Francesca Vacante

All Publications

• The LncRNA MYRACL Regulates Human Oligodendrocyte Maturation and Myelination. Molecular therapy : the journal of the American Society of Gene Therapy Tsarouchas, T. M., Vacante, F., Kazakou, N. L., Wagstaff, L., Bennett, M., Zoupi, L., Gibson, E. M., Baker, A. H., Williams, A. 2025

  Abstract

  Recent studies have described disease-associated expression patterns of long non-coding RNAs (lncRNA) associated with neurodevelopment and neurodegeneration, highlighting their potential as regulators of function and therefore potential therapeutic targets. Oligodendrocyte dysfunction drives central nervous system (CNS) myelin disruption in neurological disorders, but the mechanisms underlying impaired myelin patterns are still poorly understood. In this study, we uncover a role for the long noncoding RNA (lncRNA) MYRACL (MYelination RegulAting oligodendroCyte associated LncRNA), as regulator of functional maturation and oligodendrocyte myelination. Analysis of RNA-sequencing data performed in human post-mortem brain tissue revealed MYRACL among the top enriched genes expressed in the oligodendrocyte (OL) population compared to the oligodendrocyte precursor cell (OPC) cluster. We validated this finding in an embryonic stem cell (ESC)-derived oligodendroglia cell culture model. Analysis of evolutionary conservation and protein coding potential showed that MYRACL is non-coding and may exhibit conserved regions across mammalian species. Further co-expression analysis of lncRNAs-mRNAs suggested that expression of MYRACL positively correlates with genes known to be involved in driving oligodendroglia differentiation. GapmeR-mediated knockdown of nuclear MYRACL disrupted OL maturation in vitro, while lentivirus-mediated overexpression promoted OL differentiation with enhancement of myelin formation in-vitro. Our findings highlight MYRACL as a novel regulatory mechanism in human OL maturation and myelination. By providing a human, translationally relevant platform, this work advances our ability to model human myelination in vitro and paves the way for precision medicine approaches targeting lncRNA-mediated dysregulation in neurodevelopmental and neurodegenerative diseases.

  View details for DOI 10.1016/j.ymthe.2025.08.011

  View details for PubMedID 40783783

• Effective Transcriptional Induction of the CARMN/miR-143/145 Complex Locus in Smooth Muscle Cells Using CRISPR Activation. Arteriosclerosis, thrombosis, and vascular biology Vacante, F., Sanchez-Esteban, S., Tsarouchas, T., Rodor, J., Bennett, M., Carroll, M. S., Beqqali, A., Baker, A. H. 2025

  View details for DOI 10.1161/ATVBAHA.124.322353

  View details for PubMedID 40740134

• Generation of two induced pluripotent stem cell lines from patients with Facioscapulohumeral muscular dystrophy. Stem cell research Venkateshappa, R., Vacante, F., Xu, L., Canel-Rivero, G., Day, J. W., Wu, J. C. 2025; 87: 103794

  Abstract

  Facioscapulohumeral muscular dystrophy (FSHD) is a genetically complex condition marked by progressive skeletal muscle weakness, primarily affecting the face, shoulders, and upper arms. Here, we generated human induced pluripotent stem cell (iPSC) lines from two clinically diagnosed FSHD patients and characterized their pluripotency and germline markers. Both lines exhibited pluripotency markers, maintained normal karyotypes, and were capable of differentiating into all three germ layers. These iPSC lines are valuable resources for studying FSHD mechanisms and potential drug discovery applications.

  View details for DOI 10.1016/j.scr.2025.103794

  View details for PubMedID 40773824

• Targeting Cis-regulatory elements for CRISPR-mediated transcriptional activation of the human MIR503HG locus. Vascular pharmacology Monteiro, J. P., Vacante, F., De Pace, A., Bennett, M., Rodor, J., O'Carroll, D., Wu, J. C., Quertermous, T., Baker, A. H. 2025: 107521

