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Jaeger J, Masselot C, Greshake Tzovaras B, Senabre Hidalgo E, Haklay M(M, Santolini M. An epistemology for democratic citizen science. R Soc Open Sci 2023; 10:231100. [PMID: 38026019 PMCID: PMC10646465 DOI: 10.1098/rsos.231100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023]
Abstract
More than ever, humanity relies on robust scientific knowledge of the world and our place within it. Unfortunately, our contemporary view of science is still suffused with outdated ideas about scientific knowledge production based on a naive kind of realism. These ideas persist among members of the public and scientists alike. They contribute to an ultra-competitive system of academic research, which sacrifices long-term productivity through an excessive obsession with short-term efficiency. Efforts to diversify this system come from a movement called democratic citizen science, which can serve as a model for scientific inquiry in general. Democratic citizen science requires an alternative theory of knowledge with a focus on the role that diversity plays in the process of discovery. Here, we present such an epistemology, based on three central philosophical pillars: perspectival realism, a naturalistic process-based epistemology, and deliberative social practices. They broaden our focus from immediate research outcomes towards cognitive and social processes which facilitate sustainable long-term productivity and scientific innovation. This marks a shift from an industrial to an ecological vision of how scientific research should be done, and how it should be assessed. At the core of this vision are research communities that are diverse, representative, and democratic.
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Affiliation(s)
- Johannes Jaeger
- Complexity Science Hub (CSH) Vienna, Josefstädter Straße 39, 1080 Vienna, Austria
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, 75004 Paris, France
- Learning Planet Institute, 8 bis Rue Charles V, 75004 Paris, France
- Institut d’Études Avancées de Paris, 17 quai d'Anjou, 75004 Paris, France
- Université Paris-Saclay, 3 rue Joliot Curie, 91190 Gif-sur-Yvette, France
| | - Camille Masselot
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, 75004 Paris, France
- Learning Planet Institute, 8 bis Rue Charles V, 75004 Paris, France
| | - Bastian Greshake Tzovaras
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, 75004 Paris, France
- Learning Planet Institute, 8 bis Rue Charles V, 75004 Paris, France
| | - Enric Senabre Hidalgo
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, 75004 Paris, France
- Learning Planet Institute, 8 bis Rue Charles V, 75004 Paris, France
- Universitat Oberta de Catalunya, Rambla del Poblenou 156, 08018 Barcelona, Spain
| | | | - Marc Santolini
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, 75004 Paris, France
- Learning Planet Institute, 8 bis Rue Charles V, 75004 Paris, France
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Wurmser M, Madani R, Chaverot N, Backer S, Borok M, Dos Santos M, Comai G, Tajbakhsh S, Relaix F, Santolini M, Sambasivan R, Jiang R, Maire P. Overlapping functions of SIX homeoproteins during embryonic myogenesis. PLoS Genet 2023; 19:e1010781. [PMID: 37267426 DOI: 10.1371/journal.pgen.1010781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 05/10/2023] [Indexed: 06/04/2023] Open
Abstract
Four SIX homeoproteins display a combinatorial expression throughout embryonic developmental myogenesis and they modulate the expression of the myogenic regulatory factors. Here, we provide a deep characterization of their role in distinct mouse developmental territories. We showed, at the hypaxial level, that the Six1:Six4 double knockout (dKO) somitic precursor cells adopt a smooth muscle fate and lose their myogenic identity. At the epaxial level, we demonstrated by the analysis of Six quadruple KO (qKO) embryos, that SIX are required for fetal myogenesis, and for the maintenance of PAX7+ progenitor cells, which differentiated prematurely and are lost by the end of fetal development in qKO embryos. Finally, we showed that Six1 and Six2 are required to establish craniofacial myogenesis by controlling the expression of Myf5. We have thus described an unknown role for SIX proteins in the control of myogenesis at different embryonic levels and refined their involvement in the genetic cascades operating at the head level and in the genesis of myogenic stem cells.
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Affiliation(s)
- Maud Wurmser
- Université de Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| | - Rouba Madani
- Université de Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| | - Nathalie Chaverot
- Université de Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| | - Stéphanie Backer
- Université de Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| | - Matthew Borok
- Univ Paris Est Creteil, INSERM, EnvA, EFS, AP-HP, IMRB, Creteil, France
| | | | - Glenda Comai
- Stem Cells & Development, Institut Pasteur, Paris, France
- CNRS UMR 3738, Institut Pasteur, Paris, France
| | - Shahragim Tajbakhsh
- Stem Cells & Development, Institut Pasteur, Paris, France
- CNRS UMR 3738, Institut Pasteur, Paris, France
| | - Frédéric Relaix
- Univ Paris Est Creteil, INSERM, EnvA, EFS, AP-HP, IMRB, Creteil, France
| | - Marc Santolini
- Université de Paris Cité, Interaction Data Lab, CRI Paris, INSERM. Paris, France
| | - Ramkumar Sambasivan
- Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, India
| | - Rulang Jiang
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Pascal Maire
- Université de Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
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Graham CL, Landrain TE, Vjestica A, Masselot C, Lawton E, Blondel L, Haenal L, Greshake Tzovaras B, Santolini M. Community review: a robust and scalable selection system for resource allocation within open science and innovation communities. F1000Res 2023; 11:1440. [PMID: 38283124 PMCID: PMC10818098 DOI: 10.12688/f1000research.125886.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/31/2023] [Indexed: 01/30/2024] Open
Abstract
Resource allocation is essential to selection and implementation of innovative projects in science and technology. Current "winner-take-all" models for grant applications require significant researcher time in writing extensive project proposals, and rely on the availability of a few time-saturated volunteer experts. Such processes usually carry over several months, resulting in high effective costs compared to expected benefits. We devised an agile "community review" system to allocate micro-grants for the fast prototyping of innovative solutions. Here we describe and evaluate the implementation of this community review across 147 projects from the "Just One Giant Lab's OpenCOVID19 initiative" and "Helpful Engineering" open research communities. The community review process uses granular review forms and requires the participation of grant applicants in the review process. Within a year, we organised 7 rounds of review, resulting in 614 reviews from 201 reviewers, and the attribution of 48 micro-grants of up to 4,000 euros. The system is fast, with a median process duration of 10 days, scalable, with a median of 4 reviewers per project independent of the total number of projects, and fair, with project rankings highly preserved after the synthetic removal of reviewers. Regarding potential bias introduced by involving applicants in the process, we find that review scores from both applicants and non-applicants have a similar correlation of r=0.28 with other reviews within a project, matching traditional approaches. Finally, we find that the ability of projects to apply to several rounds allows to foster the further implementation of successful early prototypes, as well as provide a pathway to constructively improve an initially failing proposal in an agile manner. Overall, this study quantitatively highlights the benefits of a frugal, community review system acting as a due diligence for rapid and agile resource allocation in open research and innovation programs, with implications for decentralised communities.
