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Experimental & Molecular Medicine

Springer Science and Business Media LLC

All preprints, ranked by how well they match Experimental & Molecular Medicine's content profile, based on 14 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit. Older preprints may already have been published elsewhere.

1
Endothelial TET2 Regulates Cardiac Remodeling by Modifying Endothelial-to-Mesenchymal Transition

Kou, W.; Shi, Y.; Li, B.; Zeng, Y.; Zhai, M.; You, S.; Yu, Q.; Gong, S.-y.; Zhuang, J.; Zhao, Y.; Xia, J.; Xu, Y.-W.; Peng, W.

2022-06-16 genetics 10.1101/2022.06.15.496224 medRxiv
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DNA methylation modification has been proved to play an important role in heart diseases. In this study, the role of Ten-Eleven Translocation-2 (TET2), which is a key demethylation enzyme, is investigated in cardiac remodeling. TET2 is abundant in endothelial cells but decreased in hypertrophic hearts. TET2 knockdown in endothelial cells triggers endothelial-to-mesenchymal transition (EndMT), while overexpression of TET2 inhibits the EndMT. In vivo, Cdh5-CreERT2/TET2flox/flox; Rosa26-mTmG+/- mice are developed and undergo transverse aortic constriction (TAC) subsequently to induce pathological cardiac hypertrophy model. Hearts of Cdh5-CreERT2/TET2flox/flox mice show more severe hypertrophy and fibrosis than controls in the TAC model. Furthermore, EGLN3 is identified to participate in EndMT as the downstream target of TET2 by using RNA sequencing and whole-genome bisulfite sequencing (WGBS). Finally, vitamin C, which can mimic TET2 restoration, is found to partially improve cardiac function and inhibit myocardial fibrosis. These insights into how TET2 alleviates cardiac fibrosis may open new avenues for treating cardiac remodeling in the future.

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Functional impact of pathogenic Runt domain mutations in Runx2 on skeletal and dental development in cleidocranial dysplasia

Ogawa, S.; Higuchi, S.; Yoshimoto, Y.; Hoshino, M.; Miura, S.; Hamada, A.; Watanabe, H.; Sakuma, T.; Hu, K.; Ogata, S.; Uchibe, K.; Fujimoto, K.; Yamamoto, T.; Okamoto, T.; Kunimatsu, R.; Sotomaru, Y.; Tanimoto, K.; Kondoh, G.; Komori, T.; Docheva, D.; Shukunami, C.

2025-07-15 genetics 10.1101/2025.06.18.660258 medRxiv
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Runt-related transcription factor 2 (RUNX2) is essential for skeletogenesis, and mutations in its gene cause cleidocranial dysplasia (CCD), an autosomal dominant skeletal disorder. The evolutionarily conserved 128-amino acid Runt homology domain (RHD) of human RUNX2 is essential for DNA binding and heterodimerization, and serves as a mutation hotspot associated with severe CCD phenotypes. To elucidate the functional impact of pathogenic RHD mutations in vivo, we generated two novel mouse lines: one carrying a missense mutation, c.695G>A (p.R232Q) (Runx2m/+), corresponding to the human RUNX2 c.674G>A (p.R225Q), and the other harboring a frameshift mutation, c.697_698delGA (p.E233TfsTer9) (Runx2112/+), causing a premature stop codon. Homozygous Runx2m/mand Runx2112/112 mice lacked membranous ossification, whereas heterozygous Runx2m/+ and Runx2112/+ mice displayed typical CCD-like skeletal features, including an open anterior fontanelle and clavicle hypoplasia. Unexpectedly, heterozygotes carrying pathogenic mutations in RHD developed an accessory root-like protrusion at the furcation of three-rooted maxillary first molars, representing a previously unrecognized dental phenotype during root development. Dual luciferase assays revealed impaired transactivation of the p.R232Q mutant Runx2 on the osteocalcin enhancer/promoter. Wild-type Runx2 was robustly expressed in osteoblasts and hypertrophic chondrocytes during bone formation, but the mutant Runx2 exhibited reduced expression in hypertrophic chondrocytes and partially impaired nuclear localization, resulting in arrested osteoblast and chondrocyte maturation. Our mutant mouse model provides a valuable in vivo platform to study CCD pathogenesis, mechanisms of tooth root furcation, and therapeutic interventions targeting dysfunctional RHD.

