Modeling human age-related neurodegenerative diseases (NDDs), including synucleinopathies, by using human induced pluripotent stem cells (hiPSCs) leverages the use of cell culture systems in research of neurodegenerative diseases. The hiPSC system has several advantages crucial to accomplishing our research goals. First, as an isogenic system, it allows us to examine the direct effects of specific genetic variants on a common human genetic background, in a cell-specific manner. Second, it enables us to perform comprehensive assessments of molecular phenotypes and cellular functions using living cells.

We have developed isogenic hiPSC-derived aged cholinergic and dopaminergic neurons, and astrocytes involved in age-related NDDs, including AD, PD and DLB. These 2D model systems are suitable for investigating cell-specific disease mechanisms and genetic etiologies, and to validate causal genetic factors.

A deeper understanding of the interplay between brain cell types is feasible with novel 3D co-culture systems. The isogenic hiPSC-derived 3D triculture technique recapitulates the brain microenvironment in vitro and enables to study the interactions between the different brain cell types. Working with the Bursac group, we initiate the development of 3D triculture systems composed of various combinations of isogenic neurons, astrocytes, and microglia as human-based disease models for exploring the mechanistic complexity of NDDs.

Additionally, in collaboration with the Kantor and Akkari research teams, our overarching goal is to translate the mechanistic understanding to clinical applications. The hiPSC-derived models facilitate the validation of therapeutic targets and the establishment of proof-of-concept for next generation gene-therapy approaches, including CRISPR/Cas (genome and epigenome editing) and antisense oligonucleotide (ASO) technologies, as a precision medicine for individuals at high risk for NDDs due to gene dysregulation.

Identifying neuron-, astrocyte- and microglia-specific alterations in regulatory elements, the epigenome landscape, and gene expression profiles between normal and LOAD-pathological stages will advance the identification of target genes within the LOAD-associated loci.

In collaboration with the Crawford and the Ashley-Koch labs we investigate chromatin accessibility and gene expression profiles in affected brain tissues from LOAD patients. The heterogeneity of brain tissue makes it difficult to assess molecular characteristics of individual cell types. Frozen tissue presents additional challenges, as intact cell bodies are more difficult to isolate than intact nuclei. Therefore, we used fluorescence-activated nuclei sorting (FANS) to distinguish between neuronal and non-neuronal nuclei. Unexpectedly, we detected LOAD-specific differential chromatin accessibility in non-neuronal cells from female but not male subjects. This has prompted further investigation to determine the specific non-neuronal cell types underlying this sex-specific genetic regulatory landscape.

To interrogate cellular diversity in the brain at an even higher resolution, our lab employs the 10X Genomics microfluidics system to generate single-nuclei (sn) barcoded libraries for RNA-sequencing (seq) and ATAC-seq. We perform snRNA-seq and snATAC-seq in parallel from the same sample, such that chromatin accessibility and gene expression profiles can be assessed from the same pool of nuclei. We utilize advanced data science methods to process and analyze these large datasets and generate cell type-specific clusters. Ultimately, we are able to characterize and integrate cell subtype-specific multi-omic profiles to identify regulatory elements implicated in LOAD pathogenesis and progression.

In the post genome-wide-association-studies (GWAS) era we are shifting gears toward translation of genetic disease loci to molecular mechanisms of pathogenesis. Large multi-center GWAS have found associations between >30 genomic loci and late-onset Alzheimer’s disease (LOAD), and candidate genes were inferred by the proximity to the associated-SNP. However, the precise target genes within the LOAD-associated genomic regions and the causal variants affecting LOAD-risk have yet to be uncovered. In collaboration with Dr. Lutz, we developed a bioinformatics pipeline based on functional genomic datasets to advance the interpretation of Alzheimer's disease GWAS discoveries. This pipeline can be applied to other complex genetic diseases.

Several key observations have provided evidence for the interrelationship between Alzheimer’s disease (AD) and neuropsychiatric symptoms (NPS). Neuropsychiatric conditions have been shown to increase the risk for developing dementia, and patients with AD frequently manifest comorbid NPS with wide heterogeneity. This evidence suggests shared genetic etiology and intersecting pathways between AD and neuropsychiatric conditions, which contributes to the comorbid phenotypes of NPS, such as depression and anxiety. In collaboration with Drs. Lutz, Williamson, and Sheng, we have been testing the hypothesis that genetic variability, epigenetic signatures, and gene expression changes in specific genes are common between AD and neuropsychiatric conditions, and that these shared molecular phenotypes are responsible, at least in part, for the heterogeneity of NPS in AD.

