1
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Yin L, Zander M, Huang SSC, Xie M, Song L, Saldierna Guzmán JP, Hann E, Shanbhag BK, Ng S, Jain S, Janssen BJ, Clark NM, Walley JW, Beddoe T, Bar-Joseph Z, Lewsey MG, Ecker JR. Transcription Factor Dynamics in Cross-Regulation of Plant Hormone Signaling Pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531630. [PMID: 36945593 PMCID: PMC10028877 DOI: 10.1101/2023.03.07.531630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Cross-regulation between hormone signaling pathways is indispensable for plant growth and development. However, the molecular mechanisms by which multiple hormones interact and co-ordinate activity need to be understood. Here, we generated a cross-regulation network explaining how hormone signals are integrated from multiple pathways in etiolated Arabidopsis (Arabidopsis thaliana) seedlings. To do so we comprehensively characterized transcription factor activity during plant hormone responses and reconstructed dynamic transcriptional regulatory models for six hormones; abscisic acid, brassinosteroid, ethylene, jasmonic acid, salicylic acid and strigolactone/karrikin. These models incorporated target data for hundreds of transcription factors and thousands of protein-protein interactions. Each hormone recruited different combinations of transcription factors, a subset of which were shared between hormones. Hub target genes existed within hormone transcriptional networks, exhibiting transcription factor activity themselves. In addition, a group of MITOGEN-ACTIVATED PROTEIN KINASES (MPKs) were identified as potential key points of cross-regulation between multiple hormones. Accordingly, the loss of function of one of these (MPK6) disrupted the global proteome, phosphoproteome and transcriptome during hormone responses. Lastly, we determined that all hormones drive substantial alternative splicing that has distinct effects on the transcriptome compared with differential gene expression, acting in early hormone responses. These results provide a comprehensive understanding of the common features of plant transcriptional regulatory pathways and how cross-regulation between hormones acts upon gene expression.
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Affiliation(s)
- Lingling Yin
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Agriculture Biomedicine and Environment, AgriBio Building, La Trobe University, Melbourne, VIC 3086, Australia
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Mark Zander
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Present address: Waksman Institute of Microbiology, Department of Plant Biology, Rutgers, The State University of New Jersey, NJ 08854, USA
| | - Shao-shan Carol Huang
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Present address: Department of Biology, New York University, New York, NY 10003, USA
| | - Mingtang Xie
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Present address: Cibus, San Diego, CA 92121, USA
| | - Liang Song
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Present address: Department of Botany, The University of British Columbia, Vancouver, British Columbia, Canada
| | - J. Paola Saldierna Guzmán
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Present address: Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Elizabeth Hann
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Present address: Department of Chemical and Environmental Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Bhuvana K. Shanbhag
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Agriculture Biomedicine and Environment, AgriBio Building, La Trobe University, Melbourne, VIC 3086, Australia
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Sophia Ng
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Agriculture Biomedicine and Environment, AgriBio Building, La Trobe University, Melbourne, VIC 3086, Australia
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Siddhartha Jain
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Bart J. Janssen
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - Natalie M. Clark
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA, 50011 USA
| | - Justin W. Walley
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA, 50011 USA
| | - Travis Beddoe
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Agriculture Biomedicine and Environment, AgriBio Building, La Trobe University, Melbourne, VIC 3086, Australia
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Mathew G. Lewsey
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Agriculture Biomedicine and Environment, AgriBio Building, La Trobe University, Melbourne, VIC 3086, Australia
- Australian Research Council Industrial Transformation Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
- Australian Research Council Centre of Excellence in Plants For Space, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Joseph R. Ecker
- Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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2
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Ding J, Lugo-Martinez J, Yuan Y, Huang J, Hume AJ, Suder EL, Mühlberger E, Kotton DN, Bar-Joseph Z. Reconstructed signaling and regulatory networks identify potential drugs for SARS-CoV-2 infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.06.01.127589. [PMID: 33083801 PMCID: PMC7574259 DOI: 10.1101/2020.06.01.127589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Several molecular datasets have been recently compiled to characterize the activity of SARS-CoV-2 within human cells. Here we extend computational methods to integrate several different types of sequence, functional and interaction data to reconstruct networks and pathways activated by the virus in host cells. We identify key proteins in these networks and further intersect them with genes differentially expressed at conditions that are known to impact viral activity. Several of the top ranked genes do not directly interact with virus proteins. We experimentally tested treatments for a number of the predicted targets. We show that blocking one of the predicted indirect targets significantly reduces viral loads in stem cell-derived alveolar epithelial type II cells (iAT2s).
