Biology subjects

Carroll, J. B.

Publications and source records attributed to Carroll, J. B..

17 recordsLinked to original sources

bioRxiv2026

VO659, a CAG repeat-targeting antisense oligonucleotide, lowers multiple neurotoxic mutant huntingtin proteins in Huntington's disease

Huntington's disease (HD) is caused by a CAG repeat expansion in the huntingtin (HTT) gene, encoding an elongated polyglutamine stretch in the corresponding mutant HTT (mHTT) protein. HD pathogenesis is driven by multiple neurotoxic mHTT protein species, including HTT1a and repeat-associated non-AUG translation (RAN) proteins, which increase in expression as mutant CAG repeats lengthen due to somatic expansion. VO659 is an investigational CAG repeat-targeting antisense oligonucleotide (ASO) that lowers mHTT protein levels by blocking translation. Here, we show that VO659 allele-preferentially lowers levels of multiple neurotoxic mHTT protein species in a CAG repeat length-dependent manner, relatively sparing wild-type HTT, while becoming more efficacious as somatic expansion occurs. VO659 reduced HTT1a mRNA levels in HD fibroblasts with an ultra-long CAG repeat, blocked the translation of HTT1a and polyalanine-containing RAN proteins derived from HTT exon 1 overexpression constructs, and displayed a long tissue half-life in mouse brain, supporting an infrequent dosing regimen. A first-in-human, open-label phase 1/2a clinical trial (NCT05822908) is currently ongoing in HD patients. VO659's unique CAG repeat-dependent and allele-preferential mechanism of action holds promise for its therapeutic effect in HD patients by targeting multiple core neurotoxic proteins derived from (somatically) expanded mHTT CAG repeats, while sparing wild-type HTT expression.

neuroscience↗

bioRxiv2026

Hepatic huntingtin loss drives an acute phase response and liver injury in multiple mouse models

Multiple therapeutic strategies are being developed to slow Huntingtons disease (HD) progression through targeted reduction of huntingtin (HTT) protein or mRNA. Despite HTTs discovery over 30 years ago, its cellular functions remain incompletely understood, and the long-term consequences of HTT-lowering therapies remain unclear. We previously demonstrated that hepatic HTT loss in mice disrupts hepatocyte zonation and metabolism. Here, we investigate the physiological consequences of hepatic Htt loss. Across multiple models of Htt loss--including ubiquitous and hepatocyte-specific genetic knockouts and a therapeutically relevant Htt-targeting siRNA--there was elevated expression of IL-6/STAT3-driven acute phase response genes. Single-nucleus RNA sequencing reveals a zonal pattern of hepatocyte stress, most highly upregulated in pericentral hepatocytes, and identifies a distinct pericentral cluster of stressed hepatocytes that was enriched [~]9.6-fold following Htt knockout. Histological examination reveals that Htt loss results in increased hepatic pathology, including hepatic intranuclear inclusions, apoptosis, and necrosis, as well as prevalence of granulomas. Transcriptomic analysis reveals significant upregulation of metallothionein genes following Htt loss, as confirmed by elevated plasma metallothionein-1 (MT1) levels in knockout mice. These findings underscore important safety considerations for HTT-lowering therapies and suggest candidate biomarkers for monitoring hepatic off-target effects in clinical trials.

molecular biology↗

bioRxiv2026

scVIP: personalized modeling of single-cell transcriptomes for developmental and disease phenotypes

Single-cell transcriptomics resolves cellular heterogeneity within individuals, but connecting molecular states to individual-level phenotypes requires frameworks that explicitly bridge these scales. We present scVIP, a generative model that links gene expression, cell-type composition, and phenotypic measurements within a single probabilistic model, which enables accurate phenotype prediction and interpretable trajectory inference. A cell-type-aware multi-instance learning architecture learns donor embeddings that capture progression while localizing phenotype-associated signals to specific cell populations. Applied across four settings, scVIP accurately predicts cortical developmental age (Pearson r = 0.95), characterizes Huntingtons disease progression (concordance correlation coefficient = 0.90), integrates two Alzheimers disease cohorts recovering disease-relevant microglial and astrocytic programs, and distinguishes healthy from ACPA-positive individuals and non-progressors from early RA individuals, identifying inflammatory T cell programs associated with disease. scVIP enables principled analysis of how cellular states collectively shape organism-level phenotypes across development and disease.

bioinformatics↗

bioRxiv2025

Selective targeting of mutant huntingtin intron-1 improves rescue provided by antisense oligonucleotides