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DUSP4 knockdown in BRAF V600E mutant colorectal cancer induces cell cycle arrest and halts tumor growth

Hopfgartner, B.; Kriz, M.; Alpar, D.; Westermaier, Y.; Hofmann, M. H.; Neumuller, R. A.; Grosche, S.

2026-01-15 genetics 10.64898/2026.01.15.699635 medRxiv
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Oncogenic signaling in cancer cells is essential for proliferation, and its disruption, either through inhibition or overactivation, can provide therapeutic opportunities. Dual specificity phosphatase 4 (DUSP4), a negative regulator of the MAPK pathway that dephosphorylates ERK, has been proposed as a potential target; however, its therapeutic relevance has not been evaluated in vivo. In this study, we show that DUSP4 knock-down induces G1 cell cycle arrest and reduces proliferation in BRAFV600E-mutant and BRAF inhibitor-resistant colorectal cancer models, both in vitro and in vivo, and induces a rapid DUSP5-mediated adaptive response. While treatment achieved tumor stasis indicating disease control, it did not yield tumor regression, suggesting that DUSP4 may have limited efficacy as a monotherapy target in cancer.

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Long-lasting Analgesia via Targeted in vivo Epigenetic Repression of Nav1.7

Moreno, A. M.; Catroli, G. F.; Aleman, F.; Pla, A.; Woller, S. A.; Hu, M.; Yaksh, T.; Mali, P.

2019-07-24 genetics 10.1101/711812 medRxiv
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Current treatments for chronic pain rely largely on opioids despite their unwanted side effects and risk of addiction. Genetic studies have identified in humans key targets pivotal to nociceptive processing, with the voltage-gated sodium channel, NaV1.7 (SCN9A), being perhaps the most promising candidate for analgesic drug development. Specifically, a hereditary loss-of-function mutation in NaV1.7 leads to insensitivity to pain without other neurodevelopmental alterations. However, the high sequence similarity between NaV subtypes has frustrated efforts to develop selective inhibitors. Here, we investigated targeted epigenetic repression of NaV1.7 via genome engineering approaches based on clustered regularly interspaced short palindromic repeats (CRISPR)-dCas9 and zinc finger proteins as a potential treatment for chronic pain. Towards this end, we first optimized the efficiency of NaV1.7 repression in vitro in Neuro2A cells, and then by the lumbar intrathecal route delivered both genome-engineering platforms via adeno-associated viruses (AAVs) to assess their effects in three mouse models of pain: carrageenan-induced inflammatory pain, paclitaxel-induced neuropathic pain and BzATP-induced pain. Our results demonstrate: one, effective repression of NaV1.7 in lumbar dorsal root ganglia; two, reduced thermal hyperalgesia in the inflammatory state; three, decreased tactile allodynia in the neuropathic state; and four, no changes in normal motor function. We anticipate this genomically scarless and non-addictive pain amelioration approach enabling Long-lasting Analgesia via Targeted in vivo Epigenetic Repression of Nav1.7, a methodology we dub pain LATER, will have significant therapeutic potential, such as for preemptive administration in anticipation of a pain stimulus (pre-operatively), or during an established chronic pain state.\n\nOne sentence summaryIn situ epigenome engineering approach for genomically scarless, durable, and non-addictive management of pain.

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Expression of C5aR1 in Cutaneous Squamous Cell Carcinoma is Associated with Invasion, Metastasis and Poor Prognosis

Heiskanen, L.; Nissinen, L.; Siljamaki, E.; Knuutila, J.; Pellinen, T.; Kallajoki, M.; Heino, J.; Riihila, P.; Kahari, V.-M.

2024-08-19 dermatology 10.1101/2024.08.16.24312116 medRxiv
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Cutaneous squamous cell carcinoma (cSCC) is the most common metastatic skin cancer, and the metastatic disease is associated with poor prognosis. We have examined the role of complement C5a receptor, C5aR1, in the progression and metastasis of cSCC. C5aR1 expression was increased in cSCC cells in 3D spheroid co-culture model in the presence of fibroblasts, and that treatment with recombinant C5a enhanced the invasion of cSCC cells. Staining for C5aR1 was detected on the surface of tumor cells at the invasive edge of human cSCC xenografts in vivo. Staining of metastatic and non-metastatic primary human cSCCs, premalignant and benign epidermal lesions and normal skin for C5aR1 with multiplex immunofluorescence and chromogenic immunohistochemistry revealed increased expression of C5aR1 on the surface of tumor cells and fibroblasts in invasive cSCCs and recessive dystrophic epidermolysis bullosa-associated cSCCs compared to cSCC in situ, actinic keratoses, seborrheic keratoses and normal skin. Increased expression of C5aR1 on the tumor cell surface and in fibroblasts was associated with metastatic risk and poor disease-specific survival of patients with primary cSCC. These findings reveal the role of C5aR1 in cSCC invasion and identify C5aR1 as a novel biomarker for metastasis risk and poor prognosis in patients with cSCC. The results also suggest that C5aR1 could be a novel therapeutic target for treatment of locally advanced and metastatic cSCC.