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Affiliation(s)
- Jun Ding
- Meakins-Christie Laboratories, Department of Medicine, McGill University Health Centre, Montreal, Quebec, H4A 3J1, Canada
| | - Jose Lugo-Martinez
- Department of Computer Science, University of Puerto Rico, San Juan, Puerto Rico, 00925, USA
| | - Ye Yuan
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Adam J. Hume
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ellen L. Suder
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Elke Mühlberger
- National Emerging Infectious Diseases Laboratory (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, 15213, USA
- Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, 15213, USA
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3
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Siahpirani AF, Chasman D, Roy S. Integrative Approaches for Inference of Genome-Scale Gene Regulatory Networks. Methods Mol Biol 2019; 1883:161-194. [PMID: 30547400 DOI: 10.1007/978-1-4939-8882-2_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Transcriptional regulatory networks specify the regulatory proteins of target genes that control the context-specific expression levels of genes. With our ability to profile the different types of molecular components of cells under different conditions, we are now uniquely positioned to infer regulatory networks in diverse biological contexts such as different cell types, tissues, and time points. In this chapter, we cover two main classes of computational methods to integrate different types of information to infer genome-scale transcriptional regulatory networks. The first class of methods focuses on integrative methods for specifically inferring connections between transcription factors and target genes by combining gene expression data with regulatory edge-specific knowledge. The second class of methods integrates upstream signaling networks with transcriptional regulatory networks by combining gene expression data with protein-protein interaction networks and proteomic datasets. We conclude with a section on practical applications of a network inference algorithm to infer a genome-scale regulatory network.
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Affiliation(s)
- Alireza Fotuhi Siahpirani
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA.,Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Deborah Chasman
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA.
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4
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Köksal AS, Beck K, Cronin DR, McKenna A, Camp ND, Srivastava S, MacGilvray ME, Bodík R, Wolf-Yadlin A, Fraenkel E, Fisher J, Gitter A. Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data. Cell Rep 2018; 24:3607-3618. [PMID: 30257219 PMCID: PMC6295338 DOI: 10.1016/j.celrep.2018.08.085] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 04/16/2018] [Accepted: 08/29/2018] [Indexed: 12/25/2022] Open
Abstract
We present a method for automatically discovering signaling pathways from time-resolved phosphoproteomic data. The Temporal Pathway Synthesizer (TPS) algorithm uses constraint-solving techniques first developed in the context of formal verification to explore paths in an interaction network. It systematically eliminates all candidate structures for a signaling pathway where a protein is activated or inactivated before its upstream regulators. The algorithm can model more than one hundred thousand dynamic phosphosites and can discover pathway members that are not differentially phosphorylated. By analyzing temporal data, TPS defines signaling cascades without needing to experimentally perturb individual proteins. It recovers known pathways and proposes pathway connections when applied to the human epidermal growth factor and yeast osmotic stress responses. Independent kinase mutant studies validate predicted substrates in the TPS osmotic stress pathway.
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Affiliation(s)
- Ali Sinan Köksal
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA
| | - Kirsten Beck
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Dylan R Cronin
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA; Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, USA
| | - Aaron McKenna
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Nathan D Camp
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Saurabh Srivastava
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA
| | | | - Rastislav Bodík
- Paul G. Allen Center for Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | | | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jasmin Fisher
- Microsoft Research, Cambridge, UK; Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Anthony Gitter
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA; Morgridge Institute for Research, Madison, WI, USA.
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5
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Ray S, Maulik U. Discovering Perturbation of Modular Structure in HIV Progression by Integrating Multiple Data Sources Through Non-Negative Matrix Factorization. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:869-877. [PMID: 28029629 DOI: 10.1109/tcbb.2016.2642184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Detecting perturbation in modular structure during HIV-1 disease progression is an important step to understand stage specific infection pattern of HIV-1 virus in human cell. In this article, we proposed a novel methodology on integration of multiple biological information to identify such disruption in human gene module during different stages of HIV-1 infection. We integrate three different biological information: gene expression information, protein-protein interaction information, and gene ontology information in single gene meta-module, through non negative matrix factorization (NMF). As the identified meta-modules inherit those information so, detecting perturbation of these, reflects the changes in expression pattern, in PPI structure and in functional similarity of genes during the infection progression. To integrate modules of different data sources into strong meta-modules, NMF based clustering is utilized here. Perturbation in meta-modular structure is identified by investigating the topological and intramodular properties and putting rank to those meta-modules using a rank aggregation algorithm. We have also analyzed the preservation structure of significant GO terms in which the human proteins of the meta-modules participate. Moreover, we have performed an analysis to show the change of coregulation pattern of identified transcription factors (TFs) over the HIV progression stages.
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6
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Lin C, Jain S, Kim H, Bar-Joseph Z. Using neural networks for reducing the dimensions of single-cell RNA-Seq data. Nucleic Acids Res 2017; 45:e156. [PMID: 28973464 PMCID: PMC5737331 DOI: 10.1093/nar/gkx681] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/24/2017] [Indexed: 12/11/2022] Open
Abstract
While only recently developed, the ability to profile expression data in single cells (scRNA-Seq) has already led to several important studies and findings. However, this technology has also raised several new computational challenges. These include questions about the best methods for clustering scRNA-Seq data, how to identify unique group of cells in such experiments, and how to determine the state or function of specific cells based on their expression profile. To address these issues we develop and test a method based on neural networks (NN) for the analysis and retrieval of single cell RNA-Seq data. We tested various NN architectures, some of which incorporate prior biological knowledge, and used these to obtain a reduced dimension representation of the single cell expression data. We show that the NN method improves upon prior methods in both, the ability to correctly group cells in experiments not used in the training and the ability to correctly infer cell type or state by querying a database of tens of thousands of single cell profiles. Such database queries (which can be performed using our web server) will enable researchers to better characterize cells when analyzing heterogeneous scRNA-Seq samples.