AbstractHuntingtons disease (HD) arises from the toxic gain of function caused by a CAG expansion in the coding region of the HTT gene. HD is increasingly appreciated to emerge from multiple pathogenic processes, including somatic instability in mutant HTTs (mHTT) CAG repeat tract, which leads to diverse deleterious consequences. These include the alternative processing of HTT pre-mRNA to generate the HTT1a transcript that encodes the very toxic, mHTT isoform referred to as HTT1a. We set out to compare the efficacy and safety of allele-selective lowering of mHTT compared to non-allele-selective lowering using antisense oligonucleotides (ASOs) in heterozygous HttQ111 (Q111) mice. We developed a mutant specific ASO (MutASO) targeting Htt intron-1 that selectively reduced mutant full-length HTT, as well as HTT1a, in the brains of Q111 mice. Compared to the rescue provided by a pan-allele-targeting ASO (PanASO) that lowers wild-type HTT and full-length mHTT (sparing HTT1a), the MutASO essentially eliminated aggregate formation, and provided marked protection from transcriptional dysregulation in HD knock-in mice. Thus, by targeting the ASO to the region upstream of the cryptic polyadenylation sites required to generate the HTT1a transcript, our allele-selective MutASO potently reduced HTT1a protein levels. Here, our findings advocate that HTT1a may have a disproportionate impact on aggregate formation and transcriptional dysregulation and that lowering the levels of HTT1a could provide benefit when designing HTT-lowering based therapeutic strategies for HD.

neuroscience↗

bioRxiv2025

Atrophin-1 Antisense Oligonucleotide Provides Robust Protection from Pathology in a Fully Humanized DRPLA Model

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, including aggregation of mutant ATN1 (mATN1), 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.

neuroscience↗

bioRxiv2024

Suppression of Huntington's Disease Somatic Instability by Transcriptional Repression and Direct CAG Repeat Binding

Huntingtons disease (HD) arises from a CAG expansion in the huntingtin (HTT) gene beyond a critical threshold. A major thrust of current HD therapeutic development is lowering levels of mutant HTT mRNA (mHTT) and protein (mHTT) with the aim of reducing the toxicity of these product(s). Human genetic data also support a key role for somatic instability (SI) in HTTs CAG repeat - whereby it lengthens with age in specific somatic cell types - as a key driver of age of motor dysfunction onset. Thus, an attractive HD therapy would address both mHTT toxicity and SI, but to date the relationship between SI and HTT lowering remains unexplored. Here, we investigated multiple therapeutically-relevant HTT-lowering modalities to establish the relationship between HTT lowering and SI in HD knock-in mice. We find that repressing transcription of mutant Htt (mHtt) provides robust protection from SI, using diverse genetic and pharmacological approaches (antisense oligonucleotides, CRISPR-Cas9 genome editing, the Lac repressor, and virally delivered zinc finger transcriptional repressor proteins, ZFPs). However, we find that small interfering RNA (siRNA), a potent HTT-lowering treatment, lowers HTT levels without influencing SI and that SI is also normal in mice lacking 50% of total HTT levels, suggesting HTT levels, per se, do not modulate SI in trans. Remarkably, modified ZFPs that bind the mHtt locus, but lack a repressive domain, robustly protect from SI, despite not reducing HTT mRNA or protein levels. These results have important therapeutic implications in HD, as they suggest that DNA-targeted HTT-lowering treatments may have significant advantages compared to other HTT-lowering approaches, and that interaction of a DNA-binding protein and HTTs CAG repeats may provide protection from SI while sparing HTT expression.

neuroscience↗

bioRxiv2024

Identification of genetic modifiers of Huntington's disease somatic CAG repeat instability by in vivo CRISPR-Cas9 genome editing

Huntingtons disease (HD), one of >50 inherited repeat expansion disorders (Depienne and Mandel, 2021), is a dominantly-inherited neurodegenerative disease caused by a CAG expansion in HTT (The Huntingtons Disease Collaborative Research Group, 1993). Inherited CAG repeat length is the primary determinant of age of onset, with human genetic studies underscoring that the property driving disease is the CAG length-dependent propensity of the repeat to further expand in brain (Swami et al., 2009; GeM-HD, 2015; Hensman Moss et al., 2017; Ciosi et al., 2019; GeM-HD, 2019; Hong et al., 2021). Routes to slowing somatic CAG expansion therefore hold great promise for disease-modifying therapies. Several DNA repair genes, notably in the mismatch repair (MMR) pathway, modify somatic expansion in HD mouse models (Wheeler and Dion, 2021). To identify novel modifiers of somatic expansion, we have used CRISPR-Cas9 editing in HD knock-in mice to enable in vivo screening of expansion-modifier candidates at scale. This has included testing of HD onset modifier genes emerging from human genome-wide association studies (GWAS), as well as interactions between modifier genes, thereby providing new insight into pathways underlying CAG expansion and potential therapeutic targets.