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Affiliation(s)
- Chris L.B. Graham
- Just One Giant Lab, Paris, France
- University of Warwick, Coventry, UK
| | | | | | | | | | | | | | | | - Marc Santolini
- Just One Giant Lab, Paris, France
- Learning Planet Institute, Université de Paris, Paris, France
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Bergmark RW, Jin G, Semco RS, Santolini M, Olsen MA, Dhand A. Association of hospital centrality in inter-hospital patient-sharing networks with patient mortality and length of stay. PLoS One 2023; 18:e0281871. [PMID: 36920981 PMCID: PMC10016671 DOI: 10.1371/journal.pone.0281871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 02/02/2023] [Indexed: 03/16/2023] Open
Abstract
OBJECTIVE The interdependence of hospitals is underappreciated in patient outcomes studies. We used a network science approach to foreground this interdependence. Specifically, within two large state-based interhospital networks, we examined the relationship of a hospital's network position with in-hospital mortality and length of stay. METHODS We constructed interhospital network graphs using data from the Healthcare Cost and Utilization Project and the American Hospital Association Annual Survey for Florida (2014) and California (2011). The exposure of interest was hospital centrality, defined as weighted degree (sum of all ties to a given hospital from other hospitals). The outcomes were in-hospital mortality and length of stay with sub-analyses for four acute medical conditions: pneumonia, heart failure, ischemic stroke, myocardial infarction. We compared outcomes for each quartile of hospital centrality relative to the most central quartile (Q4), independent of patient- and hospital-level characteristics, in this retrospective cross-sectional study. RESULTS The inpatient cohorts had 1,246,169 patients in Florida and 1,415,728 in California. Compared to Florida's central hospitals which had an overall mortality 1.60%, peripheral hospitals had higher in-hospital mortality (1.97%, adjusted OR (95%CI): Q1 1.61 (1.37, 1.89), p<0.001). Hospitals in the middle quartiles had lower in-hospital mortality compared to central hospitals (%, adjusted OR (95% CI): Q2 1.39%, 0.79 (0.70, 0.89), p<0.001; Q3 1.33%, 0.78 (0.70, 0.87), p<0.001). Peripheral hospitals had longer lengths of stay (adjusted incidence rate ratio (95% CI): Q1 2.47 (2.44, 2.50), p<0.001). These findings were replicated in California, and in patients with heart failure and pneumonia in Florida. These results show a u-shaped distribution of outcomes based on hospital network centrality quartile. CONCLUSIONS The position of hospitals within an inter-hospital network is associated with patient outcomes. Specifically, hospitals located in the peripheral or central positions may be most vulnerable to diminished quality outcomes due to the network. Results should be replicated with deeper clinical data.
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Affiliation(s)
- Regan W. Bergmark
- Center for Surgery and Public Health, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States of America
- Brigham and Women’s Hospital and Dana Farber Cancer Institute and Department of Otolaryngology-Head and Neck Surgery, Division of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA, United States of America
| | - Ginger Jin
- Center for Surgery and Public Health, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Robert S. Semco
- Center for Surgery and Public Health, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Marc Santolini
- Université Paris Cité, Inserm, System Engineering and Evolution Dynamics, Paris, France
- Network Science Institute, Northeastern University, Boston, MA, United States of America
| | - Margaret A. Olsen
- Department of Medicine, Division of Infectious Disease, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Amar Dhand
- Network Science Institute, Northeastern University, Boston, MA, United States of America
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
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Graham CLB, Akligoh H, Ori JK, Adzaho G, Salekwa L, Campbell P, Saba CKS, Landrain TE, Santolini M. Education-based grant programmes for bottom-up distance learning and project catalysis: antimicrobial resistance in Sub-Saharan Africa. Access Microbiol 2023; 5:000472.v3. [PMID: 37091736 PMCID: PMC10118251 DOI: 10.1099/acmi.0.000472.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/29/2023] [Indexed: 03/18/2023] Open
Abstract
International development and aid are often conducted through the allocation of funding determined by decisions of non-locals, especially in the west for those in the global south. In addition, such funding is often disassociated from local expertise, therefore providing little long-term developmental impact and generating distrust. This is particularly true for conservation, as well as environmental and educational programmes. We hypothesize that by granting local people the educational tools and the necessary funding to develop their own projects through the use of an applicant-driven peer-review approach, it is possible to relocalize the decision-making process to the programme participants, with the potential to generate and select more relevant projects with developmental outcomes of higher quality. Here we created an online curriculum for antimicrobial resistance (AMR) education that was followed by 89 participants across Ghana, Tanzania, Nigeria and Uganda. We then created an open research programme that facilitated the creation of eight de novo projects on AMR. Finally, we organized an applicant-driven grant round to allocate funding to the ‘Neonatal Sepsis in Nigeria’ project to conduct a pilot study and awareness campaign. This work opens perspectives for the design of frugal educational programmes and the funding of context-specific, community-driven projects aimed at empowering local stakeholders in the global South.
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Affiliation(s)
| | | | | | | | - Linda Salekwa
- Mbeya University of Science and Technology, Mbeya, Tanzania
| | | | | | | | - Marc Santolini
- Université Paris Cité, INSERM, U1284, F-75004 Paris, France
- Just One Giant Lab, Paris, France
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Akmaev VR, Ghiassian SD, Withers JB, Santolini M, Saleh A. Retraction notice to "Network-based response module comprised of gene expression biomarkers predicts response to infliximab at treatment initiation in ulcerative colitis" Translational Research 239C (2021) 35-43. Transl Res 2022; 244:137. [PMID: 35589246 DOI: 10.1016/j.trsl.2022.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
| | | | | | - Marc Santolini
- Center for Research and Interdisciplinarity (CRI), University Paris Descartes, Paris, France
| | - Alif Saleh
- Scipher Medicine Corporation, Waltham, MA
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Masselot C, Greshake Tzovaras B, Graham CLB, Finnegan G, Jeyaram R, Vitali I, Landrain T, Santolini M. Implementing the Co-Immune Open Innovation Program to Address Vaccination Hesitancy and Access to Vaccines: Retrospective Study. J Particip Med 2022; 14:e32125. [PMID: 35060917 PMCID: PMC8817221 DOI: 10.2196/32125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/30/2021] [Accepted: 10/03/2021] [Indexed: 11/29/2022] Open
Abstract
Background The rise of major complex public health problems, such as vaccination hesitancy and access to vaccination, requires innovative, open, and transdisciplinary approaches. Yet, institutional silos and lack of participation on the part of nonacademic citizens in the design of solutions hamper efforts to meet these challenges. Against this background, new solutions have been explored, with participatory research, citizen science, hackathons, and challenge-based approaches being applied in the context of public health. Objective Our aim was to develop a program for creating citizen science and open innovation projects that address the contemporary challenges of vaccination in France and around the globe. Methods We designed and implemented Co-Immune, a program created to tackle the question of vaccination hesitancy and access to vaccination through an online and offline challenge-based open innovation approach. The program was run on the open science platform Just One Giant Lab. Results Over a 6-month period, the Co-Immune program gathered 234 participants of diverse backgrounds and 13 partners from the public and private sectors. The program comprised 10 events to facilitate the creation of 20 new projects, as well as the continuation of two existing projects, to address the issues of vaccination hesitancy and access, ranging from app development and data mining to analysis and game design. In an open framework, the projects made their data, code, and solutions publicly available. Conclusions Co-Immune highlights how open innovation approaches and online platforms can help to gather and coordinate noninstitutional communities in a rapid, distributed, and global way toward solving public health issues. Such initiatives can lead to the production and transfer of knowledge, creating novel solutions in the public health sector. The example of Co-Immune contributes to paving the way for organizations and individuals to collaboratively tackle future global challenges.
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Affiliation(s)
| | | | | | | | - Rathin Jeyaram
- Center for Research and Interdisciplinarity, INSERM U1284, Universite de Paris, Paris, France
| | | | | | - Marc Santolini
- Just One Giant Lab Association, Paris, France
- Center for Research and Interdisciplinarity, INSERM U1284, Universite de Paris, Paris, France
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Ghiassian SD, Withers JB, Santolini M, Saleh A, Akmaev VR. RETRACTED: Network-based response module comprised of gene expression biomarkers predicts response to infliximab at treatment initiation in ulcerative colitis. Transl Res 2022; 239:35-43. [PMID: 33965585 DOI: 10.1016/j.trsl.2021.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/12/2021] [Accepted: 04/28/2021] [Indexed: 11/25/2022]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been retracted at the request of the authors after consulting with the Editors. During a follow-up study, the authors regretfully discovered that the microarray probe-to-gene mapping was incorrect. Although the methodology and primary findings remain the same, the identity of the biomarker genes are incorrect as a result of this honest mistake. The extent of the changes to correct this information necessitated the publication of a corrected version of this article: https://doi.org/10.1016/j.trsl.2022.03.006.