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Affiliation(s)
- Chieh Lin
- Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Siddhartha Jain
- Computer Science Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Hannah Kim
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Ziv Bar-Joseph
- Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.,Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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7
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Ruffalo M, Stojanov P, Pillutla VK, Varma R, Bar-Joseph Z. Reconstructing cancer drug response networks using multitask learning. BMC SYSTEMS BIOLOGY 2017; 11:96. [PMID: 29017547 PMCID: PMC5635550 DOI: 10.1186/s12918-017-0471-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 10/02/2017] [Indexed: 01/03/2023]
Abstract
BACKGROUND Translating in vitro results to clinical tests is a major challenge in systems biology. Here we present a new Multi-Task learning framework which integrates thousands of cell line expression experiments to reconstruct drug specific response networks in cancer. RESULTS The reconstructed networks correctly identify several shared key proteins and pathways while simultaneously highlighting many cell type specific proteins. We used top proteins from each drug network to predict survival for patients prescribed the drug. CONCLUSIONS Predictions based on proteins from the in-vitro derived networks significantly outperformed predictions based on known cancer genes indicating that Multi-Task learning can indeed identify accurate drug response networks.
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Affiliation(s)
- Matthew Ruffalo
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Petar Stojanov
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Venkata Krishna Pillutla
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Rohan Varma
- Electrical and Computer Engineering, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA. .,Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
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8
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Rioualen C, Da Costa Q, Chetrit B, Charafe-Jauffret E, Ginestier C, Bidaut G. HTS-Net: An integrated regulome-interactome approach for establishing network regulation models in high-throughput screenings. PLoS One 2017; 12:e0185400. [PMID: 28949986 PMCID: PMC5614607 DOI: 10.1371/journal.pone.0185400] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 09/12/2017] [Indexed: 12/28/2022] Open
Abstract
High-throughput RNAi screenings (HTS) allow quantifying the impact of the deletion of each gene in any particular function, from virus-host interactions to cell differentiation. However, there has been less development for functional analysis tools dedicated to RNAi analyses. HTS-Net, a network-based analysis program, was developed to identify gene regulatory modules impacted in high-throughput screenings, by integrating transcription factors-target genes interaction data (regulome) and protein-protein interaction networks (interactome) on top of screening z-scores. HTS-Net produces exhaustive HTML reports for results navigation and exploration. HTS-Net is a new pipeline for RNA interference screening analyses that proves better performance than simple gene rankings by z-scores, by re-prioritizing genes and replacing them in their biological context, as shown by the three studies that we reanalyzed. Formatted input data for the three studied datasets, source code and web site for testing the system are available from the companion web site at http://htsnet.marseille.inserm.fr/. We also compared our program with existing algorithms (CARD and hotnet2).
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Affiliation(s)
- Claire Rioualen
- Aix-Marseille Univ, Marseille, France
- Inserm, U1068, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- CNRS, UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, France
| | - Quentin Da Costa
- Aix-Marseille Univ, Marseille, France
- Inserm, U1068, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- CNRS, UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, France
| | - Bernard Chetrit
- Aix-Marseille Univ, Marseille, France
- Inserm, U1068, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- CNRS, UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, France
| | - Emmanuelle Charafe-Jauffret
- Aix-Marseille Univ, Marseille, France
- Inserm, U1068, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- CNRS, UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, France
| | - Christophe Ginestier
- Aix-Marseille Univ, Marseille, France
- Inserm, U1068, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- CNRS, UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, France
| | - Ghislain Bidaut
- Aix-Marseille Univ, Marseille, France
- Inserm, U1068, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- CNRS, UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- * E-mail:
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9
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Jain S, Arrais J, Venkatachari NJ, Ayyavoo V, Bar-Joseph Z. Reconstructing the temporal progression of HIV-1 immune response pathways. Bioinformatics 2017; 32:i253-i261. [PMID: 27307624 PMCID: PMC4908338 DOI: 10.1093/bioinformatics/btw254] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Motivation: Most methods for reconstructing response networks from high throughput data generate static models which cannot distinguish between early and late response stages. Results: We present TimePath, a new method that integrates time series and static datasets to reconstruct dynamic models of host response to stimulus. TimePath uses an Integer Programming formulation to select a subset of pathways that, together, explain the observed dynamic responses. Applying TimePath to study human response to HIV-1 led to accurate reconstruction of several known regulatory and signaling pathways and to novel mechanistic insights. We experimentally validated several of TimePaths’ predictions highlighting the usefulness of temporal models. Availability and Implementation: Data, Supplementary text and the TimePath software are available from http://sb.cs.cmu.edu/timepath Contact:zivbj@cs.cmu.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Siddhartha Jain
- Computer Science Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Joel Arrais
- Department of Computer Science, University of Coimbra, Coimbra, Portugal
| | | | - Velpandi Ayyavoo
- Department of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ziv Bar-Joseph
- Computational Biology and Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA, USA
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10
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Korla K, Chandra N. A Systems Perspective of Signalling Networks in Host–Pathogen Interactions. J Indian Inst Sci 2017. [DOI: 10.1007/s41745-016-0017-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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Ray S, Bandyopadhyay S. Discovering Condition Specific Topological Pattern Changes in Coexpression Network: An Application to HIV-1 Progression. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016; 13:1086-1099. [PMID: 26661789 DOI: 10.1109/tcbb.2015.2505300] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The natural progression of HIV-1 begins with a short acute retroviral syndrome which typically transit to chronic and clinical latency stages and subsequently progresses to a symptomatic, life-threatening immunodeficiency disease known as AIDS. Microarray analysis based on gene coexpression is widely used to investigate the coregulation pattern of a group (or cluster) of genes in a specific phenotype. Moreover, an investigation on the topological patterns across multiple phenotypes can facilitate the understanding of stage specific infection pattern of HIV-1 virus. Here, we develop a novel framework to identify topological patterns of gene co-expression network and detect changes of modular structure across different stages of HIV progression. This is achieved by comparing the topological and intramodular properties of HIV infection modules. To capture the diversity in modular structure, some topological, correlation based, and eigengene based measures are utilized here. We have applied a rank aggregation scheme to rank all the modules to provide a good agreement between these measures. Some novel transcription factors like 'FOXO1', 'GATA3', 'GFI1', 'IRF1', 'IRF7', 'MAX', 'STAT1', 'STAT3', 'XBP1', and 'YY1' that merge from the modules show significant change in expression pattern over HIV progression stages. Moreover, we have performed an eigengene based analysis to reveal the perturbation in modular structure across three stages of HIV-1 progression.