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A postzygotic GNA13 variant upregulates the RHOA/ROCK pathway and alters melanocyte function in a mosaic skin hypopigmentation syndrome

El Masri, R.; Iannuzzo, A.; Kuentz, P.; Tacine, R.; Vincent, M.; Barbarot, S.; Morice-Picard, F.; Boralevi, F.; Oillarburu, N.; Mazereeuw-Hautier, J.; Duffourd, Y.; Faivre, L.; Sorlin, A.; Vabres, P.; Delon, J.

2024-07-24 dermatology 10.1101/2024.07.24.24310661 medRxiv
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The genetic bases of mosaic pigmentation disorders have increasingly been identified, but these conditions remain poorly characterised, and their pathophysiology is unclear. Here, we report in four unrelated patients that a recurrent postzygotic mutation in GNA13 is responsible for a recognizable syndrome with hypomelanosis of Ito associated with developmental anomalies. GNA13 encodes G13, a subunit of {beta}{gamma} heterotrimeric G proteins coupled to specific transmembrane receptors known as G-protein coupled receptors. In-depth functional investigations revealed that this R200K mutation provides a gain of function to G13. Mechanistically, we show that this variant hyperactivates the RHOA/ROCK signalling pathway that consequently increases actin polymerisation and myosin light chains phosphorylation, and promotes melanocytes rounding. Our results also indicate that R200K G13 hyperactivates the YAP signalling pathway. All these changes appear to affect cell migration and adhesion but not the proliferation. Our results suggest that hypopigmentation can result from a defect in melanosome transfer to keratinocytes due to cell shape alterations. These findings highlight the interaction between heterotrimeric G proteins and the RHOA pathway, and their role in melanocyte function.

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Interleaved intersectional strategy enables genetic lineage tracing with enhanced specificity

han, m.; liu, z.; huang, x.; liu, l.; zhou, b.; Lui, K.; shu, q.; Zhou, B.

2024-03-11 genetics 10.1101/2024.03.06.583635 medRxiv
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BACKGROUNDDual recombinases have been increasingly employed for enhanced precision in genetic targeting. A recent study utilizing an intersectional genetic approach through dual recombinases (Dre + CreER) has revealed that endocardium-derived fibroblasts (EndoFbs) play a pivotal role in cardiac fibrosis after pressure overload. However, this intersectional strategy has limitations, primarily due to ectopic genetic labeling of non-target cells within the adult heart by the constitutively active Dre recombinase. METHODSTo address this issue, we have developed an advanced, interleaved and intersectional reporter (IIR) strategy in this study. This IIR strategy leverages an inducible CreER to prevent inadvertent Dre-rox recombination during development or disease progression by designing an interleaved reporter to allow for more specific tracing of EndoFbs. Moreover, our IIR system also incorporates Diphtheria Toxin Receptor (DTR) in targeted cells, enabling functional characterization of these cells after genetic ablation. RESULTSEndoFbs were regionally distributed in the heart during homeostasis and proliferated preferentially in response to pressure overload, leading to cardiac fibrosis in defined regions. The IIR strategy enables the tracing of EndoFbs with a more prominent regional pattern and facilitates genetic ablation of EndoFbs through DT injection. In addition, we have applied this IIR strategy to specifically target fibroblasts derived from the epicardium (EpiFbs). Genetic lineage tracing of EpiFb reveals that their distribution pattern is complementary to that of EndoFbs in the adult heart. When a substantial number of EpiFbs were genetically ablated, EndoFbs could replace the loss of EpiFbs in some specific regions of hearts. CONCLUSIONSThe IIR strategy refines the precision of genetic lineage tracing while still employing the constitutively active Dre recombinase in tandem with inducible Cre. EndoFbs and EpiFbs are complementary in their distribution pattern in the heart, where EndoFbs have the potential to replace the loss of EpiFbs in some regions.