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Affiliation(s)
| | | | - Marc Santolini
- Center for Research and Interdisciplinarity (CRI), University Paris Descartes, Paris, France
| | - Alif Saleh
- Scipher Medicine Corporation, Waltham, Massachusetts
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De Ridder D, Loizeau AJ, Sandoval JL, Ehrler F, Perrier M, Ritch A, Violot G, Santolini M, Greshake Tzovaras B, Stringhini S, Kaiser L, Pradeau JF, Joost S, Guessous I. Detection of Spatiotemporal Clusters of COVID-19-Associated Symptoms and Prevention Using a Participatory Surveillance App: Protocol for the @choum Study. JMIR Res Protoc 2021; 10:e30444. [PMID: 34449403 PMCID: PMC8496683 DOI: 10.2196/30444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/18/2021] [Accepted: 07/19/2021] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND The early detection of clusters of infectious diseases such as the SARS-CoV-2-related COVID-19 disease can promote timely testing recommendation compliance and help to prevent disease outbreaks. Prior research revealed the potential of COVID-19 participatory syndromic surveillance systems to complement traditional surveillance systems. However, most existing systems did not integrate geographic information at a local scale, which could improve the management of the SARS-CoV-2 pandemic. OBJECTIVE The aim of this study is to detect active and emerging spatiotemporal clusters of COVID-19-associated symptoms, and to examine (a posteriori) the association between the clusters' characteristics and sociodemographic and environmental determinants. METHODS This report presents the methodology and development of the @choum (English: "achoo") study, evaluating an epidemiological digital surveillance tool to detect and prevent clusters of individuals (target sample size, N=5000), aged 18 years or above, with COVID-19-associated symptoms living and/or working in the canton of Geneva, Switzerland. The tool is a 5-minute survey integrated into a free and secure mobile app (CoronApp-HUG). Participants are enrolled through a comprehensive communication campaign conducted throughout the 12-month data collection phase. Participants register to the tool by providing electronic informed consent and nonsensitive information (gender, age, geographically masked addresses). Symptomatic participants can then report COVID-19-associated symptoms at their onset (eg, symptoms type, test date) by tapping on the @choum button. Those who have not yet been tested are offered the possibility to be informed on their cluster status (information returned by daily automated clustering analysis). At each participation step, participants are redirected to the official COVID-19 recommendations websites. Geospatial clustering analyses are performed using the modified space-time density-based spatial clustering of applications with noise (MST-DBSCAN) algorithm. RESULTS The study began on September 1, 2020, and will be completed on February 28, 2022. Multiple tests performed at various time points throughout the 5-month preparation phase have helped to improve the tool's user experience and the accuracy of the clustering analyses. A 1-month pilot study performed among 38 pharmacists working in 7 Geneva-based pharmacies confirmed the proper functioning of the tool. Since the tool's launch to the entire population of Geneva on February 11, 2021, data are being collected and clusters are being carefully monitored. The primary study outcomes are expected to be published in mid-2022. CONCLUSIONS The @choum study evaluates an innovative participatory epidemiological digital surveillance tool to detect and prevent clusters of COVID-19-associated symptoms. @choum collects precise geographic information while protecting the user's privacy by using geomasking methods. By providing an evidence base to inform citizens and local authorities on areas potentially facing a high COVID-19 burden, the tool supports the targeted allocation of public health resources and promotes testing. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/30444.
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Affiliation(s)
- David De Ridder
- Division of Primary Care, Geneva University Hospitals, Geneva, Switzerland
- Department of Health and Community Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Group of Geographic Information Research and Analysis in Population Health, Geneva University Hospitals, Geneva, Switzerland
- Laboratory of Geographic Information Systems, School of Architecture, Civil and Environmental Engineering, Swiss Federal Institute of Technology Lausanne, Lausanne, Switzerland
| | - Andrea Jutta Loizeau
- Division of Primary Care, Geneva University Hospitals, Geneva, Switzerland
- Department of Health and Community Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - José Luis Sandoval
- Group of Geographic Information Research and Analysis in Population Health, Geneva University Hospitals, Geneva, Switzerland
- Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
| | - Frédéric Ehrler
- Direction of Information Systems, Geneva University Hospitals, Geneva, Switzerland
| | - Myriam Perrier
- Direction of Information Systems, Geneva University Hospitals, Geneva, Switzerland
| | - Albert Ritch
- Direction of Information Systems, Geneva University Hospitals, Geneva, Switzerland
| | - Guillemette Violot
- Communication Directorate, Geneva University Hospitals, Geneva, Switzerland
| | - Marc Santolini
- Center for Research and Interdisciplinarity, INSERM U1284, University of Paris, Paris, France
| | | | - Silvia Stringhini
- Division of Primary Care, Geneva University Hospitals, Geneva, Switzerland
- Department of Health and Community Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Laurent Kaiser
- Department of Health and Community Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Infectious Disease and Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland
- Center for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
| | | | - Stéphane Joost
- Group of Geographic Information Research and Analysis in Population Health, Geneva University Hospitals, Geneva, Switzerland
- Laboratory of Geographic Information Systems, School of Architecture, Civil and Environmental Engineering, Swiss Federal Institute of Technology Lausanne, Lausanne, Switzerland
| | - Idris Guessous
- Division of Primary Care, Geneva University Hospitals, Geneva, Switzerland
- Department of Health and Community Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Group of Geographic Information Research and Analysis in Population Health, Geneva University Hospitals, Geneva, Switzerland
- Laboratory of Geographic Information Systems, School of Architecture, Civil and Environmental Engineering, Swiss Federal Institute of Technology Lausanne, Lausanne, Switzerland
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Meignié A, Combredet C, Santolini M, Kovács IA, Douché T, Gianetto QG, Eun H, Matondo M, Jacob Y, Grailhe R, Tangy F, Komarova AV. Proteomic Analysis Uncovers Measles Virus Protein C Interaction With p65-iASPP Protein Complex. Mol Cell Proteomics 2021; 20:100049. [PMID: 33515806 PMCID: PMC7950213 DOI: 10.1016/j.mcpro.2021.100049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/30/2022] Open
Abstract
Viruses manipulate the central machineries of host cells to their advantage. They prevent host cell antiviral responses to create a favorable environment for their survival and propagation. Measles virus (MV) encodes two nonstructural proteins MV-V and MV-C known to counteract the host interferon response and to regulate cell death pathways. Several molecular mechanisms underlining MV-V regulation of innate immunity and cell death pathways have been proposed, whereas MV-C host-interacting proteins are less studied. We suggest that some cellular factors that are controlled by MV-C protein during viral replication could be components of innate immunity and the cell death pathways. To determine which host factors are targeted by MV-C, we captured both direct and indirect host-interacting proteins of MV-C protein. For this, we used a strategy based on recombinant viruses expressing tagged viral proteins followed by affinity purification and a bottom-up mass spectrometry analysis. From the list of host proteins specifically interacting with MV-C protein in different cell lines, we selected the host targets that belong to immunity and cell death pathways for further validation. Direct protein interaction partners of MV-C were determined by applying protein complementation assay and the bioluminescence resonance energy transfer approach. As a result, we found that MV-C protein specifically interacts with p65–iASPP protein complex that controls both cell death and innate immunity pathways and evaluated the significance of these host factors on virus replication. Measles virus controls immune response and cell death pathways to achieve replication. Host proteins interaction network with measles virulence factor C protein. Cellular p65–iASPP complex is targeted by measles virus C protein.