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12
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Wang CH, Zhong Y, Zhang Y, Liu JP, Wang YF, Jia WN, Wang GC, Li Z, Zhu Y, Gao XM. A network analysis of the Chinese medicine Lianhua-Qingwen formula to identify its main effective components. MOLECULAR BIOSYSTEMS 2016; 12:606-13. [PMID: 26687282 DOI: 10.1039/c5mb00448a] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Chinese medicine is known to treat complex diseases with multiple components and multiple targets. However, the main effective components and their related key targets and functions remain to be identified. Herein, a network analysis method was developed to identify the main effective components and key targets of a Chinese medicine, Lianhua-Qingwen Formula (LQF). The LQF is commonly used for the prevention and treatment of viral influenza in China. It is composed of 11 herbs, gypsum and menthol with 61 compounds being identified in our previous work. In this paper, these 61 candidate compounds were used to find their related targets and construct the predicted-target (PT) network. An influenza-related protein-protein interaction (PPI) network was constructed and integrated with the PT network. Then the compound-effective target (CET) network and compound-ineffective target network (CIT) were extracted, respectively. A novel approach was developed to identify effective components by comparing CET and CIT networks. As a result, 15 main effective components were identified along with 61 corresponding targets. 7 of these main effective components were further experimentally validated to have antivirus efficacy in vitro. The main effective component-target (MECT) network was further constructed with main effective components and their key targets. Gene Ontology (GO) analysis of the MECT network predicted key functions such as NO production being modulated by the LQF. Interestingly, five effective components were experimentally tested and exhibited inhibitory effects on NO production in the LPS induced RAW 264.7 cell. In summary, we have developed a novel approach to identify the main effective components in a Chinese medicine LQF and experimentally validated some of the predictions.
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Affiliation(s)
- Chun-Hua Wang
- Tianjin Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China. +86-571-88208427
| | - Yi Zhong
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yan Zhang
- Tianjin Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China. +86-571-88208427
| | - Jin-Ping Liu
- Tianjin Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China. +86-571-88208427
| | - Yue-Fei Wang
- Tianjin Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China. +86-571-88208427
| | - Wei-Na Jia
- Tianjin Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China. +86-571-88208427
| | - Guo-Cai Wang
- Institute of TCM and Natural Medicine, Jinan University, Guangzhou 510632, China.
| | - Zheng Li
- Tianjin Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China. +86-571-88208427
| | - Yan Zhu
- Tianjin Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China. +86-571-88208427
| | - Xiu-Mei Gao
- Tianjin Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China. +86-571-88208427
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13
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Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens. PLoS Comput Biol 2016; 12:e1005013. [PMID: 27403523 PMCID: PMC4942116 DOI: 10.1371/journal.pcbi.1005013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 06/06/2016] [Indexed: 12/17/2022] Open
Abstract
Mammalian host response to pathogenic infections is controlled by a complex regulatory network connecting regulatory proteins such as transcription factors and signaling proteins to target genes. An important challenge in infectious disease research is to understand molecular similarities and differences in mammalian host response to diverse sets of pathogens. Recently, systems biology studies have produced rich collections of omic profiles measuring host response to infectious agents such as influenza viruses at multiple levels. To gain a comprehensive understanding of the regulatory network driving host response to multiple infectious agents, we integrated host transcriptomes and proteomes using a network-based approach. Our approach combines expression-based regulatory network inference, structured-sparsity based regression, and network information flow to infer putative physical regulatory programs for expression modules. We applied our approach to identify regulatory networks, modules and subnetworks that drive host response to multiple influenza infections. The inferred regulatory network and modules are significantly enriched for known pathways of immune response and implicate apoptosis, splicing, and interferon signaling processes in the differential response of viral infections of different pathogenicities. We used the learned network to prioritize regulators and study virus and time-point specific networks. RNAi-based knockdown of predicted regulators had significant impact on viral replication and include several previously unknown regulators. Taken together, our integrated analysis identified novel module level patterns that capture strain and pathogenicity-specific patterns of expression and helped identify important regulators of host response to influenza infection. An important challenge in infectious disease research is to understand how the human immune system responds to different types of pathogenic infections. An important component of mounting proper response is the transcriptional regulatory network that specifies the context-specific gene expression program in the host cell. However, our understanding of this regulatory network and how it drives context-specific transcriptional programs is incomplete. To address this gap, we performed a network-based analysis of host response to influenza viruses that integrated high-throughput mRNA- and protein measurements and protein-protein interaction networks to identify virus and pathogenicity-specific modules and their upstream physical regulatory programs. We inferred regulatory networks for human cell line and mouse host systems, which recapitulated several known regulators and pathways of the immune response and viral life cycle. We used the networks to study time point and strain-specific subnetworks and to prioritize important regulators of host response. We predicted several novel regulators, both at the mRNA and protein levels, and experimentally verified their role in the virus life cycle based on their ability to significantly impact viral replication.
