1
|
Oubounyt M, Adlung L, Patroni F, Wenke NK, Maier A, Hartung M, Baumbach J, Elkjaer ML. Inference of differential key regulatory networks and mechanistic drug repurposing candidates from scRNA-seq data with SCANet. Bioinformatics 2023; 39:btad644. [PMID: 37862243 PMCID: PMC10628438 DOI: 10.1093/bioinformatics/btad644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/07/2023] [Accepted: 10/19/2023] [Indexed: 10/22/2023] Open
Abstract
MOTIVATION The reconstruction of small key regulatory networks that explain the differences in the development of cell (sub)types from single-cell RNA sequencing is a yet unresolved computational problem. RESULTS To this end, we have developed SCANet, an all-in-one package for single-cell profiling that covers the whole differential mechanotyping workflow, from inference of trait/cell-type-specific gene co-expression modules, driver gene detection, and transcriptional gene regulatory network reconstruction to mechanistic drug repurposing candidate prediction. To illustrate the power of SCANet, we examined data from two studies. First, we identify the drivers of the mechanotype of a cytokine storm associated with increased mortality in patients with acute respiratory illness. Secondly, we find 20 drugs for eight potential pharmacological targets in cellular driver mechanisms in the intestinal stem cells of obese mice. AVAILABILITY AND IMPLEMENTATION SCANet is a free, open-source, and user-friendly Python package that can be seamlessly integrated into single-cell-based systems medicine research and mechanistic drug discovery.
Collapse
Affiliation(s)
- Mhaned Oubounyt
- Institute for Computational Systems Biology, University of Hamburg, Hamburg 22607, Germany
| | - Lorenz Adlung
- Department of Medicine, Hamburg Center for Translational Immunology (HCTI) and Center for Biomedical AI (bAIome), University Medical Center Hamburg-Eppendorf (UKE), Hamburg 20246, Germany
| | - Fabio Patroni
- Institute for Computational Systems Biology, University of Hamburg, Hamburg 22607, Germany
- Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas (Unicamp), Campinas, SP 13083-875, Brazil
| | - Nina Kerstin Wenke
- Institute for Computational Systems Biology, University of Hamburg, Hamburg 22607, Germany
| | - Andreas Maier
- Institute for Computational Systems Biology, University of Hamburg, Hamburg 22607, Germany
| | - Michael Hartung
- Institute for Computational Systems Biology, University of Hamburg, Hamburg 22607, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Hamburg 22607, Germany
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense 5000, Denmark
| | - Maria L Elkjaer
- Institute for Computational Systems Biology, University of Hamburg, Hamburg 22607, Germany
- Department of Neurology, Odense University Hospital, Odense 5000, Denmark
- Institute of Clinical Research, University of Southern Denmark, Odense 5000, Denmark
- Institute of Molecular Medicine, University of Southern Denmark, Odense 5000, Denmark
| |
Collapse
|
2
|
Agramunt J, Parke B, Mena S, Ubels V, Jimenez F, Williams G, Rhodes ADY, Limbu S, Hexter M, Knight L, Hashemi P, Kozlov AS, Higgins CA. Mechanical stimulation of human hair follicle outer root sheath cultures activates adjacent sensory neurons. SCIENCE ADVANCES 2023; 9:eadh3273. [PMID: 37889977 PMCID: PMC10610912 DOI: 10.1126/sciadv.adh3273] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023]
Abstract
Mechanical stimuli, such as stroking or pressing on the skin, activate mechanoreceptors transmitting information to the sensory nervous system and brain. It is well accepted that deflection of the hair fiber that occurs with a light breeze or touch directly activates the sensory neurons surrounding the hair follicle, facilitating transmission of mechanical information. Here, we hypothesized that hair follicle outer root sheath cells act as transducers of mechanical stimuli to sensory neurons surrounding the hair follicle. Using electrochemical analysis on human hair follicle preparations in vitro, we were able to show that outer root sheath cells release ATP and the neurotransmitters serotonin and histamine in response to mechanical stimulation. Using calcium imaging combined with pharmacology in a coculture of outer root sheath cells with sensory neurons, we found that the release of these three molecules from hair follicle cells leads to activation of sensory neurons.
