Detecting human iPSC-derived neuron effect in chromatin dynamics and genetic variants using in situ Hi-C assay

I am currently a freshman attending FCLC and double majoring in Integrative Neuroscience and English on the pre-medical track. On Thursdays, I volunteer in the Surgical Acute Care Unit at NYU Tisch Hospital. During one of my shifts, I had a conversation with a physician-scientist who introduced me to the world of research. Since that conversation, I have pursued research. I am interested in hands-on work and an environment that allows me to apply the knowledge I gained from the science courses I have taken. Just two months ago, I reached out and received the chance to assist in a neuroscience lab at the Icahn Medical Institute at Mount Sinai.

I find the brain intriguing, especially the way it enables humans to think, act, memorize, feel, and experience. Currently, my colleagues and I are using a human induced pluripotent stem cell model to study human proneness to psychiatric disease, and this model allows us to test variants in human cells. Variants are differences that differentiate every person’s genome by making it unique. One example of the variants tested is copy number variants (CNVs), which are repeated genome sections dispersed throughout the human genome. The hiPSC model helps my colleagues and I better understand complex gene interactions and look at the types of variants that affect human cells. In the lab, we are taking skin cells that are donated by patients with Schizophrenia and turning them into human induced pluripotent stem cells (iPSC) using viruses. Once we have human iPSC-derived neurons, which are derived from Schizophrenic patients with neuropsychiatric disease, the neurons are grouped into cultures, fed growth medium, and tested for genetic effects, particularly changes in gene expression that are key to being able to memorize and think, and drugs such as heroin and marijuana.

Additionally, human induced pluripotent stem cells (hiPSC) and cells sorted postmortem are solidified to see how psychosis risk-loci disrupts chromatin dynamics. Locus, or loci, are the locations of specific genes on a chromosome. Chromatin dynamics change the amount of DNA that is available for proteins that recognize specific DNA sequences called regulatory factors. Cells sorted post mortem refer to neural cells acquired by a medical examination of the body; in this case, the brain. I assist by taking dopaminergic neurons and Gamma-aminobutyric acid (GABAergic) neurons and carrying out an in situ Hi-C assay. The in situ Hi-C assay is a chromosome conformation capture that characterizes genome-wide chromatin organization. The chromosome conformation capture can detect the way chromatin is organized inside a cell, and it applies to postmortem tissue because it depicts preserved brain tissue after death. In the in situ, also known as in position, Hi-C assay, a bead mill homogenizer thoroughly mixes the bead-bound DNA by moving beads at high speed to break up tissues and disrupt cells, and a magnet separates the bead-bound DNA to obtain the “good” DNA. 

I was able to incorporate knowledge gained from a psychology course I took last semester, where I learned about mental disorders such as Bipolar disorder and Schizophrenia, into the current research I assist in. Although I initially pursued research as a means of getting my feet wet, joining a lab has made me realize the importance of neuroscience research. Despite starting eager and clueless, I learned and am still currently learning the essential techniques required of research and, more importantly, am gaining experience that requires me to read papers, brainstorm, and fix failures. 

By: Sophie Chen, FCLC ‘23

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