming: Genetic animal models, such as those in mice, flies, and worms, have been widely used to model human diseases. While these models are enormously valuable and essential, ADRD research has been steadily moving toward modeling human neurodegenerative disease in human neurons as well. In fact, induced pluripotent stem cells (iPSCs) have now become the de facto gold standard for neuronal disease research in NIH grants and high-impact publications. The use of human neurons converted from iPSCs is not only entirely feasible but is also now an essential part of ADRD research toolset. Another emerging technology for generation of human neurons is direct reprogramming of human patient-derived fibroblasts or epithelial cells into neurons. This method has a key advantage in that while the generation of iPSCs to their stemness erases the epigenetic profile from the original “age” to an embryonic state, direct reprogramming to neurons retains the epigenetic “age” of cells, thereby allowing aging and disease states to be examined in the same form as in the diseased patients (original source of cells). The presence of the dementia clinic and Parkinson’s clinic within the Byrd building greatly facilitates the establishment of a primary fibroblast bank from which to derive neurons. Since primary fibroblasts are not a renewable resource, the fibroblast bank will be highly valued not only by Byrd and NSI investigators but also other neuroscientists worldwide in need of patient-derived primary fibroblasts.  However, no investigator at Byrd or NSI has national prominence in the expertise for generating iPSCs or direct reprogramming of cells into neurons. These types of innovative methods are not easily learned from scratch but require extensive expertise and experience, and a technology that is really in an infant stage and continually evolving. An investigator with leading-edge expertise in these methods will provide huge synergy for all investigators at Byrd and NSI. This investigator would also be instrumental in the development of a new ‘Cellular Reprogramming Core” and establishment of a patient-derived “Fibroblast Bank” at USF Health in collaboration with clinicians and biomarker investigators (see below).

The Insolublome in Aging: Aging is the primary risk factor driving all major diseases, including ADRDs. Studies from flies, C. elegans and mice have clearly shown that genetic and environmental factors promoting healthy aging or extending healthy lifespan also protect against most major diseases, including proteinopathies and mitochondrial dysfunction seen in ADRDs. The concept of “geroscience” advances the idea that ADRDs are different forms of aberrant or accelerated brain aging – that proteinopathies emerging during the normal aging process accelerate during the onset ADRDs. This concept considers the idea of the insolublome, the content of the insoluble proteasomes that advances with age, as a major driving force behind the pathogenesis of ADRDs. Genetic and pharmacological approaches to reduce the insolublome or its content may mitigate proteinopathies in ADRDs. This highly quantitative and unbiased approach utilizes advanced mass spectrometry-based proteomics, which are not widely used at Byrd. These approaches can also take advantage of simpler animal models such as flies and worms, leading to rapid translation to higher level species and human neurons. Very often, genes or agents that extend healthy lifespan are those that activate autophagy, impact mitochondrial function, and/or modify epigenetic profiles. An investigator with the “geroscience” scientific background and expertise in the insolubiome would inject a fresh perspective and strengthen all aspects of ADRD research at the Byrd and NSI. This investigator would also be instrumental in aggregating resources for proteomics studies at Byrd and NSI (i.e. the Proteomics Core).

Neurovascular component of dementia: Vascular dementia has been explicitly named as an ADRD by the NIH, as vascular abnormalities are seen in more than 40% of AD patients. While Ab is known to be cleared out of the brain via the blood-brain-barrier (BBB) and often deposited on the walls of blood vessels (vascular amyloid), this area has historically been understudied. Disruption of the BBB is one of the early features of ADRDs, whether via vascular amyloid or other mechanisms. At present, one Byrd investigator, Dr. Lianchun Wang, is the only person who has started to work on the vascular component of ADRDs. Dr. Wang’s scientific background is in the cancer and cardiovascular fields, so another neurovascular investigator with specific expertise in neurodegeneration would greatly strengthen research on the vascular component of ADRDs at Byrd and NSI.

