# Development of TDP-43 nuclear targeting aptamers for ALS/FTD

> **NIH NIH R03** · JOHNS HOPKINS UNIVERSITY · 2022 · $81,875

## Abstract

Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are closely-related, fatal
neurodegenerative diseases with considerable genetic and pathologic overlap. Postmortem analysis of more
than 97% of ALS cases and nearly half of FTD cases demonstrates nuclear clearance and cytoplasmic
aggregation of TDP-43, a primarily nuclear DNA- and RNA-binding protein that regulates pre-mRNA splicing.
Moreover, abundant evidence shows that the loss of TDP-43 nuclear function drives the evolution of many
aspects of ALS/FTD pathogenesis. This proposal seeks to build on recent data from our laboratory showing that
RNA critically tethers TDP-43 within the nucleus and limits its passive nuclear export. We propose to design a
novel RNA-based strategy to oppose TDP-43 nuclear export, guided by two observations: 1) TDP-43 nuclear
residence depends on its binding to GU-rich nuclear RNAs, and 2) small GU-rich RNA oligomers transfected into
live cells efficiently target and modulate the nuclear/cytoplasmic shuttling of TDP-43. Here, we will develop
bivalent RNA oligomers, termed TDP-43 nuclear targeting aptamers (TNTAs), to bind and retain the pool of free
TDP-43 that would otherwise diffuse out of the nucleus. The TNTA will consist of a reversible GU-rich TDP-43
targeting sequence (TTS), a linker, and a nucleus-targeting sequence (NTS), to anchor the TNTA-TDP-43
complex within stable nuclear ribonucleoprotein assemblies. Using the (GU)6 sequence as a starting point,
studies in aim 1 will further optimize the TTS motif, using the TDP-43 nuclear displacement assay as a readout
for successful TTS-TDP-43 interaction. Cells will be transfected by synthetic GU-rich RNAs (or poly-A, as a
negative control), and the nuclear exit of endogenous TDP-43 will be monitored by immunofluorescence with
automated confocal high-content microscopy. The direct TTS-TDP-43 interaction, its selectivity towards TDP-
43, and reversibility over time will then be evaluated to identify the optimal TTS sequence. In the second aim,
the nuclear retention sequences of several classes of endogenous nuclear RNAs will be tested to identify optimal
NTS sequences, that, when combined with the TTS can promote TDP-43 nuclear localization. Nuclear tethering
of TNTAs via the bacteriophage MS2-loop RNA-MCP system will be utilized as a positive control. TNTAs
combining the endogenous validated NTS linked to the GU-rich TTS will then be tested for activity in preventing
TDP-43 exit. Finally, the selectivity and reversibility of the TNTAs towards TDP-43 will be determined, and cryptic
exon incorporation will be evaluated to ensure no interference with TDP-43 nuclear function. Together, these
studies will identify and optimize a new tool to promote TDP-43 nuclear localization, to enable further therapy
development and improve our understanding of the regulation of TDP-43 nuclear/cytoplasmic shuttling.

## Key facts

- **NIH application ID:** 10427644
- **Project number:** 1R03NS127011-01
- **Recipient organization:** JOHNS HOPKINS UNIVERSITY
- **Principal Investigator:** Lindsey Renae Hayes
- **Activity code:** R03 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $81,875
- **Award type:** 1
- **Project period:** 2022-02-01 → 2024-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10427644

## Citation

> US National Institutes of Health, RePORTER application 10427644, Development of TDP-43 nuclear targeting aptamers for ALS/FTD (1R03NS127011-01). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10427644. Licensed CC0.

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