Research
We use powerful gene perturbation tools — such as CRISPR, RNAi and small molecule screening — to investigate how genes function, contribute to disease and can be targeted to develop better treatments.
Functional Genomic Screening in Complex Cell Models
Complex cell models, such as co-culture systems, primary cells, spheroids, organoids, and iPSC-differentiated cells, better replicate the cellular interactions, spatial organization, and microenvironment of human tissues. These models provide more physiologically relevant insights into cell behavior, drug responses, and disease mechanisms, making them essential tools to advance research in health and disease.
However, applying functional genomic tools like CRISPR and RNAi in these complex systems presents several challenges. Efficient delivery of genetic material into dense or structured tissues is difficult. The inherent heterogeneity of spheroids, organoids, and iPSC-derived neuronal cells can complicate data interpretation. Moreover, the cellular interactions in these models can lead to variable or unexpected biological responses. Overcoming these obstacles requires continuous innovation in both delivery technologies and analytical methods to ensure reliable and reproducible outcomes.
At FGL, we develop customized protocols for complex cell models on a project-specific basis. With the NCATS 3-D Bioprinting Group, led by Marc Ferrer, Ph.D., we have established a high-throughput, image-based screening workflow using spheroids in 1536-well plates. Our efforts include both arrayed and pooled CRISPR screening in spheroids, as well as using CRISPR technology to 3D-bioprint tissues and iPSC-derived neurons.
High-throughput small molecule screening to identify inhibitors of unesterified cholesterol accumulation in NPC1-deficient neurons
High-throughput small molecule screening to identify inhibitors of unesterified cholesterol accumulation in NPC1-deficient neurons
- Confocal image of human cortical neuron stained for nuclei (blue) and MAP2 (green), a neuronal marker.
- Accumulation of unesterified cholesterol in NPC-deficient i3Neurons, visualized using perfringolysin O (PFO) staining.
Images were acquired using the Opera Phenix high-content imaging system in 384-well format. This project is conducted in collaboration with Dr. Forbes Porter (NICHD).
High-throughput small molecule screening to identify inhibitors of unesterified cholesterol accumulation in NPC1-deficient neurons
- Confocal image of human cortical neuron stained for nuclei (blue) and MAP2 (green), a neuronal marker.
- Accumulation of unesterified cholesterol in NPC-deficient i3Neurons, visualized using perfringolysin O (PFO) staining.
Images were acquired using the Opera Phenix high-content imaging system in 384-well format. This project is conducted in collaboration with Dr. Forbes Porter (NICHD).
Therapeutics for Rare Diseases
Developing therapies for rare diseases presents significant preclinical challenges that deter large pharmaceutical companies from pursuing these critical areas of research. Despite being classified as “rare,” these diseases collectively impact millions of people worldwide, yet they remain underfunded and underexplored. The private sector generally prioritizes broader market opportunities. The high cost of research and lower profit makes rare disease projects less attractive. As a result, many rare diseases lack effective therapies, leaving patients with few options.
The Functional Genomics Laboratory is committed to advancing research in rare diseases. We identify novel therapeutic targets and develop treatments using cutting-edge functional genomics technologies. Our goal is to uncover key insights that can lead to the development of targeted therapies, improving patient outcomes and expanding treatment options for those affected by these conditions.
Our research focuses on diseases such as sickle cell disease, a genetic blood disorder characterized by abnormal hemoglobin leading to chronic pain and organ damage, and Niemann-Pick Disease Type C1 (NPC1), a rare neurodegenerative disorder caused by defects in how cholesterol acts within cells. Studying these and other conditions helps us better understand disease mechanisms and identify promising therapeutic targets.
FGL is leading several rare disease research initiatives and collaborating with the Bespoke Gene Therapy Consortium (BGTC; https://ncats.nih.gov/research/research-activities/BGTC) to improve adeno-associated virus (AAV)-based gene therapies. Through these innovative efforts, we aim to make meaningful strides toward life-changing solutions for people with rare diseases.