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Single-cell analysis of psoriasis resolution reveals an inflammatory fibroblast state targeted by IL-23 blockade

Francis, L.; McCluskey, D.; Ganier, C.; Jiang, T.; Du-Harpur, X.; Gabriel, J.; Dhami, P.; Kamra, Y.; Visvanathan, S.; Barker, J. N.; Smith, C. H.; Capon, F.; Mahil, S. K.

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Biologics targeting the IL-23/IL-17 axis have transformed the treatment of psoriasis. However, the early mechanisms of action of these drugs remain poorly understood. Here, we performed longitudinal single-cell RNA-sequencing in affected individuals receiving IL-23 inhibitor therapy. By profiling skin at baseline, day 3 and day 14 of treatment, we demonstrated that IL-23 blockade causes marked gene expression shifts, with fibroblast and myeloid populations displaying the most extensive changes at day 3. We also identified a transient WNT5A+/IL24+ fibroblast state, which was only detectable in lesional skin. In-silico and in-vitro studies indicated that signals stemming from these WNT5A+/IL24+ fibroblasts upregulated multiple inflammatory genes in keratinocytes. Importantly, the abundance of WNT5A+/IL24+ fibroblasts was significantly reduced after treatment. This observation was validated in-silico, by deconvolution of multiple transcriptomic datasets, and experimentally, by RNA in-situ hybridization. These findings demonstrate that the evolution of inflammatory fibroblast states is a key feature of resolving psoriasis skin.

9
Disentangling Schwann Cell and Neuronal TRPA1 Function in Mouse Models of Familial Episodic Pain Syndrome

Marini, M.; Chieca, M.; Coppi, E.; Bonacchi, L.; Landini, L.; Scuffi, I.; Kwan, K.; Papini, A.; De Siena, G.; Bellantoni, E.; Timotei, L.; Albanese, V.; Ferroni, G.; do Nascimento Melo, E. D.; Birling, M.-C.; Lorentz, R.; Nassini, R.; De Logu, F.

2026-02-17 genetics 10.64898/2026.02.14.705765 medRxiv
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Familial Episodic Pain Syndrome (FEPS) is a rare inherited disorder characterized by episodes of severe upper-body pain triggered by different stimuli including cold, stress, or fasting. A gain-of-function point mutation (N855S) in the Transient Receptor Potential Ankyrin 1 (TRPA1) ion channel has been identified in affected individuals, altering its biophysical properties, and leading to sustained nociceptive signaling. While TRPA1 is predominantly studied in sensory neurons, recent findings highlight its key modulatory role for Schwann cells in chronic pain. Here, we investigated the cell-specific contributions of mutant TRPA1 (TRPA1*) in FEPS by developing mouse models with TRPA1* selectively expressed in either Schwann cells or sensory neurons, using CRISPR-based and Cre-loxP strategies. Patch-clamp analyses confirmed that TRPA1* exhibits enhanced current responses to agonists compared to wild-type. Through behavioral assays we revealed that TRPA1* expressed in sensory neurons mediates acute nociception, while TRPA1* in Schwann cells drives mechanical allodynia in response to subthreshold doses of TRPA1 agonists and to physiological pain triggers commonly observed in FEPS patients, including fasting, cold exposure, and restraint stress. Pain responses were associated with the increase in reactive oxygen species (ROS) and accumulation of 4-hydroxynonenal (4-HNE) in TRPA1* sciatic nerves and these effects were reduced by a treatment with an antioxidant. We reveal distinct roles of neuronal and non-neuronal TRPA1 in pain and provide novel in vivo models to investigate the mechanisms of chronic pain in FEPS and related channelopathies. Overall, this study offers new insights into the development of targeted therapies for Schwann cell-TRPA1 to relieve pain in affected individuals.

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Distinct heterozygous TTC7A missense variants lead to different intestinal epithelial phenotypes in pediatric IBD

Jeshvaghani, Z. S.; Deenichina, P.; Collen, L.; de Vries, M.; Brunsveld, J.; Kotlarz, D.; Koletzko, S.; Klein, C.; Beekman, J.; Snapper, S.; Lindemans, C.; Mokry, M.; Argmann, C.; Kuijk, E.; Nieuwenhuis, E.