In particular, we have been studying two neuropsychiatric disorders, Major Depressive Disorder (MDD) and Post-traumatic Stress Disorder (PTSD). For both we found a moderate enrichment for SNPs associated with LOAD across increasingly stringent levels of significance with the MDD and the PTSD GWAS findings. Association analysis identified numerous pleiotropic risk-loci, with the primary and most significant SNPs positioned in two regions of chromosome 11 (SPI1 gene and MS4A genes cluster). Functional genomic studies, including eQTLs and pathway analyses, pointed to the immune response as a common pathway.

A neuropathological hallmark of a group of neurodegenerative diseases, known as human synucleinopathies, is the presence of intracellular protein aggregates named Lewy bodies (LBs) and Lewy neurites (LNs). The alpha-synuclein protein is a major component of LBs. Parkinson’s disease (PD) is the archetypal human synucleinopathy and has been studied extensively. Genome-wide association studies (GWAS) have implicated the alpha-synuclein gene (SNCA) in PD, DLB and MSA. Several studies in cell-culture and animal models reported that overexpression of wild-type SNCA can be toxic and may lead to cell death. Moreover, we documented that elevated SNCA expression in patients correlated with Lewy body presentation.
 
We utilize a multi-faceted strategy in our experiments to decipher the role of SNCA in health and disease, whether that be LB pathologies in general or in a particular disease within the spectrum.

One of the leading projects in our lab aims to uncover the molecular mechanisms regulating SNCA expression (such as transcription, RNA metabolism), and any genetic variability that impinges on this regulation. Another more recent study in our lab suggested a role for SNCA in the nucleus in the context of aging. Specifically, we found that when SNCA is mutated or overexpressed, it disrupts the nucleocytoplasmic transport leading to impairment of nuclear function and exacerbation of aging. 

APOE ε4 is the strongest and most replicated genetic risk factor for late-onset Alzheimer’s disease (LOAD). APOE is located on chromosome 19 (19q13.32) in the tight gene cluster TOMM40-APOE-APOC1-APOC4-APOC2 that exhibits strong linkage disequilibrium (LD). Genome wide association studies (GWAS) reported that the strongest association signal (by a wide margin) was also in the APOE LD region. This top association signal was attributed to the APOE ε4 haplotype; however, it has been acknowledged that other genetic factors within this LD block may also explain the strong genome-wide significant signal and contribute, in part, to disease risk attributed to this genomic region. This work has been carried out in collaborations with the late Dr. Allen Roses and team, and Drs. Lutz and Gottschalk.

We investigated the TOMM40-APOE genomic region associated with the risk and age of onset of LOAD to determine the functional consequences of a highly polymorphic, intronic polyT within this region (rs10524523) discovered by Roses et al. The TOMM40-polyT was associated with LOAD age of onset and other disease related endophenotypes, and we have identified an association with cognitive performance in normal aging. Specifically, we have been studying the regional regulatory effect of the TOMM40-polyT site on gene expression. In these investigations, we are using multiple model systems, including human brain tissues, cell-based reporter systems, mESCs, and humanized mouse models. We have found that the polyT acts as a regional transcriptional regulator of TOMM40 and APOE genes, suggesting that the TOMM40-polyT locus may contribute to LOAD susceptibility by modulating TOMM40 and/or APOE mRNA expression levels. We have also manipulated the transcriptional effects on TOMM40 and APOE-C1 genes in vitro using two approaches: knockdown of PPARgamma with shRNA, and treatment with pharmacological agents that are known PPARgamma agonists, particularly low doses of the Pioglitazone and Rosiglitazone compounds.

Dysregulation of gene expression has been implicated in the etiology of several age-related neurodegenerative diseases. Translating the knowledge of the mechanisms involved in the regulation of firmly established key-genes in disease, such as SNCA in PD and APOE in LOAD, will facilitate next generation drug discovery based on targeted manipulation of gene expression in a fine-tuned manner. This therapeutic strategy is efficient for fine modulation of gene expression to restore physiological levels of critical proteins. In collaboration with the Kantor lab, we developed a novel strategy to intervene with transcriptional regulation programs of SNCA and APOE, based on targeted epigenome editing. Specifically, we have established a system for targeted DNA-methylation editing that comprises an all-in-one lentiviral vector, for the delivery of CRISPR/dCas9 fused with the catalytic domain of DNA-methyltransferase 3A (DNMT3A).