genetics↗

bioRxiv2024

Global Huntingtin Knockout in Adult Mice Leads to Fatal Neurodegeneration that Spares the Pancreas

Huntingtons disease (HD) is a fatal neurogenerative disorder caused by an expanded glutamine-coding CAG tract in the Huntingtin (Htt) gene. HD is believed to primarily arise via a toxic gain of function, and as a result a wide range of Htt-lowering treatments are in clinical trials. The safety of these trials is contingent on the risks imposed by Htt lowering: Htt is widely conserved, ubiquitously expressed and its complete loss causes severe developmental symptoms in mice and humans. Recently, multiple labs have reported on the consequences of widespread inducible Htt loss in mice. One report describes that early induction of global Htt loss causes fatal pancreatitis, but that later onset lowering is benign. Another study did not report fatal pancreatitis but suggested that postnatal Htt loss was associated with widespread progressive phenotypes, including subcortical calcification and neurodegeneration. To better understand the risks posed by widespread inducible Htt loss we established the phenotypes of mice in which we knocked out Htt with two tamoxifen inducible Cre lines, which we have here extensively characterized. In short, we find that widespread loss of Htt at 2 months of age leads to a wide range of phenotypes, including subcortical calcification, but does not result in acute pancreatitis or histological changes in the pancreas. Additionally, we report here for the first time that Htt loss is followed by robust and sustained increases in the levels of neurofilament light chain (NfL), a peripherally accessible biomarker of neuroaxonal stress. These results confirm that complete loss of Htt in mice is associated with pronounced risks, including progressive subcortical calcification and neurodegeneration.

neuroscience↗

bioRxiv2023

Huntingtin loss in hepatocytes is associated with altered metabolism, adhesion, and liver zonation

Huntingtons disease arises from a toxic gain of function in the huntingtin (HTT) gene. As a result, many HTT-lowering therapies are being pursued in clinical studies, including those that reduce HTT RNA and protein expression in the liver. To investigate potential impacts, we characterized molecular, cellular, and metabolic impacts of chronic HTT lowering in mouse hepatocytes. Lifelong hepatocyte HTT loss is associated with multiple physiological changes, including increased circulating bile acids, cholesterol and urea, hypoglycemia, and impaired adhesion. HTT loss causes a clear shift in the normal zonal patterns of liver gene expression, such that pericentral gene expression is reduced. These alterations in liver zonation in livers lacking HTT are observed at the transcriptional, histological and plasma metabolite level. We have extended these phenotypes physiologically with a metabolic challenge of acetaminophen, for which the HTT loss results in toxicity resistance. Our data reveal an unexpected role for HTT in regulating hepatic zonation, and we find that loss of HTT in hepatocytes mimics the phenotypes caused by impaired hepatic {beta}-catenin function. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/546334v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@1dd0f15org.highwire.dtl.DTLVardef@938f7org.highwire.dtl.DTLVardef@17ae025org.highwire.dtl.DTLVardef@11cd15_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2021

HAP40 orchestrates huntingtin structure for differential interaction with polyglutamine expanded exon 1

Huntingtons disease results from expansion of a glutamine-coding CAG tract in the huntingtin (HTT) gene, producing an aberrantly functioning form of HTT. Both wildtype and disease-state HTT form a hetero-dimer with HAP40 of unknown functional relevance. We demonstrate in vivo that HTT and HAP40 cellular abundance are coupled. Integrating data from a 2.6 [A] cryo-electron microscopy structure, cross-linking mass spectrometry, small-angle X-ray scattering, and modeling, we provide a near-atomic-level view of HTT, its molecular interaction surfaces and compacted domain architecture, orchestrated by HAP40. Native mass-spectrometry reveals a remarkably stable hetero-dimer, potentially explaining the cellular inter-dependence of HTT and HAP40. The polyglutamine tract containing N-terminal exon 1 region of HTT is dynamic, but shows greater conformational variety in the mutant than wildtype exon 1. By providing novel insight into the structural consequences of HTT polyglutamine expansion, our data provide a foundation for future functional and drug discovery studies targeting Huntingtons disease.