2025-06-13 genetics 10.1101/2025.06.11.659065 medRxiv
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Pathogenic mutations in Tetratricopeptide repeat domain 7A (TTC7A) result in gastrointestinal and immunological disorders of which the pathobiology is not fully understood. Previous case reports indicate that TTC7A plays an important role in preserving intestinal epithelial integrity, but thus far only few variants have been investigated and it is unclear if different variants exert the same effects. Here, we aim to study the effects of different variants on the intestinal epithelium. We present three instances of pediatric inflammatory bowel disease (IBD), displaying varying clinical symptoms and severity levels, and associated with different heterozygous missense mutations in TTC7A. Intestinal organoids derived from patients show dissimilar epithelial phenotypes and exhibit differences in growth, morphology, apicobasal polarity, responses to specific drugs, TTC7A expression, and transcriptional profiles. The findings of our study suggest differences in pathobiology between individuals with different TTC7A mutations. This investigation enhances our comprehension of TTC7A-related conditions and can have implications for developing targeted therapies for TTC7A-associated disorders.

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The robust, high-throughput, and temporally regulated roxCre and loxCre reporting systems for genetic modifications in vivo

Shi, M.; Li, J.; Liu, X.; Liu, K.; He, L.; Pu, W.; Weng, W.; Zhang, S.; Zhao, H.; Lui, K.; Zhou, B.

2025-01-21 genetics 10.1101/2024.04.23.590680 medRxiv
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Cre-loxP technology, a cornerstone in fate mapping and in vivo gene function studies, faces challenges in achieving precise and efficient conditional mutagenesis through inducible systems. This study introduces two innovative genetic tools designed to overcome these limitations. The first, roxCre, enables DreER-mediated Cre release, paving the way for intersectional genetic manipulation that permits increased precision and efficiency. The second, loxCre, facilitates conditional gene targeting by allowing CreER lines to induce Cre expression with significantly enhanced efficiency. These tools incorporate a fluorescent reporter for genetic lineage tracing, simultaneously revealing efficient gene knockout in cells marked by the reporter. These strategies hold great potential for precise and efficient exploration of lineage-specific gene functions, marking a significant advancement in genetic research methodologies.

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A Comprehensive Proteogenomic and Spatial Analysis of Innate and Acquired Resistance of Metastatic Melanoma to Immune Checkpoint Blockade Therapies

wei, s.; Du, K.; Lan, H.; Yang, Z.; Deng, Y.; Wei, Z.; Frederick, D. T.; Lee, J.; Labrie, M.; Tian, T.; Moll, T.; Chen, Y.; Sullivan, R. J.; Mills, G. B.; Boland, G. M.; Flaherty, K.; liu, l.; Herlyn, M.; Zhang, G.

2024-09-15 genetics 10.1101/2024.09.12.612675 medRxiv
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While a subset of patients with metastatic melanoma achieves durable responses to immune checkpoint blockade (ICB) therapies, the majority ultimately exhibit either innate or acquired resistance to these treatments. However, the molecular mechanisms underlying resistance to ICB therapies remain elusive and are warranted to elucidate. Here, we comprehensively investigated the tumor and tumor immune microenvironment (TIME) of paired pre- and post-treatment tumor specimens from metastatic melanoma patients who were primary or secondary resistance to anti-CTLA-4 and/or anti-PD-1/PD-L1 therapies. Differentially expressed gene (DEG) analysis and single-sample gene set enrichment analysis (ssGSEA) with transcriptomic data identified cell cycle and c-MYC signaling as pathway-based resistance signatures. And weighted gene co-expression network analysis (WGCNA) revealed the activation of a cross-resistance meta-program involving key signaling pathways related to tumor progression in ICB resistant melanoma. Moreover, spatially-resolved, image-based immune monitoring analysis by using NanoStrings digital spatial profiling (DSP) and Cyclic Immunofluorescence (CyCIF) showed infiltration of suppressive immune cells in the tumor microenvironment of melanoma with resistance to ICB therapies. Our study reveals the molecular mechanisms underlying resistance to ICB therapies in patients with metastatic melanoma by conducting such integrated analyses of multi-dimensional data, and provides rationale for salvage therapies that will potentially overcome resistance to ICB therapies. Statement of translational relevanceThis study paves the way for the creation of innovative therapeutic strategies, aimed at subverting resistance to immune checkpoint blockade (ICB) therapies in metastatic melanoma patients. By unraveling the specific molecular mechanisms underlying resistance, scientists can design effective alternative treatments that target pathways such as pathways associated with cell cycle dysregulation and c-MYC signaling. Furthermore, through the application of advanced immune monitoring techniques such as NanoString Digital Spatial Profiling (DSP) and Cyclic Immunofluorescence (CyCIF), this study has significantly enriched our understanding of the tumor microenvironment. This enhanced characterization facilitates the discovery of potential biomarkers that may forecast a patients response to ICB treatment. Ultimately, these advancements could potentially refine patient outcomes and foster the development of more personalized cancer treatments in the future.

