Biology subjects

Joenson, L.

Publications and source records attributed to Joenson, L..

4 recordsLinked to original sources

bioRxiv2026

Antisense oligonucleotides targeting transcription termination windows disrupt mRNA 3' end processing and decrease gene expression

Antisense oligonucleotides (ASOs) are short, synthetic nucleic acids that bind to complementary RNA sequences and alter gene expression, making them versatile therapeutic agents. Here, we identify transcription termination windows of protein-coding genes as previously unrecognized targets for ASOs. We show that ASOs can act on nascent RNA synthesised downstream of the annotated genes, leading to a pronounced decrease in the corresponding mRNA levels. These downstream-of-gene ASOs (DG-ASOs) induce RNase H1-dependent cleavage, impairing mRNA 3 end processing, directing the unprocessed mRNAs for exosome-dependent degradation and creating early entry points in the nascent RNA for the XRN2 exonuclease termination factor. Altogether, we show that termination windows are genuine ASO targets which can be exploited to suppress gene expression. Importantly, we also reveal an underappreciated source of off-target effects which may arise from ASOs binding downstream of genes. Our findings indicate the necessity to expand ASO design and off-target assessment guidelines to include termination window sequences, thereby improving therapeutic efficacy and safety.

molecular biology↗

bioRxiv2026

Cell-Type Specific Molecular and Functional Consequences of TDP-43 Loss-of-Function in Human Induced Neurons

Amyotrophic Lateral Sclerosis (ALS) is a devastating neurodegenerative disorder characterized by the cytoplasmic aggregation and nuclear depletion of the TDP-43 protein. The latter impairs TDP-43 function as an RNA-binding protein and compromises the repression of cryptic splicing events, affecting both glutamatergic upper motor neurons and cholinergic lower motor neurons. This study systematically investigated the molecular and functional consequences of TDP-43 knockdown in human induced pluripotent stem cell (hiPSC)-derived glutamatergic neurons (iGNs) and cholinergic motor neurons (iMNs) using antisense oligonucleotides. The results demonstrated that TDP-43 loss elicits widespread, cell-type-specific changes in gene expression and alternative splicing. Notably, a shared subset of ALS-associated targets, including STMN2 and UNC13A, were consistently downregulated and mis-spliced across both neuronal subtypes. Functionally, Microelectrode Array (MEA) electrophysiology recordings revealed that TDP-43 knockdown induces a hyperexcitable phenotype in both neuronal populations, though they exhibited distinct network patterns: iGNs displayed synchronized bursting and significant shifts in overall electrophysiological profiles, while iMNs showed asynchronous firing. Furthermore, the inclusion of astrocytes in co-culture models expanded the repertoire of detectable cryptic splicing, including an event in HDGFL2 previously identified in patient cerebrospinal fluid. Despite these profound molecular and functional deficits, TDP-43 depletion did not impact neuronal viability or increase susceptibility to glutamate-induced excitotoxicity. These findings validate hiPSC-derived iGNs and iMNs as relevant models for ALS and highlight the critical necessity of considering cell-type specificity when elucidating pathogenesis and developing targeted therapies.

neuroscience↗

bioRxiv2023

(CA)n oligonucleotides correct RNA mis-splicing in TDP-43 pathology

Withdrawal StatementThe authors have withdrawn their manuscript owing to not all authors having approved the manuscript. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

molecular biology↗

bioRxiv2022

Angelman syndrome patient neuron screen identifies a potent and selective clinical ASO targeting UBE3A-ATS with long lasting effect in cynomolgus monkey

Angelman syndrome (AS) is a severe neurodevelopmental disorder caused by the loss of neuronal E3 ligase UBE3A with no available treatment. Restoring UBE3A levels via downregulation of the paternally cis-acting long non-coding antisense transcript (UBE3A-ATS) is a potential disease modifying. Developing molecules targeting human UBE3A-ATS is challenging because it is expressed only in neurons and lacks animal species sequence conservation. To overcome this, we performed a library screen of locked-nucleic acid (LNA)-modified antisense oligonucleotides (ASOs) on AS patient-derived neurons, identifying initial sequences. Further optimization led to the identification of the ASO, RO7248824, which selectively and potently reduces UBE3A-ATS, while concomitantly upregulating the UBE3A mRNA and protein. These properties held true in both human AS patient- and neurotypical-, as well as cynomolgus monkey-derived neurons. In vivo use of tool molecules in wild-type (WT) and AS Ube3am-/p+ mice, revealed a steep relationship between UBE3A-ATS knock-down and UBE3A mRNA/protein upregulation, whereby an almost 90% downregulation was needed to achieve a 50% upregulation, respectively. This relationship was confirmed in cynomolgus monkeys. Whereby, repeated lumbar intrathecal administrations of RO7248824 was well tolerated without adverse in-life effects or tissue pathology and produced a robust, long lasting (up to 3 months) paternal reactivation of UBE3A mRNA/protein across key monkey brain regions. Our results demonstrate that AS human pluripotent stem cell neurons serve as an excellent translational tool and furthermore LNA-modified ASOs exhibit excellent drug-like properties. Sustained efficacy translated to infrequent, intrathecal dosing and serves as the basis for the ongoing clinical development of RO7248824 for AS. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/495066v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1c2a97eorg.highwire.dtl.DTLVardef@1059954org.highwire.dtl.DTLVardef@95835aorg.highwire.dtl.DTLVardef@1e2adea_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract.C_FLOATNO From AS patient blood to a neuronal screen, identifies clinical ASO with excellent in vivo properties. (1) Patients were recruited. (2) Whereby blood was reprogrammed into hIPSC and subsequently differentiated into neurons. (3) ASOs were designed and screened on human neurons to downregulate the UBE3A-ATS likely via directed RNase H Cleavage of Nascent Transcripts. (4a) RO7248824 was identified that potently and selective reduces UBE3A-ATS, concomitantly with upregulating the UBE3A sense transcript and protein which was used for in vitro pk/pd. (4b) In parallel tool murine ASO were used demonstrate in vivo POC.(5) Pivotal nonhuman primate studies to monitor safety and predict the human dose. (6) RO7248824 is in AS clinical trial. C_FIG One Sentence SummaryFrom angelman syndrome human neuron screen to cynomolgus monkey proof of concept identifies the clinical molecule RO7248824

neuroscience↗