Collapse
Affiliation(s)
- Julià Agramunt
- Department of Bioengineering, Imperial College London, London, UK
| | - Brenna Parke
- Department of Bioengineering, Imperial College London, London, UK
| | - Sergio Mena
- Department of Bioengineering, Imperial College London, London, UK
| | - Victor Ubels
- Department of Bioengineering, Imperial College London, London, UK
| | - Francisco Jimenez
- Mediteknia Clinic, Las Palmas, Gran Canaria, Spain
- University Fernando Pessoa Canarias, Gran Canaria, Spain
| | | | - Anna DY Rhodes
- Department of Bioengineering, Imperial College London, London, UK
| | - Summik Limbu
- Department of Bioengineering, Imperial College London, London, UK
| | - Melissa Hexter
- Department of Bioengineering, Imperial College London, London, UK
| | | | - Parastoo Hashemi
- Department of Bioengineering, Imperial College London, London, UK
| | - Andriy S. Kozlov
- Department of Bioengineering, Imperial College London, London, UK
| | | |
Collapse
|
3
|
Taliani V, Buonaiuto G, Desideri F, Setti A, Santini T, Galfrè S, Schirone L, Mariani D, Frati G, Valenti V, Sciarretta S, Perlas E, Nicoletti C, Musarò A, Ballarino M. The long noncoding RNA Charme supervises cardiomyocyte maturation by controlling cell differentiation programs in the developing heart. eLife 2023; 12:81360. [PMID: 36877136 PMCID: PMC10023161 DOI: 10.7554/elife.81360] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 03/03/2023] [Indexed: 03/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are emerging as critical regulators of heart physiology and disease, although the studies unveiling their modes of action are still limited to few examples. We recently identified pCharme, a chromatin-associated lncRNA whose functional knockout in mice results in defective myogenesis and morphological remodeling of the cardiac muscle. Here, we combined Cap-Analysis of Gene Expression (CAGE), single-cell (sc)RNA sequencing, and whole-mount in situ hybridization analyses to study pCharme cardiac expression. Since the early steps of cardiomyogenesis, we found the lncRNA being specifically restricted to cardiomyocytes, where it assists the formation of specific nuclear condensates containing MATR3, as well as important RNAs for cardiac development. In line with the functional significance of these activities, pCharme ablation in mice results in a delayed maturation of cardiomyocytes, which ultimately leads to morphological alterations of the ventricular myocardium. Since congenital anomalies in myocardium are clinically relevant in humans and predispose patients to major complications, the identification of novel genes controlling cardiac morphology becomes crucial. Our study offers unique insights into a novel lncRNA-mediated regulatory mechanism promoting cardiomyocyte maturation and bears relevance to Charme locus for future theranostic applications.
Collapse
Affiliation(s)
- Valeria Taliani
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
| | - Giulia Buonaiuto
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
| | - Fabio Desideri
- Center for Life Nano- and Neuro-Science, Istituto Italiano di Tecnologia (IIT)RomeItaly
| | - Adriano Setti
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
| | - Tiziana Santini
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
| | - Silvia Galfrè
- Center for Life Nano- and Neuro-Science, Istituto Italiano di Tecnologia (IIT)RomeItaly
| | - Leonardo Schirone
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of RomeLatinaItaly
| | - Davide Mariani
- Center for Human Technologies, Istituto Italiano di TecnologiaGenovaItaly
| | - Giacomo Frati
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of RomeLatinaItaly
| | - Valentina Valenti
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of RomeLatinaItaly
| | - Sebastiano Sciarretta
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of RomeLatinaItaly
| | - Emerald Perlas
- Epigenetics and Neurobiology Unit, EMBL-RomeMonterotondoItaly
| | - Carmine Nicoletti
- DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of RomeRomeItaly
| | - Antonio Musarò
- DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of RomeRomeItaly
| | - Monica Ballarino
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
| |
Collapse
|
4
|
Chen Z, King WC, Hwang A, Gerstein M, Zhang J. DeepVelo: Single-cell transcriptomic deep velocity field learning with neural ordinary differential equations. SCIENCE ADVANCES 2022; 8:eabq3745. [PMID: 36449617 PMCID: PMC9710871 DOI: 10.1126/sciadv.abq3745] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Recent advances in single-cell sequencing technologies have provided unprecedented opportunities to measure the gene expression profile and RNA velocity of individual cells. However, modeling transcriptional dynamics is computationally challenging because of the high-dimensional, sparse nature of the single-cell gene expression measurements and the nonlinear regulatory relationships. Here, we present DeepVelo, a neural network-based ordinary differential equation that can model complex transcriptome dynamics by describing continuous-time gene expression changes within individual cells. We apply DeepVelo to public datasets from different sequencing platforms to (i) formulate transcriptome dynamics on different time scales, (ii) measure the instability of cell states, and (iii) identify developmental driver genes via perturbation analysis. Benchmarking against the state-of-the-art methods shows that DeepVelo can learn a more accurate representation of the velocity field. Furthermore, our perturbation studies reveal that single-cell dynamical systems could exhibit chaotic properties. In summary, DeepVelo allows data-driven discoveries of differential equations that delineate single-cell transcriptome dynamics.