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Affiliation(s)
- Alice Meignié
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, CNRS UMR-3569, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Chantal Combredet
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Marc Santolini
- Center for Research and Interdisciplinarity (CRI), Université de Paris, INSERM U1284, Paris, France; Network Science Institute and Department of Physics, Northeastern University, Boston, Massachusetts, USA
| | - István A Kovács
- Network Science Institute and Department of Physics, Northeastern University, Boston, Massachusetts, USA; Department of Physics and Astronomy, Northwestern University, Evanston, Illinois, USA; Department of Network and Data Science, Central European University, Budapest, Hungary
| | - Thibaut Douché
- Proteomics platform, Mass Spectrometry for Biology Unit (MSBio), Institut Pasteur, CNRS USR 2000, Paris, France
| | - Quentin Giai Gianetto
- Proteomics platform, Mass Spectrometry for Biology Unit (MSBio), Institut Pasteur, CNRS USR 2000, Paris, France; Bioinformatics and Biostatistics Hub, Computational Biology Department, Institut Pasteur, CNRS USR 3756, Paris, France
| | - Hyeju Eun
- Technology Development Platform, Institut Pasteur Korea, Seongnam-si, Republic of Korea
| | - Mariette Matondo
- Proteomics platform, Mass Spectrometry for Biology Unit (MSBio), Institut Pasteur, CNRS USR 2000, Paris, France
| | - Yves Jacob
- Laboratory of Molecular Genetics of RNA Viruses, Institut Pasteur, CNRS UMR-3569, Paris, France
| | - Regis Grailhe
- Technology Development Platform, Institut Pasteur Korea, Seongnam-si, Republic of Korea
| | - Frédéric Tangy
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, CNRS UMR-3569, Paris, France.
| | - Anastassia V Komarova
- Viral Genomics and Vaccination Unit, Department of Virology, Institut Pasteur, CNRS UMR-3569, Paris, France; Laboratory of Molecular Genetics of RNA Viruses, Institut Pasteur, CNRS UMR-3569, Paris, France.
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11
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Mellors T, Withers JB, Ameli A, Jones A, Wang M, Zhang L, Sanchez HN, Santolini M, Do Valle I, Sebek M, Cheng F, Pappas DA, Kremer JM, Curtis JR, Johnson KJ, Saleh A, Ghiassian SD, Akmaev VR. Clinical Validation of a Blood-Based Predictive Test for Stratification of Response to Tumor Necrosis Factor Inhibitor Therapies in Rheumatoid Arthritis Patients. Network and Systems Medicine 2020. [DOI: 10.1089/nsm.2020.0007] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
| | | | - Asher Ameli
- Scipher Medicine, Waltham, Massachusetts, USA
| | - Alex Jones
- Scipher Medicine, Waltham, Massachusetts, USA
| | | | - Lixia Zhang
- Scipher Medicine, Waltham, Massachusetts, USA
| | | | - Marc Santolini
- Center for Research and Interdisciplinarity (CRI), University Paris Descartes, Paris, France
| | - Italo Do Valle
- Center for Complex Network Research, Department of Physics, Northeastern University, Boston, Massachusetts, USA
| | - Michael Sebek
- Center for Complex Network Research, Department of Physics, Northeastern University, Boston, Massachusetts, USA
| | - Feixiong Cheng
- Center for Complex Network Research, Department of Physics, Northeastern University, Boston, Massachusetts, USA
| | - Dimitrios A. Pappas
- Division of Rheumatology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
- CORRONA, LCC, Waltham, Massachusetts, USA
| | - Joel M. Kremer
- CORRONA, LCC, Waltham, Massachusetts, USA
- Albany Medical College, The Center for Rheumatology, Albany, New York, USA
| | - Jeffery R. Curtis
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Alif Saleh
- Scipher Medicine, Waltham, Massachusetts, USA
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12
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Kılıç A, Ameli A, Park JA, Kho AT, Tantisira K, Santolini M, Cheng F, Mitchel JA, McGill M, O'Sullivan MJ, De Marzio M, Sharma A, Randell SH, Drazen JM, Fredberg JJ, Weiss ST. Mechanical forces induce an asthma gene signature in healthy airway epithelial cells. Sci Rep 2020; 10:966. [PMID: 31969610 PMCID: PMC6976696 DOI: 10.1038/s41598-020-57755-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/23/2019] [Indexed: 12/27/2022] Open
Abstract
Bronchospasm compresses the bronchial epithelium, and this compressive stress has been implicated in asthma pathogenesis. However, the molecular mechanisms by which this compressive stress alters pathways relevant to disease are not well understood. Using air-liquid interface cultures of primary human bronchial epithelial cells derived from non-asthmatic donors and asthmatic donors, we applied a compressive stress and then used a network approach to map resulting changes in the molecular interactome. In cells from non-asthmatic donors, compression by itself was sufficient to induce inflammatory, late repair, and fibrotic pathways. Remarkably, this molecular profile of non-asthmatic cells after compression recapitulated the profile of asthmatic cells before compression. Together, these results show that even in the absence of any inflammatory stimulus, mechanical compression alone is sufficient to induce an asthma-like molecular signature.
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Affiliation(s)
- Ayşe Kılıç
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Asher Ameli
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Jin-Ah Park
- Program in Molecular Integrative Phyisological Sciences, Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Alvin T Kho
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Kelan Tantisira
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Marc Santolini
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Centre for Research and Interdisciplinarity (CRI), Paris, F-75014, France
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, 44106, USA
| | - Jennifer A Mitchel
- Program in Molecular Integrative Phyisological Sciences, Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Maureen McGill
- Program in Molecular Integrative Phyisological Sciences, Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Michael J O'Sullivan
- Program in Molecular Integrative Phyisological Sciences, Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Margherita De Marzio
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Program in Molecular Integrative Phyisological Sciences, Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Amitabh Sharma
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Scott H Randell
- Marsico Lung Institute/Cystic Fibrosis Center, University of North Carolina, Chapel Hill, NC, USA
| | - Jeffrey M Drazen
- Program in Molecular Integrative Phyisological Sciences, Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Jeffrey J Fredberg
- Program in Molecular Integrative Phyisological Sciences, Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Program in Molecular Integrative Phyisological Sciences, Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA.
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13
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Sharma A, Kitsak M, Cho MH, Ameli A, Zhou X, Jiang Z, Crapo JD, Beaty TH, Menche J, Bakke PS, Santolini M, Silverman EK. Integration of Molecular Interactome and Targeted Interaction Analysis to Identify a COPD Disease Network Module. Sci Rep 2018; 8:14439. [PMID: 30262855 PMCID: PMC6160419 DOI: 10.1038/s41598-018-32173-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 08/20/2018] [Indexed: 12/21/2022] Open
Abstract
The polygenic nature of complex diseases offers potential opportunities to utilize network-based approaches that leverage the comprehensive set of protein-protein interactions (the human interactome) to identify new genes of interest and relevant biological pathways. However, the incompleteness of the current human interactome prevents it from reaching its full potential to extract network-based knowledge from gene discovery efforts, such as genome-wide association studies, for complex diseases like chronic obstructive pulmonary disease (COPD). Here, we provide a framework that integrates the existing human interactome information with experimental protein-protein interaction data for FAM13A, one of the most highly associated genetic loci to COPD, to find a more comprehensive disease network module. We identified an initial disease network neighborhood by applying a random-walk method. Next, we developed a network-based closeness approach (CAB) that revealed 9 out of 96 FAM13A interacting partners identified by affinity purification assays were significantly close to the initial network neighborhood. Moreover, compared to a similar method (local radiality), the CAB approach predicts low-degree genes as potential candidates. The candidates identified by the network-based closeness approach were combined with the initial network neighborhood to build a comprehensive disease network module (163 genes) that was enriched with genes differentially expressed between controls and COPD subjects in alveolar macrophages, lung tissue, sputum, blood, and bronchial brushing datasets. Overall, we demonstrate an approach to find disease-related network components using new laboratory data to overcome incompleteness of the current interactome.