biochemistry↗

bioRxiv2020

Huntingtin lowering reduces somatic instability at CAG-expanded loci

Expanded trinucleotide repeats cause many human diseases, including Huntingtons disease (HD). Recent studies indicate that somatic instability of these repeats contributes to pathogenesis in several expansion disorders. We find that lowering huntingtin protein (HTT) levels reduces somatic instability of both the Htt and Atxn2 CAG tracts in knockin mouse models, and the HTT CAG tract in human iPSC-derived neurons, revealing an unexpected role for HTT in regulating somatic instability.

neuroscience↗

bioRxiv2020

Altered Huntingtin-Chromatin Interactions Predict Transcriptional and Epigenetic Changes in Huntingtons Disease

Progressive striatal gene expression changes and epigenetic alterations are a prominent feature of Huntingtons disease (HD), but the mechanistic basis remains poorly understood. Using chromatin immunoprecipitation and sequencing (ChIP-seq), we show that the huntingtin protein (HTT) reproducibly occupies specific locations in the mouse genome. Moreover, many genomic loci were differentially occupied by HTT in striatal tissue from a homozygous knock-in mouse model of HD (B6.HttQ111/Q111) when compared to wildtype controls. Huntingtin ChIP-seq peaks were enriched in the coding regions of cell identity genes important for striatal function, with many of these genes found to have reduced expression in the striata of HD patients and mouse models, as well as reduced HTT occupancy in HttQ111/Q111mice compared to controls. Conversely, HTT ChIP-seq peaks were depleted near genes that are up-regulated in HD. ChIP-seq of bulk striatal histone modifications, generated in parallel, revealed genotype-specific colocalization of HTT with active chromatin marks (H3K4me3 and H3K27ac), and with enhancer of zeste homolog 2 (EZH2), a key enzymatic component of the PRC2 complex. Near genes that are differentially regulated in HD, greater HTT occupancy in HttQ111/Q111 vs. wildtype mice was associated with increased EZH2 binding, increased histone H3 lysine 4 (H3K4me3), and decreased histone H3 lysine 27 (H3K27me3). Our study suggests that huntingtin-chromatin interactions may play a direct role in organizing chromatin and promoting cell type-specific gene expression, with loss of HTT occupancy predicting decreased gene expression in HD.

neuroscience↗

bioRxiv2020

Prion protein lowering is a disease-modifying therapy across prion strains, disease stages, and endpoints

Lowering of prion protein (PrP) expression in the brain is a genetically validated therapeutic hypothesis in prion disease. We recently showed that antisense oligonucleotide (ASO)-mediated PrP suppression extends survival and delays disease onset in intracerebrally prion-infected mice in both prophylactic and delayed dosing paradigms. Here, we examine the efficacy of this therapeutic approach across diverse paradigms, varying the dose and dosing regimen, prion strain, treatment timepoint, and examining symptomatic, survival, and biomarker readouts. We recapitulate our previous findings with additional PrP-targeting ASOs, and demonstrate therapeutic benefit against four additional prion strains. We demonstrate that less than 25% PrP suppression is sufficient to extend survival and delay symptoms in a prophylactic paradigm. Rise in both neuroinflammation and neuronal injury markers can be reversed by a single dose of PrP-lowering ASO administered after the detection of pathological change. Chronic ASO-mediated suppression of PrP beginning at any time up to early signs of neuropathology confers benefit similar to constitutive heterozygous PrP knockout. Remarkably, even after emergence of frank symptoms including weight loss, a single treatment prolongs survival by months in a subset of animals. These results support ASO-mediated PrP lowering, and PrP-lowering therapeutics in general, as a promising path forward against prion disease.

neuroscience↗

bioRxiv2017

Early Detection of Apathetic Phenotypes in Huntington’s Disease Knock-in Mice Using Open Source Tools

Apathy is one of the most prevalent and progressive psychiatric symptom in Huntingtons disease (HD) patients. However, preclinical work in HD mouse models tend to focus on molecular and motor, rather than affective, phenotypes. Measuring behavior in mice often produces noisy data and requires large cohorts to detect phenotypic rescue with appropriate power. The operant equipment necessary for measuring affective phenotypes is typically expensive, proprietary to commercial entities, and bulky which can render adequately sized mouse cohorts as cost-prohibitive. Thus, we describe here a home-built open-source alternative to commercial hardware that is reliable, scalable, and reproducible. Using off-the-shelf hardware, we adapted and built several of the rodent operant buckets (ROBucket) designed to test HttQ111/+ mice for attention deficits in fixed ratio (FR) and progressive ratio (PR) tasks. We find that, despite normal performance in reward attainment in the FR task, HttQ111/+ mice exhibit reduced PR performance at 9-11 months of age, suggesting motivational deficits. We replicated this in two independent cohorts, which demonstrates the reliability and utility of both the apathetic phenotype, and these ROBuckets, for preclinical HD studies.

