DOI: 10.5061/dryad.1vhhmgr7k
title: Data in support of: Atrophin-1 antisense oligonucleotide provides robust protection from pathology in a fully humanized DRPLA model

description: Dentatorubral-pallidoluysian atrophy (DRPLA) is a fatal neurodegenerative
 disease arising from a CAG repeat expansion in the atrophin-1 (ATN1) gene.
 Because DRPLA, like many repeat expansion disorders (REDs), arises
 predominantly from toxic gain-of-function mechanisms, we hypothesized that
 ATN1 knockdown would have therapeutic potential. To test this, we
 established the first fully humanized mouse model of a RED, in which one
 allele of mouse Atn1 is completely replaced by human ATN1, including 112
 pure CAG repeats. This novel approach to exploring RED biology provides
 significant advantages, notably the ability to test sequence-specific
 therapeutics targeting human sequences, even in introns and untranslated
 regions of pre-mRNA. We found that our model—the Atn1Q112/+
 mouse—recapitulates key features of human DRPLA, including behavioral
 alterations, reduced brain size, and aggregate accumulation. We treated
 Atn1Q112/+ mice with antisense oligonucleotides (ASOs) targeting mouse
 Atn1 (to probe for loss of function concerns), human ATN1, or a
 combination. Treatment with human, but not mouse, ATN1-targeting ASOs
 provides remarkable protection from a range of disease-related behavioral
 phenotypes and marked rescue of transcriptional dysregulation in the
 cerebellum. These results have helped motivate an ongoing human clinical
 study of ASOs targeting ATN1 for DRPLA.
description: # Data in support of: Atrophin-1 antisense oligonucleotide provides robust
 protection from pathology in a fully humanized DRPLA model Dataset DOI:
 [10.5061/dryad.1vhhmgr7k](https://doi.org/10.5061/dryad.1vhhmgr7k) ##
 Description of the data and file structure Dataset and R scripts used to
 generate all statistics and figures for the associated manuscript are
 deposited here in the .xlsx file
 'ATN1_manuscript_rProject_source_data.xlsx'. The .xlsx file
 comprises 24 separate worksheets with a leading number (e.g. 02C, 03Ac,
 etc.) which indicates where the data was used in the manuscript, along
 with a short identifying text (e.g. Cortex ATN1 Levels) which gives
 additional context about what the data corresponds to. Each worksheet and
 it's column headings are defined below. Corresponding R scripts for
 analysis are also included. R scripts pull data from the .xlsx sheet and
 make plots and/or run statistics used in the manuscript and include basic
 annotation. R script naming follows the same convention as the data, for
 example the script '02C - Cortex ATN1 Levels.R' is the script
 that plots and analyzes the data underlying Figure 02C in the manuscript.
 ### Files and variables # README: Data in support of atrophin-1 antisense
 oligonucleotide provides robust protection from pathology in a fully
 humanized DRPLA model **Descriptions** | Sheet | Column Header |
 Definition | | :------------------------------ | :------------------------
 |