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Affiliation(s)
- Amitabh Sharma
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA. .,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA. .,Center for Complex Networks Research and Department of Physics, Northeastern University, Boston, MA, 02115, USA. .,Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
| | - Maksim Kitsak
- Center for Complex Networks Research and Department of Physics, Northeastern University, Boston, MA, 02115, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA.,Pulmonary and Critical Care Division, Brigham and Women's Hospital and Harvard Medical School, Boston, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Asher Ameli
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA.,Department of Physics, Northeastern University, Boston, MA, 02115, United States
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Zhiqiang Jiang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA
| | - James D Crapo
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jörg Menche
- Department of Bioinformatics, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, A-1090, Vienna, Austria
| | - Per S Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Marc Santolini
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA.,Center for Complex Networks Research and Department of Physics, Northeastern University, Boston, MA, 02115, USA.,Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA. .,Pulmonary and Critical Care Division, Brigham and Women's Hospital and Harvard Medical School, Boston, USA. .,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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14
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Rees CM, Yang JH, Santolini M, Lusis AJ, Weiss JN, Karma A. The Ca 2+ transient as a feedback sensor controlling cardiomyocyte ionic conductances in mouse populations. eLife 2018; 7:36717. [PMID: 30251624 PMCID: PMC6205808 DOI: 10.7554/elife.36717] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 09/24/2018] [Indexed: 12/13/2022] Open
Abstract
Conductances of ion channels and transporters controlling cardiac excitation may vary in a population of subjects with different cardiac gene expression patterns. However, the amount of variability and its origin are not quantitatively known. We propose a new conceptual approach to predict this variability that consists of finding combinations of conductances generating a normal intracellular Ca2+ transient without any constraint on the action potential. Furthermore, we validate experimentally its predictions using the Hybrid Mouse Diversity Panel, a model system of genetically diverse mouse strains that allows us to quantify inter-subject versus intra-subject variability. The method predicts that conductances of inward Ca2+ and outward K+ currents compensate each other to generate a normal Ca2+ transient in good quantitative agreement with current measurements in ventricular myocytes from hearts of different isogenic strains. Our results suggest that a feedback mechanism sensing the aggregate Ca2+ transient of the heart suffices to regulate ionic conductances.
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Affiliation(s)
- Colin M Rees
- Physics Department, Northeastern University, Boston, United states.,Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, United States
| | - Jun-Hai Yang
- Department of Medicine (Cardiology), Cardiovascular Research Laboratory, David Geffen School of Medicine, University of California, Los Angeles, United states.,Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, United States
| | - Marc Santolini
- Physics Department, Northeastern University, Boston, United states.,Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, United States
| | - Aldons J Lusis
- Department of Medicine (Cardiology), Cardiovascular Research Laboratory, David Geffen School of Medicine, University of California, Los Angeles, United states.,Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, United States.,Department of Microbiology, David Geffen School of Medicine, University of California, Los Angeles, United States.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, United States
| | - James N Weiss
- Department of Medicine (Cardiology), Cardiovascular Research Laboratory, David Geffen School of Medicine, University of California, Los Angeles, United states.,Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, United States
| | - Alain Karma
- Physics Department, Northeastern University, Boston, United states.,Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, United States
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15
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Sharma A, Halu A, Decano JL, Padi M, Liu YY, Prasad RB, Fadista J, Santolini M, Menche J, Weiss ST, Vidal M, Silverman EK, Aikawa M, Barabási AL, Groop L, Loscalzo J. Controllability in an islet specific regulatory network identifies the transcriptional factor NFATC4, which regulates Type 2 Diabetes associated genes. NPJ Syst Biol Appl 2018; 4:25. [PMID: 29977601 PMCID: PMC6028434 DOI: 10.1038/s41540-018-0057-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 04/09/2018] [Accepted: 05/04/2018] [Indexed: 01/14/2023] Open
Abstract
Probing the dynamic control features of biological networks represents a new frontier in capturing the dysregulated pathways in complex diseases. Here, using patient samples obtained from a pancreatic islet transplantation program, we constructed a tissue-specific gene regulatory network and used the control centrality (Cc) concept to identify the high control centrality (HiCc) pathways, which might serve as key pathobiological pathways for Type 2 Diabetes (T2D). We found that HiCc pathway genes were significantly enriched with modest GWAS p-values in the DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) study. We identified variants regulating gene expression (expression quantitative loci, eQTL) of HiCc pathway genes in islet samples. These eQTL genes showed higher levels of differential expression compared to non-eQTL genes in low, medium, and high glucose concentrations in rat islets. Among genes with highly significant eQTL evidence, NFATC4 belonged to four HiCc pathways. We asked if the expressions of T2D-associated candidate genes from GWAS and literature are regulated by Nfatc4 in rat islets. Extensive in vitro silencing of Nfatc4 in rat islet cells displayed reduced expression of 16, and increased expression of four putative downstream T2D genes. Overall, our approach uncovers the mechanistic connection of NFATC4 with downstream targets including a previously unknown one, TCF7L2, and establishes the HiCc pathways' relationship to T2D.
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Affiliation(s)
- Amitabh Sharma
- 1Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115 USA.,2Center for Complex Network Research and Department of Physics, Northeastern University, Boston, MA 02115 USA.,3Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215 USA.,4Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215 USA
| | - Arda Halu
- 1Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115 USA.,4Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215 USA
| | - Julius L Decano
- 4Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215 USA
| | - Megha Padi
- 5Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721 USA
| | - Yang-Yu Liu
- 1Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Rashmi B Prasad
- 6Lund University Diabetes Center, Department of Clinical Sciences, Diabetes & Endocrinology, Skåne University Hospital Malmö, Lund University, Malmö, 20502 Sweden
| | - Joao Fadista
- 6Lund University Diabetes Center, Department of Clinical Sciences, Diabetes & Endocrinology, Skåne University Hospital Malmö, Lund University, Malmö, 20502 Sweden
| | - Marc Santolini
- 1Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115 USA.,2Center for Complex Network Research and Department of Physics, Northeastern University, Boston, MA 02115 USA
| | - Jörg Menche
- 2Center for Complex Network Research and Department of Physics, Northeastern University, Boston, MA 02115 USA.,7 CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090 Austria
| | - Scott T Weiss
- 1Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Marc Vidal
- 3Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215 USA.,8Department of Genetics, Harvard Medical School, Boston, MA 02115 USA
| | - Edwin K Silverman
- 1Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Masanori Aikawa
- 4Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215 USA
| | - Albert-László Barabási
- 1Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115 USA.,2Center for Complex Network Research and Department of Physics, Northeastern University, Boston, MA 02115 USA.,3Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215 USA.,9Center for Network Science, Central European University, Nador u. 9, 1051 Budapest, Hungary
| | - Leif Groop
- 6Lund University Diabetes Center, Department of Clinical Sciences, Diabetes & Endocrinology, Skåne University Hospital Malmö, Lund University, Malmö, 20502 Sweden.,10Department of Clinical Sciences, Islet cell physiology, Skåne University Hospital Malmö, Lund University, Malmö, 20502 Sweden
| | - Joseph Loscalzo
- 11Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115 USA
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16
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Kılıç A, Santolini M, Nakano T, Schiller M, Teranishi M, Gellert P, Ponomareva Y, Braun T, Uchida S, Weiss ST, Sharma A, Renz H. A systems immunology approach identifies the collective impact of 5 miRs in Th2 inflammation. JCI Insight 2018; 3:97503. [PMID: 29875322 DOI: 10.1172/jci.insight.97503] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 03/29/2018] [Indexed: 12/20/2022] Open
Abstract
Allergic asthma is a chronic inflammatory disease dominated by a CD4+ T helper 2 (Th2) cell signature. The immune response amplifies in self-enforcing loops, promoting Th2-driven cellular immunity and leaving the host unable to terminate inflammation. Posttranscriptional mechanisms, including microRNAs (miRs), are pivotal in maintaining immune homeostasis. Since an altered expression of various miRs has been associated with T cell-driven diseases, including asthma, we hypothesized that miRs control mechanisms ensuring Th2 stability and maintenance in the lung. We isolated murine CD4+ Th2 cells from allergic inflamed lungs and profiled gene and miR expression. Instead of focusing on the magnitude of miR differential expression, here we addressed the secondary consequences for the set of molecular interactions in the cell, the interactome. We developed the Impact of Differential Expression Across Layers, a network-based algorithm to prioritize disease-relevant miRs based on the central role of their targets in the molecular interactome. This method identified 5 Th2-related miRs (mir27b, mir206, mir106b, mir203, and mir23b) whose antagonization led to a sharp reduction of the Th2 phenotype. Overall, a systems biology tool was developed and validated, highlighting the role of miRs in Th2-driven immune response. This result offers potentially novel approaches for therapeutic interventions.
