Cell-type-specific dysregulation and genetic control of alternative polyadenylation in neurodegeneration

PROJECT SUMMARY/ABSTRACT
Alternative polyadenylation (APA) is the fundamental mechanism for 3’ UTR choice during mRNA maturation,
directly affecting mRNA localization, translation, and stability. Proper control of 3’UTR choice is crucial in the
brain, especially for precise localization of stable mRNAs in highly structured and compartmentalized neurons.
mRNA metabolism and processing is dysregulated in both Alzheimers’ disease (AD) and Parkinson’s disease
(PD). mRNA processing is altered by alpha-synuclein and cell-type-specific 3’UTR choice is critical for the
proper function of key neurodegenerative genes. Therefore, there is a critical need to understand APA in
neurodegenerative disease. In addition, genetic variants controlling 3’UTR choice may explain specific disease
risk loci that are not explained by other molecular quantitative trait loci (QTLs), providing mechanisms for
disease risk. As the immediate molecular effects of 3’UTRs are encoded through its sequence, there is also an
important opportunity to determine and potentially modulate the molecular cascade downstream of variants
regulating 3’UTR choice in disease. My objective is to determine the role of APA in neurodegenerative disease
and in disease risk. My overall goal is to close the gap in mapping altered molecular processes in
neurodegenerative disease, map genetic risk for disease onto mRNA molecular phenotypes, and understand
the roles of the downstream mechanisms of 3’UTR choice in neurodegenerative disease.
I will repurpose 3’-biased single-nucleus RNA-seq from over 350 post-mortem human brain samples to
map APA at the single-cell level in neurodegenerative diseases. I will develop a method for identifying
differential APA, determine disease-specific and shared changes across cell types in AD and PD, and predict
regulators of APA choice in health and in disease. To investigate the genetic control of 3’UTR choice, I will
identify both 3’UTR QTLs (3’aQTLs) and expression QTLs at the single-cell level. I will determine the extent to
which 3’aQTLs overlap with other molecular QTLs and identify neurodegenerative disease risk loci acting
through 3’aQTLs. I will extend this work in my independent phase to understand how the immediate molecular
consequences of 3’UTR choice impact neurodegenerative diseases and disease risk.
I will work with my mentor Dr. Shamil Sunyaev; my co-mentors, Dr. Vikram Khurana and Dr. Rudolph
Tanzi; and my technical support and advisory committee, Dr. Evan Macosko, Dr. David Bennett, and Dr. Chris
Cassa to carry out my proposed research and training plan. I will gain experience in complex disease genetics,
statistical genetics, and variant effect prediction. I will audit relevant courses in my training period to bridge the
gap in my training on neurodegenerative diseases and genetics. I will receive additional mentoring from Dr.
Vikram Khurana on PD biology, genetics, and mRNA processing. I will also receive mentoring and technical
support from Dr. Rudolph Tanzi and Dr. David Bennett on neuropathology and AD biology and genetics.

Grant Number: 1K99AG095208-01
NIH Institute/Center: NIH
Principal Investigator: Carles Boix