animal behavior and cognition↗

bioRxiv2016

Peripheral Htt silencing does not ameliorate central signs of disease in the B6.HttQ111/+ mouse model of Huntington’s Disease

Huntingtons disease (HD) is an autosomal dominant neurodegenerative disease whose neuropathological signature is a selective loss of medium spiny neurons in the striatum. Despite this selective neuropathology, the mutant protein (huntingtin) is found in virtually every cell so far studied, and, consequently, phenotypes are observed in a wide range of organ systems both inside and outside the central nervous system. We, and others, have suggested that peripheral dysfunction could contribute to the rate of progression of striatal phenotypes of HD. To test this hypothesis, we lowered levels of huntingtin by treating mice with antisense oligonucleotides (ASOs) targeting the murine Huntingtin gene. To study the relationship between peripheral huntingtin levels and striatal HD phenotypes, we utilized a knock-in model of the human HD mutation (the B6.HttQ111/+ mouse). We treated mice with ASOs from 2-10 months of age, a time period over which significant HD-relevant signs progressively develop in the brains of HttQ111+ mice. Peripheral treatment with ASOs led to persistent reduction of huntingtin protein in peripheral organs, including liver, brown and white adipose tissues. This reduction was not associated with alterations in the severity of HD-relevant signs in the striatum of HttQ111/+ mice at the end of the study, including transcriptional dysregulation, the accumulation of neuronal intranuclear inclusions, and behavioral changes such as subtle hypoactivity and reduced exploratory drive. These results suggest that the amount of peripheral reduction achieved in the current study does not significantly impact the progression of HD-relevant signs in the central nervous system.

neuroscience↗

bioRxiv2016

Genome-scale transcriptional regulatory network models for the mouse and human striatum predict roles for SMAD3 and other transcription factors in Huntington’s disease

Transcriptional changes occur presymptomatically and throughout Huntingtons Disease (HD), motivating the study of transcriptional regulatory networks (TRNs) in HD. We reconstructed a genome-scale model for the target genes of 718 TFs in the mouse striatum by integrating a model of the genomic binding sites with transcriptome profiling of striatal tissue from HD mouse models. We identified 48 differentially expressed TF-target gene modules associated with age- and Htt allele-dependent gene expression changes in the mouse striatum, and replicated many of these associations in independent transcriptomic and proteomic datasets. Strikingly, many of these predicted target genes were also differentially expressed in striatal tissue from human disease. We experimentally validated a key model prediction that SMAD3 regulates HD-related gene expression changes using chromatin immunoprecipitation and deep sequencing (ChIP-seq) of mouse striatum. We found Htt allele-dependent changes in the genomic occupancy of SMAD3 and confirmed our models prediction that many SMAD3 target genes are down-regulated early in HD. Importantly, our study provides a mouse and human striatal-specific TRN and prioritizes a hierarchy of transcription factor drivers in HD.

systems biology↗

bioRxiv2016

Motivational, proteostatic and transcriptional deficits precede synapse loss, gliosis and neurodegeneration in the B6.HttQ111/+ model of Huntington’s disease

We investigated the appearance and progression of disease-relevant signs in the B6.HttQ111/+ mouse, a genetically precise model of the mutation that causes Huntingtons disease (HD). We find that B6.HttQ111/+ mice are healthy, show no overt signs of central or peripheral inflammation, and no gross motor impairment as late as 12 months of age. Behaviorally, we find that 4-9 month old B6.HttQ111/+ mice have normal activity levels and show no clear signs of anxiety or depression, but do show clear signs of reduced motivation. The neuronal density, neuronal size, synaptic density and number of glia is normal in B6.HttQ111/+ striatum, the most vulnerable brain region in HD, up to 12 months of age. Despite this preservation of the synaptic and cellular composition of the striatum, we observe clear progressive, striatal-specific, transcriptional dysregulation and accumulation of neuronal intranuclear inclusions (NIIs). Simulation studies suggest these molecular endpoints are sufficiently robust for future preclinical studies, and that B6.HttQ111/+ mice are a useful tool for modeling disease-modifying or neuroprotective strategies for disease processes before the onset of overt phenotypes.

neuroscience↗