Biology subjects

Vincenti, F.

Publications and source records attributed to Vincenti, F..

5 recordsLinked to original sources

bioRxiv2023

CIA: a Cluster Independent Annotation method to investigate cell identities in scRNA-seq data

Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of the transcriptional landscape of complex tissues, enabling the discovery of novel cell types and biological functions. However, the identification and classification of cells from scRNA-seq datasets remain significant challenges. To address this, we developed a new computational tool called CIA (Cluster Independent Annotation), which accurately identifies cell types across different datasets without requiring a fully annotated reference dataset or complex machine learning processes. Based on predefined cell type signatures, CIA provides a highly user-friendly and practical solution to functional annotation of single cells. Our results demonstrate that CIA outperforms other state-of-the-art approaches, while also having significantly lower computational running time. Overall, CIA simplifies the process of obtaining reproducible signature-based cell assignments that can be easily interpreted through graphical summaries providing researchers with a powerful tool to explore the complex transcriptional landscape of single cells. The CIA framework is implemented in both the Python and R programming languages, making it applicable to all main single-cell analysis frameworks, and it is available under the MIT license with its documentation at the following links: Python package: https://pypi.org/project/cia-python/ Python tutorial: https://cia-python.readthedocs.io/en/latest/tutorial/Cluster_Independent_Annotation.html R package and tutorial: https://github.com/ingmbioinfo/CIA_R

bioinformatics↗

bioRxiv2023

Human Bone Marrow Plasma Cell Atlas: Maturation and Survival Pathways Unraveled by Single Cell Analyses

Human bone marrow (BM) plasma cells are heterogeneous, ranging from newly arrived antibody-secreting cells (ASC) to long-lived plasma cells (LLPC). We provide single cell transcriptional resolution of 17,347 BM ASC from 5 healthy adults. Fifteen clusters were identified ranging from newly minted ASC (cluster 1) expressing MKI67 and high MHC Class II that progressed to late clusters 5-8 through intermediate clusters 2-4. Additional clusters included early and late IgM-predominant ASC of likely extra-follicular origin; IFN-responsive; and high mitochondrial activity ASC. Late ASCs were distinguished by differences in G2M checkpoints, MTOR signaling, distinct metabolic pathways, CD38 expression, and utilization of TNF-receptor superfamily members. They mature through two distinct paths differentiated by the degree of TNF signaling through NFKB. This study provides the first single cell resolution atlas and molecular roadmap of LLPC maturation, thereby providing insight into differentiation trajectories and molecular regulation of these essential processes in the human BM microniche. This information enables investigation of the origin of protective and pathogenic antibodies in multiple diseases and development of new strategies targeted to the enhancement or depletion of the corresponding ASC. One Sentence Summary: The single cell transcriptomic atlas of human bone marrow plasma cell heterogeneity shows maturation of class-switched early and late subsets, specific IgM and Interferon-driven clusters, and unique heterogeneity of the late subsets which encompass the long-lived plasma cells.

immunology↗

bioRxiv2022

Perturbations in podocyte transcriptome and biological pathways induced by FSGS associated circulating factors.