  Abstract

  Advances in genome annotation have revealed a striking increase in the number and complexity of non-coding RNA (ncRNA) genes, particularly multi-transcript loci that harbor long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) within the same genomic region. These loci can often function as coordinated regulatory units, with their transcription modulated by shared cis-acting regulatory elements (CREs). Traditional gene manipulation approaches, which typically target individual transcripts, are insufficient to capture the full regulatory and therapeutic potential of these complex loci. Here, we present "cis-ON" a single-vector lentiviral delivery system based on CRISPR activation (CRISPRa), designed to simultaneously upregulate multiple noncoding RNA transcripts by targeting a single CRE. We focused on the evolutionarily conserved MIR503HG locus, which encodes seven lncRNA isoforms and hosts the miR-424/503 cluster, both implicated in various cellular processes, including proliferation, angiogenesis, and endothelial-to-mesenchymal transition. Using integrative analysis of histone marks (H3K27Ac, H3K4Me3), DNase hypersensitivity, and CAGE-seq data, we identified the primary promoter of the MIR503HG locus. A dual fluorescent reporter screen selected optimal single guide RNAs (sgRNAs) for targeting this region. We then engineered cis-ON, a novel lentiviral system combining dCas9-VPR and sgRNA to enable a streamlined single-vector delivery approach. Transduction of primary human endothelial cells with this system robustly activated the entire locus including the MIR503HG isoforms and co-embedded miRNAs miR-424 and miR-503, demonstrating coordinated transcriptional regulation. Additionally, the neighboring LINC00629 lncRNA locus remained unaffected, highlighting regulatory specificity. This approach demonstrates the feasibility of modulating complex ncRNA loci across a ~ 10 kb genomic region by targeting a single CRE, bypassing limitations of transcriptspecific strategies. By enabling simultaneous upregulation of lncRNAs and miRNAs, the cis-ON platform provides a streamlined strategy for restoring regulatory networks disrupted in disease.

  View details for DOI 10.1016/j.vph.2025.107521

  View details for PubMedID 40653285

• Framework for Cultivating Leadership and Driving Growth. Circulation Vacante, F., Yildirim, Z., Wu, J. C. 2025; 151 (7): 430-432

  View details for DOI 10.1161/CIRCULATIONAHA.124.073352

  View details for PubMedID 39960988

• Functional screening identifies miRNAs with a novel function inhibiting vascular smooth muscle cell proliferation. Molecular therapy : the journal of the American Society of Gene Therapy Rodor, J., Klimi, E., Brown, S. D., Krilis, G., Braga, L., Ring, N. A., Ballantyne, M. D., Kesidou, D., Nguyen Dinh Cat, A., Miscianinov, V., Vacante, F., Miteva, K., Bennett, M., Beqqali, A., Giacca, M., Zacchigna, S., Baker, A. H. 2025; 33 (2): 615-630

  Abstract

  Proliferation of vascular smooth muscle cells (vSMCs) is a crucial contributor to pathological vascular remodeling. MicroRNAs (miRNAs) are powerful gene regulators and attractive therapeutic agents. Here, we aimed to systematically identify and characterize miRNAs with therapeutic potential in targeting vSMC proliferation. Using high-throughput screening, we assessed the impact of 2,042 human miRNA mimics on vSMC proliferation and identified seven miRNAs with novel vSMC anti-proliferative function: miR-323a-3p, miR-449b-5p, miR-491-3p, miR-892b, miR-1827, miR-4774-3p, and miR-5681b. miRNA-mimic treatment affects proliferation of vSMCs from different vascular beds. Focusing on vein graft failure, where miRNA-based therapeutics can be applied to the graft ex vivo, we showed that these miRNAs reduced human saphenous vein smooth muscle cell (HSVSMC) proliferation without toxic effect. HSVSMC transcriptomics revealed a distinct set of targets for each miRNA, leading to the common downregulation of a cell-cycle gene network for all miRNAs. For miR-449b-5p, we showed that its candidate target, CCND1, contributes to HSVSMC proliferation. In contrast to HSVSMCs, miRNA overexpression in endothelial cells led to a limited response in terms of proliferation and transcriptomics. In an ex vivo vein organ model, overexpression of miR-323a-3p and miR-449b-5p reduced medial proliferation. Collectively, the results of our study show the therapeutic potential of seven miRNAs to target pathological vascular remodeling.