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Gene editing is suitable to treat GM1 Gangliosidosis: a proof-of-concept study

Leclerc, D.; Goujon, L.; Jaillard, S.; Nouyou, B.; Cluzeau, L.; Damaj, L.; Dubourg, C.; Etcheverry, A.; Levade, T.; Froissart, R.; Dreano, S.; Guillory, X.; Eriksson, L. A.; Launay, E.; Mouriaux, F.; Belaud-Rotureau, M.-A.; Odent, S.; Gilot, D.

2022-04-17 genetics 10.1101/2022.04.17.488473 medRxiv
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Ganglioside-monosialic acid (GM1) gangliosidosis, a rare autosomal recessive disorder, is frequently caused by deleterious single nucleotide variants (SNVs) in GLB1 gene. These variants result in reduced {beta}-galactosidase ({beta}-gal) activity, leading to neurodegeneration associated with premature death. Currently, no effective therapy for GM1 gangliosidosis is available. Three ongoing clinical trials aim to deliver a functional copy of the GLB1 gene to stop disease progression. Here, we show that 41% of GLB1 pathogenic SNVs might be cured by adenine base editors (ABEs). Our results demonstrate that ABE efficiently corrects the pathogenic allele in patient-derived fibroblasts, restoring a therapeutic level of {beta}-gal activity. Unbiased off-target DNA analysis did not detect off-target editing activity in treated patients cells except a bystander edit without consequences on {beta}-gal activity. Altogether our results suggest that gene editing is an alternative strategy to cure GM1 gangliosidosis, by correcting the root cause of disease and avoiding repetitive adeno-associated virus injections.

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Inflammatory bowel disease risk gene C1ORF106 regulates actin dynamics in intestinal epithelial cells

Hebert-Milette, I.; Levesque, C.; Paquette, J.; Rivard, M.-E.; Villeneuve, L.; Boucher, G.; Goyette, P.; Charron, G.; Rioux, J. D.

2025-03-15 genetics 10.1101/2025.03.14.643205 medRxiv
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Background and aimsC1ORF106 has previously been associated with inflammatory bowel diseases (IBD) via large-scale genetic studies. Increased intestinal permeability is a hallmark of IBD and is observed in at-risk individuals prior to the appearance of clinical symptoms. C1ORF106 was previously shown to regulate intestinal barrier permeability through the regulation of adherens junction stability and through the formation of tight junctions, which impacted actin assembly. However, the downstream impact and molecular mechanisms involved in actin regulation by C1ORF106 havent been explored. Our study aimed at identifying which pathways involved in intestinal epithelial barrier regulation and F-actin regulation are impacted by C1ORF106 and its IBD-associated variant. MethodsWe knocked down (KD) the expression of C1ORF106 in human colonic epithelial cells and characterized the function of the 333F variant in intestinal epithelial spheroid cultures obtained from patient-derived human induced pluripotent stem cell (hiPSC). We measured barrier permeability and characterized spheroid formation, actin regulation and cell migration though immunofluorescence, western blots and permeability assays. ResultsC1ORF106 KD leads to impaired cortical actin belt dynamics and regulation of stress fiber formation, resulting in increased cell constriction, impaired barrier permeability, cell polarity and cell migration. Moreover, we demonstrated that an inhibition of ROCK rescues the actin belt and cell polarity phenotypes in C1ORF106 KD cells, demonstrating that C1ORF106 regulates these phenotypes through a ROCK-dependent mechanism. We also observed an altered nmMYO2-P localization in C1ORF106 KD cells associated with the formation of Vacuolar Apical Compartments (VACs), which are important for 3D epithelial spheroid formation. We observed a similar impact on cell polarity in intestinal epithelial spheroids obtained from hiPSC carrying the 333F variant, providing additional support that this pathway is involved in disease development. ConclusionWe provide insights into the molecular mechanisms by which C1ORF106 controls actin dynamics to regulate intestinal epithelial integrity. summaryC1ORF106 and its inflammatory bowel disease-associated genetic variant regulate intestinal barrier permeability through the regulation of tight junction formation and cell polarity in epithelial cells. This regulation is associated with altered F-actin dynamics that are ROCK-dependent.

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STX18-AS1 is a Long Noncoding RNA predisposing to Atrial Septal Defect via downregulation of NKX2-5 in differentiating cardiomyocytes

Liu, Y.; Choy, M.-k.; Abraham, S.; Tenin, G.; Black, G. C.; Keavney, B.

