Evidence map›Paper›PMID 40258535›Full record

ArticleNeurobiology of disease2025

Intersecting impact of CAG repeat and huntingtin knockout in stem cell-derived cortical neurons.

Jennifer T Stocksdale, Matthew J Leventhal, Stephanie Lam, Yu-Xin Xu, Yang Oliver Wang, Keona Q Wang, Reuben Thomas, Zohreh Faghihmonzavi, Yogindra Raghav, Charlene Smith and 21 more

Abstract read
In one paragraph

Article in Neurobiology of disease, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

31 authors.

Jennifer T StocksdaleDepartment of Neurobiology and Behavior, UC Irvine, Irvine, CA 92677, USA.
Matthew J LeventhalMIT PhD Program in Computational and Systems Biology, Cambridge, MA 02139, USA; MIT Department of Biological Engineering, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Stephanie LamCenter for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA.
Yu-Xin XuDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Yang Oliver WangAdvanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
Keona Q WangDepartment of Neurobiology and Behavior, UC Irvine, Irvine, CA 92677, USA.
Reuben ThomasInstitute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA.
Zohreh FaghihmonzaviCenter for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA.
Yogindra RaghavDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Charlene SmithDepartment of Psychiatry and Human Behavior, UC Irvine, Irvine, CA 92697, USA.
Jie WuDepartment of Biological Chemistry, UC Irvine, Irvine, CA 92697, USA.
Ricardo MiramontesInstitute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA.
Kanchan SardaCenter for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA.
Heather JohnstonCenter for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA.
Min-Gyoung ShinInstitute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA.
Terry HuangCenter for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA.
Mikelle FosterCenter for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA.
Mariya BarchCenter for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA.
Naufa AmiraniCenter for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA.
Chris PaizCenter for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA.
Lindsay EasterCenter for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA.
Erse DuderstadtCenter for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA.
Vineet VaibhavAdvanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
Niveda SundararamanAdvanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
Dan P FelsenfeldCHDI Management, Inc, New York, NY 10001, USA.
Thomas F VogtCHDI Management, Inc, New York, NY 10001, USA.
Jennifer Van EykAdvanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
Steve FinkbeinerInstitute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA; Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA; Taube/Koret Center for Neurodegenerative Disease Research, Gladstone Institutes, San Francisco, CA 94158, USA.
Julia A KayeCenter for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA 94158, USA; Taube/Koret Center for Neurodegenerative Disease Research, Gladstone Institutes, San Francisco, CA 94158, USA.
Ernest FraenkelMIT PhD Program in Computational and Systems Biology, Cambridge, MA 02139, USA; MIT Department of Biological Engineering, Cambridge, MA 02139, USA.
Leslie M ThompsonDepartment of Neurobiology and Behavior, UC Irvine, Irvine, CA 92677, USA; Department of Psychiatry and Human Behavior, UC Irvine, Irvine, CA 92697, USA; Department of Biological Chemistry, UC Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA 92697, USA. Electronic address: lmthomps@uci.edu.

Funding

Univ.of Calif., Irvine Cancer Center Support GrantP30CA062203 · NCI · UNIVERSITY OF CALIFORNIA-IRVINE · PI Melanie Funes · 1994 to 2026
$57.9M
Molecular Mechanisms of Pathogenesis in Huntington’s diseaseR35NS116872 · NINDS · UNIVERSITY OF CALIFORNIA-IRVINE · PI Leslie Michels Thompson · 2020 to 2026
$8.5M
Epigenetic Pathology and Therapy in Huntington's DiseaseR01NS089076 · NINDS · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI FRAENKEL, ERNEST, HOUSMAN, DAVID · 2015 to 2024
$4.9M
Graduate Training in Computational and Systems BiologyT32GM087237 · NIGMS · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI BURGE, CHRISTOPHER B · 2009 to 2023
$4.6M
Rare Variant Whole Genome Analysis and iPSC Validation of Putative Genetic Modifiers of Huntington DiseaseR37NS101996 · NINDS · J. DAVID GLADSTONE INSTITUTES · PI FINKBEINER, STEVEN M · 2017 to 2023
$4.4M
Training Program in Stem Cell Translational Medicine for Neurological DisordersT32NS082174 · NINDS · UNIVERSITY OF CALIFORNIA-IRVINE · PI PETER John DONOVAN, Leslie Michels Thompson · 2013 to 2026
$3.3M
Neuroimmunology Training Program at the University of California, IrvineT32NS121727 · NINDS · UNIVERSITY OF CALIFORNIA-IRVINE · PI Kim Green, Thomas E Lane · 2022 to 2026
$854k
NCI NIH HHS P30 CA062203NIGMS NIH HHS T32 GM087237NINDS NIH HHS R01 NS089076NINDS NIH HHS R35 NS116872NINDS NIH HHS R37 NS101996NINDS NIH HHS T32 NS082174NINDS NIH HHS T32 NS121727
6 · The paper itself

Abstract

Huntington's Disease (HD) is caused by a CAG repeat expansion in the gene encoding huntingtin (HTT). While normal HTT function appears impacted by the mutation, the specific pathways unique to CAG repeat expansion versus loss of normal function are unclear. To understand the impact of the CAG repeat expansion, we evaluated biological signatures of HTT knockout (HTT KO) versus those that occur from the CAG repeat expansion by applying multi-omics, live cell imaging, survival analysis and a novel feature-based pipeline to study cortical neurons (eCNs) derived from an isogenic human embryonic stem cell series (RUES2). HTT KO and the CAG repeat expansion influence developmental trajectories of eCNs, with opposing effects on growth. Network analyses of differentially expressed genes and proteins associated with enriched epigenetic motifs identified subnetworks common to CAG repeat expansion and HTT KO that include neuronal differentiation, cell cycle regulation, and mechanisms related to transcriptional repression, and may represent gain-of-function mechanisms that cannot be explained by HTT loss of function alone. A combination of dominant and loss-of-function mechanisms are likely involved in the aberrant neurodevelopmental and neurodegenerative features of HD that can help inform therapeutic strategies.

Indexed as

Cerebral CortexHuntingtin ProteinNeuronsTrinucleotide Repeat ExpansionCell DifferentiationGene Knockout TechniquesHumansHuntington DiseaseHTT protein, humanHuntingtin ProteinEmbryonic stem cellsFeaturesHuntington's diseaseMachine learningMulti-omicsNetwork analysisRobotic microscopyRUES2

Identifiers

PMID40258535
PMCPMC12668206

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.