Cleavage stimulating factor 64 depletion mitigates cardiac fibrosis through alternative polyadenylation

Unraveling the role of MiR-181 in skin fibrosis pathogenesis by targeting NUDT21

Systemic sclerosis (SSc) is a life-threatening autoimmune disease characterized by widespread fibrosis in the skin and several internal organs. Nudix Hydrolase 21 (NUDT2 or CFIm25) downregulation in fibroblasts is known to play detrimental roles in both skin and lung fibrosis. This study aims to investigate the upstream mechanisms that lead to NUDT21 repression in skin fibrosis. We identified transforming growth factor β (TGFβ1) as the primary cytokine that downregulated NUDT21 in normal skin fibroblasts. In the bleomycin-induced dermal fibrosis model, consistent with the peak activation of TGFβ1 at the late fibrotic stage, NUDT21 was downregulated at this stage, and delayed NUDT21 knockdown during this fibrotic phase led to enhanced fibrotic response to bleomycin. Further investigation suggested TGFβ downregulated NUDT21 through microRNA (miRNA) 181a and 181b induction. Both miR-181a and miR-181b were elevated in bleomycin-induced skin fibrosis in mice and primary fibroblasts isolated from SSc patients, and they directly targeted NUDT21 and led to its downregulation in skin fibroblasts. Functional studies demonstrated that miR-181a and miR-181b inhibitors attenuated bleomycin-induced skin fibrosis in mice in association with decreased NUDT21 expression, while miR-181a and miR-181b mimics promoted bleomycin-induced fibrosis. Overall, these findings suggest a novel role for miR-181a/b in SSc pathogenesis by repressing NUDT21 expression.

An AluYa5 Insertion in the 3'UTR of COL4A1 and Cerebral Small Vessel Disease

Importance

Cerebral small vessel diseases (CSVDs) account for one-fifth of stroke cases. Numerous familial cases remain unresolved after routine screening of known CSVD genes.

Objective

To identify novel genes and mechanisms associated with familial CSVD.

Design, Setting, and Participants

This 2-stage study involved linkage analysis and a case-control study; linkage analysis and whole exome and genome sequencing were used to identify candidate gene variants in 2 large families with CSVD (9 patients with CSVD). Then, a case-control analysis was conducted on 246 unrelated probands, including probands from these 2 families and 244 additional probands. All probands (clinical onset

Main Outcomes and Measures

A pathogenic AluYa5 insertion was identified within the COL4A1 3'UTR in the 2 large families with CSVD. Reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR), Western blot, and long-read RNA sequencing were used to investigate outcomes associated with the insertion using patient fibroblasts. Clinical and magnetic resonance imaging features of probands with variants and available relatives were assessed.

Results

Among 246 probands (141 females [57.3%]; median [IQR] age at referral, 56 [49-64] years), 7 patients of French ancestry carried the insertion. This insertion was absent in 467 healthy French individuals in a control group (odds ratio, ∞; 95% CI, 2.78 to ∞; P = 5 × 10-4) and 10 847 individuals from the gnomAD structural variant database (odds ratio, ∞; 95% CI, 64.77 to ∞; P = 2.42 × 10-12). In these 7 patients' families, 19 family members with CSVD carried the insertion. RT-qPCR and Western blot showed an upregulation of COL4A1 mRNA (10.6-fold increase; 95% CI, 1.4-fold to 17.1-fold increase) and protein levels (2.8-fold increase; 95% CI, 2.1-fold to 3.5-fold increase) in patient vs control group fibroblasts. Long-read RNA sequencing data showed that the insertion was associated with perturbation in the use of canonical COL4A1 polyadenylation signals (approximately 87% of isoforms transcribed from the wild type allele vs 5% of isoforms transcribed from the allele with the insertion used the 2 distal canonical polyadenylation signals). The main clinical feature of individuals with CSVD was the recurrence of pontine ischemic lesions starting at an early age (17 of 19 patients [89.5%]).

Conclusions and relevance

This study found a novel mechanism associated with COL4A1 upregulation and a highly penetrant adult-onset CSVD. These findings suggest that quantitative alterations of the cerebrovascular matrisome are associated with CSVD pathogenesis, with diagnostic and therapeutic implications.

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MESH Headings

• Adult
• Female
• Humans
• Middle Aged
• 3' Untranslated Regions/genetics
• Alleles
• Case-Control Studies
• Cerebral Small Vessel Diseases/genetics
• Collagen Type IV/metabolism
• Protein Isoforms
• Mutagenesis, Insertional

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Affiliation(s)