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14
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Chasman D, Fotuhi Siahpirani A, Roy S. Network-based approaches for analysis of complex biological systems. Curr Opin Biotechnol 2016; 39:157-166. [PMID: 27115495 DOI: 10.1016/j.copbio.2016.04.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 04/04/2016] [Accepted: 04/05/2016] [Indexed: 12/22/2022]
Abstract
Cells function and respond to changes in their environment by the coordinated activity of their molecular components, including mRNAs, proteins and metabolites. At the heart of proper cellular function are molecular networks connecting these components to process extra-cellular environmental signals and drive dynamic, context-specific cellular responses. Network-based computational approaches aim to systematically integrate measurements from high-throughput experiments to gain a global understanding of cellular function under changing environmental conditions. We provide an overview of recent methodological developments toward solving two major computational problems within this field in the past two years (2013-2015): network reconstruction and network-based interpretation. Looking forward, we envision development of methods that can predict phenotypes with high accuracy as well as provide biologically plausible mechanistic hypotheses.
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Affiliation(s)
- Deborah Chasman
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, United States
| | - Alireza Fotuhi Siahpirani
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 53706, United States; Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, United States; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53792, United States
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, United States; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53792, United States; Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 53706, United States.
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15
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Tuncbag N, Gosline SJC, Kedaigle A, Soltis AR, Gitter A, Fraenkel E. Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package. PLoS Comput Biol 2016; 12:e1004879. [PMID: 27096930 PMCID: PMC4838263 DOI: 10.1371/journal.pcbi.1004879] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 03/23/2016] [Indexed: 02/07/2023] Open
Abstract
High-throughput, ‘omic’ methods provide sensitive measures of biological responses to perturbations. However, inherent biases in high-throughput assays make it difficult to interpret experiments in which more than one type of data is collected. In this work, we introduce Omics Integrator, a software package that takes a variety of ‘omic’ data as input and identifies putative underlying molecular pathways. The approach applies advanced network optimization algorithms to a network of thousands of molecular interactions to find high-confidence, interpretable subnetworks that best explain the data. These subnetworks connect changes observed in gene expression, protein abundance or other global assays to proteins that may not have been measured in the screens due to inherent bias or noise in measurement. This approach reveals unannotated molecular pathways that would not be detectable by searching pathway databases. Omics Integrator also provides an elegant framework to incorporate not only positive data, but also negative evidence. Incorporating negative evidence allows Omics Integrator to avoid unexpressed genes and avoid being biased toward highly-studied hub proteins, except when they are strongly implicated by the data. The software is comprised of two individual tools, Garnet and Forest, that can be run together or independently to allow a user to perform advanced integration of multiple types of high-throughput data as well as create condition-specific subnetworks of protein interactions that best connect the observed changes in various datasets. It is available at http://fraenkel.mit.edu/omicsintegrator and on GitHub at https://github.com/fraenkel-lab/OmicsIntegrator.
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Affiliation(s)
- Nurcan Tuncbag
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Sara J. C. Gosline
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Amanda Kedaigle
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Anthony R. Soltis
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Anthony Gitter
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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16
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Abstract
Genes are often combinatorially regulated by multiple transcription factors (TFs). Such combinatorial regulation plays an important role in development and facilitates the ability of cells to respond to different stresses. While a number of approaches have utilized sequence and ChIP-based datasets to study combinational regulation, these have often ignored the combinational logic and the dynamics associated with such regulation. Here we present cDREM, a new method for reconstructing dynamic models of combinatorial regulation. cDREM integrates time series gene expression data with (static) protein interaction data. The method is based on a hidden Markov model and utilizes the sparse group Lasso to identify small subsets of combinatorially active TFs, their time of activation, and the logical function they implement. We tested cDREM on yeast and human data sets. Using yeast we show that the predicted combinatorial sets agree with other high throughput genomic datasets and improve upon prior methods developed to infer combinatorial regulation. Applying cDREM to study human response to flu, we were able to identify several combinatorial TF sets, some of which were known to regulate immune response while others represent novel combinations of important TFs.