 :------------------------------------------------------------------------------ | |  02C - Cortex ATN1 Levels | mouse | Individual Mouse Identification number | |  02C - Cortex ATN1 Levels | sex | Animal sex; Male (M) or female (F) | |  02C - Cortex ATN1 Levels | genotype | Mouse genotype; Wildtype (WT) or Atn1^Q112/+^ (Q112/+) | |  02C - Cortex ATN1 Levels | treatment | Treatment; Saline, human ASO (hASO), mouse ASO (mASO), or Combo (hASO and mASO) | |  02C - Cortex ATN1 Levels | fold\_change | ddCT normalized to the control genotype (Q112/+) | |  02C - Cortex ATN1 Levels | atn1\_species | ATN1/Atn1 primer used; human or mouse | | 03A - Rotarod | mouse | Individual Mouse Identification number | | 03A - Rotarod | sex | Animal sex; Male (M) or female (F) | | 03A - Rotarod | genotype | Mouse genotype; Wildtype (WT) or Atn1^Q112/+^ (Q112/+) | | 03A - Rotarod | treatment | Treatment; Saline, human ASO (hASO), mouse ASO (mASO), or Combo (hASO and mASO) | | 03A - Rotarod | RPM | Rounds per minute; 4 or 8 | | 03A - Rotarod | trial\_1 | Rotarod trial 1 in seconds | | 03A - Rotarod | trial\_2 | Rotarod trial 2 in seconds | | 03A - Rotarod | trial\_3 | Rotarod trial 3 in seconds | | 03A - Rotarod | average | Average of all 3 rotarod trials in seconds | | 03A - Rotarod | n/a | Unfinished trial | | 03B - Balance Beam | mouse | Individual Mouse Identification number | | 03B - Balance Beam | sex | Animal sex; Male (M) or female (F) | | 03B - Balance Beam | genotype | Mouse genotype; Wildtype (WT) or Atn1^Q112/+^ (Q112/+) | | 03B - Balance Beam | treatment | Treatment; Saline, human ASO (hASO), mouse ASO (mASO), or Combo (hASO and mASO) | | 03B - Balance Beam | trial\_1 | Balance beam trial 1 in seconds | | 03B - Balance Beam | trial\_2 | Balance beam trial 2 in seconds | | 03B - Balance Beam | trial\_3 | Balance beam trial 3 in seconds | | 03B - Balance Beam | average | Average of all 3 balance beam trials in seconds | | 03B - Balance Beam | n/a | Unfinished trial | | 03C - Distance Traveled in OF | mouse | Individual Mouse Identification number | | 03C - Distance Traveled in OF | sex | Animal sex; Male (M) or female (F) | | 03C - Distance Traveled in OF | genotype | Mouse genotype; Wildtype (WT) or Atn1^Q112/+^ (Q112/+) | | 03C - Distance Traveled in OF | treatment | Treatment; Saline, human ASO (hASO), mouse ASO (mASO), or Combo (hASO and mASO) | | 03C - Distance Traveled in OF | distance\_traveled | Total distance mice traveled during open field testing in centimeters | | 03D - SHIRPA Tremor Score | mouse | Individual Mouse Identification number | | 03D - SHIRPA Tremor Score | sex | Animal sex; Male (M) or female (F) | | 03D - SHIRPA Tremor Score | genotype | Mouse genotype; Wildtype (WT) or Atn1^Q112/+^ (Q112/+) | | 03D - SHIRPA Tremor Score | treatment | Treatment; Saline, human ASO (hASO), mouse ASO (mASO), or Combo (hASO and mASO) | | 03D - SHIRPA Tremor Score | tremor\_score | SHIRPA tremor score; 0-2 | | 03E - SHIRPA Total Score | mouse | Individual Mouse Identification number | | 03E - SHIRPA Total Score | sex | Animal sex; Male (M) or female (F) | | 03E - SHIRPA Total Score | genotype | Mouse genotype; Wildtype (WT) or Atn1^Q112/+^ (Q112/+) | | 03E - SHIRPA Total Score | treatment | Treatment; Saline, human ASO (hASO), mouse ASO (mASO), or Combo (hASO and mASO) | | 03E - SHIRPA Total Score | total\_score | Combined score of all SHIRPA observations | | 05A - Brain Weights | mouse | Individual Mouse Identification number | | 05A - Brain Weights | sex | Animal sex; Male (M) or female (F) | | 05A - Brain Weights | genotype | Mouse genotype; Wildtype (WT) or Atn1^Q112/+^ (Q112/+) | | 05A - Brain