Biophysical and Therapeutic Approaches to Neurodegenerative Disease: Insights From Lysosomal and RNA-Binding Protein Systems

Neurodegenerative diseases arise from progressive failures in the cellular systems that maintain protein and RNA homeostasis, yet how distinct molecular defects contribute to the disease pathogenesis is incompletely understood. This dissertation investigates two complementary arms of this network: lysosomal quality control mediated by tripeptidyl peptidase 1 (TPP1), and RNA‑regulated proteostasis governed by the RNA‑binding protein TDP‑43. First, I reviewed general mechanisms of proteostasis disruption, highlighting how lysosomal storage disorders and RNA‑binding proteinopathies exemplify convergent routes to neurodegeneration and motivate a cross‑disease, mechanistically grounded therapeutic perspective. I also examined the cellular fate of TPP1 from its synthesis in the endoplasmic reticulum to its delivery and maturation in lysosomes, highlighting specific steps in this pathway that can be pharmacologically targeted to develop chemical modulators capable of enhancing lysosomal TPP1 activity in disease models.Building on this framework, I developed a protein structure‑based drug discovery pipeline for CLN2 Batten disease centered on TPP1. Using structural and biophysical analyses, including comparison of cryo‑electron microscopy reconstructions with existing crystal structures, alongside enzyme kinetics and cell‑based assays, I identified and characterized small‑molecule modulators with the potential to stabilize or enhance TPP1 function in the lysosomal environment. In parallel, I examined the biophysical behavior of TDP‑43, focusing on how its N‑terminal domain and RNA recognition motifs coordinate oligomerization, RNA binding, and liquid–liquid phase separation. Through in vitro and cellular studies, I delineate conditions under which RNA‑dependent condensates remain dynamic and functional versus transition toward more stable assemblies associated with ALS‑linked pathology. By integrating insights from these lysosomal and RNA‑binding protein systems, the dissertation reveals how discrete perturbations, defective lysosomal degradation, and misregulated RNA‑protein condensates contribute to neurodegeneration and proteinopathy. Together, these findings advance a unified view of neurodegeneration in which biophysical and structural approaches not only clarify disease mechanisms but also guide rational, target‑centric strategies for therapeutic intervention across mechanistically diverse disorders.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

doctoral

Discipline thesis:degree_discipline

Graduate College

Grantor dc:publisher

The University of Arizona.

Year dc:date.issued

2026

Author dc:creator

• Jena, Lipsa

Advisors dc:contributor.advisor

• Tomasiak, Thomas M.
• Khanna, May

Committee members dc:contributor.committeemember

• Schwartz, Jacob C.
• Montfort, William R.
• Weimer, Jill

Statement dc:rights

• Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction, presentation (such as public display or performance) of protected items is prohibited except with permission of the author.

Licence dc:rights.uri

• http://rightsstatements.org/vocab/InC/1.0/

Language dc:language.iso

en

Handle dc:identifier.uri

http://hdl.handle.net/10150/680192

OAI identifier oai:identifier

oai:repository.arizona.edu:10150/680192