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Affiliation(s)
- Aaron Wise
- Lane Center for Computational Biology, Carnegie Mellon University , Pittsburgh, Pennsylvania
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17
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Castrillo JI, Oliver SG. Alzheimer's as a Systems-Level Disease Involving the Interplay of Multiple Cellular Networks. Methods Mol Biol 2016; 1303:3-48. [PMID: 26235058 DOI: 10.1007/978-1-4939-2627-5_1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Alzheimer's disease (AD), and many neurodegenerative disorders, are multifactorial in nature. They involve a combination of genomic, epigenomic, interactomic and environmental factors. Progress is being made, and these complex diseases are beginning to be understood as having their origin in altered states of biological networks at the cellular level. In the case of AD, genomic susceptibility and mechanisms leading to (or accompanying) the impairment of the central Amyloid Precursor Protein (APP) processing and tau networks are widely accepted as major contributors to the diseased state. The derangement of these networks may result in both the gain and loss of functions, increased generation of toxic species (e.g., toxic soluble oligomers and aggregates) and imbalances, whose effects can propagate to supra-cellular levels. Although well sustained by empirical data and widely accepted, this global perspective often overlooks the essential roles played by the main counteracting homeostatic networks (e.g., protein quality control/proteostasis, unfolded protein response, protein folding chaperone networks, disaggregases, ER-associated degradation/ubiquitin proteasome system, endolysosomal network, autophagy, and other stress-protective and clearance networks), whose relevance to AD is just beginning to be fully realized. In this chapter, an integrative perspective is presented. Alzheimer's disease is characterized to be a result of: (a) intrinsic genomic/epigenomic susceptibility and, (b) a continued dynamic interplay between the deranged networks and the central homeostatic networks of nerve cells. This interplay of networks will underlie both the onset and rate of progression of the disease in each individual. Integrative Systems Biology approaches are required to effect its elucidation. Comprehensive Systems Biology experiments at different 'omics levels in simple model organisms, engineered to recapitulate the basic features of AD may illuminate the onset and sequence of events underlying AD. Indeed, studies of models of AD in simple organisms, differentiated cells in culture and rodents are beginning to offer hope that the onset and progression of AD, if detected at an early stage, may be stopped, delayed, or even reversed, by activating or modulating networks involved in proteostasis and the clearance of toxic species. In practice, the incorporation of next-generation neuroimaging, high-throughput and computational approaches are opening the way towards early diagnosis well before irreversible cell death. Thus, the presence or co-occurrence of: (a) accumulation of toxic Aβ oligomers and tau species; (b) altered splicing and transcriptome patterns; (c) impaired redox, proteostatic, and metabolic networks together with, (d) compromised homeostatic capacities may constitute relevant 'AD hallmarks at the cellular level' towards reliable and early diagnosis. From here, preventive lifestyle changes and tailored therapies may be investigated, such as combined strategies aimed at both lowering the production of toxic species and potentiating homeostatic responses, in order to prevent or delay the onset, and arrest, alleviate, or even reverse the progression of the disease.
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Affiliation(s)
- Juan I Castrillo
- Department of Biochemistry & Cambridge Systems Biology Centre, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA, UK,
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18
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Gitter A, Bar-Joseph Z. The SDREM Method for Reconstructing Signaling and Regulatory Response Networks: Applications for Studying Disease Progression. Methods Mol Biol 2016; 1303:493-506. [PMID: 26235087 DOI: 10.1007/978-1-4939-2627-5_30] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The Signaling and Dynamic Regulatory Events Miner (SDREM) is a powerful computational approach for identifying which signaling pathways and transcription factors control the temporal cellular response to a stimulus. SDREM builds end-to-end response models by combining condition-independent protein-protein interactions and transcription factor binding data with two types of condition-specific data: source proteins that detect the stimulus and changes in gene expression over time. Here we describe how to apply SDREM to study human diseases, using epidermal growth factor (EGF) response impacting neurogenesis and Alzheimer's disease as an example.
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19
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Mei S, Zhu H. Multi-label multi-instance transfer learning for simultaneous reconstruction and cross-talk modeling of multiple human signaling pathways. BMC Bioinformatics 2015; 16:417. [PMID: 26718335 PMCID: PMC4697333 DOI: 10.1186/s12859-015-0841-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 07/13/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Signaling pathways play important roles in the life processes of cell growth, cell apoptosis and organism development. At present the signal transduction networks are far from complete. As an effective complement to experimental methods, computational modeling is suited to rapidly reconstruct the signaling pathways at low cost. To our knowledge, the existing computational methods seldom simultaneously exploit more than three signaling pathways into one predictive model for the discovery of novel signaling components and the cross-talk modeling between signaling pathways. RESULTS In this work, we propose a multi-label multi-instance transfer learning method to simultaneously reconstruct 27 human signaling pathways and model their cross-talks. Computational results show that the proposed method demonstrates satisfactory multi-label learning performance and rational proteome-wide predictions. Some predicted signaling components or pathway targeted proteins have been validated by recent literature. The predicted signaling components are further linked to pathways using the experimentally derived PPIs (protein-protein interactions) to reconstruct the human signaling pathways. Thus the map of the cross-talks via common signaling components and common signaling PPIs is conveniently inferred to provide valuable insights into the regulatory and cooperative relationships between signaling pathways. Lastly, gene ontology enrichment analysis is conducted to gain statistical knowledge about the reconstructed human signaling pathways. CONCLUSIONS Multi-label learning framework has been demonstrated effective in this work to model the phenomena that a signaling protein belongs to more than one signaling pathway. As results, novel signaling components and pathways targeted proteins are predicted to simultaneously reconstruct multiple human signaling pathways and the static map of their cross-talks for further biomedical research.