Applying this novel CRISPR/dCas9-based technology offers an unprecedented tool to modify a particular epigenetic mark. Specifically, this technology resulted in effective fine-tuned reduction of SNCA expression levels in hiPSC-derived neurons from a PD patient that was sufficient for reversing PD-associated phenotypic perturbations. These proof-of-concept experiments provide the foundation and validation for advancing this novel epigenetic editing-based system towards a PD therapeutic strategy applicable in a clinical setting. Our innovative platform that allows for fine-tuned regulation of gene expression would be highly appealing and translational for developing ‘next generation drugs’ as prevention and/or disease modifying interventions for PD, Alzheimer’s disease and other neurodegenerative diseases and pathologies associated with dysregulation of gene expression.

Our Alumni

Graduates and former employees of the Chiba-Falek laboratory have gone on to excel both in clinical medicine and laboratory research. The list below lists former members of our laboratory as well as their current positions.

Peter Nicholls, MD 

Lab position: Research Scientist

Julio Barrera 

Lab Position: Laboratory Manager

Julia Gamache, PhD 

Lab Position: Postdoctoral Associate

Jeison Valencia 

Lab Position: Research Technician II

Suraj Upadhya

Lab Position: Student

Cordelia Hume

Lab Position: Student

Angela Wei 

Lab Position: Student

Anna Yang

Lab Position: Student

Chesney Birshing

Lab Position: Summer Student | Genome Science and Medicine

Delaney Hill

Lab Position: Summer Student | Genome Science and Medicine

Danielle Chipman

Undergraduate, Class of 2021
Major: Neuroscience

Kennedy Lofton

Undergraduate, Class of 2022 (NCCU)
Major: Pharmaceutical Sciences

Gabriella MacDougall, PhD
Postdoctoral associate

Daniel Sprague
Undergraduate, Class of 2021
Major: Biophysics

Jeffrey Gu
Undergraduate, Class of 2020
Current position: Medical scribe

Vivian Chen
Undergraduate, Class of 2020
Current position: Duke Medical School, Class of 2026

Manish Kumar
Undergraduate, Class of 2020
Current position: Consultant, Accenture

Dominic Tringali
Research Technician
Current position: Gene therapy operations specialist I, Pfizer

Young Yun
Previous position: Research Technician
Current position: Gene therapy operations specialist I, Pfizer

Lidia Tagliafierro, PhD
Previous position: Postdoctoral associate
Current position: Investigator, GSK

Ivana Premasinghe
Undergraduate, Class of 2019
Major: Biology & Spanish, Minor: Chemistry
Current position: Duke Medical School, Class of 2024

Ahlia Sriskanda
Lab Position: Research technician
Current position: Gene therapy operations specialist II, Pfizer

George Crawley, IV
Undergraduate, Class of 2020
Major: Biology
Minors: Chemistry, African and African-American Studies

Madison Zamora
Undergraduate, Class of 2018
Current Position: Dental Student, Harvard School of Dental Medicine (Class of 2023)

Kathy Ziyue Dai
Undergraduate, Class of 2018
Current Position: Medical Student, Duke University School of Medicine, Class of 2023

Omolara-Chinue Glenn
Lab position: Research technician
Current position: Premedical post-baccalaureate student, Virginia Commonwealth University

Shobana Subramanian
Lab position: Undergraduate, Class of 2017
Current position: Medical student, Yale School of Medicine

Kirsten Bonawitz
Lab position: Undergraduate researcher Class of 2017
Current position: Medical Fellow, Global Public Service Academies (GPSA), Guatemala

Haylee Bergstrom
Lab position: Undergraduate, class of 2016
Current position: UC-San Diego Post-baccalaureate Premedical Program, medical school applicant, summer 2018

Taylor Novice
Lab position: Undergraduate, Class of 2015
Current position: medical student, University of Michigan Medical School

Christina He
Lab position: Undergraduate, class of 2015
Current position: medical student, Weill Cornell Medical College

Natalie Miller
Lab position: Undergraduate, Class of 2014
Current position: medical student, Uniformed Services University of the Health Sciences (Walter Reed)

Jawara Allen
Lab position: Undergraduate, class of 2012
Current position:MD/PhD student, Johns Hopkins School of Medicine

Sunita Saith
Lab position:Undergraduate, class of 2011
Medical School: OUWB School of Medicine, class of 2016
Current position: Residency (internal medicine), University of Louisville School of Medicine, Kentucky

Jennifer Byrne
Lab position: Research technician
Current position: Oncology Remote Site Monitor, PPD® Clinical Trials

Laura Saucier
Lab position: Undergraduate, class of 2010
Current position: MD (Stanford University School of Medicine, class of 2016)