Biomarkers for ADRDs: The cellular buildup of Ab, tau, and other proteins begins 10-20 years prior to any clinical signs of dementia. By the time clinical symptoms arise, the brain already has significant proteinopathy with pathologic degeneration. This is a huge challenge for clinical trials, because treating patients who have already deteriorated is far more difficult than prevention. New technologies for detecting amyloid or metabolic defects in brain by PET imaging are currently available, but neither are foolproof, and both are expensive (>$2000/scan). At present, CSF-based biomarkers are somewhat more accurate than blood-based ones but obtaining CSF by lumbar puncture is invasive and nonroutine. Therefore, it is critically important to develop accurate blood-based biomarkers for ADRDs. Recent studies indicate that detecting pathological proteins from brain-derived exosomes in blood may serve as early biochemical signatures of ADRDs prior to the onset of symptoms. These types of detection methods together with proteomics, genomics, epigenomics, and transcriptomics may greatly enhance the diagnostic potential. Such biomarkers can also be used as surrogates for prognosis during clinical trials and treatment regimens. The Byrd Center boasts outstanding dementia and Parkinson’s clinics and many ongoing clinical trials, and yet, no one at Byrd or NSI has taken a systematic approach to obtain blood samples (or CSF) from patients for this purpose and to conduct traditional and novel biomarker studies for ADRDs in our patients for Byrd-centric studies. A scientist with both a clinical and basic research background as well as a history of biomarker research would be the investigator of choice, who could take advantage of valuable clinical resources from the Byrd clinic and systematically propel biomarker research. He/she would also work closely with the proteomics and genomics cores for biomarker studies. If a physician scientist, this investigator may also see patients at the clinic and be involved in clinical trials. Ultimately Byrd, and this investigator, would lead national trials to move this field forward using resources from NIH grants, foundations, and public/private partnerships.

The Microbiome in ADRDs: Emerging evidence shows that gut microbial imbalance (dysbiosis) could greatly contribute to ADRD pathogenesis and neurodegeneration. Not only is the diversity of the gut microbiome significantly reduced in AD patients, the populations of microbiota found in the AD gut are also highly different. Fecal microbiota from normal gut given to AD animal models reduce amyloid and tau in the brain and improve cognitive performance. A phenomenon known as “leaky gut” can lead to the release of microbiota-generated molecules into the blood circulation and enter the brain, many of which are pro-inflammatory. Thus, the gut-brain axis is an emerging area of study with huge implications for brain function and ADRD pathogenesis. Moreover, modification of the GI track is therapeutically tractable by diet, exercise, prebiotics, probiotics, and direct microbiota transfer from healthy donors. A recruit in this field of study would not only take advantage of existing resources such as animal models and the Genomics Core at Byrd and USF, but also develop a Metabolomics Core alongside the Proteomics Core, which would be a new core capability at USF Health.

Single cell, subcellular, microdomain, and in vivo imaging: Research in molecular targets of neurodegeneration requires advanced microscopic and nanoscopic imaging capabilities. The Byrd Microscopy Core is presently equipped with a scanning microscope, several confocal fluorescence microscopes, an atomic force microscope, a multi-photon microscope for deep tissue in vivo imaging, and a soon-to-be acquired super-resolution confocal microscope. Dr. Tian Liu, an Assistant Professor of Molecular Medicine, is currently putting 50% of his effort in the Microscopy Core by training investigators and maintaining Core equipment (confocal, scanning, and atomic force microscopes). However, he has limited expertise in super-resolution and multiphoton microscopy techniques. These types of sophisticated instruments require continual optimization using off-the-shelf components and troubleshooting with high-level technical expertise. A recruit with demonstrated expertise in various sophisticated microscopy techniques (particularly super-resolution and multiphoton) would provide great synergy for Byrd and NSI investigators as well as introduce new core capabilities to the Byrd and NSI. He/she would not only be a technical person, but one who applies these high-level techniques to the study of ADRDs.


David E. Kang, PhD
Professor and Director of Basic Research, Byrd Alzheimer’s Center

Stephen B. Liggett, MD
Professor and Vice Dean for Research, Morsani College of Medicine


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