Focal segmental glomerulosclerosis (FSGS) is frequently associated with heavy proteinuria and progressive renal failure requiring dialysis or kidney transplantation. However, primary FSGS also has 40-80% risk of recurrence of disease in the transplanted kidney (rFSGS). Multiple circulating factors have been proposed to contribute to the pathogenesis of primary and rFSGS. However, neither the factors nor the downstream effectors specific to individual factors have been identified. The tumor necrosis factor, TNF pathway activation by one or more circulating factors present in the sera of patients with FSGS has been supported by multiple studies. The proposed circulating factors include soluble urokinase-type plasminogen activator receptor (suPAR) and patient derived CD40 autoantibody (CD40autoAb) in the development and recurrence of FSGS. In a human in vitro model, using two novel human antibodies-anti uPAR (2G10) and anti CD40 antibody, we show that the podocyte injury caused by sera from FSGS patients is at least in part mediated by CD40 and suPAR. Additionally, we employ gene expression studies to compare the molecules and pathways activated in response to CD40 autoantibody from rFSGS patients (rFSGS/CD40autoAb) and suPAR, and delineate the unique pathways associated with FSGS injury and transcriptional podocyte alterations with targeted blockade of suPAR and CD40 pathways. Clinical ImpactFocal Segmental Glomerulosclerosis remains a disease without specific therapy for primary disease and high rate of recurrence after kidney transplantation. Circulating factors are implicated in the pathogenesis of FSGS but targeting them for therapy has remained elusive. We propose two potential therapeutic molecules for rFSGS treatment-a human anti-uPAR antibody (2G10) and a humanized anti-CD40 blocking antibody (Bristol Meyer Squibb, 986090) that reverse podocyte injury associated with FSGS in cultured podocytes and can be further tested in pre-clinical and clinical models. Furthermore, we use microarray profiling to identify transcriptional pathways specific to podocyte injury from patient-derived CD40 autoantibodies (rFSGS/CD40autoAb) and suPAR and selective blockade of these pathways to abrogate podocyte injury.

immunology↗

bioRxiv2021

TNFa and IL-6 promote ex-vivo proliferation of lineage-committed human regulatory T cells

Treg therapy is being tested in clinical trials in transplantation and autoimmune diseases, however, the impact of inflammation on Tregs is unclear. In this study, we challenged human Tregs ex-vivo with pro-inflammatory cytokines, TNF and IL-6. These cytokines enhanced Treg proliferation induced by anti-CD3 and anti-CD28 or CD28 superagonist (CD28SA) while maintaining high expression of FOXP3 and HELIOS, demethylated FOXP3 enhancer, and low expression of cytokines IFNg, IL-4 and IL-17. Blocking TNF receptor signaling using etanercept or deletion of TNF receptor 2 using CRISPR/Cas9 blunted Treg proliferation and attenuated FOXP3 and HELIOS expression, revealing the importance of TNFR2 signaling in Treg proliferation and lineage stability. The robust proliferation induced by CD28SA with IL-6 and TNF may be adopted for the expansion of therapeutic Tregs. Metabolomics analysis showed that Tregs expanded with CD28SA plus cytokines had more active glycolysis and oxidative phosphorylation, increased energy production, and higher antioxidant potential. Finally, CD28SA plus cytokine-expanded Tregs had comparable suppressive activity in vitro and in vivo in a humanized mouse model of graft-versus-host-disease when compared to Tregs expanded using the conventional protocol. These results demonstrate that human Tregs positively respond to proinflammatory cytokines with enhanced proliferation without compromising their lineage identity or function.

immunology↗

bioRxiv2020

ZFP423 regulates early patterning and multiciliogenesis in the hindbrain choroid plexus

The choroid plexus (ChP) is a secretory tissue that produces cerebrospinal fluid (CSF) and secretes it into the ventricular system. CSF flows from the lateral to the third ventricle, and then to the fourth ventricle through the cerebral aqueduct. Recent studies have uncovered new, active roles for this structure in the regulation of neural stem cell maintenance and differentiation into neurons. Zfp423, encoding a Kruppel-type zinc finger transcription factor essential for cerebellar development and mutated in rare cases of cerebellar vermis hypoplasia / Joubert syndrome and other ciliopathies, is expressed in the hindbrain roof plate (RP), from which the IV ventricle ChP arises, and in mesenchymal cells giving rise to the stroma and leptomeninges. Zfp423 mutants display a marked reduction of the hindbrain ChP (hChP), which fails to express key markers of its secretory function and genes implicated in its development and maintenance (Lmx1a, Otx2). The mutant hChP displays a complete lack of multiciliated ependymal cells. A transcriptome analysis conducted at the earliest stages of hChP development and subsequent validations demonstrate that the mutant hChp displays a strong deregulation of pathways involved in early hindbrain patterning and multiciliated cell fate specification. Our results propose Zfp423 as a master gene and one of the earliest known determinants of hChP development.

developmental biology↗