2020-05-30 genetics 10.1101/2020.05.27.118349 medRxiv
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Previous genome-wide association studies (GWAS) have identified a region of chromosome 4p16 associated with the risk of Atrial Septal Defect (ASD), which is among the commonest Congenital Heart Disease (CHD) phenotypes. Here, we identify the responsible gene in the region and elucidate disease mechanisms. Linkage disequilibrium in the region, eQTL analyses in human atrial tissues, and spatio-temporal gene expression studies in human embryonic hearts concordantly suggested the long noncoding RNA (lncRNA) STX18-AS1 as the causative gene in the region. Using CRISPR/Cas9 knockdown in HepG2 cells, STX18-AS1 was shown to regulate the expression of the key cardiac transcription factor NKX2-5 via a trans-acting effect on promoter histone methylation. Furthermore, STX18-AS1 knockdown depleted the potential of human embryonic stem cells (H9) to differentiate into cardiomyocytes, without affecting their viability and pluripotency, providing a mechanistic explanation for the clinical association.

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AAV-based gene replacement reverses Neurexin-2 downregulation in the cerebellum of a mouse model of phosphomannomutase 2 deficiency (PMM2-CDG)

Zhong, M.-l.; Lai, K.

2025-08-14 genetics 10.1101/2025.08.11.669733 medRxiv
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Phosphomannomutase 2 (PMM2) deficiency is the most common congenital disorders of glycosylation (CDG) with an estimated incidence ranging from 1:20,000 to 1:80,000. Patients manifest a broad spectrum of clinical manifestations, with neurological deficits often emerging as the earliest sign, and may progress to severe multi-organ dysfunction. Mortality reaches 20% by the age of six, primarily due to severe infections, liver insufficiency, or cardiomyopathy. The pathophysiology of the tissue-specific complications remains unclear and there is currently no cure for the disease. In this study, we performed omics analyses of cerebella isolated from a mouse model of PMM2-CDG. RNA-Seq analysis revealed altered gene expression in pathways involved in immune responses and coagulation, while proteomic analysis of proteins enriched by lectin-affinity chromatography identified proteins required for neurodevelopment and neurotransmission. We validated our results by demonstrating significant downregulation of Neurexin-2 in the Pmm2 knockout (KO) mouse cerebella and showed that its reduced abundance can be reversed by AAV9-PMM2 gene treatment of the Pmm2 KO mice.

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A Novel TRPC6 Mutation Causes Autosomal Dominant FSGS

Bhattacharya, R.; Mou, X.; Leeman, S. M.; Mishra, A.; Kalejaiye, T. D.; Stangl, M.; Silas, D.; Soldano, K.; Sperati, C. J.; Olabisi, O.; Hall, G.; Musah, S.

2025-02-15 genetics 10.1101/2025.02.11.637765 medRxiv
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FSGS is the most common primary glomerular lesion that causes kidney failure in the US. FSGS results from injury or loss of glomerular visceral epithelial cells (i.e. podocytes). Pathogenic variants in TRPC6 can cause FSGS through dysregulated calcium conductance and associated disturbances in podocyte physiology. Here, we describe a 5-generation kindred with FSGS caused by a novel compound C-terminal TRPC6 mutation. Analysis of patient-specific iPSC-derived podocytes and glomerular capillary wall-on-a-chip systems revealed that the compound variants disrupt TRPC6 protein structure, intermolecular interactions, and membrane localization. Combined therapy with Sildenafil and Losartan ameliorated these disturbances compared to conventional immunosuppressive treatment.

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DNA-PKcs Inhibition Improves Sequential Gene Insertion of the Full-Length CFTR cDNA in Airway Stem Cells

Stack, J. T.; Rayner, R. E.; Nouri, R.; Suarez, C. J.; Kim, S. H.; Kanke, K. L.; Vetter, T. A.; Cormet-Boyaka, E.; Vaidyanathan, S.