Collapse
Affiliation(s)
- Zhanlin Chen
- Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
| | - William C. King
- Healthcare and Life Sciences, Microsoft, Redmond, WA 98052, USA
| | - Aheyon Hwang
- Mathematical, Computational, and Systems Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Mark Gerstein
- Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
- Corresponding author. (M.G.); (J.Z.)
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, Irvine, CA 92697, USA
- Corresponding author. (M.G.); (J.Z.)
| |
Collapse
|
5
|
Dunville K, Tonelli F, Novelli E, Codino A, Massa V, Frontino AM, Galfrè S, Biondi F, Gustincich S, Caleo M, Pandolfini L, Alia C, Cremisi F. Laminin 511 and WNT signalling sustain prolonged expansion of hiPSC-derived hippocampal progenitors. Development 2022; 149:276383. [DOI: 10.1242/dev.200353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 08/08/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Using the timely re-activation of WNT signalling in neuralizing human induced pluripotent stem cells (hiPSCs), we have produced neural progenitor cells with a gene expression profile typical of human embryonic dentate gyrus (DG) cells. Notably, in addition to continuous WNT signalling, a specific laminin isoform is crucial to prolonging the neural stem state and to extending progenitor cell proliferation for over 200 days in vitro. Laminin 511 is indeed specifically required to support proliferation and to inhibit differentiation of hippocampal progenitor cells for extended time periods when compared with a number of different laminin isoforms assayed. Global gene expression profiles of these cells suggest that a niche of laminin 511 and WNT signalling is sufficient to maintain their capability to undergo typical hippocampal neurogenesis. Moreover, laminin 511 signalling sustains the expression of a set of genes responsible for the maintenance of a hippocampal neurogenic niche. Finally, xenograft of human DG progenitors into the DG of adult immunosuppressed host mice produces efficient integration of neurons that innervate CA3 layer cells spanning the same area of endogenous hippocampal neuron synapses.
Collapse
Affiliation(s)
- Keagan Dunville
- Laboratorio di Biologia, Scuola Normale Superiore 1 , Pisa, 56126 , Italy
| | - Fabrizio Tonelli
- Laboratorio di Biologia, Scuola Normale Superiore 1 , Pisa, 56126 , Italy
| | - Elena Novelli
- Istituto di Neuroscienze, Consiglio Nazionale delle Ricerche 2 , Pisa, 56124 , Italy
| | - Azzurra Codino
- Center for Human Technologies, Central RNA Lab, Istituto Italiano di Tecnologia 3 , Genova, 16152 , Italy
| | - Verediana Massa
- Istituto di Neuroscienze, Consiglio Nazionale delle Ricerche 2 , Pisa, 56124 , Italy
| | | | - Silvia Galfrè
- Department of Biology and Biotechnologies ‘Charles Darwin’, Università La Sapienza 4 , Roma, 00185 , Italy
| | - Francesca Biondi
- Istituto di Neuroscienze, Consiglio Nazionale delle Ricerche 2 , Pisa, 56124 , Italy
| | - Stefano Gustincich
- Center for Human Technologies, Central RNA Lab, Istituto Italiano di Tecnologia 3 , Genova, 16152 , Italy
| | - Matteo Caleo
- Istituto di Neuroscienze, Consiglio Nazionale delle Ricerche 2 , Pisa, 56124 , Italy
| | - Luca Pandolfini
- Center for Human Technologies, Central RNA Lab, Istituto Italiano di Tecnologia 3 , Genova, 16152 , Italy
| | - Claudia Alia
- Istituto di Neuroscienze, Consiglio Nazionale delle Ricerche 2 , Pisa, 56124 , Italy
| | - Federico Cremisi
- Laboratorio di Biologia, Scuola Normale Superiore 1 , Pisa, 56126 , Italy
| |
Collapse
|
6
|
Carvelli A, Setti A, Desideri F, Galfrè SG, Biscarini S, Santini T, Colantoni A, Peruzzi G, Marzi MJ, Capauto D, Di Angelantonio S, Ballarino M, Nicassio F, Laneve P, Bozzoni I. A multifunctional locus controls motor neuron differentiation through short and long noncoding RNAs. EMBO J 2022; 41:e108918. [PMID: 35698802 PMCID: PMC9251839 DOI: 10.15252/embj.2021108918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 12/12/2022] Open
Abstract