Chaker Aloui NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France
Lisa Neumann NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France
Françoise Bergametti NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France
Eric Sartori Service de Neurologie, Centre Hospitalier Bretagne Sud, Lorient, France
Marc Herbreteau Service de Neurologie, Centre Hospitalier Bretagne Sud, Lorient, France
Arnaud Maillard Assistance Publique-Hôpitaux de Paris, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, Paris, France
Thibault Coste NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France Assistance Publique-Hôpitaux de Paris, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, Paris, France
Hélène Morel NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France Assistance Publique-Hôpitaux de Paris, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, Paris, France
Dominique Hervé NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France Assistance Publique-Hôpitaux de Paris, Service de Neurologie, Hôpital Lariboisière, Paris, France
Hugues Chabriat NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France Assistance Publique-Hôpitaux de Paris, Service de Neurologie, Hôpital Lariboisière, Paris, France
Serge Timsit Service de Neurologie Vasculaire, Centre Hospitalier Régional Universitaire de Brest, Brest, France
Irina Viakhireva Service de Neurologie Vasculaire, Centre Hospitalier Régional Universitaire de Brest, Brest, France
Yves Denoyer Service de Neurologie, Centre Hospitalier Bretagne Sud, Lorient, France Université de Rennes, Laboratoire Traitement du Signal et de l'Image, Institut National de la Santé Et de la Recherche Médicale Unité Mixte de Recherche 1099, Rennes, France
Rémi Allibert Service de Neurologie, Unité Neurovasculaire, Centre Hospitalier Universitaire de Saint Etienne, Saint Etienne, France
Florence Demurger Service de Neurologie, Unité Neurovasculaire, Centre Hospitalier Bretagne Atlantique, Vannes, France
Cedric Gollion Service de Neurologie, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
Patrick Vermersch Univ. Lille, Institut National de la Santé Et de la Recherche Médicale Unité Mixte de Recherche 1172 LilNCog, Centre Hospitalier Universitaire Lille, Fédérations Hospitalo-Universitaire Precise, Lille, France
Florence Marchelli Assistance Publique-Hôpitaux de Paris, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, Paris, France
Corinne Blugeon GenomiqueENS, Institut de Biologie de l’Ecole Normale Supérieur, Département de biologie, École Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé Et de la Recherche Médicale, Université Paris Sciences et Lettres, Paris, France
Sophie Lemoine GenomiqueENS, Institut de Biologie de l’Ecole Normale Supérieur, Département de biologie, École Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé Et de la Recherche Médicale, Université Paris Sciences et Lettres, Paris, France
Claire Tourtier-Bellosta Service de Neurologie, Centre Hospitalier Bretagne Sud, Lorient, France
Alexis Brouazin Service de neurologie, Centre Hospitalier de Cornouaille, Quimper, France
Anne-Louise Leutenegger NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France
Eva Pipiras NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France Assistance Publique-Hôpitaux de Paris, Hôpitaux Jean Verdier et Armand Trousseau, Université Sorbonne Paris Nord, Bobigny, France
Elisabeth Tournier-Lasserve NeuroDiderot, Université Paris Cité, Institut National de la Santé Et de la Recherche Médicale, Unité Mixte de Recherche 1141, Paris, France Assistance Publique-Hôpitaux de Paris, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, Paris, France

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siRNA Delivery from Cationic Nanocarriers Prepared by Diffusion-assisted Loading in the Presence and Absence of Electrostatic Interactions

In this study, we use modified cationic nanocarriers as vehicles for the intracellular delivery of therapeutic siRNA. After developing nanocarrier formulations with appropriate pKa, size, swellability, and cytocompatibility, we investigated the importance of siRNA loading methods by studying the impact of the pH and time over which siRNA is loaded into the nanocarriers. We concentrate on diffusion-based loading in the presence and absence of electrostatic interactions. siRNA release kinetics were studied using samples prepared from nanocarriers loaded by both mechanisms. In addition, siRNA delivery was evaluated for two formulations. While previous studies were conducted with samples prepared by siRNA loading at low pH values, this research provides evidence that loading conditions of siRNA affect the release behavior. This study concludes that this concept could prove advantageous for eliciting prolonged intracellular release of nucleic acids and negatively charged molecules, effectively decreasing dose frequency and contributing to more effective therapies and improved patient outcomes. In addition, our findings could be leveraged for enhanced control over siRNA release kinetics, providing novel methods for the continued optimization of cationic nanoparticles in a wide array of RNA interference-based applications.

Alternative polyadenylation regulation in cardiac development and cardiovascular disease

Cleavage and polyadenylation of pre-mRNAs is a necessary step for gene expression and function. Majority of human genes exhibit multiple polyadenylation sites, which can be alternatively used to generate different mRNA isoforms from a single gene. Alternative polyadenylation (APA) of pre-mRNAs is important for the proteome and transcriptome landscape. APA is tightly regulated during development and contributes to tissue-specific gene regulation. Mis-regulation of APA is linked to a wide range of pathological conditions. APA-mediated gene regulation in the heart is emerging as a new area of research. Here, we will discuss the impact of APA on gene regulation during heart development and in cardiovascular diseases. First, we will briefly review how APA impacts gene regulation and discuss molecular mechanisms that control APA. Then, we will address APA regulation during heart development and its dysregulation in cardiovascular diseases. Finally, we will discuss pre-mRNA targeting strategies to correct aberrant APA patterns of essential genes for the treatment or prevention of cardiovascular diseases. The RNA field is blooming due to advancements in RNA-based technologies. RNA-based vaccines and therapies are becoming the new line of effective and safe approaches for the treatment and prevention of human diseases. Overall, this review will be influential for understanding gene regulation at the RNA level via APA in the heart and will help design RNA-based tools for the treatment of cardiovascular diseases in the future.