2024-08-12 genetics 10.1101/2024.08.12.607571 medRxiv
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Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Although many people with CF (pwCF) are treated using CFTR modulators, some are non-responsive due to their genotype or other uncharacterized reasons. Autologous airway stem cell therapies, in which the CFTR cDNA has been replaced, may enable a durable therapy for all pwCF. Previously, CRISPR-Cas9 with two AAVs was used to sequentially insert two halves of the CFTR cDNA and an enrichment cassette into the CFTR locus. However, the editing efficiency was <10% and required enrichment to restore CFTR function. Further improvement in gene insertion may enhance cell therapy production. To improve CFTR cDNA insertion in human airway basal stem cells (ABCs), we evaluated the use of the small molecules AZD7648 and ART558 which inhibit non-homologous end joining (NHEJ) and micro-homology mediated end joining (MMEJ). Adding AZD7648 alone improved gene insertion by 2-3-fold. Adding both ART558 and AZD7648 improved gene insertion but induced toxicity. ABCs edited in the presence of AZD7648 produced differentiated airway epithelial sheets with restored CFTR function after enrichment. Adding AZD7648 did not increase off-target editing. Further studies are necessary to validate if AZD7648 treatment enriches cells with oncogenic mutations.

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Systemic genome-epigenome analysis captures the lineage specificity and functional significance for MYB associated super-enhancer in gastrointestinal adenocarcinoma

Li, F.; Wang, S.; Chen, L.; Jiang, N.; Chen, X.; Li, J.

2024-11-12 genetics 10.1101/2024.11.11.622904 medRxiv
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The gastrointestinal adenocarcinoma is a major cancer type for the digestive system, ranking as the top cause of cancer-related deaths worldwide. In contrast to the large body of studies on the protein-coding regions mutations, the knowledge about the landscape of its non-coding regulatory elements is still insufficient. Combining the analysis of active enhancers profile and genomic structural variation, we discovered and validated a lineage-specific super-enhancer for MYB in gastrointestinal adenocarcinoma. This super-enhancer is constituted by a predominant enhancer e4 and multiple facilitator enhancers, whose transcriptional activity is controlled by the direct binding of HNF4A and MYB itself. Suppression of the super-enhancer downregulated the expression of MYB, inhibited the downstream Notch signaling and prevented the development of gastrointestinal adenocarcinoma in vitro and in vivo. Our study revealed a non-coding variation-based mechanism to affect MYB expression in a lineage-specific manner, which provided an inspiring insight into the carcinogenic mechanism and therapeutic strategies for gastrointestinal adenocarcinoma.

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MARK2 variants cause autism spectrum disorder via the downregulation of WNT/β-catenin signaling pathway

Gong, M.; Li, J.; Liu, Y.; Matheus, V. M. B. W.; Li, Q.; Liu, H.; Liang, C.; Joel A, M.-R.; Cohen, A. S. A.; Hughes, S. S.; Sullivan, B. R.; Waddell, V.; Henriette van den Boogaard, M. J.; van Jaarsveld, R. H.; Binsbergen, E. v.; van Gassen, K. L.; Wang, T.; Hiatt, S. M.; Amaral, M. D.; Kelley, W. V.; Zhao, J.; Feng, W.; Ren, C.; Yu, Y.; Boczek, N. J.; Ferber, M. J.; Lahner, C.; Elliott, S.; Ruan, Y.; Mignot, C.; Keren, B.; Xie, H.; Wang, X.; Popp, B.; Zweier, C.; Piard, J.; Coubes, C.; Tran-Mau-Them, F.; Safraou, H.; Innes, M.; Gauthier, J.; Michaud, J. L.; Koboldt, D. C.; Sylvie, O.; Willems

2024-04-25 genetic and genomic medicine 10.1101/2024.04.24.24304501 medRxiv
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MARK2, a member of the evolutionarily conserved PAR1/MARK serine/threonine kinase family, has been identified as a novel risk gene for autism spectrum disorder (ASD) based on the enrichment of de novo loss-of-function (Lof) variants in large-scale sequencing studies of ASD individuals. However, the features shared by affected individuals and the molecular mechanism of MARK2 variants during early neural development remained unclear. Here, we report 31 individuals carrying heterozygous MARK2 variants and presenting with ASD, other neurodevelopmental disorders, and typical facial dysmorphisms. Lof variants predominate (81%) in affected individuals, while computational analysis and in vitro transfection assay also point to MARK2 loss resulting from missense variants. Using patient-derived and CRISPR-engineered isogenic induced pluripotent stem cells (iPSCs), and Mark2+/- (HET) mice, we show that MARK2 loss leads to systemic neurodevelopmental deficits, including anomalous polarity in neural rosettes, imbalanced proliferation and differentiation in neural progenitor cells (NPCs), abnormal cortical development and ASD-like behaviors in mice. Further using RNA-Seq and lithium treatment, we link MARK2 loss to the downregulated WNT/{beta}-catenin signaling pathway and identify lithium as a potential drug for treating MARK2-related ASD.