The transition from dividing progenitors to postmitotic motor neurons (MNs) is orchestrated by a series of events, which are mainly studied at the transcriptional level by analyzing the activity of specific programming transcription factors. Here, we identify a post‐transcriptional role of a MN‐specific transcriptional unit (MN2) harboring a lncRNA (lncMN2‐203) and two miRNAs (miR‐325‐3p and miR‐384‐5p) in this transition. Through the use of in vitro mESC differentiation and single‐cell sequencing of CRISPR/Cas9 mutants, we demonstrate that lncMN2‐203 affects MN differentiation by sponging miR‐466i‐5p and upregulating its targets, including several factors involved in neuronal differentiation and function. In parallel, miR‐325‐3p and miR‐384‐5p, co‐transcribed with lncMN2‐203, act by repressing proliferation‐related factors. These findings indicate the functional relevance of the MN2 locus and exemplify additional layers of specificity regulation in MN differentiation.
Collapse
Affiliation(s)
- Andrea Carvelli
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Adriano Setti
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Fabio Desideri
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Silvia Giulia Galfrè
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Silvia Biscarini
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Tiziana Santini
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Alessio Colantoni
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Giovanna Peruzzi
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Matteo Jacopo Marzi
- Center for Genomic Science of Istituto of Italiano di Tecnologia (IIT), Milan, Italy
| | - Davide Capauto
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | | | - Monica Ballarino
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Francesco Nicassio
- Center for Genomic Science of Istituto of Italiano di Tecnologia (IIT), Milan, Italy
| | - Pietro Laneve
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Irene Bozzoni
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy.,Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| |
Collapse
|
7
|
Quattrocolo G, Dunville K, Nigro MJ. Resurgent Sodium Current in Neurons of the Cerebral Cortex. Front Cell Neurosci 2021; 15:760610. [PMID: 34658797 PMCID: PMC8517112 DOI: 10.3389/fncel.2021.760610] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 09/13/2021] [Indexed: 11/29/2022] Open
Abstract
In the late ’90, Dr. Indira Raman, at the time a postdoctoral fellow with Dr. Bruce Bean, at Harvard University, identified a new type of sodium current, flowing through the channels that reopens when the membrane is repolarized. This current, called “resurgent Sodium current,” was originally identified in cerebellar Purkinje neurons and has now been confirmed in around 20 different neuronal types. Since moving to Northwestern University in 1999 to establish her own research group, Dr. Raman has dedicated great efforts in identifying the mechanisms supporting the resurgent Sodium current and how its biophysical properties shape the firing of the different cell types. Her work has impacted greatly the field of cellular neurophysiology, from basic research to translation neuroscience. In fact, alterations in the resurgent sodium currents have been observed in several neuropathologies, from Huntington’s disease to epilepsy. In this Perspective we will focus on the current knowledge on the expression and function of the resurgent Sodium current in neurons of the cerebral cortex and hippocampus. We will also briefly highlight the role of Dr. Raman’s as teacher and mentor, not only for her pupils, but for the whole scientific community.
Collapse
Affiliation(s)
- Giulia Quattrocolo
- Center for Neural Computation, Egil and Pauline Braathen and Fred Kavli Center for Cortical Microcircuits, Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| | - Keagan Dunville
- Center for Neural Computation, Egil and Pauline Braathen and Fred Kavli Center for Cortical Microcircuits, Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| | - Maximiliano José Nigro
- Center for Neural Computation, Egil and Pauline Braathen and Fred Kavli Center for Cortical Microcircuits, Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| |
Collapse
|