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Affiliation(s)
- Suyu Mei
- Software College, Shenyang Normal University, Shenyang, China. .,Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
| | - Hao Zhu
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
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20
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Venkatachari NJ, Zerbato JM, Jain S, Mancini AE, Chattopadhyay A, Sluis-Cremer N, Bar-Joseph Z, Ayyavoo V. Temporal transcriptional response to latency reversing agents identifies specific factors regulating HIV-1 viral transcriptional switch. Retrovirology 2015; 12:85. [PMID: 26438393 PMCID: PMC4594640 DOI: 10.1186/s12977-015-0211-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 09/25/2015] [Indexed: 12/27/2022] Open
Abstract
Background Latent HIV-1 reservoirs are identified as one of the major challenges to achieve HIV-1 cure. Currently available strategies are associated with wide variability in outcomes both in patients and CD4+ T cell models. This underlines the critical need to develop innovative strategies to predict and recognize ways that could result in better reactivation and eventual elimination of latent HIV-1 reservoirs. Results and discussion In this study, we combined genome wide transcriptome datasets post activation with Systems Biology approach (Signaling and Dynamic Regulatory Events Miner, SDREM analyses) to reconstruct a dynamic signaling and regulatory network involved in reactivation mediated by specific activators using a latent cell line. This approach identified several critical regulators for each treatment, which were confirmed in follow-up validation studies using small molecule inhibitors. Results indicate that signaling pathways involving JNK and related factors as predicted by SDREM are essential for virus reactivation by suberoylanilide hydroxamic acid. ERK1/2 and NF-κB pathways have the foremost role in reactivation with prostratin and TNF-α, respectively. JAK-STAT pathway has a central role in HIV-1 transcription. Additional evaluation, using other latent J-Lat cell clones and primary T cell model, also confirmed that many of the cellular factors associated with latency reversing agents are similar, though minor differences are identified. JAK-STAT and NF-κB related pathways are critical for reversal of HIV-1 latency in primary resting T cells. Conclusion These results validate our combinatorial approach to predict the regulatory cellular factors and pathways responsible for HIV-1 reactivation in latent HIV-1 harboring cell line models. JAK-STAT have a role in reversal of latency in all the HIV-1 latency models tested, including primary CD4+ T cells, with additional cellular pathways such as NF-κB, JNK and ERK 1/2 that may have complementary role in reversal of HIV-1 latency. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0211-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Narasimhan J Venkatachari
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh/GSPH, Room A435, Crabtree Hall, 130 DeSoto Street, Pittsburgh, PA, 15261, USA.
| | - Jennifer M Zerbato
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
| | - Siddhartha Jain
- Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA, 15217, USA.
| | - Allison E Mancini
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh/GSPH, Room A435, Crabtree Hall, 130 DeSoto Street, Pittsburgh, PA, 15261, USA.
| | - Ansuman Chattopadhyay
- Molecular Biology Information Service, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
| | - Nicolas Sluis-Cremer
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
| | - Ziv Bar-Joseph
- Computer Science Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, 15217, USA.
| | - Velpandi Ayyavoo
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh/GSPH, Room A435, Crabtree Hall, 130 DeSoto Street, Pittsburgh, PA, 15261, USA.
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21
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Jain S, Gitter A, Bar-Joseph Z. Multitask learning of signaling and regulatory networks with application to studying human response to flu. PLoS Comput Biol 2014; 10:e1003943. [PMID: 25522349 PMCID: PMC4270428 DOI: 10.1371/journal.pcbi.1003943] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 09/28/2014] [Indexed: 01/04/2023] Open
Abstract
Reconstructing regulatory and signaling response networks is one of the major goals of systems biology. While several successful methods have been suggested for this task, some integrating large and diverse datasets, these methods have so far been applied to reconstruct a single response network at a time, even when studying and modeling related conditions. To improve network reconstruction we developed MT-SDREM, a multi-task learning method which jointly models networks for several related conditions. In MT-SDREM, parameters are jointly constrained across the networks while still allowing for condition-specific pathways and regulation. We formulate the multi-task learning problem and discuss methods for optimizing the joint target function. We applied MT-SDREM to reconstruct dynamic human response networks for three flu strains: H1N1, H5N1 and H3N2. Our multi-task learning method was able to identify known and novel factors and genes, improving upon prior methods that model each condition independently. The MT-SDREM networks were also better at identifying proteins whose removal affects viral load indicating that joint learning can still lead to accurate, condition-specific, networks. Supporting website with MT-SDREM implementation: http://sb.cs.cmu.edu/mtsdrem To understand why some flu strains are more virulent than others, researchers attempt to profile and model the molecular human response to these strains and identify similarities and differences between the resulting models. So far, the modeling and analysis part has been done independently for each strain and the results contrasted in a post-processing step. Here we present a new method, termed MT-SDREM, that simultaneously models the response to all strains allowing us to identify both, the core response elements that are shared among the strains, and factors that are uniquely activated or repressed by individual strains. We applied this method to study the human response to three flu strains: H1N1, H3N2 and H5N1. As we show, the method was able to correctly identify several common and known factors regulating immune response to such strains and also identified unique factors for each of the strains. The models reconstructed by the simultaneous analysis method improved upon those generated by methods that model each strain response separately. Our joint models can be used to identify strain specific treatments as well as treatments that are likely to be effective against all three strains.