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Affiliation(s)
- Ayşe Kılıç
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Philipps University Marburg, Marburg, Germany
| | - Marc Santolini
- Center for Complex Network Research, Department of Physics, Northeastern University, Boston, Massachusetts, USA.,Brigham and Women's Hospital, Channing Division of Network Medicine, Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Taiji Nakano
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Philipps University Marburg, Marburg, Germany
| | - Matthias Schiller
- Clinic for Dermatology and Venereology, University Medical Center Rostock, Rostock, Germany
| | - Mizue Teranishi
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Pascal Gellert
- Breast Cancer Now Research Centre at The Institute of Cancer Research, London, United Kingdom
| | - Yuliya Ponomareva
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe- University Frankfurt, Frankfurt Germany
| | - Thomas Braun
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Shizuka Uchida
- Cardiovascular Innovation Institute, University of Louisville, Louisville, Kentucky, USA
| | - Scott T Weiss
- Brigham and Women's Hospital, Channing Division of Network Medicine, Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Amitabh Sharma
- Brigham and Women's Hospital, Channing Division of Network Medicine, Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Harald Renz
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Philipps University Marburg, Marburg, Germany
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17
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Benchoufi M, Fournier M, Magrez D, Macaux G, Barué V, Mansilla Sanchez A, de Fresnoye O, Fillaudeau R, Tauvel-Mocquet O, Chalabi N, Petit-Nivard JF, Blondel L, Santolini M, Ben Hadj Yahia B. Epidemium: A multidisciplinary community to tackle cancer using big and open data. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.e13604] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Mehdi Benchoufi
- Centre d’Épidémiologie Clinique, Hôpital Hôtel Dieu, Assistance Publique des Hôpitaux de Paris, Paris, France
| | | | - David Magrez
- ROCHE S.A.S - Medical Affairs, Boulogne-Billancourt, France
| | | | - Vanessa Barué
- ROCHE S.A.S - Medical Affairs, Boulogne Billancourt, France
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18
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Rau CD, Romay MC, Tuteryan M, Wang JJC, Santolini M, Ren S, Karma A, Weiss JN, Wang Y, Lusis AJ. Systems Genetics Approach Identifies Gene Pathways and Adamts2 as Drivers of Isoproterenol-Induced Cardiac Hypertrophy and Cardiomyopathy in Mice. Cell Syst 2017; 4:121-128.e4. [PMID: 27866946 PMCID: PMC5338604 DOI: 10.1016/j.cels.2016.10.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 09/09/2016] [Accepted: 10/19/2016] [Indexed: 10/20/2022]
Abstract
We previously reported a genetic analysis of heart failure traits in a population of inbred mouse strains treated with isoproterenol to mimic catecholamine-driven cardiac hypertrophy. Here, we apply a co-expression network algorithm, wMICA, to perform a systems-level analysis of left ventricular transcriptomes from these mice. We describe the features of the overall network but focus on a module identified in treated hearts that is strongly related to cardiac hypertrophy and pathological remodeling. Using the causal modeling algorithm NEO, we identified the gene Adamts2 as a putative regulator of this module and validated the predictive value of NEO using small interfering RNA-mediated knockdown in neonatal rat ventricular myocytes. Adamts2 silencing regulated the expression of the genes residing within the module and impaired isoproterenol-induced cellular hypertrophy. Our results provide a view of higher order interactions in heart failure with potential for diagnostic and therapeutic insights.
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Affiliation(s)
- Christoph D Rau
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Departments of Anesthesiology, Physiology, and Medicine, Cardiovascular Research Laboratories, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Milagros C Romay
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mary Tuteryan
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jessica J-C Wang
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marc Santolini
- Center for Interdisciplinary Research on Complex Systems, Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Shuxun Ren
- Departments of Anesthesiology, Physiology, and Medicine, Cardiovascular Research Laboratories, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alain Karma
- Center for Interdisciplinary Research on Complex Systems, Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - James N Weiss
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yibin Wang
- Departments of Anesthesiology, Physiology, and Medicine, Cardiovascular Research Laboratories, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aldons J Lusis
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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19
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Mirzakhani H, Litonjua AA, McElrath TF, O'Connor G, Lee-Parritz A, Iverson R, Macones G, Strunk RC, Bacharier LB, Zeiger R, Hollis BW, Handy DE, Sharma A, Laranjo N, Carey V, Qiu W, Santolini M, Liu S, Chhabra D, Enquobahrie DA, Williams MA, Loscalzo J, Weiss ST. Early pregnancy vitamin D status and risk of preeclampsia. J Clin Invest 2016; 126:4702-4715. [PMID: 27841759 DOI: 10.1172/jci89031] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/16/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Low vitamin D status in pregnancy was proposed as a risk factor of preeclampsia. METHODS We assessed the effect of vitamin D supplementation (4,400 vs. 400 IU/day), initiated early in pregnancy (10-18 weeks), on the development of preeclampsia. The effects of serum vitamin D (25-hydroxyvitamin D [25OHD]) levels on preeclampsia incidence at trial entry and in the third trimester (32-38 weeks) were studied. We also conducted a nested case-control study of 157 women to investigate peripheral blood vitamin D-associated gene expression profiles at 10 to 18 weeks in 47 participants who developed preeclampsia. RESULTS Of 881 women randomized, outcome data were available for 816, with 67 (8.2%) developing preeclampsia. There was no significant difference between treatment (N = 408) or control (N = 408) groups in the incidence of preeclampsia (8.08% vs. 8.33%, respectively; relative risk: 0.97; 95% CI, 0.61-1.53). However, in a cohort analysis and after adjustment for confounders, a significant effect of sufficient vitamin D status (25OHD ≥30 ng/ml) was observed in both early and late pregnancy compared with insufficient levels (25OHD <30 ng/ml) (adjusted odds ratio, 0.28; 95% CI, 0.10-0.96). Differential expression of 348 vitamin D-associated genes (158 upregulated) was found in peripheral blood of women who developed preeclampsia (FDR <0.05 in the Vitamin D Antenatal Asthma Reduction Trial [VDAART]; P < 0.05 in a replication cohort). Functional enrichment and network analyses of this vitamin D-associated gene set suggests several highly functional modules related to systematic inflammatory and immune responses, including some nodes with a high degree of connectivity. CONCLUSIONS Vitamin D supplementation initiated in weeks 10-18 of pregnancy did not reduce preeclampsia incidence in the intention-to-treat paradigm. However, vitamin D levels of 30 ng/ml or higher at trial entry and in late pregnancy were associated with a lower risk of preeclampsia. Differentially expressed vitamin D-associated transcriptomes implicated the emergence of an early pregnancy, distinctive immune response in women who went on to develop preeclampsia. TRIAL REGISTRATION ClinicalTrials.gov NCT00920621. FUNDING Quebec Breast Cancer Foundation and Genome Canada Innovation Network. This trial was funded by the National Heart, Lung, and Blood Institute. For details see Acknowledgments.