Weights | treatment | Treatment; Saline, human ASO (hASO), mouse ASO (mASO), or Combo (hASO and mASO) | | 05A - Brain Weights | brain\_weight | Brain weight of mice in grams | | 05B - Normalized Brain Weights | mouse | Individual Mouse Identification number | | 05B - Normalized Brain Weights | sex | Animal sex; Male (M) or female (F) | | 05B - Normalized Brain Weights | genotype | Mouse genotype; Wildtype (WT) or Atn1^Q112/+^ (Q112/+) | | 05B - Normalized Brain Weights | treatment | Treatment; Saline, human ASO (hASO), mouse ASO (mASO), or Combo (hASO and mASO) | | 05B - Normalized Brain Weights | normalized\_brain\_weight | Brain weight normalized to mouse body weight in grams | | S5B - Pilot Midbrain ATN1 | mouse | Individual Mouse Identification number | | S5B - Pilot Midbrain ATN1 | sex | Animal sex; Male (M) or female (F) | | S5B - Pilot Midbrain ATN1 | genotype | Mouse genotype; Wildtype (WT) or Atn1^Q112/+^ (Q112/+) | | S5B - Pilot Midbrain ATN1 | treatment\_time | Timepoint of treatment; Late, None, Early, or Early\_Late | | S5B - Pilot Midbrain ATN1 | treatment\_type | Treatment; Saline or human ASO (hASO) | | S5B - Pilot Midbrain ATN1 | fold\_change | ddCT normalized to the control genotype (Q112/+) | | S6 - Cerebellum ATN1 Levels | mouse | Individual Mouse Identification number | | S6 - Cerebellum ATN1 Levels | sex | Animal sex; Male (M) or female (F) | | S6 - Cerebellum ATN1 Levels | genotype | Mouse genotype; Wildtype (WT) or Atn1^Q112/+^ (Q112/+) | | S6 - Cerebellum ATN1 Levels | treatment | Treatment; Saline, human ASO (hASO), mouse ASO (mASO), or Combo (hASO and mASO) | | S6 - Cerebellum ATN1 Levels | fold\_change | ddCT normalized to the control genotype (Q112/+) | | S6 - Cerebellum ATN1 Levels | atn1\_species | ATN1/Atn1 primer used; human or mouse | | S7A - All Body Weights | mouse | Individual Mouse Identification number | | S7A - All Body Weights | sex | Animal sex; Male (M) or female (F) | | S7A - All Body Weights | genotype | Mouse genotype; Wildtype (WT) or Atn1^Q112/+^ (Q112/+) | | S7A - All Body Weights | treatment | Treatment; Saline, human ASO (hASO), mouse ASO (mASO), or Combo (hASO and mASO) | | S7A - All Body Weights | week\_5 | Body weight at 5 weeks of age in grams | | S7A - All Body Weights | week\_6 | Body weight at 6 weeks of age in grams | | S7A - All Body Weights | week\_7 | Body weight at 7 weeks of age in grams | | S7A - All Body Weights | week\_8 | Body weight at 8 weeks of age in grams | | S7A - All Body Weights | week\_9 | Body weight at 9 weeks of age in grams | | S7A - All Body Weights | weight\_mean | Mean of all body weights in grams | | S7A - All Body Weights | n/a | 
 
 | | S7B - Sal, hASO, Body Weights | mouse | Individual Mouse
 Identification number | | S7B - Sal, hASO, Body Weights | sex | Animal
 sex; Male (M) or female (F) | | S7B - Sal, hASO, Body Weights | genotype |
 Mouse genotype; Wildtype (WT) or Atn1^Q112/+^ (Q112/+) | | S7B - Sal,
 hASO, Body Weights | treatment | Treatment; Saline or human ASO (hASO) | |
 S7B - Sal, hASO, Body Weights | week\_5 | Body weight at 5 weeks of age in
 grams | | S7B - Sal, hASO, Body Weights | week\_6 | Body weight at 6 weeks
 of age in grams | | S7B - Sal, hASO, Body Weights | week\_7 | Body weight
 at 7 weeks of age in grams | | S7B - Sal, hASO, Body Weights | week\_8 |