  View details for DOI 10.1016/j.ymthe.2024.12.037

  View details for PubMedID 39736815

  View details for PubMedCentralID PMC11852670

• Effective CRISPR modulation of complex non-coding RNA loci. Nature reviews. Cardiology Vacante, F., Baker, A. H. 2025

  View details for DOI 10.1038/s41569-025-01117-2

  View details for PubMedID 39810048

• Protocol to study electrophysiological properties of hPSC-derived 3D cardiac organoids using MEA and sharp electrode techniques. STAR protocols Venkateshappa, R., Yildirim, Z., Zhao, S. R., Wu, M. A., Vacante, F., Abilez, O. J., Wu, J. C. 2024; 5 (4): 103406

  Abstract

  Continuing advancements in human pluripotent stem cell (hPSC)-derived complex three-dimensional (3D) cardiac tissues require the development of novel technologies or adaptation of existing technologies to understand the physiology of the derived 3D cardiac tissues. In this protocol, we describe the use of multielectrode array (MEA) and sharp electrode electrophysiology techniques to investigate the electrical properties of 3D cardiac organoids. This protocol deciphers the electrical behavior of 3D cardiac organoids at both the single-cell level and tissue level.

  View details for DOI 10.1016/j.xpro.2024.103406

  View details for PubMedID 39514393

• Generation of Marfan syndrome-specific induced pluripotent stem cells harboring FBN1 mutations. Stem cell research Vacante, F., Venkateshappa, R., Htet, M., Yan, C., Wu, J. C. 2024; 80: 103518

  Abstract

  Marfan syndrome (MFS) is a hereditary condition caused by mutations in the FBN1 gene. Genetic mutations in the FBN1 locus impact the function of the encoded protein, Fibrillin 1, a structural molecule forming microfibrils found in the connective tissue. MFS patients develop severe cardiovascular complications including thoracic aortic aneurysm and aortic dissection, which predispose them to an enhanced risk of premature death. Here, we generated two induced pluripotent stem cell (iPSC) lines harboring mutations in the FBN1 gene (p.C1942C>A and c.1954 T>C), directly derived from MFS patients. We have shown that both iPSC lines displayed expression of pluripotency markers, normal karyotype and ability of trilineage differentiation, representing a valuable tool for the identification of new therapeutic strategies for intervening in this disease.

  View details for DOI 10.1016/j.scr.2024.103518

  View details for PubMedID 39096853

• Lnc-ing epicardium-derived cells to cardiac remodelling: lncRNA-TARID as a novel antifibrotic option. European heart journal Wu, X., Vacante, F., Wu, J. C. 2023

  View details for DOI 10.1093/eurheartj/ehad058

  View details for PubMedID 36928295

• CARMN Loss Regulates Smooth Muscle Cells and Accelerates Atherosclerosis in Mice. Circulation research Vacante, F., Rodor, J., Lalwani, M. K., Mahmoud, A. D., Bennett, M., De Pace, A. L., Miller, E., Van Kuijk, K., de Bruijn, J., Gijbels, M., Williams, T. C., Clark, M. B., Scanlon, J. P., Doran, A. C., Montgomery, R., Newby, D. E., Giacca, M., O'Carroll, D., Hadoke, P. W., Denby, L., Sluimer, J. C., Baker, A. H. 2021; 128 (9): 1258-1275

  Abstract

  [Figure: see text].

  View details for DOI 10.1161/CIRCRESAHA.120.318688

  View details for PubMedID 33622045

  View details for PubMedCentralID PMC7610708

• The function of miR-143, miR-145 and the MiR-143 host gene in cardiovascular development and disease. Vascular pharmacology Vacante, F., Denby, L., Sluimer, J. C., Baker, A. H. 2019; 112: 24-30

  Abstract

  Noncoding RNAs (long noncoding RNAs and small RNAs) are emerging as critical modulators of phenotypic changes associated with physiological and pathological contexts in a variety of cardiovascular diseases (CVDs). Although it has been well established that hereditable genetic alterations and exposure to risk factors are crucial in the development of CVDs, other critical regulators of cell function impact on disease processes. Here we discuss noncoding RNAs have only recently been identified as key players involved in the progression of disease. In particular, we discuss micro RNA (miR)-143/145 since they represent one of the most characterised microRNA clusters regulating smooth muscle cell (SMC) differentiation and phenotypic switch in response to vascular injury and remodelling. MiR143HG is a well conserved long noncoding RNA (lncRNA), which is the host gene for miR-143/145 and recently implicated in cardiac specification during heart development. Although the lncRNA-miRNA interactions have not been completely characterised, their crosstalk is now beginning to emerge and likely requires further research focus. In this review we give an overview of the biology of the genomic axis that is miR-143/145 and MiR143HG, focusing on their important functional role(s) in the cardiovascular system.

  View details for DOI 10.1016/j.vph.2018.11.006

  View details for PubMedID 30502421

  View details for PubMedCentralID PMC6395947