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Sakakibara I, Wurmser M, Dos Santos M, Santolini M, Ducommun S, Davaze R, Guernec A, Sakamoto K, Maire P. Six1 homeoprotein drives myofiber type IIA specialization in soleus muscle. Skelet Muscle 2016; 6:30. [PMID: 27597886 PMCID: PMC5011358 DOI: 10.1186/s13395-016-0102-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 08/16/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Adult skeletal muscles are composed of slow and fast myofiber subtypes which each express selective genes required for their specific contractile and metabolic activity. Six homeoproteins are transcription factors regulating muscle cell fate through activation of myogenic regulatory factors and driving fast-type gene expression during embryogenesis. RESULTS We show here that Six1 protein accumulates more robustly in the nuclei of adult fast-type muscles than in adult slow-type muscles, this specific enrichment takes place during perinatal growth. Deletion of Six1 in soleus impaired fast-type myofiber specialization during perinatal development, resulting in a slow phenotype and a complete lack of Myosin heavy chain 2A (MyHCIIA) expression. Global transcriptomic analysis of wild-type and Six1 mutant myofibers identified the gene networks controlled by Six1 in adult soleus muscle. This analysis showed that Six1 is required for the expression of numerous genes encoding fast-type sarcomeric proteins, glycolytic enzymes and controlling intracellular calcium homeostasis. Parvalbumin, a key player of calcium buffering, in particular, is a direct target of Six1 in the adult myofiber. CONCLUSIONS This analysis revealed that Six1 controls distinct aspects of adult muscle physiology in vivo, and acts as a main determinant of fast-fiber type acquisition and maintenance.
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Affiliation(s)
- Iori Sakakibara
- INSERM U1016, Institut Cochin, Paris, 75014 France ; CNRS UMR 8104, Paris, 75014 France ; Université Paris Descartes, Sorbonne Paris Cité, Paris, 75014 France ; Division of Integrative Pathophysiology, Proteo-Science Center, Graduate School of Medicine, Ehime University, Ehime, Japan
| | - Maud Wurmser
- INSERM U1016, Institut Cochin, Paris, 75014 France ; CNRS UMR 8104, Paris, 75014 France ; Université Paris Descartes, Sorbonne Paris Cité, Paris, 75014 France
| | - Matthieu Dos Santos
- INSERM U1016, Institut Cochin, Paris, 75014 France ; CNRS UMR 8104, Paris, 75014 France ; Université Paris Descartes, Sorbonne Paris Cité, Paris, 75014 France
| | - Marc Santolini
- Laboratoire de Physique Statistique, CNRS, Université P. et M. Curie, Université D. Diderot, École Normale Supérieure, Paris, 75005 France
| | - Serge Ducommun
- Nestlé Institute of Health Sciences SA, EPFL Innovation Park, Lausanne, Switzerland
| | - Romain Davaze
- INSERM U1016, Institut Cochin, Paris, 75014 France ; CNRS UMR 8104, Paris, 75014 France ; Université Paris Descartes, Sorbonne Paris Cité, Paris, 75014 France
| | - Anthony Guernec
- INSERM U1016, Institut Cochin, Paris, 75014 France ; CNRS UMR 8104, Paris, 75014 France ; Université Paris Descartes, Sorbonne Paris Cité, Paris, 75014 France
| | - Kei Sakamoto
- Nestlé Institute of Health Sciences SA, EPFL Innovation Park, Lausanne, Switzerland
| | - Pascal Maire
- INSERM U1016, Institut Cochin, Paris, 75014 France ; CNRS UMR 8104, Paris, 75014 France ; Université Paris Descartes, Sorbonne Paris Cité, Paris, 75014 France
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Santolini M, Sakakibara I, Gauthier M, Ribas-Aulinas F, Takahashi H, Sawasaki T, Mouly V, Concordet JP, Defossez PA, Hakim V, Maire P. MyoD reprogramming requires Six1 and Six4 homeoproteins: genome-wide cis-regulatory module analysis. Nucleic Acids Res 2016; 44:8621-8640. [PMID: 27302134 PMCID: PMC5062961 DOI: 10.1093/nar/gkw512] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 05/26/2016] [Indexed: 11/12/2022] Open
Abstract
Myogenic regulatory factors of the MyoD family have the ability to reprogram differentiated cells toward a myogenic fate. In this study, we demonstrate that Six1 or Six4 are required for the reprogramming by MyoD of mouse embryonic fibroblasts (MEFs). Using microarray experiments, we found 761 genes under the control of both Six and MyoD. Using MyoD ChIPseq data and a genome-wide search for Six1/4 MEF3 binding sites, we found significant co-localization of binding sites for MyoD and Six proteins on over a thousand mouse genomic DNA regions. The combination of both datasets yielded 82 genes which are synergistically activated by Six and MyoD, with 96 associated MyoD+MEF3 putative cis-regulatory modules (CRMs). Fourteen out of 19 of the CRMs that we tested demonstrated in Luciferase assays a synergistic action also observed for their cognate gene. We searched putative binding sites on these CRMs using available databases and de novo search of conserved motifs and demonstrated that the Six/MyoD synergistic activation takes place in a feedforward way. It involves the recruitment of these two families of transcription factors to their targets, together with partner transcription factors, encoded by genes that are themselves activated by Six and MyoD, including Mef2, Pbx-Meis and EBF.
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Affiliation(s)
- Marc Santolini
- Institut Cochin, Université Paris-Descartes, Centre National de la Recherche Scientifique (CNRS), UMR 8104, Paris, France Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, Paris, France Ecole Normale Supérieure, CNRS, Laboratoire de Physique Statistique, PSL Research University, Université Pierre-et-Marie Curie, Paris, France
| | - Iori Sakakibara
- Institut Cochin, Université Paris-Descartes, Centre National de la Recherche Scientifique (CNRS), UMR 8104, Paris, France Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, Paris, France Division of Integrative Pathophysiology, Proteo-Science Center, Graduate School of Medicine, Ehime University, Ehime, Japan
| | - Morgane Gauthier
- Institut Cochin, Université Paris-Descartes, Centre National de la Recherche Scientifique (CNRS), UMR 8104, Paris, France Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, Paris, France
| | - Francesc Ribas-Aulinas
- Institut Cochin, Université Paris-Descartes, Centre National de la Recherche Scientifique (CNRS), UMR 8104, Paris, France Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, Paris, France
| | | | | | - Vincent Mouly
- Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology, 75013 Paris, France
| | - Jean-Paul Concordet
- Institut Cochin, Université Paris-Descartes, Centre National de la Recherche Scientifique (CNRS), UMR 8104, Paris, France Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, Paris, France
| | | | - Vincent Hakim
- Ecole Normale Supérieure, CNRS, Laboratoire de Physique Statistique, PSL Research University, Université Pierre-et-Marie Curie, Paris, France
| | - Pascal Maire
- Institut Cochin, Université Paris-Descartes, Centre National de la Recherche Scientifique (CNRS), UMR 8104, Paris, France Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, Paris, France
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Santolini M, Mora T, Hakim V. A general pairwise interaction model provides an accurate description of in vivo transcription factor binding sites. PLoS One 2014; 9:e99015. [PMID: 24926895 PMCID: PMC4057186 DOI: 10.1371/journal.pone.0099015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 05/09/2014] [Indexed: 11/19/2022] Open
Abstract
The identification of transcription factor binding sites (TFBSs) on genomic DNA is of crucial importance for understanding and predicting regulatory elements in gene networks. TFBS motifs are commonly described by Position Weight Matrices (PWMs), in which each DNA base pair contributes independently to the transcription factor (TF) binding. However, this description ignores correlations between nucleotides at different positions, and is generally inaccurate: analysing fly and mouse in vivo ChIPseq data, we show that in most cases the PWM model fails to reproduce the observed statistics of TFBSs. To overcome this issue, we introduce the pairwise interaction model (PIM), a generalization of the PWM model. The model is based on the principle of maximum entropy and explicitly describes pairwise correlations between nucleotides at different positions, while being otherwise as unconstrained as possible. It is mathematically equivalent to considering a TF-DNA binding energy that depends additively on each nucleotide identity at all positions in the TFBS, like the PWM model, but also additively on pairs of nucleotides. We find that the PIM significantly improves over the PWM model, and even provides an optimal description of TFBS statistics within statistical noise. The PIM generalizes previous approaches to interdependent positions: it accounts for co-variation of two or more base pairs, and predicts secondary motifs, while outperforming multiple-motif models consisting of mixtures of PWMs. We analyse the structure of pairwise interactions between nucleotides, and find that they are sparse and dominantly located between consecutive base pairs in the flanking region of TFBS. Nonetheless, interactions between pairs of non-consecutive nucleotides are found to play a significant role in the obtained accurate description of TFBS statistics. The PIM is computationally tractable, and provides a general framework that should be useful for describing and predicting TFBSs beyond PWMs.