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Affiliation(s)
- Siddhartha Jain
- Computer Science Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Anthony Gitter
- Microsoft Research, Cambridge, Massachusetts, United States of America
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Ziv Bar-Joseph
- Lane Center for Computational Biology and Machine Learning Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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22
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Chasman D, Gancarz B, Hao L, Ferris M, Ahlquist P, Craven M. Inferring host gene subnetworks involved in viral replication. PLoS Comput Biol 2014; 10:e1003626. [PMID: 24874113 PMCID: PMC4038467 DOI: 10.1371/journal.pcbi.1003626] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 02/06/2014] [Indexed: 12/16/2022] Open
Abstract
Systematic, genome-wide loss-of-function experiments can be used to identify host factors that directly or indirectly facilitate or inhibit the replication of a virus in a host cell. We present an approach that combines an integer linear program and a diffusion kernel method to infer the pathways through which those host factors modulate viral replication. The inputs to the method are a set of viral phenotypes observed in single-host-gene mutants and a background network consisting of a variety of host intracellular interactions. The output is an ensemble of subnetworks that provides a consistent explanation for the measured phenotypes, predicts which unassayed host factors modulate the virus, and predicts which host factors are the most direct interfaces with the virus. We infer host-virus interaction subnetworks using data from experiments screening the yeast genome for genes modulating the replication of two RNA viruses. Because a gold-standard network is unavailable, we assess the predicted subnetworks using both computational and qualitative analyses. We conduct a cross-validation experiment in which we predict whether held-aside test genes have an effect on viral replication. Our approach is able to make high-confidence predictions more accurately than several baselines, and about as well as the best baseline, which does not infer mechanistic pathways. We also examine two kinds of predictions made by our method: which host factors are nearest to a direct interaction with a viral component, and which unassayed host genes are likely to be involved in viral replication. Multiple predictions are supported by recent independent experimental data, or are components or functional partners of confirmed relevant complexes or pathways. Integer program code, background network data, and inferred host-virus subnetworks are available at http://www.biostat.wisc.edu/~craven/chasman_host_virus/.
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Affiliation(s)
- Deborah Chasman
- Department of Computer Sciences, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Brandi Gancarz
- Luminex Corporation, Madison, Wisconsin, United States of America
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Linhui Hao
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Howard Hughes Medical Institute, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Michael Ferris
- Department of Computer Sciences, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Paul Ahlquist
- Institute for Molecular Virology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Howard Hughes Medical Institute, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Mark Craven
- Department of Computer Sciences, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
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23
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GITTER ANTHONY, BRAUNSTEIN ALFREDO, PAGNANI ANDREA, BALDASSI CARLO, BORGS CHRISTIAN, CHAYES JENNIFER, ZECCHINA RICCARDO, FRAENKEL ERNEST. Sharing information to reconstruct patient-specific pathways in heterogeneous diseases. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2014:39-50. [PMID: 24297532 PMCID: PMC3910098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Advances in experimental techniques resulted in abundant genomic, transcriptomic, epigenomic, and proteomic data that have the potential to reveal critical drivers of human diseases. Complementary algorithmic developments enable researchers to map these data onto protein-protein interaction networks and infer which signaling pathways are perturbed by a disease. Despite this progress, integrating data across different biological samples or patients remains a substantial challenge because samples from the same disease can be extremely heterogeneous. Somatic mutations in cancer are an infamous example of this heterogeneity. Although the same signaling pathways may be disrupted in a cancer patient cohort, the distribution of mutations is long-tailed, and many driver mutations may only be detected in a small fraction of patients. We developed a computational approach to account for heterogeneous data when inferring signaling pathways by sharing information across the samples. Our technique builds upon the prize-collecting Steiner forest problem, a network optimization algorithm that extracts pathways from a protein-protein interaction network. We recover signaling pathways that are similar across all samples yet still reflect the unique characteristics of each biological sample. Leveraging data from related tumors improves our ability to recover the disrupted pathways and reveals patient-specific pathway perturbations in breast cancer.
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Affiliation(s)
- ANTHONY GITTER
- Microsoft Research, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - ALFREDO BRAUNSTEIN
- DISAT and Center for Computational Sciences, Politecnico di Torino, Turin, Italy
- Human Genetics Foundation, Turin, Italy
| | - ANDREA PAGNANI
- DISAT and Center for Computational Sciences, Politecnico di Torino, Turin, Italy
- Human Genetics Foundation, Turin, Italy
| | - CARLO BALDASSI
- DISAT and Center for Computational Sciences, Politecnico di Torino, Turin, Italy
- Human Genetics Foundation, Turin, Italy
| | | | | | - RICCARDO ZECCHINA
- DISAT and Center for Computational Sciences, Politecnico di Torino, Turin, Italy
- Human Genetics Foundation, Turin, Italy
| | - ERNEST FRAENKEL
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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