 Body weight at 8 weeks of age in grams | | S7B - Sal, hASO, Body Weights |
 week\_9 | Body weight at 9 weeks of age in grams | | S7B - Sal, hASO, Body
 Weights | weight\_mean | Mean of all body weights in grams | | S7C - Sal,
 mASO, Body Weights | mouse | Individual Mouse Identification number | |
 S7C - Sal, mASO, Body Weights | sex | Animal sex; Male (M) or female (F) |
 | S7C - Sal, mASO, Body Weights | genotype | Mouse genotype; Wildtype (WT)
 or Atn1^Q112/+^ (Q112/+) | | S7C - Sal, mASO, Body Weights | treatment |
 Treatment; Saline or mouse ASO (mASO) | | S7C - Sal, mASO, Body Weights |
 week\_5 | Body weight at 5 weeks of age in grams | | S7C - Sal, mASO, Body
 Weights | week\_6 | Body weight at 6 weeks of age in grams | | S7C - Sal,
 mASO, Body Weights | week\_7 | Body weight at 7 weeks of age in grams | |
 S7C - Sal, mASO, Body Weights | week\_8 | Body weight at 8 weeks of age in
 grams | | S7C - Sal, mASO, Body Weights | week\_9 | Body weight at 9 weeks
 of age in grams | | S7C - Sal, mASO, Body Weights | weight\_mean | Mean of
 all body weights in grams | | S8A - SHIRPA Gait Score | mouse | Individual
 Mouse Identification number | | S8A - SHIRPA Gait Score | sex | Animal
 sex; Male (M) or female (F) | | S8A - SHIRPA Gait Score | genotype | Mouse
 genotype; Wildtype (WT) or Atn1^Q112/+^ (Q112/+) | | S8A - SHIRPA Gait
 Score | treatment | Treatment; Saline, human ASO (hASO), mouse ASO (mASO),
 or Combo (hASO and mASO) | | S8A - SHIRPA Gait Score | gait\_score |
 SHIRPA gait score; 0-3 | | S8B - SHIRPA Lethargy Score | mouse |
 Individual Mouse Identification number | | S8B - SHIRPA Lethargy Score |
 sex | Animal sex; Male (M) or female (F) | | S8B - SHIRPA Lethargy Score |
 genotype | Mouse genotype; Wildtype (WT) or Atn1^Q112/+^ (Q112/+) | | S8B
 - SHIRPA Lethargy Score | treatment | Treatment; Saline, human ASO (hASO),
 mouse ASO (mASO), or Combo (hASO and mASO) | | S8B - SHIRPA Lethargy Score
 | lethargy\_score | SHIRPA lethargy score; 0-4 | | S8C - SHIRPA Hindlimb
 Grasping | mouse | Individual Mouse Identification number | | S8C - SHIRPA
 Hindlimb Grasping | sex | Animal sex; Male (M) or female (F) | | S8C -
 SHIRPA Hindlimb Grasping | genotype | Mouse genotype; Wildtype (WT)
 or Atn1^Q112/+^ (Q112/+) | | S8C - SHIRPA Hindlimb Grasping | treatment |
 Treatment; Saline, human ASO (hASO), mouse ASO (mASO), or Combo (hASO and
 mASO) | | S8C - SHIRPA Hindlimb Grasping | hindlimb\_grasping\_score |
 SHIRPA hindlimb grasping score; 0-3 | | S8D - SHIRPA Forelimb Grasping |
 mouse | Individual Mouse Identification number | | S8D - SHIRPA Forelimb
 Grasping | sex | Animal sex; Male (M) or female (F) | | S8D - SHIRPA
 Forelimb Grasping | genotype | Mouse genotype; Wildtype (WT)
 or Atn1^Q112/+^ (Q112/+) | | S8D - SHIRPA Forelimb Grasping | treatment |
 Treatment; Saline, human ASO (hASO), mouse ASO (mASO), or Combo (hASO and
 mASO) | | S8D - SHIRPA Forelimb Grasping | forelimb\_grasping\_score |
 SHIRPA forelimb grasping score; 0-2 | | S8E - SHIRPA Touch Escape Score |
 mouse | Individual Mouse Identification number | | S8E - SHIRPA Touch
 Escape Score | sex | Animal sex; Male (M) or female (F) | | S8E - SHIRPA
 Touch Escape Score | genotype | Mouse genotype; Wildtype (WT)
 or Atn1^Q112/+^ (Q112/+) | | S8E - SHIRPA Touch Escape Score | treatment |
 Treatment; Saline, human ASO (hASO), mouse ASO (mASO), or Combo (hASO and