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Affiliation(s)
- Marc Santolini
- Laboratoire de Physique Statistique, CNRS, Université P. et M. Curie, Université D. Diderot, École Normale Supérieure, Paris, France
| | - Thierry Mora
- Laboratoire de Physique Statistique, CNRS, Université P. et M. Curie, Université D. Diderot, École Normale Supérieure, Paris, France
| | - Vincent Hakim
- Laboratoire de Physique Statistique, CNRS, Université P. et M. Curie, Université D. Diderot, École Normale Supérieure, Paris, France
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Sakakibara I, Santolini M, Ferry A, Hakim V, Maire P. Six homeoproteins and a Iinc-RNA at the fast MYH locus lock fast myofiber terminal phenotype. PLoS Genet 2014; 10:e1004386. [PMID: 24852826 PMCID: PMC4031048 DOI: 10.1371/journal.pgen.1004386] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 04/02/2014] [Indexed: 12/18/2022] Open
Abstract
Thousands of long intergenic non-coding RNAs (lincRNAs) are encoded by the mammalian genome. However, the function of most of these lincRNAs has not been identified in vivo. Here, we demonstrate a role for a novel lincRNA, linc-MYH, in adult fast-type myofiber specialization. Fast myosin heavy chain (MYH) genes and linc-MYH share a common enhancer, located in the fast MYH gene locus and regulated by Six1 homeoproteins. linc-MYH in nuclei of fast-type myofibers prevents slow-type and enhances fast-type gene expression. Functional fast-sarcomeric unit formation is achieved by the coordinate expression of fast MYHs and linc-MYH, under the control of a common Six-bound enhancer.
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Affiliation(s)
- Iori Sakakibara
- INSERM U1016, Institut Cochin, Paris, France
- CNRS UMR 8104, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Marc Santolini
- Laboratoire de Physique Statistique, CNRS, Université P. et M. Curie, Université D. Diderot, École Normale Supérieure, Paris, France
| | - Arnaud Ferry
- CNRS UMR 8104, Paris, France
- Université Pierre et Marie Curie-Paris 6, Sorbonne Universités, UMR S794, INSERM U974, CNRS UMR7215, Institut de Myologie, Paris, France
| | - Vincent Hakim
- Laboratoire de Physique Statistique, CNRS, Université P. et M. Curie, Université D. Diderot, École Normale Supérieure, Paris, France
| | - Pascal Maire
- INSERM U1016, Institut Cochin, Paris, France
- CNRS UMR 8104, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- * E-mail:
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Rouault H, Santolini M, Schweisguth F, Hakim V. Imogene: identification of motifs and cis-regulatory modules underlying gene co-regulation. Nucleic Acids Res 2014; 42:6128-45. [PMID: 24682824 PMCID: PMC4041412 DOI: 10.1093/nar/gku209] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Cis-regulatory modules (CRMs) and motifs play a central role in tissue and condition-specific gene expression. Here we present Imogene, an ensemble of statistical tools that we have developed to facilitate their identification and implemented in a publicly available software. Starting from a small training set of mammalian or fly CRMs that drive similar gene expression profiles, Imogene determines de novocis-regulatory motifs that underlie this co-expression. It can then predict on a genome-wide scale other CRMs with a regulatory potential similar to the training set. Imogene bypasses the need of large datasets for statistical analyses by making central use of the information provided by the sequenced genomes of multiple species, based on the developed statistical tools and explicit models for transcription factor binding site evolution. We test Imogene on characterized tissue-specific mouse developmental CRMs. Its ability to identify CRMs with the same specificity based on its de novo created motifs is comparable to that of previously evaluated ‘motif-blind’ methods. We further show, both in flies and in mammals, that Imogene de novo generated motifs are sufficient to discriminate CRMs related to different developmental programs. Notably, purely relying on sequence data, Imogene performs as well in this discrimination task as a previously reported learning algorithm based on Chromatin Immunoprecipitation (ChIP) data for multiple transcription factors at multiple developmental stages.
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Affiliation(s)
- Hervé Rouault
- Developmental and Stem Cell Biology Department, Institut Pasteur, F-75015 Paris, France CNRS, URA2578, F-75015 Paris, France
| | - Marc Santolini
- Laboratoire de Physique Statistique, CNRS, École Normale Supérieure, Université P. et M. Curie, Université Paris-Diderot
| | - François Schweisguth
- Developmental and Stem Cell Biology Department, Institut Pasteur, F-75015 Paris, France CNRS, URA2578, F-75015 Paris, France
| | - Vincent Hakim
- Laboratoire de Physique Statistique, CNRS, École Normale Supérieure, Université P. et M. Curie, Université Paris-Diderot
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Menoret D, Santolini M, Fernandes I, Spokony R, Zanet J, Gonzalez I, Latapie Y, Ferrer P, Rouault H, White KP, Besse P, Hakim V, Aerts S, Payre F, Plaza S. Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization. Genome Biol 2013; 14:R86. [PMID: 23972280 PMCID: PMC4053989 DOI: 10.1186/gb-2013-14-8-r86] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 08/23/2013] [Indexed: 12/17/2022] Open
Abstract
Background Developmental programs are implemented by regulatory interactions between Transcription Factors (TFs) and their target genes, which remain poorly understood. While recent studies have focused on regulatory cascades of TFs that govern early development, little is known about how the ultimate effectors of cell differentiation are selected and controlled. We addressed this question during late Drosophila embryogenesis, when the finely tuned expression of the TF Ovo/Shavenbaby (Svb) triggers the morphological differentiation of epidermal trichomes. Results We defined a sizeable set of genes downstream of Svb and used in vivo assays to delineate 14 enhancers driving their specific expression in trichome cells. Coupling computational modeling to functional dissection, we investigated the regulatory logic of these enhancers. Extending the repertoire of epidermal effectors using genome-wide approaches showed that the regulatory models learned from this first sample are representative of the whole set of trichome enhancers. These enhancers harbor remarkable features with respect to their functional architectures, including a weak or non-existent clustering of Svb binding sites. The in vivo function of each site relies on its intimate context, notably the flanking nucleotides. Two additional cis-regulatory motifs, present in a broad diversity of composition and positioning among trichome enhancers, critically contribute to enhancer activity. Conclusions Our results show that Svb directly regulates a large set of terminal effectors of the remodeling of epidermal cells. Further, these data reveal that trichome formation is underpinned by unexpectedly diverse modes of regulation, providing fresh insights into the functional architecture of enhancers governing a terminal differentiation program.
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Sirtori C, Paganuzzi M, Lombardo C, Ruzzon T, Santolini M, Dutto P, Lapide M, Chiola S. [Cooking meat in microwave ovens does not cause formation of mutagenic substances]. Minerva Med 1983; 74:2803-6. [PMID: 6657121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
UNLABELLED During the cooking process of meat, mutagenic and/or carcinogenic substances can be formed that can induce tumours of the gastro-intestinal tract or of other organs in the rat. The formation of these substances is proportionate to the cooking time, the cooking surface and the quantity of fats contained in meat. A comparison is made between beef cooked on a grid where the temperature reaches 200 degrees C, and cooked in a microwave oven (Cuocorapido Candy 500 CL, frequency 2450 Mhz) where the temperature does not exceed 100 degrees C. Mutagenic substances were extracted by the Commoner technique and mutagenic activity was assayed with the Ames test. RESULTS no mutagenic activity was demonstrated in the extracts of meat cooked in microwave ovens, while mutagenic activity was clearly demonstrated in the extracts of meat cooked on a grid.
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