 mASO) | | S8E - SHIRPA Touch Escape Score | touch\_escape\_score | SHIRPA
 touch escape score; 0-3 | | S8F - SHIRPA Respiration Rate | mouse |
 Individual Mouse Identification number | | S8F - SHIRPA Respiration Rate |
 sex | Animal sex; Male (M) or female (F) | | S8F - SHIRPA Respiration Rate
 | genotype | Mouse genotype; Wildtype (WT) or Atn1^Q112/+^ (Q112/+) | |
 S8F - SHIRPA Respiration Rate | treatment | Treatment; Saline, human ASO
 (hASO), mouse ASO (mASO), or Combo (hASO and mASO) | | S8F - SHIRPA
 Respiration Rate | respiration\_rate\_score | SHIRPA respiration rate
 score; 0-3 | | S9A - SHIRPA Pelvic Elevation | mouse | Individual Mouse
 Identification number | | S9A - SHIRPA Pelvic Elevation | sex | Animal
 sex; Male (M) or female (F) | | S9A - SHIRPA Pelvic Elevation | genotype |
 Mouse genotype; Wildtype (WT) or Atn1^Q112/+^ (Q112/+) | | S9A - SHIRPA
 Pelvic Elevation | treatment | Treatment; Saline, human ASO (hASO), mouse
 ASO (mASO), or Combo (hASO and mASO) | | S9A - SHIRPA Pelvic Elevation |
 pelvic\_elevation\_score | SHIRPA pelvic elevation score; 0-3 | | S9B -
 SHIRPA Piloerection Score | mouse | Individual Mouse Identification number
 | | S9B - SHIRPA Piloerection Score | sex | Animal sex; Male (M) or female
 (F) | | S9B - SHIRPA Piloerection Score | genotype | Mouse
 genotype; Wildtype (WT) or Atn1^Q112/+^ (Q112/+) | | S9B - SHIRPA
 Piloerection Score | treatment | Treatment; Saline, human ASO (hASO),
 mouse ASO (mASO), or Combo (hASO and mASO) | | S9B - SHIRPA Piloerection
 Score | piloerection\_score | SHIRPA piloerection score; 0-1 | | S9C -
 SHIRPA Tail Elevation | mouse | Individual Mouse Identification number | |
 S9C - SHIRPA Tail Elevation | sex | Animal sex; Male (M) or female (F) | |
 S9C - SHIRPA Tail Elevation | genotype | Mouse genotype; Wildtype (WT)
 or Atn1^Q112/+^ (Q112/+) | | S9C - SHIRPA Tail Elevation | treatment |
 Treatment; Saline, human ASO (hASO), mouse ASO (mASO), or Combo (hASO and
 mASO) | | S9C - SHIRPA Tail Elevation | tail\_elevation\_score | SHIRPA
 tail elevation score; 0-2 | | S9D - Freezing Percentage in OF | mouse |
 Individual Mouse Identification number | | S9D - Freezing Percentage in OF
 | sex | Animal sex; Male (M) or female (F) | | S9D - Freezing Percentage
 in OF | genotype | Mouse genotype; Wildtype (WT) or Atn1^Q112/+^ (Q112/+)
 | | S9D - Freezing Percentage in OF | treatment | Treatment; Saline, human
 ASO (hASO), mouse ASO (mASO), or Combo (hASO and mASO) | | S9D - Freezing
 Percentage in OF | freezing\_percentage | Freezing percentage in open
 field testing | | S11 - Terminal NEFL Levels | mouse | Individual Mouse
 Identification number | | S11 - Terminal NEFL Levels | sex | Animal sex;
 Male (M) or female (F) | | S11 - Terminal NEFL Levels | genotype | Mouse
 genotype; Wildtype (WT) or Atn1^Q112/+^ (Q112/+) | | S11 - Terminal NEFL
 Levels | treatment | Treatment; Saline, human ASO (hASO), mouse ASO
 (mASO), or Combo (hASO and mASO) | | S11 - Terminal NEFL Levels |
 raw\_concentration | Raw NEFL concentration in pg/mL | | S11 - Terminal
 NEFL Levels | concentration\_x10 | Raw NEFL concentration multiplied by
 dilution factor (10) in pg/mL | ## Code/software #### Usage Notes R is
 required to open all .R scripts. Scripts were generated using R 4.3.2.
 Microsoft Excel can be used to view
 *ATN1_manuscript_rProject_source_data.xlsx*